Patent Application
20240011041
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Oct. 27, 2021, is named 53240-743_601_SL.txt and is 71,774 bytes in size.
Disclosed herein, in certain embodiments, are phage compositions comprising CRISPR-Cas systems and methods of use thereof.
Disclosed herein, in certain embodiments, are bacteriophages comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising: a CRISPR array comprising one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; a Cascade polypeptide; and a Cas3 polypeptide. In some embodiments, the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array further comprises at least one repeat sequence. In some embodiments, the at least one repeat sequence is operably linked to the one or more spacer sequence at either its 5′ end or its 3′ end. In some embodiments, the repeat sequence comprises at least about 90% sequence identity to any one of SEQ ID NOS: 26-30. In some embodiments, the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
In some embodiments, provided is a cocktail system comprising one or more bacteriophage. In some embodiments, the bacteriophage included in the cocktail system includes any one of p1106, p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1, or two or more phage thereof. In some embodiments, the bacteriophage cocktail system used herein includes, one, two, three, four, five, six or more that are selected from the group consisting of p1106, p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, and PB1. In some embodiments, the bacteriophage is a bacteriophage having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to a bacteriophage selected from p1106, p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, and PB1. In some embodiments, the bacteriophage in the bacteriophage cocktail system used herein includes any one, two, three, four, five, six, or more from p1106e003, p1106wt, p1194wt, p1587e002, p1587wt, p1695wt, p1772e005, p1772wt, p1835e002, p1835wt, p2037e002, p2037wt, p2131e002, p2131wt, p2132e002, p2132wt, p2167wt, p2363e003, p2363wt, p2421e002, p2421wt, p2973e002, p2973wt, p3278wt, p4430wt, PB1e002, or PB1wt. In some embodiments, the bacteriophage in the bacteriophage cocktail system used herein includes a bacteriophage having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to p1106e003, p1106wt, p1194wt, p1587e002, p1587wt, p1695wt, p1772e005, p1772wt, p1835e002, p1835wt, p2037e002, p2037wt, p2131e002, p2131wt, p2132e002, p2132wt, p2167wt, p2363e003, p2363wt, p2421e002, p2421wt, p2973e002, p2973wt, p3278wt, p4430wt, PB1e002, or PB1wt, or two or more phage thereof. In some embodiments, the bacteriophage in the bacteriophage cocktail system used herein includes any one or more of p1106e003, p1835e002, p1772e005, p2131e002, p1194, p4430, and p1695. In some embodiments, the nucleic acid sequence is inserted in place of or adjacent to a non-essential bacteriophage gene. In some embodiments, the bacteriophage is selected from a group consisting of p1106e003, p1835e002, p1772e005, and p2131e002. In some embodiments, the bacteriophage in the bacteriophage cocktail system used herein includes any one or more of p1106e003, p1835e002, p1772e005, p2131e002, and p1194. In some embodiments, the bacteriophage in the bacteriophage cocktail system used herein includes any one or more of p1106e003, p1835e002, p1772e005, p2131e002, and p4430. In some embodiments, the bacteriophage in the bacteriophage cocktail system used herein includes any one or more of p1106e003, p1835e002, p1772e005, p2131e002, and p1695. In some embodiments, the bacteriophage in the bacteriophage cocktail system used herein includes any one or more of e p1106e003, p1835e002, p1772e005, p2131e002, p1194, and p1695. In some embodiments, the bacteriophage in the bacteriophage cocktail system used herein includes any one or more of p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695. In some embodiments, the bacteriophage cocktail system comprises the bacteriophage of CK000512 (p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695).
Disclosed herein, in certain embodiments, are pharmaceutical compositions comprising: (a) the bacteriophage described herein; and (b) a pharmaceutically acceptable excipient. In some embodiments, the bacteriophage are selected from among a PhiKZvirus, PhiKMV virus, Brunyoghevirus, Samunavirus, Nankokuvirus, Abidjanvirus, Baikalvirus, Beetrevirus, Casadabanvirus, Citexvirus, Cystovirus, Detrevirus, Elvirus, Hollowayvirus, Kochitakasuvirus, Litunavirus, Luzseptimavirus, Nipunavirus, Pakpunavirus, Pamexvirus, Paundecimvirus, Phitrevirus, Primolicivirus, Septimatrevirus, Stubburvirus, Tertilicivirus, Yuavirus, Zicotriavirus and Pbunavirus. In some embodiments, the pharmaceutical composition comprises at least six bacteriophage, wherein the bacteriophage are selected from among a p1106e003, p1835e002, p1772e005, p2131e002, p1194, and a p1695 phage. In some embodiments, the pharmaceutical composition comprises at least six bacteriophage, wherein the bacteriophage in the bacteriophage cocktail system used herein includes any one or more of p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695. In some embodiments, the pharmaceutical composition is in the form of a tablet, a liquid, a syrup, an oral formulation, an intravenous formulation, an intranasal formulation, an ocular formulation, an otic formulation, a subcutaneous formulation, an inhalable respiratory formulation, a suppository, a lyophilized formulation, a nebulizable formulation, and any combination thereof. In one embodiment, the pharmaceutical composition comprises p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695 in a nebulizable formulation for pulmonary delivery.
In certain aspects, disclosed herein is a method of killing a Pseudomonas species comprising introducing into the target bacterium a nucleic acid sequence encoding a Type I CRISPR-Cas system from a bacteriophage, the nucleic acid comprising: a CRISPR array comprising one or more spacer sequences complementary to target nucleotide sequence in the Pseudomonas species; a Cascade polypeptide; and a Cas3 polypeptide. In some embodiments, the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array further comprises at least one repeat sequence. In some embodiments, the at least one repeat sequence is operably linked to the one or more spacer sequences at either its 5′ end or its 3′ end. In some embodiments, the repeat sequence comprises at least about 90% sequence identity to any one of SEQ ID NOS: 26-30. In some embodiments, the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
In certain aspects, disclosed herein is a method of treating a disease or condition in an individual in need thereof, the method comprising administering to the individual a bacteriophage comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising: a CRISPR array; a Cascade polypeptide comprising one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; and a Cas3 polypeptide. In some embodiments, the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array further comprises at least one repeat sequence. In some embodiments, the at least one repeat sequence is operably linked to the one or more spacer sequences at either its 5′ end or its 3′ end. In some embodiments, the repeat sequence comprises at least about 90% sequence identity to any one of SEQ ID NOS: 26-30. In some embodiments, the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
In certain aspects, disclosed herein is a bacteriophage comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising: a CRISPR array comprising one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; a Cascade polypeptide comprising Cas5, CasSc and Cas7; and a Cas3 polypeptide. In some embodiments, the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array further comprises at least one repeat sequence. In some embodiments, the at least one repeat sequence is operably linked to the one or more spacer sequences at either its 5′ end or its 3′ end. In some embodiments, the repeat sequence comprises at least about 90% sequence identity to any one of SEQ ID NOS: 26-30. In some embodiments, the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
In certain aspects, disclosed herein is a method of sanitizing a surface in need thereof, the method comprising administering to the surface a bacteriophage comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising: a CRISPR array; a Cascade polypeptide comprising one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; and a Cas3 polypeptide. In some embodiments, the surface is a hospital surface, a vehicle surface, an equipment surface, or an industrial surface.
In certain aspects, disclosed herein is a method of preventing contamination in a food product or a nutritional supplement, the method comprising contacting the food product or the nutritional supplement a bacteriophage comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising: a CRISPR array; a Cascade polypeptide comprising one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; and a Cas3 polypeptide. In some embodiments, the food product or nutritional supplement comprises milk, yoghurt, curd, cheese, fermented milks, milk based fermented products, ice-creams, fermented cereal based products, milk based powders, infant formulae or tablets, liquid suspensions, dried oral supplement, wet oral supplement, or dry-tube-feeding.
In certain aspects, disclosed herein is a bacteriophage comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising: a CRISPR array comprising spacer sequences complementary to target nucleotide sequence in a Pseudomonas species, wherein the spacer sequences comprise SEQ ID NOs: 12, 16, and 20; a Cascade polypeptide; and a Cas3 polypeptide.
In certain aspects, disclosed herein is a bacteriophage comprising at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity to a phage selected from p1106, p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the bacteriophage used herein includes any one or more of a bacteriophage having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to p1106e003, p1106wt, p1194wt, p1587e002, p1587wt, p1695wt, p1772e005, p1772wt, p1835e002, p1835wt, p2037e002, p2037wt, p2131e002, p2131wt, p2132e002, p2132wt, p2167wt, p2363e003, p2363wt, p2421e002, p2421wt, p2973e002, p2973wt, p3278wt, p4430wt, PB1e002, or PB1wt, or two or more phage thereof. In some embodiments, provided is a bacteriophage cocktail system comprising two more bacteriophage. In some embodiments, the bacteriophage cocktail system comprises the bacteriophage of CK000512 (p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695). In some embodiments, the bacteriophage further comprises a CRISPR array; a Cascade polypeptide comprising one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; and a Cas3 polypeptide. In some embodiments, the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array further comprises at least one repeat sequence. In some embodiments, the at least one repeat sequence is operably linked to the one or more spacer sequences at either its 5′ end or its 3′ end. In some embodiments, the repeat sequence comprises at least about 90% sequence identity to any one of SEQ ID NOS: 26-30. In some embodiments, the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
In certain aspects, disclosed herein is a composition comprising at least four bacteriophage, comprising: a first bacteriophage comprising p1106e003 or having at least 80% sequence identity to p1106e003; a second bacteriophage comprising p1835e002 or having at least 80% sequence identity to p1835e002; a third bacteriophage comprising p1772e005 or having at least 80% sequence identity to p1772e005; and a fourth bacteriophage comprising p2131e002 or having at least 80% sequence identity to p2131e002. In some embodiments, the composition further comprises a fifth bacteriophage comprising p1194 or having at least 80% sequence identity to p1194. In some embodiments, the composition further comprises a fifth bacteriophage comprising p1695 or having at least 80% sequence identity to p1695. In some embodiments, the composition further comprises a fifth bacteriophage comprising p4430 or having at least 80% sequence identity to p4430. In some embodiments, the composition further comprises a sixth bacteriophage comprising p1695 or having at least 80% sequence identity to p1695. In some embodiments, the composition comprises the bacteriophage of CK000512 (p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695).
In any of the methods embodiments herein, the bacteriophage of the method is engineered from a bacteriophage that infects Pseudomonas. In some embodiments, bacteriophages that infect Pseudomonas include a wildtype Pbunavirus phage subtype listed in Table 5A, wherein the phage infects a target Pseudomonas as marked with a positive sign (+) (e.g., phage p1106 infects b002548). In some embodiments, bacteriophages that infect Pseudomonas include an engineered Pbunavirus phage subtype listed in Table 5A, wherein the phage infects a target Pseudomonas as marked with a positive sign (+) (e.g., p1106e003 infects b002548). In some embodiments, bacteriophages that infect Pseudomonas include a wildtype Samunavirus phage subtype, an engineered Samunavirus phage subtype, a wildtype PhiKZvirus, a wildtype PhiKMVvirus, or a wildtype Bruynoghevirus, e.g., as listed in Table 5B, wherein the phage infects a target Pseudomonas as marked with a positive sign (+). As listed in Table 5A, the wildtype Pbunavirus phage subtypes can be p1106, p1587, p1835, p2037, p2363, p2421, and/or pb1, while the engineered Pbunavirus phage subtypes can be p1106e003, p1587e002, p1835e002, p2037e002, p2363e003, and/or p2421e002. As listed in Table 5B, the wildtype Samunavirus phage subtypes can be p1772, p2131, p2132, and/or p2973, the engineered Samunavirus phage subtypes can be pb1e002, p1772e005, p2131e002, p2132e002, and/or p2973e002, the wildtype PhiKZvirus phage subtypes can be p1194, and/or p4430, the wildtype PhiKMVvirus phage subtype can be p2167, and the wildtype Bruynoghevirus phage subtypes can be p1695 and/or p3278. In some embodiments, the bacteriophage that infects Pseudomonas is a Nankokuvirus, PhiKZvirus, PhiKMV virus, Brunyoghevirus, Samunavirus, Nankokuvirus, Abidjanvirus, Baikalvirus, Beetrevirus, Casadabanvirus, Citexvirus, Cystovirus, Detrevirus, Elvirus, Hollowayvirus, Kochitakasuvirus, Litunavirus, Luzseptimavirus, Nipunavirus, Pakpunavirus, Pamexvirus, Paundecimvirus, Phitrevirus, Primolicivirus, Septimatrevirus, Stubburvirus, Tertilicivirus, Yuavirus, Zicotriavirus or Pbunavirus. In some embodiments, a bacteriophage that infects Pseudomonas kills Pseudomonas. In some embodiments, the bacteriophage that infects Pseudomonas does not infect S. aureus. In some embodiments, the bacteriophage that infects Pseudomonas does not kill S. aureus. In some embodiments, the bacteriophage that kills Pseudomonas does not infect S. aureus. In some embodiments, the bacteriophage that kills Pseudomonas does not kill S. aureus. In some embodiments, the bacteriophage that infects Pseudomonas does not infect K. pneumoniae. In some embodiments, the bacteriophage that infects Pseudomonas does not kill K. pneumoniae. In some embodiments, the bacteriophage that kills Pseudomonas does not infect K. pneumoniae. In some embodiments, the bacteriophage that kills Pseudomonas does not kill K. pneumoniae. In some embodiments, the bacteriophage that infects Pseudomonas does not infect E. faecium. In some embodiments, the bacteriophage that infects Pseudomonas does not kill E. faecium. In some embodiments, the bacteriophage that kills Pseudomonas does not infect E. faecium. In some embodiments, the bacteriophage that kills Pseudomonas does not kill E. faecium. In some embodiments, the bacteriophage that infects Pseudomonas does not infect E. cloacae. In some embodiments, the bacteriophage that infects Pseudomonas does not kill E. cloacae. In some embodiments, the bacteriophage that kills Pseudomonas does not infect E. cloacae. In some embodiments, the bacteriophage that kills Pseudomonas does not kill E. cloacae. In some embodiments, the bacteriophage that infects Pseudomonas does not infect A. baumanii. In some embodiments, the bacteriophage that infects Pseudomonas does not kill A. baumanii. In some embodiments, the bacteriophage that kills Pseudomonas does not infect A. baumanii. In some embodiments, the bacteriophage that kills Pseudomonas does not kill A. baumanii. In some embodiments, the bacteriophage that infects Pseudomonas does not infect S. epidermidis. In some embodiments, the bacteriophage that infects Pseudomonas does not kill S. epidermidis. In some embodiments, the bacteriophage that kills Pseudomonas does not infect S. epidermidis. In some embodiments, the bacteriophage that kills Pseudomonas does not kill S. epidermidis. In some embodiments, a combination of bacteriophage infect Pseudomonas. As a non-limiting example, the combination infects at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the Pseudomonas in Table 5A. As a non-limiting example, the combination infects at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the Pseudomonas in Table 5B. As a non-limiting example, the combination infects at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the Pseudomonas in Table 6B. In some embodiments, a combination of bacteriophage kill Pseudomonas. As a non-limiting example, the combination kills at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the Pseudomonas in Table 5A. As a non-limiting example, the combination kills at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the Pseudomonas in Table 5B. As a non-limiting example, the combination kills at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the Pseudomonas in Table 6B.
The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosures will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosures are utilized, and the accompanying drawings of which:
Disclosed herein, in certain embodiments, are bacteriophages comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising: (a) a CRISPR array (also referred to as “crArray”), (b) a Cascade polypeptide; and (c) a Cas3 polypeptide. Also disclosed herein, in certain embodiments, are pharmaceutical compositions comprising the bacteriophages disclosed herein. Further disclosed herein, in certain embodiments, are methods of killing a Pseudomonas species comprising introducing into the Pseudomonas species a bacteriophage comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising: (a) a CRISPR array; (b) a Cascade polypeptide; and (c) a Cas3 polypeptide. Further disclosed herein, in certain embodiments, are methods of treating a disease or condition in an individual in need thereof, the method comprising administering to the individual a bacteriophage a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising: (a) a CRISPR array; (b) a Cascade polypeptide; and (c) a Cas3 polypeptide
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. The terminology used in the description of the disclosure herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the disclosure.
Unless the context indicates otherwise, it is specifically intended that the various features of the disclosure described herein are able of being used in any combination. Moreover, the present disclosure also contemplates that in some embodiments, any feature or combination of features set forth herein are excluded or omitted. To illustrate, if the specification states that a composition comprises components A, B and C, it is specifically intended that any of A, B or C, or a combination thereof, are omitted and disclaimed singularly or in any combination.
One of skill in the art will understand the interchangeability of terms designating the various CRISPR-Cas systems and their components due to a lack of consistency in the literature and an ongoing effort in the art to unify such terminology.
As used in the description and the appended claims, the singular forms “a,” “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. Also as used herein, “and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (“or”).
The term “about” as used herein when referring to a measurable value such as a dosage or time period and the like refers to variations of ±20%, ±10%, ±5%, ±1%, ±0.5%, or even ±0.1% of the specified amount. As used herein, phrases such as “between X and Y” and “between about X and Y” should be interpreted to include X and Y. As used herein, phrases such as “between about X and Y” mean “between about X and about Y” and phrases such as “from about X to Y” mean “from about X to about Y.”
The term “comprise”, “comprises”, and “comprising”, “includes”, “including”, “have” and “having”, as used herein, specify the presence of the stated features, steps, operations, elements, and/or components, but do not preclude the presence or addition of one or more other features, steps, operations, elements, components, and/or groups thereof.
As used herein, the transitional phrase “consisting essentially of” means that the scope of a claim is to be interpreted to encompass the specified materials or steps recited in the claim and those that do not materially affect the basic and novel characteristic(s) of the claimed disclosure. Thus, the term “consisting essentially of” when used in a claim of this disclosure is not intended to be interpreted to be equivalent to “comprising.”
The term “consists of” and “consisting of”, as used herein, excludes any features, steps, operations, elements, and/or components not otherwise directly stated. The use of “consisting of” limits only the features, steps, operations, elements, and/or components set forth in that clause and does exclude other features, steps, operations, elements, and/or components from the claim as a whole.
The terms “complementary” or “complementarity”, as used herein, refer to the natural binding of polynucleotides under permissive salt and temperature conditions by base-pairing. For example, the sequence “A-G-T” binds to the complementary sequence “T-C-A.” Complementarity between two single-stranded molecules is “partial,” in which only some of the nucleotides bind, or it is complete when total complementarity exists between the single stranded molecules. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands.
“Complement” as used herein means 100% complementarity or identity with the comparator nucleotide sequence or it means less than 100% complementarity (e.g., about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and the like, complementarity). Complement or complementable may also be used in terms of a “complement” to or “complementing” a mutation.
As used herein, the term “CRISPR phage”, “CRISPR enhanced phage”, and “crPhage” refers to a bacteriophage particle comprising bacteriophage DNA comprising at least one heterologous polynucleotide that encodes at least one component of a CRISPR-Cas system (e.g., CRISPR array, crRNA; e.g., P1 bacteriophage comprising an insertion of a targeting crRNA). In some embodiments, the polynucleotide encodes at least one transcriptional activator of a CRISPR-Cas system. In some embodiments, the polynucleotide encodes at least one component of an anti-CRISPR polypeptide of a CRISPR-Cas system.
As used herein, the phrase “substantially identical,” or “substantial identity” in the context of two nucleic acid molecules, nucleotide sequences or protein sequences, refers to two or more sequences or subsequences that have at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and/or 100% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection. In some embodiments, substantial identity refers to two or more sequences or subsequences that have at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95, 96, 96, 97, 98, or 99% identity. For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.
Optimal alignment of sequences for aligning a comparison window are conducted by tools such as the local homology algorithm of Smith and Waterman, the homology alignment algorithm of Needleman and Wunsch, the search for similarity method of Pearson and Lipman, and optionally by computerized implementations of these algorithms such as GAP, BESTFIT, FASTA, and TFASTA available as part of the GCG® Wisconsin Package® (Accelrys Inc., San Diego, CA). An “identity fraction” for aligned segments of a test sequence and a reference sequence is the number of identical components which are shared by the two aligned sequences divided by the total number of components in the reference sequence segment, i.e., the entire reference sequence or a smaller defined part of the reference sequence. Percent sequence identity is represented as the identity fraction multiplied by 100. The comparison of one or more polynucleotide sequences is to a full-length polynucleotide sequence or to a portion thereof, or to a longer polynucleotide sequence. In some instances, “Percent identity” is determined using BLASTX version 2.0 for translated nucleotide sequences and BLASTN version 2.0 for polynucleotide sequences.
As used herein, a “target nucleotide sequence” refers to the portion of a target gene (i.e., target region in the genome or the “protospacer sequence,” which is adjacent to a protospacer adjacent motif (PAM) sequence) that is fully complementary or substantially complementary (e.g., at least 70% complementary (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more)) to a spacer sequence in a CRISPR array.
As used herein, the term “protospacer adjacent motif” or “PAM” refers to a DNA sequence present on the target DNA molecule adjacent to the nucleotide sequence matching the spacer sequence. This motif is found in the target gene next to the region to which a spacer sequence binds as a result of being complementary to that region and identifies the point at which base pairing with the spacer nucleotide sequence begins. The exact PAM sequence that is required varies between each different CRISPR-Cas system. Non-limiting examples of PAMs include CCA, CCT, CCG, TTC, AAG, AGG, ATG, GAG, and/or CC. In some instances, in Type I systems, the PAM is located immediately 5′ to the sequence that matches the spacer, and thus is 3′ to the sequence that base pairs with the spacer nucleotide sequence, and is directly recognized by Cascade. In some instances, for B. halodurans Type I-C systems, the PAM is YYC, where Y can be either T or C. In some instances, for the P. aeruginosa Type I-C system, the PAM is TTC. Once a cognate protospacer and PAM are recognized, Cas3 is recruited, which then cleaves and degrades the target DNA. For Type II systems, the PAM is required for a Cas9/sgRNA to form an R-loop to interrogate a specific DNA sequence through Watson-Crick pairing of its guide RNA with the genome. The PAM specificity is a function of the DNA-binding specificity of the Cas9 protein (e.g., a—protospacer adjacent motif recognition domain at the C-terminus of Cas9).
As used herein, the term “gene” refers to a nucleic acid molecule capable of being used to produce mRNA, tRNA, rRNA, miRNA, anti-microRNA, regulatory RNA, and the like. Genes may or may not be capable of being used to produce a functional protein or gene product. Genes include both coding and non-coding regions (e.g., introns, regulatory elements, promoters, enhancers, termination sequences and/or 5′ and 3′ untranslated regions). A gene is “isolated” by which is meant a nucleic acid that is substantially or essentially free from components normally found in association with the nucleic acid in its natural state. Such components include other cellular material, culture medium from recombinant production, and/or various chemicals used in chemically synthesizing the nucleic acid.
By the terms “treat,” “treating,” or “treatment,” itis intended that the severity of the subject's condition is reduced or at least partially improved or modified and that some alleviation, mitigation or decrease in at least one clinical symptom is achieved, and/or there is a delay in the progression of the disease or condition, and/or delay of the onset of a disease or illness. With respect to an infection, a disease or a condition, the term refers to a decrease in the symptoms or other manifestations of the infection, disease or condition. In some embodiments, treatment provides a reduction in symptoms or other manifestations of the infection, disease or condition by at least about 5%, e.g., about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50% or more.
The terms “prevent,” “preventing,” and “prevention” (and grammatical variations thereof) refer to prevention and/or delay of the onset of an infection, disease, condition and/or a clinical symptom(s) in a subject and/or a reduction in the severity of the onset of the infection, disease, condition and/or clinical symptom(s) relative to what would occur in the absence of carrying out the methods disclosed herein prior to the onset of the disease, disorder and/or clinical symptom(s). Thus, in some embodiments, to prevent infection, food, surfaces, medical tools and devices are treated with compositions and by methods disclosed herein.
The terms with respect to an “infection”, “a disease”, or “a condition”, used herein, refer to any adverse, negative, or harmful physiological condition in a subject due to the presence of a target bacterium in the subject. The terms are used interchangeably.
The terms “individual”, or “subject” as used herein includes any animal that has or is susceptible to an infection, disease or condition involving bacteria. Thus, in some embodiments, subjects are mammals, avians, reptiles, amphibians, fish, crustaceans, or mollusks. Mammalian subjects include but are not limited to humans, non-human primates (e.g., gorilla, monkey, baboon, and chimpanzee, etc.), dogs, cats, goats, horses, pigs, cattle, sheep, and the like, and laboratory animals (e.g., rats, guinea pigs, mice, gerbils, hamsters, and the like). Avian subjects include but are not limited to chickens, ducks, turkeys, geese, quail, pheasants, and birds kept as pets (e.g., parakeets, parrots, macaws, cockatoos, canaries, and the like). Fish subjects include but are not limited to species used in aquaculture (e.g., tuna, salmon, tilapia, catfish, carp, trout, cod, bass, perch, snapper, and the like). Crustacean subjects include but are not limited to species used in aquaculture (e.g., shrimp, prawn, lobster, crayfish, crab and the like). Mollusk subjects include but are not limited to species used in aquaculture (e.g., abalone, mussel, oyster, clams, scallop and the like). In some embodiments, suitable subjects include both males and females and subjects of any age, including embryonic (e.g., in-utero or in-ovo), infant, juvenile, adolescent, adult and geriatric subjects. In some embodiments, a subject is a human.
As used here the term “isolated” in context of a nucleic acid sequence is a nucleic acid sequence that exists apart from its native environment.
As used herein, “expression cassette” means a recombinant nucleic acid molecule comprising a nucleotide sequence of interest (e.g., the recombinant nucleic acid molecules and CRISPR arrays disclosed herein), wherein the nucleotide sequence is operably associated with at least a control sequence (e.g., a promoter).
As used herein, “chimeric” refers to a nucleic acid molecule or a polypeptide in which at least two components are derived from different sources (e.g., different organisms, different coding regions).
As used herein, “selectable marker” means a nucleotide sequence that when expressed imparts a distinct phenotype to the host cell expressing the marker and thus allows such transformed cells to be distinguished from those that do not have the marker.
As used herein, “vector” refers to a composition for transferring, delivering or introducing a nucleic acid (or nucleic acids) into a cell.
As used herein, “pharmaceutically acceptable” means a material that is not biologically or otherwise undesirable, i.e., the material are administered to a subject without causing any undesirable biological effects such as toxicity.
As used herein the term “biofilm” means an accumulation of microorganisms embedded in a matrix of polysaccharide. Biofilms form on solid biological or non-biological surfaces and are medically important, accounting for over 80 percent of microbial infections in the body.
As used herein, the term “in vivo” is used to describe an event that takes place in a subject's body.
As used herein, the term “in vitro” is used to describe an event that takes places contained in a container for holding laboratory reagent such that it is separated from the biological source from which the material is obtained. In vitro assays can encompass cell-based assays in which living or dead cells are employed. In vitro assays can also encompass a cell-free assay in which no intact cells are employed.
CRISPR-Cas systems are naturally adaptive immune systems found in bacteria and archaea. The CRISPR system is a nuclease system involved in defense against invading phages and plasmids that provides a form of acquired immunity. There is a diversity of CRISPR-Cas systems based on the set of cas genes and their phylogenetic relationship. There are at least six different types (I through VI) where Type I represents over 50% of all identified systems in both bacteria and archaea. In some embodiments, a Type I, Type II, Type II, Type IV, Type V, or Type VI CRISPR-Cas system is used herein.
Type I systems are divided into seven subtypes including: Type I-A, Type I-B, Type I-C, Type I-D, Type I-E, Type I-F, and Type I-U. Type I CRISPR-Cas systems include a multi-subunit complex called Cascade (for complex associated with antiviral defense), Cas3 (a protein with nuclease, helicase, and exonuclease activity that is responsible for degradation of the target DNA), and CRISPR array encoding crRNA (stabilizes Cascade complex and directs Cascade and Cas3 to DNA target). Cascade forms a complex with the crRNA, and the protein-RNA pair recognizes its genomic target by complementary base pairing between the 5′ end of the crRNA sequence and a predefined protospacer. This complex is directed to homologous loci of pathogen DNA via regions encoded within the crRNA and protospacer-adjacent motifs (PAMs) within the pathogen genome. Base pairing occurs between the crRNA and the target DNA sequence leading to a conformational change. In the Type I-E system, the PAM is recognized by the CasA protein within Cascade, which then unwinds the flanking DNA to evaluate the extent of base pairing between the target and the spacer portion of the crRNA. Sufficient recognition leads Cascade to recruit and activate Cas3. Cas3 then nicks the non-target strand and begins degrading the strand in a 3′-to-5′ direction.
In the Type I-C system, the proteins Cas5, Cas8c, and Cas7 form the Cascade effector complex. Cas5 processes the pre-crRNA (which can take the form of a multi-spacer array, or a single spacer between two repeats) to produce individual crRNA(s) made up of a hairpin structure formed from the remaining repeat sequence and a linear spacer. The effector complex then binds to the processed crRNA and scans DNA to identify PAM sites. In the Type I-C system, the PAM is recognized by the Cas8c protein, which then acts to unwind the DNA duplex. If the sequence 3′ of the PAM matches the crRNA spacer that is bound to effector complex, a conformational change in the complex occurs and Cas3 is recruited to the site. Cas3 then nicks the non-target strand and begins degrading the DNA. In some cases, Cas5 includes Cas5, Cas5c, Cas5d, and a sequence at least 90% identical to SEQ ID NO: 76. In some cases, Cas7 includes Cas7, Cas7c, and a sequence at least 90% identical to SEQ ID NO: 78. In some cases, Cas8 includes Cas8, Cas8c, and a sequence at least 90% identical to SEQ ID NO: 77.
In some embodiments, the CRISPR-Cas system is endogenous to a Pseudomonas species. In some embodiments, the CRISPR-Cas system is exogenous to the Pseudomonas species. In some embodiments, the CRISPR-Cas system is a Type I CRISPR-Cas system. In some embodiments, the CRISPR-Cas system is a Type I-A CRISPR-Cas system. In some embodiments, the CRISPR-Cas system is a Type I-B CRISPR-Cas system. In some embodiments, the CRISPR-Cas system is a Type I-C CRISPR-Cas system. In some embodiments, the CRISPR-Cas system is a Type I-C CRISPR-Cas system derived from Pseudomonas aeruginosa. In some embodiments, the CRISPR-Cas system is a Type I-D CRISPR-Cas system. In some embodiments, the CRISPR-Cas system is a Type I-E CRISPR-Cas system. In some embodiments, the CRISPR-Cas system is a Type I-F CRISPR-Cas system. In some embodiments, the CRISPR-Cas system is a Type I-U CRISPR-Cas system. In some embodiments, the CRISPR-Cas system is a Type II CRISPR-Cas system. In some embodiments, the CRISPR-Cas system is a Type III CRISPR-Cas system.
In some embodiments, processing of a CRISPR-array disclosed herein includes, but is not limited to, the following processes: 1) transcription of the nucleic acid encoding a pre-crRNA; 2) recognition of the pre-crRNA by Cascade and/or specific members of Cascade, such as Cas6, and (3) processing of the pre-crRNA by Cascade or members of Cascade, such as Cas6, into mature crRNAs. In some embodiments, the mode of action for a Type I CRISPR system includes, but is not limited to, the following processes: 4) mature crRNA complexation with Cascade; 5) target recognition by the complexed mature crRNA/Cascade complex; and 6) nuclease activity at the target leading to DNA degradation.
In some embodiments, provided herein are components of a CRISPR-Cas system and bacteriophage comprising CRISPR-Cas system components. As an example, provided herein is a nucleic acid sequence comprising at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to any one of SEQ ID NOS: 83-87. In some cases, the nucleic acid sequence comprises at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 83. In some cases, the nucleic acid sequence comprises at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 84. In some cases, the nucleic acid sequence comprises at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 85. In some cases, the nucleic acid sequence comprises at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 86. In some cases, the nucleic acid sequence comprises at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 87. In some cases, the nucleic acid sequence comprises at least about 90% identity to SEQ ID NO: 83. In some cases, the nucleic acid sequence comprises at least about 90% identity to SEQ ID NO: 84. In some cases, the nucleic acid sequence comprises at least about 90% identity to SEQ ID NO: In some cases, the nucleic acid sequence comprises at least about 90% identity to SEQ ID NO: 86. In some cases, the nucleic acid sequence comprises at least about 90% identity to SEQ ID NO: 87. In any of these embodiments, the nucleic acid sequence may comprise a sequence at least 90% identical to any one of SEQ ID NOS: 12-23, 31-74, or 88-120. In a non-limiting example, the nucleic acid sequence comprises one or more of: SEQ ID NO: 12, SEQ ID NO: 16, and SEQ ID NO: 20.
Further provided herein are CRISPR-Cas system components comprising a nucleic acid sequence at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 24. In some cases, the nucleic acid sequence comprises at least about 90% identity to SEQ ID NO: 24. In any of these embodiments, the nucleic acid sequence may comprise a sequence at least 90% identical to any one of SEQ ID NOS: 12-23, 31-74, or 88-120. In a non-limiting example, the nucleic acid sequence comprises one or more of: SEQ ID NO: 12, SEQ ID NO: 16, and SEQ ID NO: 20.
Provided herein are CRISPR-Cas system components comprising at least about 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 25. In some cases, the nucleic acid sequence comprises at least about 90% identity to SEQ ID NO: 25. In any of these embodiments, the nucleic acid sequence may comprise a sequence at least 90% identical to any one of SEQ ID NOS: 12-23, 31-74, or 88-120. In a non-limiting example, the nucleic acid sequence comprises one or more of: SEQ ID NO: 12, SEQ ID NO: 16, and SEQ ID NO: 20.
Disclosed herein, in certain embodiments, are bacteriophage compositions comprising CRISPR-Cas systems and methods of use thereof.
Bacteriophages or “phages” represent a group of bacterial viruses and are engineered or sourced from environmental sources. Individual bacteriophage host ranges are usually narrow, meaning, phages are highly specific to one strain or few strains of a bacterial species and this specificity makes them unique in their antibacterial action. Bacteriophages are bacterial viruses that rely on the host's cellular machinery to replicate. Bacteriophages are generally classified as virulent or temperate phages depending on their lifestyle. Virulent bacteriophages, also known as lytic bacteriophages, can only undergo lytic replication. Lytic bacteriophages infect a host cell, undergo numerous rounds of replication, and trigger cell lysis to release newly made bacteriophage particles. In some embodiments, the lytic bacteriophages disclosed herein retain their replicative ability. In some embodiments, the lytic bacteriophages disclosed herein retain their ability to trigger cell lysis. In some embodiments, the lytic bacteriophages disclosed herein retain both they replicative ability and the ability to trigger cell lysis. In some embodiments, the bacteriophages disclosed herein comprise a CRISPR array. In some embodiments, the CRISPR array does not affect the bacteriophages ability to replicate and/or trigger cell lysis. Temperate or lysogenic bacteriophages can undergo lysogeny in which the phage stops replicating and stably resides within the host cell, either integrating into the bacterial genome or being maintained as an extrachromosomal plasmid. Temperate phages can also undergo lytic replication similar to their lytic bacteriophage counterparts. Whether a temperate phage replicates lytically or undergoes lysogeny upon infection depends on a variety of factors including growth conditions and the physiological state of the cell. A bacterial cell that has a lysogenic phage integrated into its genome is referred to as a lysogenic bacterium or lysogen. Exposure to adverse conditions may trigger reactivation of the lysogenic phage, termination of the lysogenic state and resumption of lytic replication by the phage. This process is called induction. Adverse conditions which favor the termination of the lysogenic state include desiccation, exposure to UV or ionizing radiation, and exposure to mutagenic chemicals. This leads to the expression of the phage genes, reversal of the integration process, and lytic multiplication. In some embodiments, the temperate bacteriophages disclosed herein are rendered lytic. The term “lysogeny gene” refers to any gene whose gene product promotes lysogeny of a temperate phage. Lysogeny genes can directly promote, as in the case of integrase proteins that facilitate integration of the bacteriophage into the host genome. Lysogeny genes can also indirectly promote lysogeny as in the case of CI transcriptional regulators which prevent transcription of genes required for lytic replication and thus favor maintenance of lysogeny.
Bacteriophages package and deliver synthetic DNA using three general approaches. Under the first approach, the synthetic DNA is recombined into the bacteriophage genome in a targeted manner, which usually involves a selectable marker. Under the second approach, restriction sites within the phage are used to introduce synthetic DNA in-vitro. Under the third approach, a plasmid generally encoding the phage packaging sites and lytic origin of replication is packaged as part of the assembly of the bacteriophage particle. The resulting plasmids have been coined “phagemids.”
Phages are limited to a given bacterial strain for evolutionary reasons. In some cases, injecting their genetic material into an incompatible strain is counterproductive. Phages have therefore evolved to specifically infect a limited cross-section of bacterial strains. However, some phages have been discovered that inject their genetic material into a wide range of bacteria. The classic example is the P1 phage, which has been shown to inject DNA in a range of gram-negative bacteria.
Phage capsids have a limited capacity, meaning that their genome size must stay within a tight range in order to be properly packaged. Since DNA encoding the Cas operon+CRISPR array is rather large (total ˜6000 bp), other DNA must be removed from the phage genome in order to make room for the Cas system. Exemplary phage engineered herein comprise a Cas operon and CRISPR array inserted into a phage such that the phage retains viability.
Disclosed herein, in some embodiments, are bacteriophages comprising a first nucleic acid sequence encoding a first spacer sequence or a crRNA transcribed therefrom, wherein the first spacer sequence is complementary to a target nucleotide sequence from a target gene in a Pseudomonas species. In some embodiments, the bacteriophage comprises a first nucleic acid sequence encoding a first spacer sequence or a crRNA transcribed therefrom, wherein the first spacer sequence is complementary to a target nucleotide sequence from a target gene in Pseudomonas aeruginosa, provided that the bacteriophage is rendered lytic. In some embodiments, the bacteriophage is a temperate bacteriophage. In some embodiments, the bacteriophage is rendered lytic by removal, replacement, or inactivation of a lysogenic gene. In some embodiments, the lysogenic gene plays a role in the maintenance of lysogenic cycle in the bacteriophage. In some embodiments, the lysogenic gene plays a role in establishing the lysogenic cycle in the bacteriophage. In some embodiments, the lysogenic gene plays a role in both establishing the lysogenic cycle and in the maintenance of the lysogenic cycle in the bacteriophage. In some embodiments, the lysogenic gene is a repressor gene. In some embodiments, the lysogenic gene is cI repressor gene. In some embodiments, the bacteriophage is rendered lytic by the removal of a regulatory element of a lysogeny gene. In some embodiments, the bacteriophage is rendered lytic by the removal of a promoter of a lysogeny gene. In some embodiments, the bacteriophage is rendered lytic by the removal of a functional element of a lysogeny gene. In some embodiments, the lysogenic gene is an activator gene. In some embodiments, the lysogenic gene is cII gene. In some embodiments, the lysogenic gene is lexA gene. In some embodiments, the lysogenic gene is int (integrase) gene. In some embodiments, two or more lysogeny genes are removed, replaced, or inactivated to cause arrest of a bacteriophage lysogeny cycle and/or induction of a lytic cycle. In some embodiments, the bacteriophage is rendered lytic via a second CRISPR array comprising a second spacer directed to a lysogenic gene. In some embodiments, the bacteriophage is rendered lytic by the insertion of one or more lytic genes. In some embodiments, the bacteriophage is rendered lytic by the insertion of one or more genes that contribute to the induction of a lytic cycle. In some embodiments, the bacteriophage is rendered lytic by altering the expression of one or more genes that contribute to the induction of a lytic cycle. In some embodiments, the bacteriophage phenotypically changes from a lysogenic bacteriophage to a lytic bacteriophage. In some embodiments, the phenotypic change is via a self-targeting CRISPR-Cas system to render a bacteriophage lytic since it is incapable of lysogeny. In some embodiments, the self-targeting CRISPR-Cas comprises a self-targeting crRNA from the prophage genome and kills lysogens. In some embodiments, the bacteriophage is rendered lytic by environmental alterations. In some embodiments, environmental alterations include, but are not limited to, alterations in temperature, pH, or nutrients, exposure to antibiotics, hydrogen peroxide, foreign DNA, or DNA damaging agents, presence of organic carbon, and presence of heavy metal (e.g., in the form of chromium (VI)). In some embodiments, the bacteriophage that is rendered lytic is prevented from reverting to lysogenic state. In some embodiments, the bacteriophage that is rendered lytic is prevented from reverting back to lysogenic state by way of introducing an additional CRIPSR array. In some embodiments, the bacteriophage does not confer any new properties onto the Pseudomonas species beyond cellular death cause by lytic activity of the bacteriophage and/or the activity of the CRISPR array.
Further disclosed herein, in some embodiments, are temperate bacteriophages comprising a first nucleic acid sequence encoding a first spacer sequence or a crRNA transcribed therefrom, wherein the first spacer sequence is complementary to a target nucleotide sequence from a target gene in a Pseudomonas species, provided the bacteriophage is rendered lytic. In some embodiments, the bacteriophage infects multiple bacterial strains. In some embodiments, the target nucleotide sequence comprises all or a part of a promoter sequence for the target gene. In some embodiments, the target nucleotide sequence comprises all or a part of a nucleotide sequence located on a coding strand of a transcribed region of the target gene. In some embodiments, the target nucleotide sequence comprises at least a portion of an essential gene that is needed for survival of the Pseudomonas species. In some embodiments, the target nucleotide sequence comprises a highly-conserved non-coding or intergenic sequence. In some embodiments, the target sequence is an intergenic sequence that sits between the essential gene rpmF and a conserved hypothetical protein. In some embodiments, the essential gene is Tsf, acpP, gapA, infA, secY, csrA, trmD, ftsA, fusA, glyQ, eno, nusG, dnaA, dnaS, pheS, rplB, gltX, hisS, rplC, aspS, gyrB, glnS, dnaE, rpoA, rpoB, pheT, infB, rpsC, rplF, alaS, leuS, serS, rplD, gyrA, glmS, fus, adk, rpsK, rplR, ctrA, parC, tRNA-Ser, tRNA-Asn, or metK. In some embodiments, the essential gene is dnaA, ftsA, gyrB, dnaN, glnS, or rpoB. In some embodiments, the target sequence is PA4325 (hypothetical protein), PA1310 (phnW, pyruvate aminotransferase), or the boundary between PA2970 (rpmF, 50S ribosomal protein L32) and PA2971 (conserved hypothetical protein). In some embodiments, the target nucleotide sequence is in a non-essential gene. In some embodiments, the target nucleotide sequence is a noncoding sequence. In some embodiments, the noncoding sequence is an intergenic sequence. In some embodiments, the spacer sequence is complementary to a target nucleotide sequence of a highly conserved sequence in a Pseudomonas species. In some embodiments, the spacer sequence is complementary to a target nucleotide sequence of a sequence present in the Pseudomonas species. In some embodiments, the spacer sequence is complementary to a target nucleotide sequence that comprises all or a part of a promoter sequence of the essential gene. In some embodiments, the first nucleic acid sequence comprises a first CRISPR array comprising at least one repeat sequence. In some embodiments, the at least one repeat sequence is operably linked to the first spacer sequence at either its 5′ end or its 3′ end.
In some embodiments, the bacteriophage DNA is from a lysogenic or temperate bacteriophage. In some embodiments, the bacteriophage includes, but is not limited to, p1106, p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4209, p4430, or PB1, or two or more phage thereof.
In some embodiments, bacteriophages of interest are obtained from environmental sources. or commercial research vendors. In some embodiments, obtained bacteriophages are screened for lytic activity against a library of bacteria and their associated strains. In some embodiments, the bacteriophages are screened against a library of bacteria and their associated strains for their ability to generate primary resistance in the screened bacteria.
In some embodiments, a nucleic acid is inserted into the bacteriophage genome. In some embodiments, the nucleic acid comprises a crArray, a Cas system, or a combination thereof. In some embodiments, the nucleic acid is inserted into the bacteriophage genome at a transcription terminator site at the end of an operon of interest. In some embodiments, the nucleic acid is inserted into the bacteriophage genome as a replacement for one or more removed non-essential genes. In some embodiments, the nucleic acid is inserted into the bacteriophage genome as a replacement for one or more removed lysogenic genes. In some embodiments, the replacement of non-essential and/or lysogenic genes with the nucleic acid enhances the lytic activity of the bacteriophage. In some embodiments, the replacement of non-essential and/or lysogenic genes with the nucleic acid renders a lysogenic bacteriophage lytic.
In some embodiments, a nucleic acid is introduced into the bacteriophage genome at a first location while one or more non-essential and/or lysogenic genes are separately removed and/or inactivated from the bacteriophage genome at a separate location. In some embodiments, the removal of one or more non-essential and/or lysogenic genes renders a lysogenic bacteriophage into a lytic bacteriophage. Similarly, in some embodiments, one or more lytic genes are introduced into the bacteriophage so as to render a non-lytic, lysogenic bacteriophage into a lytic bacteriophage.
In some embodiments, the replacement, removal, inactivation, or any combination thereof, of one or more non-essential and/or lysogenic genes is achieved by chemical, biochemical, and/or any suitable method. In some embodiments, the insertion of one or more lytic genes is achieved by any suitable chemical, biochemical, and/or physical method by homologous recombination.
In some embodiments, the non-essential gene to be removed and/or replaced from the bacteriophage is a gene that is non-essential for the survival of the bacteriophage. In some embodiments, the non-essential gene to be removed and/or replaced from the bacteriophage is a gene that is non-essential for the induction and/or maintenance of lytic cycle.
Disclosed herein, in certain embodiments, are bacteriophages comprising a complete exogenous CRISPR-Cas system. In some embodiments, the CRISPR-Cas system is Type I CRISPR-Cas system, Type II CRISPR-Cas system, Type III CRISPR-Cas system, Type IV CRISPR-Cas system, Type V CRISPR-Cas system, or Type VI CRISPR-Cas system. Disclosed herein, in certain embodiments, are bacteriophages comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising: (a) a CRISPR array; (b) a Cascade polypeptide; and (c) a Cas3 polypeptide. In some embodiments, the CRISPR-Cas system comprises at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 24. In some embodiments, the CRISPR-Cas system comprises at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 25.
In some embodiments, the bacteriophage is p1106 (ATCC Accession No. PTA-127024), wherein the bacteriophage comprises a Type I CRISPR-Cas system. In some embodiments, the bacteriophage is p1587 (ATCC Accession No. PTA-127027), wherein the bacteriophage comprises a Type I CRISPR-Cas system. In some embodiments, the bacteriophage is p1772 (ATCC Accession No. PTA-127030), wherein the bacteriophage comprises a Type I CRISPR-Cas system. In some embodiments, the bacteriophage is p1835 (ATCC Accession No. PTA-127032), wherein the bacteriophage comprises a Type I CRISPR-Cas system. In some embodiments, the bacteriophage is p2037 (ATCC Accession No. PTA-127034), wherein the bacteriophage comprises a Type I CRISPR-Cas system. In some embodiments, the bacteriophage is p2131 (ATCC Accession No. PTA-127036), wherein the bacteriophage comprises a Type I CRISPR-Cas system. In some embodiments, the bacteriophage is p2132 (ATCC Accession No. PTA-127038), wherein the bacteriophage comprises a Type I CRISPR-Cas system. In some embodiments, the bacteriophage is p2363 (ATCC Accession No. PTA-127041), wherein the bacteriophage comprises a Type I CRISPR-Cas system. In some embodiments, the bacteriophage is p2421 (ATCC Accession No. PTA-127043), wherein the bacteriophage comprises a Type I CRISPR-Cas system. In some embodiments, the bacteriophage is p2973 (ATCC Accession No. PTA-127045), wherein the bacteriophage comprises a Type I CRISPR-Cas system. In some embodiments, the bacteriophage is PB1 (ATCC Accession No. PTA-127049), wherein the bacteriophage comprises a Type I CRISPR-Cas system. In some embodiments, the bacteriophage comprises a phage listed in Table 1A.
In some embodiments, the bacteriophage comprises a CRISPR-system having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 24. In some embodiments, the bacteriophage comprises a CRISPR-system having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 25.
In some embodiments, the bacteriophage is p1106e003 (ATCC Accession No. PTA-127023) or is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to p1106e003. In some embodiments, the bacteriophage is p1587e002 (ATCC Accession No. PTA-127026) or is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to p1587e002. In some embodiments, the bacteriophage is p1772e005 (ATCC Accession No. PTA-127029) or is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to p1772e005. In some embodiments, the bacteriophage is p1835e002 (ATCC Accession No. PTA-127031) or is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to p1835e002. In some embodiments, the bacteriophage is p2037e002 (ATCC Accession No. PTA-127033) or is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to p2037e002. In some embodiments, the bacteriophage is p2131e002 (ATCC Accession No. PTA-127035) or is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to p2131e002. In some embodiments, the bacteriophage is p2132e002 (ATCC Accession No. PTA-127037) or is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to p2132e002. In some embodiments, the bacteriophage is p2363e003 (ATCC Accession No. PTA-127040) or is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to p2363e003. In some embodiments, the bacteriophage is p2421e002 (ATCC Accession No. PTA-127042) or is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to p2421e002. In some embodiments, the bacteriophage is p2973e002 (ATCC Accession No. PTA-127044) or is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to p2973e002. In some embodiments, the bacteriophage is PB 1e002 (ATCC Accession No. PTA-127048) or is at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to PB 1e002. In some embodiments, the bacteriophage comprises a phage listed in Table 1A. In some embodiments, provided is a bacteriophage cocktail system comprising one or more engineered bacteriophage, and a wild-type phage. In some embodiments, the wild-type phage is a phage of Table 5A, Table 5B, or Table 6A. In some embodiments, the wild-type phage is a wildtype Pbunavirus. Non-limiting example wild-type Pbunavirus include p1106, p1587, p1835, p2037, p2363, p2421, and pb1. In some embodiments, the wild-type phage is a wild-type Samunavirus. Non-limiting example wild-type Samunavirus include p1772, p2121, p2132, and p2973. In some embodiments, the wild-type phage is a wild-type a Nankokuvirus. In some embodiments, the wild-type phage is a wild-type PhiKZ-virus. Non-limiting examples of wild-type PhiKZ-virus include p1194p.b008 and p4430. In some embodiments, the wild-type phage is wild-type PhiKMV-virus. A non-limiting example of a wild-type PhiKMV-virus is p2167. In some embodiments, the wild-type phage is wild-type Bruynoghevirus. Non-limiting examples of a wild-type Bruynoghevirus include p1695 and p3278. In some embodiments, the wild-type phage is p1194. In some embodiments, the wild-type phage is p4430. In some embodiments, the wild-type phage is p1695. In some embodiments, the wild-type phage is PhiKZvirus, PhiKMV virus, Brunyoghevirus, Samunavirus, Nankokuvirus, Abidjanvirus, Baikalvirus, Beetrevirus, Casadabanvirus, Citexvirus, Cystovirus, Detrevirus, Elvirus, Hollowayvirus, Kochitakasuvirus, Litunavirus, Luzseptimavirus, Nipunavirus, Pakpunavirus, Pamexvirus, Paundecimvirus, Phitrevirus, Primolicivirus, Septimatrevirus, Stubburvirus, Tertilicivirus, Yuavirus, Zicotriavirus or Pbunavirus.
In some embodiments, the bacteriophage cocktail system comprises CK000512 (p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695).
In some embodiments, a plurality of bacteriophages are used together. In some embodiments, the plurality of bacteriophages used together targets the same or different bacteria within a sample or subject. In some embodiments, a cocktail comprising a plurality of bacteriophages is used together. In some embodiments, the cocktail comprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 phages selected from Table 1A. In some embodiments, the cocktail comprises 2 phages selected from Table 1A. In some embodiments, the cocktail comprises 3 phages selected from Table 1A. In some embodiments, the cocktail comprises 3 phages selected from Table 1A. In some embodiments, the cocktail comprises 4 phages selected from Table 1A. In some embodiments, the cocktail comprises 5 phages selected from Table 1A. In some embodiments, the cocktail comprises 6 phages selected from Table 1A. In some embodiments, the cocktail comprises a cocktail selected from Table 6A. In some embodiments, at least one bacteriophage in the cocktail comprises a CRISPR array. In some embodiments, at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 bacteriophages present in the cocktail comprise a CRISPR array. In some embodiments, at least one bacteriophage in the cocktail comprises a nucleic acid sequence encoding a Cascade polypeptide. In some embodiments, at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 bacteriophages present in the cocktail comprise a nucleic acid sequence encoding a Cascade polypeptide. In some embodiments, at least one bacteriophage in the cocktail comprises a nucleic acid sequence encoding a Cas3 polypeptide. In some embodiments, at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 bacteriophages present in the cocktail comprise a nucleic acid sequence encoding a Cas3 polypeptide. In some embodiments, the cocktail comprises p1106e003, p1835e002, p1772e005, and p2131e002. In some embodiments, the cocktail further comprises p1194. In some embodiments, the cocktail further comprises p1695. In some embodiments, the cocktail further comprises p4430. In some embodiments, the cocktail comprises p1106e003, p1835e002, p1772e005, p2131e002, p1194, and p1695. In some embodiments, the cocktail comprises p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695.
In some embodiments, provided herein is a PhiKZvirus bacteriophage comprising a Type I CRISPR-Cas system. In some embodiments, the PhiKZvirus is p1194 or p4430. In some embodiments, the CRISPR-Cas system comprises one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; a Cascade polypeptide; and a Cas3 polypeptide. In some embodiments, the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array comprises at least one repeat sequence comprising at least about 90% sequence identity to any one of SEQ ID NOS: 26-30. In some embodiments, the nucleic acid sequence further comprises a promoter sequence, e.g., selected from SEQ ID NOS: 1-11. In some embodiments, the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
In some embodiments, provided herein is a PhiKMV virus bacteriophage comprising a Type I CRISPR-Cas system. In some embodiments, the PhiKMV virus is p2167. In some embodiments, the CRISPR-Cas system comprises one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; a Cascade polypeptide; and a Cas3 polypeptide. In some embodiments, the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array comprises at least one repeat sequence comprising at least about 90% sequence identity to any one of SEQ ID NOS: 26-30. In some embodiments, the nucleic acid sequence further comprises a promoter sequence, e.g., selected from SEQ ID NOS: 1-11. In some embodiments, the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
In some embodiments, provided herein is a Brunyoghevirus bacteriophage comprising a Type I CRISPR-Cas system. In some embodiments, the Brunyoghevirus is p1695 or p3278. In some embodiments, the CRISPR-Cas system comprises one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; a Cascade polypeptide; and a Cas3 polypeptide. In some embodiments, the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array comprises at least one repeat sequence comprising at least about 90% sequence identity to any one of SEQ ID NOS: 26-30. In some embodiments, the nucleic acid sequence further comprises a promoter sequence, e.g., selected from SEQ ID NOS: 1-11. In some embodiments, the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
In some embodiments, provided herein is a Samunavirus bacteriophage comprising a Type I CRISPR-Cas system. In some embodiments, the Samunavirus is p1772, p2131, p2132, or p2973. In some embodiments, the CRISPR-Cas system comprises one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; a Cascade polypeptide; and a Cas3 polypeptide. In some embodiments, the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array comprises at least one repeat sequence comprising at least about 90% sequence identity to any one of SEQ ID NOS: 26-30. In some embodiments, the nucleic acid sequence further comprises a promoter sequence, e.g., selected from SEQ ID NOS: 1-11. In some embodiments, the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
In some embodiments, provided herein is a Pbunavirus bacteriophage comprising a Type I CRISPR-Cas system. In some embodiments, the Pbunavirus is p1106, p1587, p1835, p2037, p2363, p2421, or 01. In some embodiments, the CRISPR-Cas system comprises one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; a Cascade polypeptide; and a Cas3 polypeptide. In some embodiments, the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array comprises at least one repeat sequence comprising at least about 90% sequence identity to any one of SEQ ID NOS: 26-30. In some embodiments, the nucleic acid sequence further comprises a promoter sequence, e.g., selected from SEQ ID NOS: 1-11. In some embodiments, the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
In some embodiments, provided herein is a Nankokuvirus bacteriophage comprising a Type I CRISPR-Cas system. In some embodiments, the CRISPR-Cas system comprises one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; a Cascade polypeptide; and a Cas3 polypeptide. In some embodiments, the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array comprises at least one repeat sequence comprising at least about 90% sequence identity to any one of SEQ ID NOS: 26-30. In some embodiments, the nucleic acid sequence further comprises a promoter sequence, e.g., selected from SEQ ID NOS: 1-11. In some embodiments, the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
In some embodiments, provided herein is an Abidjanvirus, Baikalvirus, Beetrevirus, Casadabanvirus, Citexvirus, Cystovirus, Detrevirus, Elvirus, Hollowayvirus, Kochitakasuvirus, Litunavirus, Luzseptimavirus, Nipunavirus, Pakpunavirus, Pamexvirus, Paundecimvirus, Phitrevirus, Primolicivirus, Septimatrevirus, Stubburvirus, Tertilicivirus, Yuavirus, or Zicotriavirus bacteriophage comprising a Type I CRISPR-Cas system. In some embodiments, the CRISPR-Cas system comprises one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; a Cascade polypeptide; and a Cas3 polypeptide. In some embodiments, the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array comprises at least one repeat sequence comprising at least about 90% sequence identity to any one of SEQ ID NOS: 26-30. In some embodiments, the nucleic acid sequence further comprises a promoter sequence, e.g., selected from SEQ ID NOS: 1-11. In some embodiments, the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
In some embodiments, the CRISPR array (crArray) comprises a spacer sequence and at least one repeat sequence. In some embodiments, the CRISPR array encodes a processed, mature crRNA. In some embodiments, the mature crRNA is introduced into a phage or a Pseudomonas species. In some embodiments, an endogenous or exogenous Cas6 processes the CRISPR array into mature crRNA. In some embodiments, an exogenous Cas6 is introduced into the phage. In some embodiments, the phage comprises an exogenous Cas6. In some embodiments, an exogenous Cas6 is introduced into a Pseudomonas species.
In some embodiments, the CRISPR array comprises a spacer sequence. In some embodiments, the CRISPR array further comprises at least one repeat sequence. In some embodiments, the at least one repeat sequence is operably linked to the spacer sequence at either its 5′ end or its 3′ end. In some embodiments, the CRISPR array is of any length and comprises any number of spacer nucleotide sequences alternating with repeat nucleotide sequences necessary to achieve the desired level of killing of a Pseudomonas species by targeting one or more essential genes. In some embodiments, the CRISPR array comprises, consists essentially of, or consists of 1 to about 100 spacer nucleotide sequences, each linked on its 5′ end and its 3′ end to a repeat nucleotide sequence. In some embodiments, the CRISPR array comprises, consists essentially of, or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, or more, spacer nucleotide sequences.
In some embodiments, the CRISPR array comprises a sequence at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 83. In some embodiments, the CRISPR array comprises a sequence at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 84. In some embodiments, the CRISPR array comprises a sequence at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 85. In some embodiments, the CRISPR array comprises a sequence at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 86. In some embodiments, the CRISPR array comprises a sequence at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 87. In some embodiments, the CRISPR array is engineered into a PhiKZ virus. In some embodiments, the PhiKZ virus is p1194 or p4430. In some embodiments, the CRISPR array is engineered into a PhiKMV virus. In some embodiments, the PhiKMV virus is p2167. In some embodiments, the CRISPR array is engineered into a Brunyoghevirus virus. In some embodiments, the Brunyoghevirus is p1695 or p3278. In some embodiments, the CRISPR array is engineered into a Samunavirus virus. In some embodiments, the Samunavirus is p1772, p2131, p2132, or p2973. In some embodiments, the CRISPR array is engineered into a Pbunavirus. In some embodiments, the Pbunavirus is p1106, p1587, p1835, p2037, p2363, p2421, or pb1. In some embodiments, the CRISPR array is engineered into a Nankokuvirus. In some embodiments, the CRISPR array is engineered into a Abidjanvirus. In some embodiments, the CRISPR array is engineered into a Baikalvirus. In some embodiments, the CRISPR array is engineered into a Beetrevirus. In some embodiments, the CRISPR array is engineered into a Casadabanvirus. In some embodiments, the CRISPR array is engineered into a Citexvirus. In some embodiments, the CRISPR array is engineered into a Cystovirus. In some embodiments, the CRISPR array is engineered into a Detrevirus. In some embodiments, the CRISPR array is engineered into a Elvirus. In some embodiments, the CRISPR array is engineered into a Hollowayvirus. In some embodiments, the CRISPR array is engineered into a Kochitakasuvirus. In some embodiments, the CRISPR array is engineered into a Litunavirus. In some embodiments, the CRISPR array is engineered into a Luzseptimavirus. In some embodiments, the CRISPR array is engineered into a Nipunavirus. In some embodiments, the CRISPR array is engineered into a Pakpunavirus. In some embodiments, the CRISPR array is engineered into a Pamexvirus. In some embodiments, the CRISPR array is engineered into a Paundecimvirus. In some embodiments, the CRISPR array is engineered into a Phitrevirus. In some embodiments, the CRISPR array is engineered into a Primolicivirus. In some embodiments, the CRISPR array is engineered into a Septimatrevirus. In some embodiments, the CRISPR array is engineered into a Stubburvirus. In some embodiments, the CRISPR array is engineered into a Tertilicivirus. In some embodiments, the CRISPR array is engineered into a Yuavirus. In some embodiments, the CRISPR array is engineered into a Zicotriavirus.
In some embodiments, the spacer sequence is complementary to a target nucleotide sequence in a Pseudomonas species. In some embodiments, the spacer sequence is complementary to a target nucleotide sequence in Pseudomonas aeruginosa. the In some embodiments, the target nucleotide sequence is a coding region. In some embodiments, the coding region is an essential gene. In some embodiments, the coding region is a nonessential gene. In some embodiments, the target nucleotide sequence is a noncoding sequence. In some embodiments, the noncoding sequence is an intergenic sequence. In some embodiments, the spacer sequence is complementary to a target nucleotide sequence of a highly conserved sequence in a Pseudomonas species. In some embodiments, the spacer sequence is complementary to a target nucleotide sequence of a sequence present in the Pseudomonas species. In some embodiments, the spacer sequence is complementary to a target nucleotide sequence that comprises all or a part of a promoter sequence of the essential gene. In some embodiments, the spacer sequence comprises one, two, three, four, or five mismatches as compared to the target nucleotide sequence. In some embodiments, the mismatches are contiguous. In some embodiments, the mismatches are noncontiguous. In some embodiments, the spacer sequence has 70% complementarity to a target nucleotide sequence. In some embodiments, the spacer sequence has 80% complementarity to a target nucleotide sequence. In some embodiments, the spacer sequence is 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% complementarity to a target nucleotide sequence. In some embodiments, the spacer sequence has 100% complementarity to the target nucleotide sequence. In some embodiments, the spacer sequence has complete complementarity or substantial complementarity over a region of a target nucleotide sequence that are at least about 8 nucleotides to about 150 nucleotides in length. In some embodiments, a spacer sequence has complete complementarity or substantial complementarity over a region of a target nucleotide sequence that is at least about 20 nucleotides to about 100 nucleotides in length. In some embodiments, the 5 ‘ region of the spacer sequence is 100% complementary to a target nucleotide sequence while the 3’ region of the spacer is substantially complementary to the target nucleotide sequence and therefore the overall complementarity of the spacer sequence to the target nucleotide sequence is less than 100%. For example, in some embodiments, the first 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 nucleotides in the 3′ region of a 20 nucleotide spacer sequence (seed region) is 100% complementary to the target nucleotide sequence, while the remaining nucleotides in the 5′ region of the spacer sequence are substantially complementary (e.g., at least about 70% complementary) to the target nucleotide sequence. In some embodiments, the first 7 to 12 nucleotides of the 3′ end of the spacer sequence is 100% complementary to the target nucleotide sequence, while the remaining nucleotides in the 5′ region of the spacer sequence are substantially complementary (e.g., at least about 50% complementary (e.g., 50%, 55%, 60%, 65%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more)) to the target nucleotide sequence. In some embodiments, the first 7 to 10 nucleotides in the 3′ end of the spacer sequence is 75%-99% complementary to the target nucleotide sequence, while the remaining nucleotides in the 5′ region of the spacer sequence are at least about 50% to about 99% complementary to the target nucleotide sequence. In some embodiments, the first 7 to 10 nucleotides in the 3′ end of the spacer sequence is 100% complementary to the target nucleotide sequence, while the remaining nucleotides in the 5′ region of the spacer sequence are substantially complementary (e.g., at least about 70% complementary) to the target nucleotide sequence. In some embodiments, the first 10 nucleotides (within the seed region) of the spacer sequence is 100% complementary to the target nucleotide sequence, while the remaining nucleotides in the 5′ region of the spacer sequence are substantially complementary (e.g., at least about 70% complementary) to the target nucleotide sequence. In some embodiment, the 5′ region of a spacer sequence (e.g., the first 8 nucleotides at the 5′ end, the first 10 nucleotides at the 5′ end, the first 15 nucleotides at the 5′ end, the first 20 nucleotides at the 5′ end) have about 75% complementarity or more (75% to about 100% complementarity) to the target nucleotide sequence, while the remainder of the spacer sequence have about 50% or more complementarity to the target nucleotide sequence. In some embodiments, the first 8 nucleotides at the 5′ end of the spacer sequence have 100% complementarity to the target nucleotide sequence or have one or two mutations and therefore is about 88% complementary or about 75% complementary to the target nucleotide sequence, respectively, while the remainder of the spacer nucleotide sequence is at least about 50% or more complementary to the target nucleotide sequence.
In some embodiments, the spacer sequence is about 15 nucleotides to about 150 nucleotides in length. In some embodiments, the spacer nucleotide sequence is about 15 nucleotides to about 100 nucleotides in length (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 nucleotides or more). In some embodiments, the spacer nucleotide sequence is a length of about 8 to about 150 nucleotides, about 8 to about 100 nucleotides, about 8 to about 50 nucleotides, about 8 to about 40 nucleotides, about 8 to about 30 nucleotides, about 8 to about 25 nucleotides, about 8 to about 20 nucleotides, about 10 to about 150 nucleotides, about 10 to about 100 nucleotides, about 10 to about 80 nucleotides, about 10 to about 50 nucleotides, about 10 to about 40, about 10 to about 30, about 10 to about 25, about 10 to about 20, about 15 to about 150, about 15 to about 100, about 15 to about 50, about 15 to about 40, about 15 to about 30, about 20 to about 150 nucleotides, about 20 to about 100 nucleotides, about 20 to about 80 nucleotides, about 20 to about 50 nucleotides, about 20 to about 40, about 20 to about 30, about 20 to about 25, at least about 8, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 32, at least about 35, at least about 40, at least about 44, at least about 50, at least about 60, at least about 70, at least about 80, at least about 90, at least about 100, at least about 110, at least about 120, at least about 130, at least about 140, at least about 150 nucleotides in length, or more, and any value or range therein. In some embodiments, the P. aeruginosa Type I-C Cas system has a spacer length of about 30 to 39 nucleotides, about 31 to about 38 nucleotides, about 32 to about 37 nucleotides, about 33 to about 36 nucleotides, about 34 to about 35 nucleotides, or about 35 nucleotides In some embodiments, the P. aeruginosa Type I-C Cas system has a spacer length of about 34 nucleotides. In some embodiments, the P. aeruginosa Type I-C Cas system has a spacer length of at least about 10, at least about 15, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 26, at least about 27, at least about 29, at least about 29, at least about 30, at least about 31, at least about 32, at least about 33, at least about 34, at least about, at least about 35, at least about 36, at least about 37, at least about 38, at least about 39, at least about 20, at least about 41, at least about 42, at least about 43, at least about 44, at least about 45, or more than about 45 nucleotides.
In some embodiments, the spacer sequence comprises at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some instances, the spacer sequence comprises at least or about 95% homology to any one of SEQ ID NOS: 12-23, 31-74, or 88-120. In some instances, the spacer sequence comprises at least or about 97% homology to any one of SEQ ID NOS: 12-23, 31-74, or 88-120. In some instances, the spacer sequence comprises at least or about 99% homology to any one of SEQ ID NOS: 12-23, 31-74, or 88-120. In some instances, the spacer sequence comprises 100% homology to any one of SEQ ID NOS: 12-23, 31-74, or 88-120. In some instances, the spacer sequence comprises at least a portion having at least or about 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or more than 34 nucleotides of any one of SEQ ID NOS: 12-23, 31-74, or 88-120.
The term “sequence identity” means that two polynucleotide sequences are identical (i.e., on a nucleotide-by-nucleotide basis) over the window of comparison. The term “percentage of sequence identity” is calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, U, or I) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity.
The term “homology” or “similarity” between two proteins is determined by comparing the amino acid sequence and its conserved amino acid substitutes of one protein sequence to the second protein sequence. Similarity may be determined by procedures which are well-known in the art, for example, a BLAST program (Basic Local Alignment Search Tool at the National Center for Biological Information).
In some embodiments, the identity of two or more spacer sequences of the CRISPR array is the same. In some embodiments, the identity of two or more spacer sequences of the CRISPR array is different. In some embodiments, the identity of two or more spacer sequences of the CRISPR array is different but are complementary to one or more target nucleotide sequences. In some embodiments, the identity of two or more spacer sequences of the CRISPR array is different and are complementary to one or more target nucleotide sequences that are overlapping sequences. In some embodiments, the identity of two or more spacer sequences of the CRISPR array is different and are complementary to one or more target nucleotide sequences that are not overlapping sequences. In some embodiments, the target nucleotide sequence is about 10 to about 40 consecutive nucleotides in length located immediately adjacent to a PAM sequence (PAM sequence located immediately 3′ of the target region) in the genome of the organism. In some embodiments, a target nucleotide sequence is located adjacent to or flanked by a PAM (protospacer adjacent motif). In some embodiments, the two or more sequences of the CRISPR array comprises at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some instances, the two or more sequences of the CRISPR array comprises at least or about 95% homology to any one of SEQ ID NOS: 12-23, 31-74, or 88-120. In some instances, the two or more sequences of the CRISPR array comprises at least or about 97% homology to any one of SEQ ID NOS: 12-23, 31-74, or 88-120. In some instances, the two or more sequences of the CRISPR array comprises at least or about 99% homology to any one of SEQ ID NOS: 12-23, 31-74, or 88-120. In some instances, the two or more sequences of the CRISPR array comprises 100% homology to any one of SEQ ID NOS: 12-23, 31-74, or 88-120. In some instances, the two or more sequences of the CRISPR array comprises at least a portion having at least or about 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or more than 34 nucleotides of any one of SEQ ID NOS: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array is engineered into a PhiKZ virus. In some embodiments, the PhiKZ virus is p1194 or p4430. In some embodiments, the CRISPR array is engineered into a PhiKMV virus. In some embodiments, the PhiKMV virus is p2167. In some embodiments, the CRISPR array is engineered into a Brunyoghevirus virus. In some embodiments, the Brunyoghevirus is p1695 or p3278. In some embodiments, the CRISPR array is engineered into a Samunavirus virus. In some embodiments, the Samunavirus is p1772, p2131, p2132, or p2973. In some embodiments, the CRISPR array is engineered into a Pbunavirus. In some embodiments, the Pbunavirus is p1106, p1587, p1835, p2037, p2363, p2421, or pb1. In some embodiments, the CRISPR array is engineered into a Nankokuvirus. In some embodiments, the CRISPR array is engineered into a Abidjanvirus. In some embodiments, the CRISPR array is engineered into a Baikalvirus. In some embodiments, the CRISPR array is engineered into a Beetrevirus. In some embodiments, the CRISPR array is engineered into a Casadabanvirus. In some embodiments, the CRISPR array is engineered into a Citexvirus. In some embodiments, the CRISPR array is engineered into a Cystovirus. In some embodiments, the CRISPR array is engineered into a Detrevirus. In some embodiments, the CRISPR array is engineered into a Elvirus. In some embodiments, the CRISPR array is engineered into a Hollowayvirus. In some embodiments, the CRISPR array is engineered into a Kochitakasuvirus. In some embodiments, the CRISPR array is engineered into a Litunavirus. In some embodiments, the CRISPR array is engineered into a Luzseptimavirus. In some embodiments, the CRISPR array is engineered into a Nipunavirus. In some embodiments, the CRISPR array is engineered into a Pakpunavirus. In some embodiments, the CRISPR array is engineered into a Pamexvirus. In some embodiments, the CRISPR array is engineered into a Paundecimvirus. In some embodiments, the CRISPR array is engineered into a Phitrevirus. In some embodiments, the CRISPR array is engineered into a Primolicivirus. In some embodiments, the CRISPR array is engineered into a Septimatrevirus. In some embodiments, the CRISPR array is engineered into a Stubburvirus. In some embodiments, the CRISPR array is engineered into a Tertilicivirus. In some embodiments, the CRISPR array is engineered into a Yuavirus. In some embodiments, the CRISPR array is engineered into a Zicotriavirus.
In some embodiments, the CRISPR array comprises a first spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 12-15; a second spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 16-19; a third spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 20-23, wherein said first spacer sequence, second spacer sequence, and third spacer sequence comprise from 0-8 nucleotide modifications. In some instances, the first spacer sequence comprises at least or about 97% homology to any one of SEQ ID NOS: 12-15; the second spacer sequence comprises at least or about 97% homology to any one of SEQ ID NOS: 16-19; and the third spacer sequence comprises at least or about 97% homology to any one of SEQ ID NOS: 20-23. In some instances, the first spacer sequence comprises at least or about 99% homology to any one of SEQ ID NOS: 12-15; the second spacer sequence comprises at least or about 99% homology to any one of SEQ ID NOS: 16-19; and the third spacer sequence comprises at least or about 99% homology to any one of SEQ ID NOS: 20-23. In some instances, the first spacer sequence comprises at least or about 100% homology to any one of SEQ ID NOS: 12-15; the second spacer sequence comprises at least or about 100% homology to any one of SEQ ID NOS: 16-19; and the third spacer sequence comprises at least or about 100% homology to any one of SEQ ID NOS: 20-23. In some embodiments, the CRISPR array is engineered into a PhiKZ virus. In some embodiments, the PhiKZ virus is p1194 or p4430. In some embodiments, the CRISPR array is engineered into a PhiKMV virus. In some embodiments, the PhiKMV virus is p2167. In some embodiments, the CRISPR array is engineered into a Brunyoghevirus virus. In some embodiments, the Brunyoghevirus is p1695 or p3278. In some embodiments, the CRISPR array is engineered into a Samunavirus virus. In some embodiments, the Samunavirus is p1772, p2131, p2132, or p2973. In some embodiments, the CRISPR array is engineered into a Pbunavirus. In some embodiments, the Pbunavirus is p1106, p1587, p1835, p2037, p2363, p2421, or pb1. In some embodiments, the CRISPR array is engineered into a Nankokuvirus. In some embodiments, the CRISPR array is engineered into a Abidjanvirus. In some embodiments, the CRISPR array is engineered into a Baikalvirus. In some embodiments, the CRISPR array is engineered into a Beetrevirus. In some embodiments, the CRISPR array is engineered into a Casadabanvirus. In some embodiments, the CRISPR array is engineered into a Citexvirus. In some embodiments, the CRISPR array is engineered into a Cystovirus. In some embodiments, the CRISPR array is engineered into a Detrevirus. In some embodiments, the CRISPR array is engineered into a Elvirus. In some embodiments, the CRISPR array is engineered into a Hollowayvirus. In some embodiments, the CRISPR array is engineered into a Kochitakasuvirus. In some embodiments, the CRISPR array is engineered into a Litunavirus. In some embodiments, the CRISPR array is engineered into a Luzseptimavirus. In some embodiments, the CRISPR array is engineered into a Nipunavirus. In some embodiments, the CRISPR array is engineered into a Pakpunavirus. In some embodiments, the CRISPR array is engineered into a Pamexvirus. In some embodiments, the CRISPR array is engineered into a Paundecimvirus. In some embodiments, the CRISPR array is engineered into a Phitrevirus. In some embodiments, the CRISPR array is engineered into a Primolicivirus. In some embodiments, the CRISPR array is engineered into a Septimatrevirus. In some embodiments, the CRISPR array is engineered into a Stubburvirus. In some embodiments, the CRISPR array is engineered into a Tertilicivirus. In some embodiments, the CRISPR array is engineered into a Yuavirus. In some embodiments, the CRISPR array is engineered into a Zicotriavirus.
In some embodiments, the CRISPR array comprises a first spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 12; a second spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 16; a third spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 20, wherein said first spacer sequence, second spacer sequence, and third spacer sequence comprise from 0-8 nucleotide modifications. In some instances, the first spacer sequence comprises at least or about 97% homology to SEQ ID NO: 12; the second spacer sequence comprises at least or about 97% homology to SEQ ID NO: 16; and the third spacer sequence comprises at least or about 97% homology to SEQ ID NO: 20. In some instances, the first spacer sequence comprises at least or about 99% homology to SEQ ID NO: 12; the second spacer sequence comprises at least or about 99% homology to SEQ ID NO: 16; and the third spacer sequence comprises at least or about 99% homology to SEQ ID NO: 20. In some instances, the first spacer sequence comprises at least or about 100% homology to SEQ ID NO: 12; the second spacer sequence comprises at least or about 100% homology to SEQ ID NO: 16; and the third spacer sequence comprises at least or about 100% homology to SEQ ID NO: 20. In some embodiments, the CRISPR array is engineered into a PhiKZ virus. In some embodiments, the PhiKZ virus is p1194 or p4430. In some embodiments, the CRISPR array is engineered into a PhiKMV virus. In some embodiments, the PhiKMV virus is p2167. In some embodiments, the CRISPR array is engineered into a Brunyoghevirus virus. In some embodiments, the Brunyoghevirus is p1695 or p3278. In some embodiments, the CRISPR array is engineered into a Samunavirus virus. In some embodiments, the Samunavirus is p1772, p2131, p2132, or p2973. In some embodiments, the CRISPR array is engineered into a Pbunavirus. In some embodiments, the Pbunavirus is p1106, p1587, p1835, p2037, p2363, p2421, or 01. In some embodiments, the CRISPR array is engineered into a Nankokuvirus. In some embodiments, the CRISPR array is engineered into a Abidjanvirus. In some embodiments, the CRISPR array is engineered into a Baikalvirus. In some embodiments, the CRISPR array is engineered into a Beetrevirus. In some embodiments, the CRISPR array is engineered into a Casadabanvirus. In some embodiments, the CRISPR array is engineered into a Citexvirus. In some embodiments, the CRISPR array is engineered into a Cystovirus. In some embodiments, the CRISPR array is engineered into a Detrevirus. In some embodiments, the CRISPR array is engineered into a Elvirus. In some embodiments, the CRISPR array is engineered into a Hollowayvirus. In some embodiments, the CRISPR array is engineered into a Kochitakasuvirus. In some embodiments, the CRISPR array is engineered into a Litunavirus. In some embodiments, the CRISPR array is engineered into a Luzseptimavirus. In some embodiments, the CRISPR array is engineered into a Nipunavirus. In some embodiments, the CRISPR array is engineered into a Pakpunavirus. In some embodiments, the CRISPR array is engineered into a Pamexvirus. In some embodiments, the CRISPR array is engineered into a Paundecimvirus. In some embodiments, the CRISPR array is engineered into a Phitrevirus. In some embodiments, the CRISPR array is engineered into a Primolicivirus. In some embodiments, the CRISPR array is engineered into a Septimatrevirus. In some embodiments, the CRISPR array is engineered into a Stubburvirus. In some embodiments, the CRISPR array is engineered into a Tertilicivirus. In some embodiments, the CRISPR array is engineered into a Yuavirus. In some embodiments, the CRISPR array is engineered into a Zicotriavirus.
In some embodiments, the CRISPR array comprises a first spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 13; a second spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 17; a third spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 21, wherein said first spacer sequence, second spacer sequence, and third spacer sequence comprise from 0-8 nucleotide modifications. In some instances, the first spacer sequence comprises at least or about 97% homology to SEQ ID NO: 13; the second spacer sequence comprises at least or about 97% homology to SEQ ID NO: 17; and the third spacer sequence comprises at least or about 97% homology to SEQ ID NO: 21. In some instances, the first spacer sequence comprises at least or about 99% homology to SEQ ID NO: 13; the second spacer sequence comprises at least or about 99% homology to SEQ ID NO: 17; and the third spacer sequence comprises at least or about 99% homology to SEQ ID NO: 21. In some instances, the first spacer sequence comprises at least or about 100% homology to SEQ ID NO: 13; the second spacer sequence comprises at least or about 100% homology to SEQ ID NO: 17; and the third spacer sequence comprises at least or about 100% homology to SEQ ID NO: 21. In some embodiments, the CRISPR array is engineered into a PhiKZ virus. In some embodiments, the PhiKZ virus is p1194 or p4430. In some embodiments, the CRISPR array is engineered into a PhiKMV virus. In some embodiments, the PhiKMV virus is p2167. In some embodiments, the CRISPR array is engineered into a Brunyoghevirus virus. In some embodiments, the Brunyoghevirus is p1695 or p3278. In some embodiments, the CRISPR array is engineered into a Samunavirus virus. In some embodiments, the Samunavirus is p1772, p2131, p2132, or p2973. In some embodiments, the CRISPR array is engineered into a Pbunavirus. In some embodiments, the Pbunavirus is p1106, p1587, p1835, p2037, p2363, p2421, or 01. In some embodiments, the CRISPR array is engineered into a Nankokuvirus. In some embodiments, the CRISPR array is engineered into a Abidjanvirus. In some embodiments, the CRISPR array is engineered into a Baikalvirus. In some embodiments, the CRISPR array is engineered into a Beetrevirus. In some embodiments, the CRISPR array is engineered into a Casadabanvirus. In some embodiments, the CRISPR array is engineered into a Citexvirus. In some embodiments, the CRISPR array is engineered into a Cystovirus. In some embodiments, the CRISPR array is engineered into a Detrevirus. In some embodiments, the CRISPR array is engineered into a Elvirus. In some embodiments, the CRISPR array is engineered into a Hollowayvirus. In some embodiments, the CRISPR array is engineered into a Kochitakasuvirus. In some embodiments, the CRISPR array is engineered into a Litunavirus. In some embodiments, the CRISPR array is engineered into a Luzseptimavirus. In some embodiments, the CRISPR array is engineered into a Nipunavirus. In some embodiments, the CRISPR array is engineered into a Pakpunavirus. In some embodiments, the CRISPR array is engineered into a Pamexvirus. In some embodiments, the CRISPR array is engineered into a Paundecimvirus. In some embodiments, the CRISPR array is engineered into a Phitrevirus. In some embodiments, the CRISPR array is engineered into a Primolicivirus. In some embodiments, the CRISPR array is engineered into a Septimatrevirus. In some embodiments, the CRISPR array is engineered into a Stubburvirus. In some embodiments, the CRISPR array is engineered into a Tertilicivirus. In some embodiments, the CRISPR array is engineered into a Yuavirus. In some embodiments, the CRISPR array is engineered into a Zicotriavirus.
In some embodiments, the CRISPR array comprises a first spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 14; a second spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 18; a third spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 22, wherein said first spacer sequence, second spacer sequence, and third spacer sequence comprise from 0-8 nucleotide modifications. In some instances, the first spacer sequence comprises at least or about 97% homology to SEQ ID NO: 14; the second spacer sequence comprises at least or about 97% homology to SEQ ID NO: 18; and the third spacer sequence comprises at least or about 97% homology to SEQ ID NO: 22. In some instances, the first spacer sequence comprises at least or about 99% homology to SEQ ID NO: 14; the second spacer sequence comprises at least or about 99% homology to SEQ ID NO: 18; and the third spacer sequence comprises at least or about 99% homology to SEQ ID NO: 22. In some instances, the first spacer sequence comprises at least or about 100% homology to SEQ ID NO: 14; the second spacer sequence comprises at least or about 100% homology to SEQ ID NO: 18; and the third spacer sequence comprises at least or about 100% homology to SEQ ID NO: 22. In some embodiments, the CRISPR array is engineered into a PhiKZ virus. In some embodiments, the PhiKZ virus is p1194 or p4430. In some embodiments, the CRISPR array is engineered into a PhiKMV virus. In some embodiments, the PhiKMV virus is p2167. In some embodiments, the CRISPR array is engineered into a Brunyoghevirus virus. In some embodiments, the Brunyoghevirus is p1695 or p3278. In some embodiments, the CRISPR array is engineered into a Samunavirus virus. In some embodiments, the Samunavirus is p1772, p2131, p2132, or p2973. In some embodiments, the CRISPR array is engineered into a Pbunavirus. In some embodiments, the Pbunavirus is p1106, p1587, p1835, p2037, p2363, p2421, or 01. In some embodiments, the CRISPR array is engineered into a Nankokuvirus. In some embodiments, the CRISPR array is engineered into a Abidjanvirus. In some embodiments, the CRISPR array is engineered into a Baikalvirus. In some embodiments, the CRISPR array is engineered into a Beetrevirus. In some embodiments, the CRISPR array is engineered into a Casadabanvirus. In some embodiments, the CRISPR array is engineered into a Citexvirus. In some embodiments, the CRISPR array is engineered into a Cystovirus. In some embodiments, the CRISPR array is engineered into a Detrevirus. In some embodiments, the CRISPR array is engineered into a Elvirus. In some embodiments, the CRISPR array is engineered into a Hollowayvirus. In some embodiments, the CRISPR array is engineered into a Kochitakasuvirus. In some embodiments, the CRISPR array is engineered into a Litunavirus. In some embodiments, the CRISPR array is engineered into a Luzseptimavirus. In some embodiments, the CRISPR array is engineered into a Nipunavirus. In some embodiments, the CRISPR array is engineered into a Pakpunavirus. In some embodiments, the CRISPR array is engineered into a Pamexvirus. In some embodiments, the CRISPR array is engineered into a Paundecimvirus. In some embodiments, the CRISPR array is engineered into a Phitrevirus. In some embodiments, the CRISPR array is engineered into a Primolicivirus. In some embodiments, the CRISPR array is engineered into a Septimatrevirus. In some embodiments, the CRISPR array is engineered into a Stubburvirus. In some embodiments, the CRISPR array is engineered into a Tertilicivirus. In some embodiments, the CRISPR array is engineered into a Yuavirus. In some embodiments, the CRISPR array is engineered into a Zicotriavirus.
In some embodiments, the CRISPR array comprises a first spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 15; a second spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 19; a third spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 23, wherein said first spacer sequence, second spacer sequence, and third spacer sequence comprise from 0-8 nucleotide modifications. In some instances, the first spacer sequence comprises at least or about 97% homology to SEQ ID NO: 15; the second spacer sequence comprises at least or about 97% homology to SEQ ID NO: 19; and the third spacer sequence comprises at least or about 97% homology to SEQ ID NO: 23. In some instances, the first spacer sequence comprises at least or about 99% homology to SEQ ID NO: 15; the second spacer sequence comprises at least or about 99% homology to SEQ ID NO: 19; and the third spacer sequence comprises at least or about 99% homology to SEQ ID NO: 23. In some instances, the first spacer sequence comprises at least or about 100% homology to SEQ ID NO: 15; the second spacer sequence comprises at least or about 100% homology to SEQ ID NO: 19; and the third spacer sequence comprises at least or about 100% homology to SEQ ID NO: 23. In some embodiments, the CRISPR array is engineered into a PhiKZ virus. In some embodiments, the PhiKZ virus is p1194 or p4430. In some embodiments, the CRISPR array is engineered into a PhiKMV virus. In some embodiments, the PhiKMV virus is p2167. In some embodiments, the CRISPR array is engineered into a Brunyoghevirus virus. In some embodiments, the Brunyoghevirus is p1695 or p3278. In some embodiments, the CRISPR array is engineered into a Samunavirus virus. In some embodiments, the Samunavirus is p1772, p2131, p2132, or p2973. In some embodiments, the CRISPR array is engineered into a Pbunavirus. In some embodiments, the Pbunavirus is p1106, p1587, p1835, p2037, p2363, p2421, or pb1. In some embodiments, the CRISPR array is engineered into a Nankokuvirus. In some embodiments, the CRISPR array is engineered into a Abidjanvirus. In some embodiments, the CRISPR array is engineered into a Baikalvirus. In some embodiments, the CRISPR array is engineered into a Beetrevirus. In some embodiments, the CRISPR array is engineered into a Casadabanvirus. In some embodiments, the CRISPR array is engineered into a Citexvirus. In some embodiments, the CRISPR array is engineered into a Cystovirus. In some embodiments, the CRISPR array is engineered into a Detrevirus. In some embodiments, the CRISPR array is engineered into a Elvirus. In some embodiments, the CRISPR array is engineered into a Hollowayvirus. In some embodiments, the CRISPR array is engineered into a Kochitakasuvirus. In some embodiments, the CRISPR array is engineered into a Litunavirus. In some embodiments, the CRISPR array is engineered into a Luzseptimavirus. In some embodiments, the CRISPR array is engineered into a Nipunavirus. In some embodiments, the CRISPR array is engineered into a Pakpunavirus. In some embodiments, the CRISPR array is engineered into a Pamexvirus. In some embodiments, the CRISPR array is engineered into a Paundecimvirus. In some embodiments, the CRISPR array is engineered into a Phitrevirus. In some embodiments, the CRISPR array is engineered into a Primolicivirus. In some embodiments, the CRISPR array is engineered into a Septimatrevirus. In some embodiments, the CRISPR array is engineered into a Stubburvirus. In some embodiments, the CRISPR array is engineered into a Tertilicivirus. In some embodiments, the CRISPR array is engineered into a Yuavirus. In some embodiments, the CRISPR array is engineered into a Zicotriavirus.
In some embodiments, the spacers are combined in plurality, in clusters within one or more bacteriophages, e.g. engineered bacteriophages. A bacteriophage or a bacteriophage cocktail may comprise one or more arrays with a first spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 12-15; a second spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 16-19; a third spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 20-23. In some embodiments, the bacteriophage cocktail may comprise one or more arrays with a first spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 12; a second or a third spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 23. In some embodiments, the bacteriophage cocktail may comprise one or more arrays with a first spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 13; a second or a third spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 22. In some embodiments, the bacteriophage cocktail may comprise one or more arrays with a first spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 14; a second or a third spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 21. In some embodiments, the bacteriophage cocktail may comprise one or more arrays with a first spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 15; a second or a third spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 20. In some embodiments, the bacteriophage cocktail may comprise one or more arrays with a first spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 16; a second or a third spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 19. In some embodiments, the bacteriophage cocktail may comprise one or more arrays with a first spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 17; a second or a third spacer sequence comprising at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 18. In some embodiments, a plurality of bacteriophages are used together. In some embodiments, the plurality of bacteriophages used together targets the same or different bacteria within a sample or subject. In some embodiments, a cocktail comprising a plurality of bacteriophages is used together. In some embodiments, the cocktail comprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 phages selected from Table 1A. In some embodiments, the cocktail comprises 2 phages selected from Table 1A. In some embodiments, cocktail comprises a wild-type or engineered PhiKZ virus. In some embodiments, the PhiKZ virus is p1194 or p4430. In some embodiments, cocktail comprises a wild-type or engineered PhiKMV virus. In some embodiments, the PhiKMV virus is p2167. In some embodiments, cocktail comprises a wild-type or engineered Brunyoghevirus virus. In some embodiments, the Brunyoghevirus is p1695 or p3278. In some embodiments, cocktail comprises a wild-type or engineered Samunavirus virus. In some embodiments, the Samunavirus is p1772, p2131, p2132, or p2973. In some embodiments, cocktail comprises a wild-type or engineered Pbunavirus. In some embodiments, the Pbunavirus is p1106, p1587, p1835, p2037, p2363, p2421, or 01. In some embodiments, cocktail comprises a wild-type or engineered Nankokuvirus. In some embodiments, cocktail comprises a wild-type or engineered Abidjanvirus. In some embodiments, cocktail comprises a wild-type or engineered Baikalvirus. In some embodiments, cocktail comprises a wild-type or engineered Beetrevirus. In some embodiments, cocktail comprises a wild-type or engineered Casadabanvirus. In some embodiments, cocktail comprises a wild-type or engineered Citexvirus. In some embodiments, cocktail comprises a wild-type or engineered Cystovirus. In some embodiments, cocktail comprises a wild-type or engineered Detrevirus. In some embodiments, cocktail comprises a wild-type or engineered Elvirus. In some embodiments, cocktail comprises a wild-type or engineered Hollowayvirus. In some embodiments, cocktail comprises a wild-type or engineered Kochitakasuvirus. In some embodiments, cocktail comprises a wild-type or engineered Litunavirus. In some embodiments, cocktail comprises a wild-type or engineered Luzseptimavirus. In some embodiments, cocktail comprises a wild-type or engineered Nipunavirus. In some embodiments, cocktail comprises a wild-type or engineered Pakpunavirus. In some embodiments, cocktail comprises a wild-type or engineered Pamexvirus. In some embodiments, cocktail comprises a wild-type or engineered Paundecimvirus. In some embodiments, cocktail comprises a wild-type or engineered Phitrevirus. In some embodiments, cocktail comprises a wild-type or engineered Primolicivirus. In some embodiments, cocktail comprises a wild-type or engineered Septimatrevirus. In some embodiments, cocktail comprises a wild-type or engineered Stubburvirus. In some embodiments, cocktail comprises a wild-type or engineered Tertilicivirus. In some embodiments, cocktail comprises a wild-type or engineered Yuavirus. In some embodiments, cocktail comprises a wild-type or engineered Zicotriavirus.
In some embodiments, the cocktail comprises a cocktail selected from Table 6A. In some embodiments, at least one bacteriophage in the cocktail comprises a CRISPR array. In some embodiments, at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 bacteriophages present in the cocktail comprise a CRISPR array. In some embodiments, at least one bacteriophage in the cocktail comprises a nucleic acid sequence encoding a Cascade polypeptide. In some embodiments, at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 bacteriophages present in the cocktail comprise a nucleic acid sequence encoding a Cascade polypeptide. In some embodiments, at least one bacteriophage in the cocktail comprises a nucleic acid sequence encoding a Cas3 polypeptide. In some embodiments, at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27 bacteriophages present in the cocktail comprise a nucleic acid sequence encoding a Cas3 polypeptide. In some embodiments, the cocktail comprises p1106e003, p1835e002, p1772e005, and p2131e002. In some embodiments, the cocktail further comprises p1194. In some embodiments, the cocktail further comprises p1695. In some embodiments, the cocktail further comprises p4430. In some embodiments, the cocktail comprises p1106e003, p1835e002, p1772e005, p2131e002, p1194, and p1695. In some embodiments, the cocktail comprises p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695.
The PAM sequence is found in the target gene next to the region to which a spacer sequence binds as a result of being complementary to that region and identifies the point at which base pairing with the spacer nucleotide sequence begins. The exact PAM sequence that is required varies between each different CRISPR-Cas system and is identified through established bioinformatics and experimental procedures. Non-limiting examples of PAMs include CCA, CCT, CCG, TTC, AAG, AGG, ATG, GAG, and/or CC. For Type I systems, the PAM is located immediately 5′ to the sequence that matches the spacer, and thus is 3′ to the sequence that base pairs with the spacer nucleotide sequence, and is directly recognized by Cascade. Once a protospacer is recognized, Cascade generally recruits the endonuclease Cas3, which cleaves and degrades the target DNA. For Type II systems, the PAM is required for a Cas9/sgRNA to form an R-loop to interrogate a specific DNA sequence through Watson-Crick pairing of its guide RNA with the genome. The PAM specificity is a function of the DNA-binding specificity of the Cas9 protein (e.g., a—protospacer adjacent motif recognition domain at the C-terminus of Cas9)
In some embodiments, the target nucleotide sequence in the bacterium to be killed is any essential target nucleotide sequence of interest. In some embodiments, the target nucleotide sequence is a non-essential sequence. In some embodiments, a target nucleotide sequence comprises, consists essentially of or consist of all or a part of a nucleotide sequence encoding a promoter, or a complement thereof, of the essential gene. In some embodiments, the spacer nucleotide sequence is complementary to a promoter, or a part thereof, of the essential gene. In some embodiments, the target nucleotide sequence comprises all or a part of a nucleotide sequence located on a coding or a non-coding strand of the essential gene. In some embodiments, the target nucleotide sequence comprises all or a part of a nucleotide sequence located on a coding of a transcribed region of the essential gene.
In some embodiments, the essential gene is any gene of an organism that is critical for its survival. However, being essential is highly dependent on the circumstances in which an organism lives. For instance, a gene required to digest starch is only essential if starch is the only source of energy. In some embodiments, the target nucleotide sequence comprises all or a part of a promoter sequence for the target gene. In some embodiments, the target nucleotide sequence comprises all or a part of a nucleotide sequence located on a coding strand of a transcribed region of the target gene. In some embodiments, the target nucleotide sequence comprises at least a portion of an essential gene that is needed for survival of the Pseudomonas species. In some embodiments, the target nucleotide sequence comprises a highly-conserved non-coding or intergenic sequence. In some embodiments, the target sequence is an intergenic sequence that sits between the essential gene rpmF and a conserved hypothetical protein. In some embodiments, the essential gene is Tsf, acpP, gapA, infA, secY, csrA, trmD, ftsA, fusA, glyQ, eno, nusG, dnaA, dnaS, pheS, rplB, gltX, hisS, rplC, aspS, gyrB, glnS, dnaE, rpoA, rpoB, pheT, infB, rpsC, rplF, alaS, leuS, serS, rplD, gyrA, glmS, fus, adk, rpsK, rplR, ctrA, parC, tRNA-Ser, tRNA-Asn, or metK. In some embodiments, the essential gene is dnaA, ftsA, gyrB, dnaN, glnS, or rpoB. In some embodiments, the target sequence is PA4325 (hypothetical protein), PA1310 (phnW, pyruvate aminotransferase), or the boundary between PA2970 (rpmF, 50S ribosomal protein L32) and PA2971 (conserved hypothetical protein). In some embodiments, a non-essential gene is any gene of an organism that is not critical for survival. However, being non-essential is highly dependent on the circumstances in which an organism lives.
In some embodiments, non-limiting examples of the target nucleotide sequence of interest includes a target nucleotide sequence encoding a transcriptional regulator, a translational regulator, a polymerase gene, a metabolic enzyme, a transporter, an RNase, a protease, a DNA replication enzyme, a DNA modifying or degrading enzyme, a regulatory RNA, a transfer RNA, or a ribosomal RNA. In some embodiments, the target nucleotide sequence is from a gene involved in cell-division, cell structure, metabolism, motility, pathogenicity, virulence, or antibiotic resistance. In some embodiments, the target nucleotide sequence is from a hypothetical gene whose function is not yet characterized. Thus, for example, these genes are any genes from any bacterium.
In some embodiments, the appropriate spacer sequences for a full-construct phage is identified by locating a search set of representative genomes, searching the genomes with relevant parameters, and determining the quality of a spacer for use in a CRISPR engineered phage.
First, a suitable search set of representative genomes is located and acquired for the organism/species/target of interest. The set of representative genomes, in some embodiments, is found in a variety of databases, including without limitations the NCBI GenBank or the PATRIC database. NCBI GenBank is one of the largest databases available and contains a mixture of reference and submitted genomes for nearly every organism sequenced to date. Specifically, for pathogenic prokaryotes, the PATRIC (Pathosystems Resource Integration Center) database provides an additional comprehensive resource of genomes and provides a focus on clinically relevant strains and genomes relevant to a drug product. Both of the above databases allow for bulk downloading of genomes via FTP (File Transfer Protocol) servers, enabling rapid and programmatic dataset acquisition
Next, the genomes are searched with relevant parameters to locate suitable spacer sequences. In some embodiments, genomes are read from start to end, in both the forward and reverse complement orientations, to locate contiguous stretches of DNA that contain a PAM (Protospacer Adjacent Motif) site. The spacer sequence will be the N-length DNA sequence 3′ or 5′ adjacent to the PAM site (depending on the CRISPR system type), where N is specific to the Cas system of interest and is generally known ahead of time. Characterizing the PAM sequence and spacer sequences, in some embodiments, is performed during the discovery and initial research of a Cas system. In some embodiments, every observed PAM-adjacent spacer is saved to a file and/or database for downstream use. The exact PAM sequence that is required varies between each different CRISPR-Cas system and is identified through established bioinformatics and experimental procedures.
Next, the quality of a spacer for use in a CRISPR engineered phage is determined. Each observed spacer, in some embodiments, is evaluated to determine how many of the evaluated genomes they are present in. In some embodiments, the observed spacers are evaluated to see how many times they may occur in each given genome. Spacers that occur in more than one location per genome, in some embodiments, are advantageous because the Cas system may not be able to recognize the target site if a mutation occurs, and each additional “backup” site increases the likelihood that a suitable, non-mutated target location will be present. In some embodiments, the observed spacers are evaluated to determine whether they occur in functionally annotated regions of the genome. If such information is available, the functional annotations may be further evaluated to determine whether those regions of the genome are “essential” for the survival and function of the organism. By focusing on spacers that occur in all, or nearly all, evaluated genomes of interest (>=99%), the spacer selection may be broadly applicable to many targeted genomes. Provided a large selection pool of conserved spacers exists, preference may be given to spacers that occur in regions of the genome that have known function, with higher preference given if those genomic regions are “essential” for survival and occur more than 1 time per genome.
The spacer sequences for a full construct phage, in some embodiments, are validated. In some embodiments, a first step comprises identifying a plasmid that replicates in the organism, species, or target of interest. In some embodiments, the plasmid has a selectable marker. In some embodiments, the selectable marker is an antibiotic-resistance gene. In some embodiments, an expression cassette includes a nucleotide sequence for a selectable marker. In some embodiments, the selectable marker is adenine deaminase (ada), blasticidin S deaminases (Bsr, BSD), bleomycin-binding protein (Ble), Neomycin phosphotransferase (neo), histidinol dehydrogenase (hisD), glutamine synthetase (GS), dihydrofolate reductase (dhfr), cytosine deaminase (codA), puromycin N-acetyltransferase (Pac), or hygromycin B phosphotransferase (Hph), ampicillin, chloramphenicol, kanamycin, tetracycline, polymyxin B, erythromycin, carbenicillin, streptomycin, spectinomycin, puromycin N-acetyltransferase (Pac), or zeocin (Sh bla). In some embodiments, the selectable marker is a gene involved in thymidylate synthase, thymidine kinase, dihydrofolate reductase, or glutamine synthetase. In some embodiments, the selectable marker is a gene encoding a fluorescent protein.
In some embodiments, a second step comprises inserting the genes encoding the Cas system into the plasmid such that they will be expressed in the organism, species, or target of interest. In some embodiments, a promoter is provided upstream of the Cas system. In some embodiments, the promoter is recognized by the organism, species, or target of interest to drive the expression of the Cas system. Exemplary promoters include, but are not limited to, L-arabinose inducible (araBAD, PBAD) promoter, any lac promoter, L-rhamnose inducible (rhaPBAD) promoter, T7 RNA polymerase promoter, trc promoter, tac promoter, lambda phage promoter (pLpL-9G-50), anhydrotetracycline-inducible (tetA) promoter, trp, Ipp, phoA, recA, proU, cst-1, cadA, nar, Ipp-lac, cspA, 11-lac operator, T3-lac operator, T4 gene 32, T5-lac operator, nprM-lac operator, Vhb, Protein A, corynebacterial-E. coli like promoters, thr, horn, diphtheria toxin promoter, sig A, sig B, nusG, SoxS, katb, α-amylase (Pamy), Ptms, P43 (comprised of two overlapping RNA polymerase a factor recognition sites, σA, σB), Ptms, P43, rplK-rplA, ferredoxin promoter, and/or xylose promoter. In some embodiments, the promoter is a BBa_J23102, BBa_J23104, or BBa_J23109. In some embodiments the promoter is derived from the organism, species, or target bacterium, such as endogenous CRISPR promoter, endogenous Cas operon promoter, p16, plpp, or ptat. In some embodiments, the promoter is a phage promoter, such as the promoter for gp105 or gp245. In some embodiments, a ribosomal binding site (RBS) is provided between the promoter and the Cas system. In some embodiments, the RBS is recognized by the organism, species, or target of interest.
In some embodiments, a third step comprises providing genome-targeting spacers into the plasmid. In some embodiments, the genome-targeting spacers are identified using bioinformatics. In some embodiments, the genome-targeting spacers are provided upstream of the repeat-spacer-repeat. In some embodiments, a promoter is provided. In some embodiments, the promoter is recognized by the organism, species, or target of interest to drive the expression of the crRNA. In some embodiments, the cloning for the third step comprises using an organism or species that is not targeted by the spacer being cloned.
In some embodiments, a fourth step comprises providing a non-target spacer into the plasmid that expresses the Cas system. In some embodiments, the non-target spacer comprises a sequence is random. In some embodiments, the non-target spacer comprises a sequence that does not comprise targeting sites in the genome of the organism, species, or target of interest. In some embodiments, the non-target spacer sequence is determined using bioinformatics to not comprise targeting sites in the genome of the organism, species, or target of interest. In some embodiments, the non-target spacer sequence is provided upstream of the repeat-spacer-repeat. In some embodiments, a promoter is provided. In some embodiments, the promoter is recognized by the organism, species, or target of interest to drive the expression of the crRNA.
In some embodiments, a fifth step comprises determining an efficacy of each spacer generated. In some embodiments, the killing efficacy is determined. In some embodiments, the efficacy of each spacer at targeting the bacterial genome is determined. In some embodiments, the plasmids comprising the spacer comprises about 0.5-fold, about 1-fold, 5-fold, 10-fold, 20-fold, 40-fold, 60-fold, 80-fold, or up to about 100 fold reduction in transfer rate as compared to a plasmid that comprises the non-targeting spacer.
In some embodiments, a repeat nucleotide sequence of the CRISPR array comprises a nucleotide sequence of any known repeat nucleotide sequence of a CRISPR-Cas system. In some embodiments, a repeat nucleotide sequence is of a synthetic sequence comprising the secondary structure of a native repeat from a CRISPR-Cas system (e.g., an internal hairpin). In some embodiments, the repeat nucleotide sequences are distinct from one another based on the known repeat nucleotide sequences of a CRISPR-Cas system. In some embodiments, the repeat nucleotide sequences are each composed of distinct secondary structures of a native repeat from a CRISPR-Cas system (e.g., an internal hairpin). In some embodiments, the repeat nucleotide sequences are a combination of distinct repeat nucleotide sequences operable with a CRISPR-Cas system.
In some embodiments, the spacer sequence is linked at its 5′ end to the 3′ end of a repeat sequence. In some embodiments, the spacer sequence is linked at its 5′ end to about 1 to about 8, about 1 to about 10, or about 1 to about 15 nucleotides of the 3′ end of a repeat sequence. In some embodiments, the about 1 to about 8, about 1 to about 10, about 1 to about 15 nucleotides of the repeat sequence are a portion of the 3′ end of a repeat sequence. In some embodiments, the spacer nucleotide sequence is linked at its 3′ end to the 5′ end of a repeat sequence. In some embodiments, the spacer is linked at its 3′ end to about 1 to about 8, about 1 to about 10, or about 1 to about 15 nucleotides of the 5′ end of a repeat sequence. In some embodiments, the about 1 to about 8, about 1 to about 10, about 1 to about 15 nucleotides of the repeat sequence are a portion of the 5′ end of a repeat sequence.
In some embodiments, the spacer nucleotide sequence is linked at its 5′ end to a first repeat sequence and linked at its 3′ end to a second repeat sequence to form a repeat-spacer-repeat sequence. In some embodiments, the spacer sequence is linked at its 5′ end to the 3′ end of a first repeat sequence and is linked at its 3′ end to the 5′ of a second repeat sequence where the spacer sequence and the second repeat sequence are repeated to form a repeat-(spacer-repeat)n sequence such that n is any integer from 1 to 100. In some embodiments, a repeat-(spacer-repeat)n sequence comprises, consists essentially of, or consists of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, or more, spacer nucleotide sequences.
In some embodiments, the repeat sequence is identical to or substantially identical to a repeat sequence from a wild-type CRISPR loci. In some embodiments, the repeat sequence is a repeat sequence found in Table 3. In some embodiments, the repeat sequence is a sequence described herein. In some embodiments, the repeat sequence comprises a portion of a wild type repeat sequence (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more contiguous nucleotides of a wild type repeat sequence). In some embodiments, the repeat sequence comprises, consists essentially of, or consists of at least one nucleotide (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, or more nucleotides, or any range therein). In some embodiments, the repeat sequence comprises, consists essentially of, or consists of no more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides. In some embodiments, the repeat sequence comprises about 20 to 40, 21 to 40, 22 to 40 23 to 40, 24 to 40, 25 to 40, 26 to 40, 27 to 40, 28 to 40, 29 to 40, 30 to 30, 31 to 40, 32 to 40, 33 to 40, 34 to 40, 35 to 40, 36 to 40, 37 to 40, 38 to 40, 39 to 40, 20 to 39, 20 to 38, 20 to 37, 20 to 36, 20 to 35, 20 to 34, 20 to 33, 20 to 32, 20 to 31, 20 to 30, 20 to 29, 20 to 28, 20 to 26, 20 to 25, 20 to 24, 20 to 23, 20 to 22, or 20 to 21 nucleotides. In some embodiments, the repeat sequence comprises about 20 to 35, 21 to 35, 22 to 35 23 to 35, 24 to 35, 25 to 35, 26 to 35, 27 to 35, 28 to 35, 29 to 35, 30 to 30, 31 to 35, 32 to 35, 33 to 35, 34 to 35, 25 to 40, 25 to 39, 25 to 38, 25 to 37, 25 to 36, 25 to 35, 25 to 34, 25 to 33, 25 to 32, 25 to 31, 25 to 30, 25 to 29, 25 to 28, 25 to 26 nucleotides. In some embodiments, the system is a P. aeruginosa Type I-C Cas system. In some embodiments, the P. aeruginosa Type I-C Cas system has a repeat length of about 25 to 38 nucleotides.
In some embodiments, the repeat sequence comprises at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 26-30. In some instances, the repeat sequence comprises at least or about 95% homology to any one of SEQ ID NOS: 26-30. In some instances, the repeat sequence comprises at least or about 97% homology to any one of SEQ ID NOS: 26-30. In some instances, the repeat sequence comprises at least or about 99% homology to any one of SEQ ID NOS: 26-30. In some instances, the repeat sequence comprises 100% homology to any one of SEQ ID NOS: 26-30. In some instances, the repeat sequence comprises at least a portion having at least or about 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, or more than 32 nucleotides of any one of SEQ ID NOS: 26-30. In some embodiments, the repeat is engineered into a PhiKZ virus. In some embodiments, the PhiKZ virus is p1194 or p4430. In some embodiments, the repeat is engineered into a PhiKMV virus. In some embodiments, the PhiKMV virus is p2167. In some embodiments, the repeat is engineered into a Brunyoghevirus virus. In some embodiments, the Brunyoghevirus is p1695 or p3278. In some embodiments, the repeat is engineered into a Samunavirus virus. In some embodiments, the Samunavirus is p1772, p2131, p2132, or p2973. In some embodiments, the repeat is engineered into a Pbunavirus. In some embodiments, the Pbunavirus is p1106, p1587, p1835, p2037, p2363, p2421, or 01. In some embodiments, the repeat is engineered into a Nankokuvirus. In some embodiments, the repeat is engineered into a Abidjanvirus. In some embodiments, the CRISPR array is engineered into a Baikalvirus. In some embodiments, the repeat is engineered into a Beetrevirus. In some embodiments, the repeat is engineered into a Casadabanvirus. In some embodiments, the repeat is engineered into a Citexvirus. In some embodiments, the CRISPR array is engineered into a Cystovirus. In some embodiments, the repeat is engineered into a Detrevirus. In some embodiments, the repeat is engineered into a Elvirus. In some embodiments, the CRISPR array is engineered into a Hollowayvirus. In some embodiments, the repeat is engineered into a Kochitakasuvirus. In some embodiments, the repeat is engineered into a Litunavirus. In some embodiments, the repeat is engineered into a Luzseptimavirus. In some embodiments, the repeat is engineered into a Nipunavirus. In some embodiments, the repeat is engineered into a Pakpunavirus. In some embodiments, the repeat is engineered into a Pamexvirus. In some embodiments, the repeat is engineered into a Paundecimvirus. In some embodiments, the repeat is engineered into a Phitrevirus. In some embodiments, the repeat is engineered into a Primolicivirus. In some embodiments, the repeat is engineered into a Septimatrevirus. In some embodiments, the repeat is engineered into a Stubburvirus. In some embodiments, the repeat is engineered into a Tertilicivirus. In some embodiments, the repeat is engineered into a Yuavirus. In some embodiments, the repeat is engineered into a Zicotriavirus. In some embodiments, the repeat is part of a CRISPR array engineered into the bacteriophage.
In some embodiments, the Type I CRISPR-Cas system is a Type I-A system, Type I-B system, Type I-C system, Type I-D system, Type I-E system, or Type I-F system. In some embodiments, the Type I CRISPR-Cas system is a Type I-A system. In some embodiments, the Type I CRISPR-Cas system is a Type I-B system. In some embodiments, the Type I CRISPR-Cas system is a Type I-C system. In some embodiments, the Type I CRISPR-Cas system is a Type I-D system. In some embodiments, the Type I CRISPR-Cas system is a Type I-E system. In some embodiments, the Type I CRISPR-Cas system is a Type I-F system. In some embodiments, the Type I CRISPR-Cas system comprises Cascade polypeptides. Type I Cascade polypeptides process CRISPR arrays to produce a processed RNA that is then used to bind the complex to a target sequence that is complementary to the spacer in the processed RNA. In some embodiments, the Type I Cascade complex is a Type I-A Cascade polypeptides, a Type I-B Cascade polypeptides, a Type I-C Cascade polypeptides, a Type I-D Cascade polypeptides, a Type I-E Cascade polypeptides, a Type I-F Cascade polypeptides, or a Type I-U Cascade polypeptides.
In some embodiments, the Type I Cascade complex comprises: (a) a nucleotide sequence encoding a Cas7 (Csa2) polypeptide, a nucleotide sequence encoding a Cas8a1 (Csx13) polypeptide or a Cas8a2 (Csx9) polypeptide, a nucleotide sequence encoding a Cas5 polypeptide, a nucleotide sequence encoding a Csa5 polypeptide, a nucleotide sequence encoding a Cas6a polypeptide, a nucleotide sequence encoding a Cas3′ polypeptide, and a nucleotide sequence encoding a Cas3″ polypeptide having no nuclease activity (Type I-A); (b) a nucleotide sequence encoding a Cas6b polypeptide, a nucleotide sequence encoding a Cas8b (Csh1) polypeptide, a nucleotide sequence encoding a Cas7 (Csh2) polypeptide, and a nucleotide sequence encoding a Cas5 polypeptide (Type I-B); (c) a nucleotide sequence encoding a Cas5d polypeptide, a nucleotide sequence encoding a Cas8c (Csd1) polypeptide, and a nucleotide sequence encoding a Cas7 (Csd2) polypeptide (Type I-C); (d) a nucleotide sequence encoding a Cas1 Od (Csc3) polypeptide, a nucleotide sequence encoding a Csc2 polypeptide, a nucleotide sequence encoding a Csc1 polypeptide, and a nucleotide sequence encoding a Cas6d polypeptide (Type I-D); (e) a nucleotide sequence encoding a Cse1 (CasA) polypeptide, a nucleotide sequence encoding a Cse2 (CasB) polypeptide, a nucleotide sequence encoding a Cas7 (CasC) polypeptide, a nucleotide sequence encoding a Cas5 (CasD) polypeptide, and a nucleotide sequence encoding a Cas6e (CasE) polypeptide (Type I-E); and/or (f) a nucleotide sequence encoding a Cys1 polypeptide, a nucleotide sequence encoding a Cys2 polypeptide, a nucleotide sequence encoding a Cas7 (Cys3) polypeptide, and a nucleotide sequence encoding a Cas6f polypeptide (Type I-F).
In some embodiments, the Type I CRISPR-Cas system is exogenous to the target bacterium. In some embodiments, the exogenous Type I CRISPR-Cas system comprises (a) a nucleotide sequence encoding a Cas7 (Csa2) polypeptide, a nucleotide sequence encoding a Cas8a1 (Csx13) polypeptide or a Cas8a2 (Csx9) polypeptide, a nucleotide sequence encoding a Cas5 polypeptide, a nucleotide sequence encoding a Csa5 polypeptide, a nucleotide sequence encoding a Cas6a polypeptide, a nucleotide sequence encoding a Cas3′ polypeptide, and a nucleotide sequence encoding a Cas3″ polypeptide having no nuclease activity (Type I-A); (b) a nucleotide sequence encoding a Cas6b polypeptide, a nucleotide sequence encoding a Cas8b (Csh1) polypeptide, a nucleotide sequence encoding a Cas7 (Csh2) polypeptide, and a nucleotide sequence encoding a Cas5 polypeptide (Type I-B); (c) a nucleotide sequence encoding a Cas5d polypeptide, a nucleotide sequence encoding a Cas8c (Csd1) polypeptide, and a nucleotide sequence encoding a Cas7 (Csd2) polypeptide (Type I-C); (d) a nucleotide sequence encoding a Cas1 Od (Csc3) polypeptide, a nucleotide sequence encoding a Csc2 polypeptide, a nucleotide sequence encoding a Csc1 polypeptide, and a nucleotide sequence encoding a Cas6d polypeptide (Type I-D); (e) a nucleotide sequence encoding a Cse1 (CasA) polypeptide, a nucleotide sequence encoding a Cse2 (CasB) polypeptide, a nucleotide sequence encoding a Cas7 (CasC) polypeptide, a nucleotide sequence encoding a Cas5 (CasD) polypeptide, and a nucleotide sequence encoding a Cas6e (CasE) polypeptide (Type I-E); and/or (f) a nucleotide sequence encoding a Cyst polypeptide, a nucleotide sequence encoding a Cys2 polypeptide, a nucleotide sequence encoding a Cas7 (Cys3) polypeptide, and a nucleotide sequence encoding a Cas6f polypeptide (Type I-F).
In some embodiments, the Type I CRISPR-Cas system exogenous to the target bacterium comprises a nucleotide sequence encoding a Cas5d polypeptide, a nucleotide sequence encoding a Cas8c (Csd1) polypeptide, and a nucleotide sequence encoding a Cas7 (Csd2) polypeptide (Type I-C).
In some embodiments, the bacteriophage is an obligate lytic bacteriophage. In some embodiments, the bacteriophage is a temperate bacteriophage with retained lysogeny genes. In some embodiments, the bacteriophage is a temperate bacteriophage with some lysogeny genes removed, replaced, or inactivated. In some embodiments, the bacteriophage is a temperate bacteriophage with a lysogeny gene removed, replaced, or inactivated, thereby rendering the bacteriophage lytic.
In some embodiments, the bacteriophage targets Pseudomonas spp. In some embodiments, the bacteriophage targets Pseudomonas aeruginosa. In some embodiments, the bacteriophage specifically targets Pseudomonas spp. over other bacterial species. In some embodiments, the bacteriophage targets Pseudomonas spp. in the absence of a CRISPR-Cas system. In some embodiments, the bacteriophage binds to lipopolysaccharide. In some embodiments, the bacteriophage binds to the Type IV pili. In some embodiments, the bacteriophage binds to outer membrane porin OprM. In some embodiments, targets refers to a bacteriophage that infects a bacteria. In some embodiments, targets refers to a bacteriophage that kills a bacteria. In some embodiments, specifically targets refers to a bacteriophage that infects a first bacterial species, but not a second bacterial species. In some embodiments, specifically targets refers to a bacteriophage that kills a first bacterial species, but not a second bacterial species.
In some embodiments, a bacteriophage herein is or is engineered from a bacteriophage that infects Pseudomonas. In some embodiments, the bacteriophage that infects Pseudomonas is PhiKZvirus, PhiKMV virus, Brunyoghevirus, Samunavirus, Nankokuvirus, Abidjanvirus, Baikalvirus, Beetrevirus, Casadabanvirus, Citexvirus, Cystovirus, Detrevirus, Elvirus, Hollowayvirus, Kochitakasuvirus, Litunavirus, Luzseptimavirus, Nipunavirus, Pakpunavirus, Pamexvirus, Paundecimvirus, Phitrevirus, Primolicivirus, Septimatrevirus, Stubburvirus, Tertilicivirus, Yuavirus, Zicotriavirus or Pbunavirus. In some embodiments, bacteriophages that infect Pseudomonas include a wildtype Pbunavirus phage subtype listed in Table 5A, wherein the phage infects a target Pseudomonas as marked with a positive sign (+) (e.g., phage p1106 infects b002548). In some embodiments, bacteriophages that infect Pseudomonas include an engineered Pbunavirus phage subtype listed in Table 5A, wherein the phage infects a target Pseudomonas as marked with a positive sign (+) (e.g., p1106e003 infects b002548). In some embodiments, bacteriophages that infect Pseudomonas include a wildtype Samunavirus phage subtype, an engineered Samunavirus phage subtype, a wildtype PhiKZvirus, a wildtype PhiKMVvirus, or a wildtype Bruynoghevirus, e.g., as listed in Table 5B, wherein the phage infects a target Pseudomonas as marked with a positive sign (+). As listed in Table 5A, the wildtype Pbunavirus phage subtypes can be p1106, p1587, p1835, p2037, p2363, p2421, and/or pb1, while the engineered Pbunavirus phage subtypes can be p1106e003, p1587e002, p1835e002, p2037e002, p2363e003, and/or p2421e002. As listed in Table 5B, the wildtype Samunavirus phage subtypes can be p1772, p2131, p2132, and/or p2973, the engineered Samunavirus phage subtypes can be pb1e002, p1772e005, p2131e002, p2132e002, and/or p2973e002, the wildtype PhiKZvirus phage subtypes can be p1194, and/or p4430, the wildtype PhiKMVvirus phage subtype can be p2167, and the wildtype Bruynoghevirus phage subtypes can be p1695, and p3278. In some embodiments, the bacteriophage that infects Pseudomonas is a Nankokuvirus. In some embodiments, the bacteriophage that infects Pseudomonas is an Abidjanvirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Baikalvirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Beetrevirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Casadabanvirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Citexvirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Cystovirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Detrevirus. In some embodiments, the bacteriophage that infects Pseudomonas is an Elvirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Hollowayvirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Kochitakasuvirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Litunavirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Luzseptimavirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Nipunavirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Pakpunavirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Pamexvirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Paundecimvirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Phitrevirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Primolicivirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Septimatrevirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Stubburvirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Tertilicivirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Yuavirus. In some embodiments, the bacteriophage that infects Pseudomonas is a Zicotriavirus. In some embodiments, a bacteriophage that infects Pseudomonas kills Pseudomonas. In some embodiments, the bacteriophage that infects Pseudomonas does not infect S. aureus. In some embodiments, the bacteriophage that infects Pseudomonas does not kill S. aureus. In some embodiments, the bacteriophage that kills Pseudomonas does not infect S. aureus. In some embodiments, the bacteriophage that kills Pseudomonas does not kill S. aureus. In some embodiments, the bacteriophage that infects Pseudomonas does not infect K. pneumoniae. In some embodiments, the bacteriophage that infects Pseudomonas does not kill K. pneumoniae. In some embodiments, the bacteriophage that kills Pseudomonas does not infect K. pneumoniae. In some embodiments, the bacteriophage that kills Pseudomonas does not kill K. pneumoniae. In some embodiments, the bacteriophage that infects Pseudomonas does not infect E. faecium. In some embodiments, the bacteriophage that infects Pseudomonas does not kill E. faecium. In some embodiments, the bacteriophage that kills Pseudomonas does not infect E. faecium. In some embodiments, the bacteriophage that kills Pseudomonas does not kill E. faecium. In some embodiments, the bacteriophage that infects Pseudomonas does not infect E. cloacae. In some embodiments, the bacteriophage that infects Pseudomonas does not kill E. cloacae. In some embodiments, the bacteriophage that kills Pseudomonas does not infect E. cloacae. In some embodiments, the bacteriophage that kills Pseudomonas does not kill E. cloacae. In some embodiments, the bacteriophage that infects Pseudomonas does not infect A. baumanii. In some embodiments, the bacteriophage that infects Pseudomonas does not kill A. baumanii. In some embodiments, the bacteriophage that kills Pseudomonas does not infect A. baumanii. In some embodiments, the bacteriophage that kills Pseudomonas does not kill A. baumanii. In some embodiments, the bacteriophage that infects Pseudomonas does not infect S. epidermidis. In some embodiments, the bacteriophage that infects Pseudomonas does not kill S. epidermidis. In some embodiments, the bacteriophage that kills Pseudomonas does not infect S. epidermidis. In some embodiments, the bacteriophage that kills Pseudomonas does not kill S. epidermidis. In some embodiments, a combination of bacteriophage infect Pseudomonas. As a non-limiting example, the combination infects at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the Pseudomonas in Table 5A. As a non-limiting example, the combination infects at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the Pseudomonas in Table 5B. As a non-limiting example, the combination infects at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the Pseudomonas in Table 6B. In some embodiments, a combination of bacteriophage kill Pseudomonas. As a non-limiting example, the combination kills at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the Pseudomonas in Table 5A. As a non-limiting example, the combination kills at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the Pseudomonas in Table 5B. As a non-limiting example, the combination kills at least 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the Pseudomonas in Table 6B.
In some embodiments, the bacteriophage is present in a cocktail comprising other bacteriophage, wherein each of the bacteriophage do not disrupt the function of the other bacteriophage in the cocktail.
In some embodiments, the bacteriophage is a PhiKZvirus, PhiKMV virus, Brunyoghevirus, Samunavirus, Nankokuvirus, Abidjanvirus, Baikalvirus, Beetrevirus, Casadabanvirus, Citexvirus, Cystovirus, Detrevirus, Elvirus, Hollowayvirus, Kochitakasuvirus, Litunavirus, Luzseptimavirus, Nipunavirus, Pakpunavirus, Pamexvirus, Paundecimvirus, Phitrevirus, Primolicivirus, Septimatrevirus, Stubburvirus, Tertilicivirus, Yuavirus, Zicotriavirus or Pbunavirus. In some embodiments, the bacteriophage is a PhiKZvirus. In some embodiments, the bacteriophage is a PhiKMV virus. In some embodiments, the bacteriophage is a Brunyoghevirus. In some embodiments, the bacteriophage is a Samunavirus. In some embodiments, the bacteriophage is a Pbunavirus. In some embodiments, the bacteriophage comprises a CRISPR-Cas3 system. In some embodiments, the bacteriophage includes, but is not limited to, p1106 (ATCC Accession No PTA-127024), p1194(ATCC Accession No PTA-127025), p1587(ATCC Accession No PTA-127027), p1695(ATCC Accession No PTA-127028), p1772(ATCC Accession No PTA-127030), p1835(ATCC Accession No PTA-127032), p2037(ATCC Accession No PTA-127034), p2131(ATCC Accession No PTA-127036), p2132(ATCC Accession No PTA-127038), p2167(ATCC Accession No PTA-127039), p2363(ATCC Accession No PTA-127041), p2421(ATCC Accession No PTA-127043), p2973(ATCC Accession No PTA-127045), p3278(ATCC Accession No PTA-127046), p4430(ATCC Accession No PTA-127047), or PB1(ATCC Accession No PTA-127049), which target Pseudomonas sp.
In some embodiments, the bacteriophage is p1106, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with that of p1106. In some embodiments, the bacteriophage is a p1106 bacteriophage comprising a CRISPR-Cas system. In some embodiments, the bacteriophage is p1106e003(ATCC Accession No. PTA-127023). In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with that of p1106e003.
In some embodiments, the bacteriophage is p1194, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with that of p1194. In some embodiments, the bacteriophage is a p1194 bacteriophage comprising a CRISPR-Cas system.
In some embodiments, the bacteriophage is p1587, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with that of p1587. In some embodiments, the bacteriophage is a p1587 bacteriophage comprising a CRISPR-Cas system. In some embodiments, the bacteriophage is p1587e002 (ATCC Accession No. PTA-127026). In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with that of 01587e002.
In some embodiments, the bacteriophage is p1695, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with that of p1695. In some embodiments, the bacteriophage is a p1695 bacteriophage comprising a CRISPR-Cas system.
In some embodiments, the bacteriophage is p1772, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with that of p1772. In some embodiments, the bacteriophage is a p1772 bacteriophage comprising a CRISPR-Cas system. In some embodiments, the bacteriophage is p1772e005 (ATCC Accession No. PTA-127029). In some embodiments, the bacteriophage comprises at least 70%, 775%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with that of p1772e005.
In some embodiments, the bacteriophage is p1835, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1835. In some embodiments, the bacteriophage is a p1835 bacteriophage comprising a CRISPR-Cas system. In some embodiments, the bacteriophage is p1835e002 (ATCC Accession No. PTA-127026). In some embodiments, the bacteriophage comprises at least 70%, 775%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1835e002.
In some embodiments, the bacteriophage is p2037, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2037. In some embodiments, the bacteriophage is a p2037 bacteriophage comprising a CRISPR-Cas system. In some embodiments, the bacteriophage is p2037e002 (ATCC Accession No. PTA-127033). In some embodiments, the bacteriophage comprises at least 70%, 775%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2037e002.
In some embodiments, the bacteriophage is p2131, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2131. In some embodiments, the bacteriophage is a p2131 bacteriophage comprising a CRISPR-Cas system. In some embodiments, the bacteriophage is p2131 (ATCC Accession No. PTA-127035). In some embodiments, the bacteriophage comprises at least 70%, 775%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2131.
In some embodiments, the bacteriophage is p2132, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2132. In some embodiments, the bacteriophage is a p2132 bacteriophage comprising a CRISPR-Cas system. In some embodiments, the bacteriophage is p2132e002 (ATCC Accession No. PTA-127037). In some embodiments, the bacteriophage comprises at least 70%, 775%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2132e002.
In some embodiments, the bacteriophage is p2167, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2167. In some embodiments, the bacteriophage is a p2167 bacteriophage comprising a CRISPR-Cas system.
In some embodiments, the bacteriophage is p2163, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2163. In some embodiments, the bacteriophage is a p2163 bacteriophage comprising a CRISPR-Cas system. In some embodiments, the bacteriophage is p2163e003 (ATCC Accession No. PTA-127040). In some embodiments, the bacteriophage comprises at least 70%, 775%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2163e003.
In some embodiments, the bacteriophage is p2421, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2421. In some embodiments, the bacteriophage is a p2421 bacteriophage comprising a CRISPR-Cas system. In some embodiments, the bacteriophage is p2141e002 (ATCC Accession No. PTA-127042). In some embodiments, the bacteriophage comprises at least 70%, 775%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2141e0002.
In some embodiments, the bacteriophage is p2973, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2973. In some embodiments, the bacteriophage is a p2973 bacteriophage comprising a CRISPR-Cas system. In some embodiments, the bacteriophage is p2973e002 (ATCC Accession No. PTA-127044). In some embodiments, the bacteriophage comprises at least 70%, 775%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2973e002.
In some embodiments, the bacteriophage is p3278, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p3278. In some embodiments, the bacteriophage is a p3278 bacteriophage comprising a CRISPR-Cas system.
In some embodiments, the bacteriophage is p4430, or a mutant thereof which retains the ability to target Pseudomonas sp. I In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p4430. In some embodiments, the bacteriophage is a p1106 bacteriophage comprising a CRISPR-Cas system. n some embodiments, the bacteriophage is PB1, or a mutant thereof which retains the ability to target Pseudomonas sp. In some embodiments, the bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with PB1. In some embodiments, the bacteriophage is a PB1 bacteriophage comprising a CRISPR-Cas system. In some embodiments, the bacteriophage is PB1e002 (ATCC Accession No. PTA-127049). In some embodiments, the bacteriophage comprises at least 70%, 775%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with PB1e002.
In some embodiments, the bacteriophage comprises a phage listed in Table 1A, or a mutant thereof which retains the ability to target Pseudomonas sp.
Also disclosed herein is a cocktail comprising two or more bacteriophage. In some embodiments, the two or more bacteriophages are selected from the lineage consisting of a PhiKZvirus, PhiKMV virus, Brunyoghevirus, Samunavirus, Nankokuvirus, Abidjanvirus, Baikalvirus, Beetrevirus, Casadabanvirus, Citexvirus, Cystovirus, Detrevirus, Elvirus, Hollowayvirus, Kochitakasuvirus, Litunavirus, Luzseptimavirus, Nipunavirus, Pakpunavirus, Pamexvirus, Paundecimvirus, Phitrevirus, Primolicivirus, Septimatrevirus, Stubburvirus, Tertilicivirus, Yuavirus, Zicotriavirus or Pbunavirus. In some embodiments, the cocktail comprises at least six bacteriophages, wherein the bacteriophages comprise a PhiKZvirus, a PhiKMV virus, a Brunyoghevirus, a Samunavirus, and a Pbunavirus. In some embodiments, the cocktail comprises at least one Pbunavirus, at least one Samunavirus, at least one PhiKZvirus, and at least one Bruynoghevirus. In some embodiments, at least one bacteriophage of the cocktail comprises a CRISPR-Cas system. In some embodiments, at least two bacteriophages of the cocktail comprise a CRISPR-Cas system. In some embodiments, at least three bacteriophages of the cocktail comprise a CRISPR-Cas system. In some embodiments, at least four bacteriophages of the cocktail comprise a CRISPR-Cas system. In some embodiments, at least one bacteriophages of the cocktail does not comprise a CRISPR-Cas system. In some embodiments, at least two bacteriophages of the cocktail do not comprise a CRISPR-Cas system.
In some embodiments, the cocktail comprises at least two bacteriophages, wherein the bacteriophages comprise p1106, p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1, or two or more phage thereof. In some embodiments, the cocktail comprises a first bacteriophage comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1106e003. In some embodiments, the cocktail comprises a second bacteriophage comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1835e002. In some embodiments, the cocktail comprises a third bacteriophage comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1772e005. In some embodiments, the cocktail comprises a fourth bacteriophage comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2131e002. In some embodiments, the cocktail comprises a fifth bacteriophage comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1194. In some embodiments, the cocktail comprises a fifth bacteriophage comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p4430. In some embodiments, the cocktail comprises a fifth bacteriophage comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1695. In some embodiments, the cocktail comprises a sixth bacteriophage comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p4430. In some embodiments, the cocktail comprises a sixth bacteriophage comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1695.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1106. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB 1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1106. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1106, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1106, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1106, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1106, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1106, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1587. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1106, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1106, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1106, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1106, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1106, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB 1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1695. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1106, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1106, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1106, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1106, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1106, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, at least one, two, three, or four bacteriophage comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophage do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1772. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1106, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third with p1194, p1587, p1695, p1106, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB 1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1106, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1106, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1106, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p1835. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1106, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1106, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB 1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1106, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1106, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1106, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2037. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p1106, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p1106, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB 1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p1106, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p1106, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p1106, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2131. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p1106, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p1106, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB 1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p1106, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p1106, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises p1106, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2132. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p1106, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p1106, p2167, p2363, p2421, p2973, p3278, p4430, or PB 1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p1106, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p1106, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p1106, p2167, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2167. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p1106, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p1106, p2363, p2421, p2973, p3278, p4430, or PB 1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p1106, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p1106, p2363, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p1106, p2363, p2421, p2973, p3278, p4430, or PB 1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2363. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p1106, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p1106, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p1106, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p1106, p2421, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p1106, p2421, p2973, p3278, p4430, or PB1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2421. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p1106, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p1106, p2973, p3278, p4430, or PB 1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p1106, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p1106, p2973, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p1106, p2973, p3278, p4430, or PB1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p2973. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p1106, p3278, p4430, or PB 1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p1106, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p1106, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p1106, p3278, p4430, or PB1. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p1106, p3278, p4430, or PB1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p3278. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p1106, p4430, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p1106, p4430, or PB 1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p1106, p4430, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p1106, p4430, or PB1. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p1106, p4430, or PB1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with p4430. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p1106, or PB1. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p1106, or PB 1. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p1106, or PB1. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p1106, or PB1. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p1106, or PB 1. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, the first bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with PB1. In some embodiments, the cocktail comprises a second bacteriophage, wherein the second bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or p1106. In some embodiments, the cocktail comprises a third bacteriophage, wherein the third bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or p1106. In some embodiments, the cocktail comprises a fourth bacteriophage, wherein the fourth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or p1106. In some embodiments, the cocktail comprises a fifth bacteriophage, wherein the fifth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or p1106. In some embodiments, the cocktail comprises a sixth bacteriophage, wherein the sixth bacteriophage comprises at least 70%, 75%, 80%, 85%, 90% 95%, 96%, 97%, 98%, 99%, or 100% with p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or p1106. In some embodiments, at least one, two, three, or four bacteriophages comprise a CRISPR-Cas system. In some embodiments, at least one or two bacteriophages do not comprise a CRISPR Cas system.
In some embodiments, bacteriophages of interest are obtained from environmental sources or from commercial research vendors. In some embodiments, obtained bacteriophages are screened for lytic activity against a library of bacteria and their associated strains. In some embodiments, the bacteriophages are screened against a library of bacteria and their associated strains for their ability to generate primary resistance in the screened bacteria.
In some embodiments, the bacterium is Pseudomonas. In some embodiments, the bacterium is Pseudomonas aeruginosa.
In some embodiments, the Pseudomonas species causes, contributes to and/or causes complications to an infection, disease, or condition, and the compositions and methods described herein are used to treat the infection, disease, or condition. In some embodiments, the infection, disease or condition is acute or chronic. In some embodiments, the infection, disease or condition is localized or systemic. In some embodiments, infection, disease or condition is idiopathic. In some embodiments, the infection, disease or condition is acquired through means including, but not limited to, respiratory inhalation, ingestion, skin and wound infections, blood stream infections, middle-ear infections, gastrointestinal tract infections, peritoneal membrane infections, urinary tract infections, urogenital tract infections, oral soft tissue infections, intra-abdominal infections, epidermal or mucosal absorption, eye infections (including contact lens contamination), endocarditis, infections in cystic fibrosis, infections of indwelling medical devices such as joint prostheses, dental implants, catheters and cardiac implants, sexual contact, and/or hospital-acquired and ventilator-associated bacterial pneumonias. In some embodiments, the Pseudomonas species causes urinary tract infection. In some embodiments, the Pseudomonas species causes and/or exacerbates an inflammatory disease. In some embodiments, the Pseudomonas species causes and/or exacerbates an autoimmune disease. In some embodiments, the Pseudomonas species causes and/or exacerbates inflammatory bowel disease (IBD). In some embodiments, the Pseudomonas species causes and/or exacerbates psoriasis. In some embodiments, the Pseudomonas species causes and/or exacerbates psoriatic arthritis (PA). In some embodiments, the Pseudomonas species causes and/or exacerbates rheumatoid arthritis (RA). In some embodiments, the Pseudomonas species causes and/or exacerbates systemic lupus erythematosus (SLE). In some embodiments, the Pseudomonas species causes and/or exacerbates multiple sclerosis (MS). In some embodiments, the Pseudomonas species causes and/or exacerbates Graves' disease. In some embodiments, the Pseudomonas species causes and/or exacerbates Hashimoto's thyroiditis. In some embodiments, the Pseudomonas species causes and/or exacerbates Myasthenia gravis. In some embodiments, the Pseudomonas species causes and/or exacerbates vasculitis. In some embodiments, the Pseudomonas species causes and/or exacerbates cancer. In some embodiments, the Pseudomonas species causes and/or exacerbates cancer progression. In some embodiments, the Pseudomonas species causes and/or exacerbates cancer metastasis. In some embodiments, the Pseudomonas species causes and/or exacerbates resistance to cancer therapy. In some embodiments, the therapy used to address cancer includes, but is not limited to, chemotherapy, immunotherapy, hormone therapy, targeted drug therapy, and/or radiation therapy. In some embodiments, the cancer develops in organs including, but not limited to the, anus, bladder, blood and blood components, bone, bone marrow, brain, breast, cervix uteri, colon and rectum, esophagus, kidney, larynx, lymphatic system, muscle (i.e., soft tissue), oral cavity and pharynx, ovary, pancreas, prostate, skin, small intestine, stomach, testis, thyroid, uterus, and/or vulva. In some embodiments, the Pseudomonas species causes and/or exacerbates disorders of the central nervous system (CNS). In some embodiments, the Pseudomonas species causes and/or exacerbates attention deficit/hyperactivity disorder (ADHD). In some embodiments, the Pseudomonas species causes and/or exacerbates autism. In some embodiments, the Pseudomonas species causes and/or exacerbates bipolar disorder. In some embodiments, the Pseudomonas species causes and/or exacerbates major depressive disorder. In some embodiments, the Pseudomonas species causes and/or exacerbates epilepsy. In some embodiments, the Pseudomonas species causes and/or exacerbates neurodegenerative disorders including, but not limited to, Alzheimer's disease, Huntington's disease, and/or Parkinson's disease. In some embodiments, the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat any one of the disease or condition or a symptom associated with a disease or condition described above. In some embodiments the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat a disease or condition described above, or a symptom associated with a disease described above, in combination with one or more other drugs for treatment or alleviating one or more conditions associated with the disease.
Cystic fibrosis and cystic fibrosis-associated bronchiectasis is associated with infection by Pseudomonas aeruginosa. See, e.g., P. Farrell, et al, Radiology, Vol. 252, No. 2, pp. 534-543 (2009). In some embodiments, one or more bacteriophages are administered to a patient with cystic fibrosis or cystic fibrosis-associated bronchiectasis. In some embodiments, a combination of two or more bacteriophages are administered to a patient with cystic fibrosis or cystic fibrosis-associated bronchiectasis. In some embodiments, administration of the bacteriophage to a patient with cystic fibrosis or cystic fibrosis-associated bronchiectasis results in a reduction in bacterial load in the patient. In some embodiments, the reduction in bacterial load results in a clinical improvement in the patient with cystic fibrosis or cystic fibrosis-associated bronchiectasis.
Non-cystic fibrosis bronchiectasis is associated with infection by Pseudomonas aeruginosa. See, e.g., R. Wilson, et al, Respiratory Medicine, Vol. 117, pp. 179-189 (2016). In some embodiments, one or more bacteriophages are administered to a patient with non-cystic fibrosis bronchiectasis. In some embodiments, a combination of two or more bacteriophages are administered to a patient with non-cystic fibrosis bronchiectasis. In some embodiments, administration of the bacteriophage to a patient with non-cystic fibrosis bronchiectasis results in a reduction in bacterial load in the patient. In some embodiments, the reduction in bacterial load results in a clinical improvement in the patient with non-cystic fibrosis bronchiectasis.
In some embodiments, the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein are administered to a subject having an infection by Pseudomonas aeruginosa or a disease caused directly or indirectly by Pseudomonas aeruginosa. In some embodiments, the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat a blood stream infection by Pseudomonas aeruginosa. In some embodiments, the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is suitable for treating a respiratory inhalation, ingestion, skin and wound infections by Pseudomonas aeruginosa. In some embodiments, the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat a middle-ear infections, gastrointestinal tract infections, peritoneal membrane infections, urinary tract infections, urogenital tract infections, oral soft tissue infections, intra-abdominal infections, epidermal or mucosal absorption, eye infections (including contact lens contamination), urinary tract infection endocarditis, infections in cystic fibrosis, infections of indwelling medical devices such as joint prostheses, dental implants, catheters and cardiac implants, sexual contact, and/or hospital-acquired and ventilator-associated bacterial pneumonias that is associated with an infection by Pseudomonas aeruginosa. In some embodiments, the Pseudomonas species causes and/or exacerbates an inflammatory disease and the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat the inflammatory disease. In some embodiments, the Pseudomonas species causes and/or exacerbates an autoimmune disease and the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat the autoimmune disease. In some embodiments, the Pseudomonas species causes and/or exacerbates inflammatory bowel disease (IBD) and the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat the IBD. In some embodiments, the bacteriophage is selected from the Table 1A, Table 5A, and/or from the Table 5B. In some embodiments the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat the disease reduce the bacterial burden. In some embodiments the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat the disease reduce the inflammation. In some embodiments the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat the disease reduce one or more symptoms associated with the bacterial infection, or one or more sequela of the bacterial infection.
In some embodiments, the treatment is administered as an intravenous or intramuscular drug. In some embodiments, the treatment is administered via oral route. In some embodiments, the treatment is administered via a nebulizer. In some embodiments, the treatment is administered via a patient-operable nebulizer. In some embodiments, the treatment is administered via a metered dose nebulizer. In some embodiments, the treatment is administered in combination with one or more other drugs or therapeutics.
In some embodiments, the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat cancer. In some embodiments, the bacteriophage is selected from the Table 1A, Table 5A, and/or from the Table 5B.
In some embodiments, the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat pneumonia. In some embodiments, the bacteriophage is selected from the Table 1A, Table 5A, and/or from the Table 5B.
In some embodiments, the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat cystic fibrosis bronchiectasis. In some embodiments, administration of the bacteriophage to a patient with cystic fibrosis or cystic fibrosis-associated bronchiectasis results in a reduction in bacterial load in the patient. In some embodiments, the reduction in bacterial load results in a clinical improvement in the patient with cystic fibrosis bronchiectasis. In some embodiments, the bacteriophage is selected from the Table 1A, Table 5A, and/or from the Table 5B. In some embodiments, the treatment is administered as an intravenous or intramuscular drug. In some embodiments, the treatment is administered via oral route. In some embodiments, the treatment is administered via a nebulizer. In some embodiments, the treatment is administered via a patient-operable nebulizer. In some embodiments, the treatment is administered via a metered dose nebulizer. In some embodiments, the treatment is administered in combination with one or more other drugs or therapeutics.
In some embodiments, the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat non-cystic fibrosis bronchiectasis. In some embodiments, administration of the bacteriophage to a patient with non-cystic fibrosis bronchiectasis or fibrosis-associated bronchiectasis results in a reduction in bacterial load in the patient. In some embodiments, the reduction in bacterial load results in a clinical improvement in the patient with non-cystic fibrosis bronchiectasis fibrosis-associated bronchiectasis. In some embodiments, the bacteriophage is selected from the Table 1A, Table 5A, and/or from the Table 5B. In some embodiments, the treatment is administered as an intravenous or intramuscular drug. In some embodiments, the treatment is administered via oral route. In some embodiments, the treatment is administered via a nebulizer. In some embodiments, the treatment is administered via a patient-operable nebulizer. In some embodiments, the treatment is administered via a metered dose nebulizer. In some embodiments, the treatment is administered in combination with one or more other drugs or therapeutics.
In some embodiments, the treatment comprises a composition, e.g. a pharmaceutical composition comprising one or more bacteriophages, e.g., a bacteriophage cocktail, wherein the bacteriophage in the composition e.g., the bacteriophage cocktail are from the lineage consisting of a PhiKZvirus, PhiKMV virus, Brunyoghevirus, Samunavirus, Nankokuvirus, Abidjanvirus, Baikalvirus, Beetrevirus, Casadabanvirus, Citexvirus, Cystovirus, Detrevirus, Elvirus, Hollowayvirus, Kochitakasuvirus, Litunavirus, Luzseptimavirus, Nipunavirus, Pakpunavirus, Pamexvirus, Paundecimvirus, Phitrevirus, Primolicivirus, Septimatrevirus, Stubburvirus, Tertilicivirus, Yuavirus, Zicotriavirus or Pbunavirus. In some embodiments, the composition comprises the bacteriophage cocktail 511. In some embodiments, the composition comprises the bacteriophage cocktail PACK512. In some embodiments, provided herein is a pharmaceutical composition wherein the pharmaceutical composition comprises at least six bacteriophage, wherein the bacteriophage are from a group consisting of p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695.
In some embodiments, the insertion of the nucleic acid sequence into a bacteriophage preserves the lytic activity of the bacteriophage. In some embodiments, the nucleic acid sequence is inserted into the bacteriophage genome. In some embodiments, the nucleic acid sequence is inserted into the bacteriophage genome at a transcription terminator site at the end of an operon of interest. In some embodiments, the nucleic acid sequence is inserted into the bacteriophage genome as a replacement for one or more removed non-essential genes. In some embodiments, the nucleic acid sequence is inserted into the bacteriophage genome as a replacement for one or more removed lysogenic genes. In some embodiments, the replacement of non-essential and/or lysogenic genes with the nucleic acid sequence does not affect the lytic activity of the bacteriophage. In some embodiments, the replacement of non-essential and/or lysogenic genes with the nucleic acid sequence preserves the lytic activity of the bacteriophage. In some embodiments, the replacement of non-essential and/or lysogenic genes with the nucleic acid sequence enhances the lytic activity of the bacteriophage. In some embodiments, the replacement of non-essential and/or lysogenic genes with the nucleic acid sequence renders a lysogenic bacteriophage lytic.
In some embodiments, the nucleic acid sequence is introduced into the bacteriophage genome at a first location while one or more non-essential and/or lysogenic genes are separately removed and/or inactivated from the bacteriophage genome at a separate location. In some embodiments, the nucleic acid sequence is introduced into the bacteriophage at a first location while one or more non-essential and/or lysogenic genes are separately removed and/or inactivated from the bacteriophage genome at multiple separate locations. In some embodiments, the removal and/or inactivation of one or more non-essential and/or lysogenic genes does not affect the lytic activity of the bacteriophage. In some embodiments, the removal and/or inactivation of one or more non-essential and/or lysogenic genes preserves the lytic activity of the bacteriophage. In some embodiments, the removal of one or more non-essential and/or lysogenic genes renders a lysogenic bacteriophage into a lytic bacteriophage.
In some embodiments, the bacteriophage is a temperate bacteriophage which has been rendered lytic by any of the aforementioned means. In some embodiments, a temperate bacteriophage is rendered lytic by the removal, replacement, or inactivation of one or more lysogenic genes. In some embodiments, the lytic activity of the bacteriophage is due to the removal, replacement, or inactivation of at least one lysogeny gene. In some embodiments, the lysogenic gene plays a role in the maintenance of lysogenic cycle in the bacteriophage. In some embodiments, the lysogenic gene plays a role in establishing the lysogenic cycle in the bacteriophage. In some embodiments, the lysogenic gene plays a role in both establishing the lysogenic cycle and in the maintenance of the lysogenic cycle in the bacteriophage. In some embodiments, the lysogenic gene is a repressor gene. In some embodiments, the lysogenic gene is cI repressor gene. In some embodiments, the lysogenic gene is an activator gene. In some embodiments, the lysogenic gene is cII gene. In some embodiments, the lysogenic gene is lexA gene. In some embodiments, the lysogenic gene is int (integrase) gene. In some embodiments, two or more lysogeny genes are removed, replaced, or inactivated to cause arrest of a bacteriophage lysogeny cycle and/or induction of a lytic cycle. In some embodiments, a temperate bacteriophage is rendered lytic by the insertion of one or more lytic genes. In some embodiments, a temperate bacteriophage is rendered lytic by the insertion of one or more genes that contribute to the induction of a lytic cycle. In some embodiments, a temperate bacteriophage is rendered lytic by altering the expression of one or more genes that contribute to the induction of a lytic cycle. In some embodiments, a temperate bacteriophage phenotypically changes from a lysogenic bacteriophage to a lytic bacteriophage. In some embodiments, a temperate bacteriophage is rendered lytic by environmental alterations. In some embodiments, environmental alterations include, but are not limited to, alterations in temperature, pH, or nutrients, exposure to antibiotics, hydrogen peroxide, foreign DNA, or DNA damaging agents, presence of organic carbon, and presence of heavy metal (e.g., in the form of chromium (VI). In some embodiments, a temperate bacteriophage that is rendered lytic is prevented from reverting to lysogenic state. In some embodiments, a temperate bacteriophage that is rendered lytic is prevented from reverting back to lysogenic state by way the self-targeting activity of the first introduced CRISPR array. In some embodiments, a temperate bacteriophage that is rendered lytic is prevented from reverting back to lysogenic state by way of introducing an additional CRISPR array. In some embodiments, the bacteriophage does not confer any new properties onto the Pseudomonas species beyond cellular death cause by lytic activity of the bacteriophage and/or the activity of the first or second CRISPR array.
In some embodiments, the replacement, removal, inactivation, or any combination thereof, of one or more non-essential and/or lysogenic genes is achieved by chemical, biochemical, and/or any suitable method. In some embodiments, the insertion of one or more lytic genes is achieved by any suitable chemical, biochemical, and/or physical method by homologous recombination.
In some embodiments, the non-essential gene to be removed and/or replaced from the bacteriophage is a gene that is non-essential for the survival of the bacteriophage. In some embodiments, the non-essential gene to be removed and/or replaced from the bacteriophage is a gene that is non-essential for the induction and/or maintenance of lytic cycle.
In some embodiments, the nucleic acid sequence further comprises a transcriptional activator. In some embodiments, the transcriptional activator encoded regulates the expression of genes of interest within the Pseudomonas species. In some embodiments, the transcriptional activator activates the expression of genes of interest within the Pseudomonas species whether exogenous or endogenous. In some embodiments, the transcriptional activator activates the expression genes of interest within the target bacterium by disrupting the activity of one or more inhibitory elements within the target bacterium. In some embodiments, the inhibitory element comprises a transcriptional repressor. In some embodiments, the inhibitory element comprises a global transcriptional repressor. In some embodiments the inhibitory element is a histone-like nucleoid-structuring (H-NS) protein or homologue or functional fragment thereof. In some embodiments, the inhibitory element is a leucine responsive regulatory protein (LRP). In some embodiments, the inhibitory element is a CodY protein.
In some bacteria, the CRISPR-Cas system is poorly expressed and considered silent under most environmental conditions. In these bacteria, the regulation of the CRISPR-Cas system is the result of the activity of transcriptional regulators, for example histone-like nucleoid-structuring (H-NS) protein which is widely involved in transcriptional regulation of the host genome. H-NS exerts control over host transcriptional regulation by multimerization along AT-rich sites resulting in DNA bending. In some bacteria, the regulation of the CRISPR-Cas3 operon is regulated by H-NS.
Similarly, in some bacteria, the repression of the CRISPR-Cas system is controlled by an inhibitory element, for example the leucine responsive regulatory protein (LRP). LRP has been implicated in binding to upstream and downstream regions of the transcriptional start sites. Notably, the activity of LRP in regulating expression of the CRISPR-Cas system varies from bacteria to bacteria. Unlike, H-NS which has broad inter-species repression activity, LRP has been shown to differentially regulate the expression of the host CRISPR-Cas system. As such, in some instances, LRP reflects a host-specific means of regulating CRISPR-Cas system expression in different bacteria.
In some instances, the repression of CRISPR-Cas system is also controlled by inhibitory element CodY. CodY is a GTP-sensing transcriptional repressor that acts through DNA binding. The intracellular concentration of GTP acts as an indicator for the environmental nutritional status. Under normal culture conditions, GTP is abundant and binds with CodY to repress transcriptional activity. However, as GTP concentrations decreases, CodY becomes less active in binding DNA, thereby allowing transcription of the formerly repressed genes to occur. As such, CodY acts as a stringent global transcriptional repressor.
In some embodiments, the transcriptional activator is a LeuO polypeptide, any homolog or functional fragment thereof, a leuO coding sequence, or an agent that upregulates LeuO. In some embodiments, the transcriptional activator comprises any ortholog or functional equivalent of LeuO. In some bacteria, LeuO acts in opposition to H-NS by acting as a global transcriptional regulator that responds to environmental nutritional status of a bacterium. Under normal conditions, LeuO is poorly expressed. However, under amino acid starvation and/or reaching of the stationary phase in the bacterial life cycle, LeuO is upregulated. Increased expression of LeuO leads to it antagonizing H-NS at overlapping promoter regions to effect gene expression. Overexpression of LeuO upregulates the expression of the CRISPR-Cas system.
In some embodiments, the expression of LeuO leads to disruption of an inhibitory element. In some embodiments, the disruption of an inhibitory element due to expression of LeuO removes the transcriptional repression of a CRISPR-Cas system. In some embodiments, the expression of LeuO removes transcriptional repression of a CRISPR-Cas system due to activity of H-NS. In some embodiments, the disruption of an inhibitory element due to the expression of LeuO causes an increase in the expression of a CRISPR-Cas system. In some embodiments, the increase in the expression of a CRISPR-Cas system due to the disruption of an inhibitory element caused by the expression of LeuO causes an increase in the CRISPR-Cas processing of a nucleic acid sequence comprising a CRISPR array. In some embodiments, the increase in the expression of a CRISPR-Cas system due to the disruption of an inhibitory element by the expression of LeuO causes an increase in the CRISPR-Cas processing of a nucleic acid sequence comprising a CRISPR array so as to increase the level of lethality of the CRISPR array against a bacterium. In some embodiments, transcriptional activator causes increase activity of a bacteriophage and/or the CRISPR-Cas system.
In some embodiments, the nucleic acid sequences are operatively associated with a variety of promoters, terminators and other regulatory elements for expression in various organisms or cells. In some embodiments, the nucleic acid sequence further comprises a leader sequence. In some embodiments, the nucleic acid sequence further comprises a promoter sequence. In some embodiments, at least one promoter and/or terminator is operably linked the CRISPR array. Any promoter useful with this disclosure is used and includes, for example, promoters functional with the organism of interest as well as constitutive, inducible, developmental regulated, tissue-specific/preferred-promoters, and the like, as disclosed herein. A regulatory element as used herein is endogenous or heterologous. In some embodiments, an endogenous regulatory element derived from the subject organism is inserted into a genetic context in which it does not naturally occur (e.g. a different position in the genome than as found in nature), thereby producing a recombinant or non-native nucleic acid.
In some embodiments, expression of the nucleic acid sequence is constitutive, inducible, temporally regulated, developmentally regulated, or chemically regulated. In some embodiments, the expression of the nucleic acid sequence is made constitutive, inducible, temporally regulated, developmentally regulated, or chemically regulated by operatively linking the nucleic acid sequence to a promoter functional in an organism of interest. In some embodiments, repression is made reversible by operatively linking the nucleic acid sequence to an inducible promoter that is functional in an organism of interest. The choice of promoter disclosed herein varies depending on the quantitative, temporal and spatial requirements for expression, and also depending on the host cell to be transformed.
Exemplary promoters for use with the methods, bacteriophages and compositions disclosed herein include promoters that are functional in bacteria. For example, L-arabinose inducible (araBAD, PBAD) promoter, any lac promoter, L-rhamnose inducible (rhaPBAD) promoter, T7 RNA polymerase promoter, trc promoter, tac promoter, lambda phage promoter (pLpL-9G-50), anhydrotetracycline-inducible (tetA) promoter, trp, Ipp, phoA, recA, proU, cst-1, cadA, nar, Ipp-lac, cspA, 11-lac operator, T3-lac operator, T4 gene 32, T5-lac operator, nprM-lac operator, Vhb, Protein A, corynebacterial-E. coli like promoters, thr, horn, diphtheria toxin promoter, sig A, sig B, nusG, SoxS, katb, α-amylase (Pamy), Ptms, P43 (comprised of two overlapping RNA polymerase a factor recognition sites, σA, σB), Ptms, P43, rplK-rplA, ferredoxin promoter, and/or xylose promoter. In some embodiments, the promoter is a BBa_J23102 promoter. In some embodiments, the promoter works in a broad range of bacteria, such as BBa_J23104, BBa_J23109. In some embodiments the promoter is derived from the target bacterium, such as endogenous CRISPR promoter, endogenous Cas operon promoter, p16, plpp, or ptat. In some embodiments, the promoter is a phage promoter, such as the promoter for gp105 or gp245.
In some embodiments, the promoter comprises at least or about 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 1-11. In some instances, the promoter comprises at least or about 95% homology to any one of SEQ ID NOS: 1-11. In some instances, the promoter comprises at least or about 97% homology to any one of SEQ ID NOS: 1-11. In some instances, the promoter comprises at least or about 99% homology to any one of SEQ ID NOS: 1-11. In some instances, the promoter comprises 100% homology to any one of SEQ ID NOS: 1-11. In some instances, the promoter comprises at least a portion having at least or about 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or more than 50 nucleotides of any one of SEQ ID NOS: 1-11. In some instances, the promoter comprises at least a portion having at least or about 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, or more than 215 nucleotides of any one of SEQ ID NOS: 1-11.
In some embodiments, inducible promoters are used. In some embodiments, chemical-regulated promoters are used to modulate the expression of a gene in an organism through the application of an exogenous chemical regulator. The use of chemically regulated promoters enables RNAs and/or the polypeptides encoded by the nucleic acid sequence to be synthesized only when, for example, an organism is treated with the inducing chemicals. In some embodiments where a chemical-inducible promoter is used, the application of a chemical induces gene expression. In some embodiments wherein a chemical-repressible promoter is used, the application of the chemical represses gene expression. In some embodiments, the promoter is a light-inducible promoter, where application of specific wavelengths of light induces gene expression. In some embodiments, a promoter is a light-repressible promoter, where application of specific wavelengths of light represses gene expression.
In some embodiments, the nucleic acid sequence is an expression cassette or in an expression cassette. In some embodiments, the expression cassettes are designed to express the nucleic acid sequence disclosed herein. In some embodiments, the nucleic acid sequence is an expression cassette encoding components of a CRISPR-Cas system. In some embodiments, the nucleic acid sequence is an expression cassette encoding components of a Type I CRISPR-Cas system. In some embodiments, the nucleic acid sequence is an expression cassette encoding an operable CRISPR-Cas system. In some embodiments, the nucleic acid sequence is an expression cassette encoding the operable components of a Type I CRISPR-Cas system, including Cascade and Cas3. In some embodiments, the nucleic acid sequence is an expression cassette encoding the operable components of a Type I CRISPR-Cas system, including a crRNA, Cascade and Cas3.
In some embodiments, an expression cassette comprising a nucleic acid sequence of interest is chimeric, meaning that at least one of its components is heterologous with respect to at least one of its other components. In some embodiments, an expression cassette is naturally occurring but has been obtained in a recombinant form useful for heterologous expression.
In some embodiments, an expression cassette includes a transcriptional and/or translational termination region (i.e. termination region) that is functional in the selected host cell. In some embodiments, termination regions are responsible for the termination of transcription beyond the heterologous nucleic acid sequence of interest and for correct mRNA polyadenylation. In some embodiments, the termination region is native to the transcriptional initiation region, is native to the operably linked nucleic acid sequence of interest, is native to the host cell, or is derived from another source (i.e., foreign or heterologous to the promoter, to the nucleic acid sequence of interest, to the host, or any combination thereof). In some embodiments, terminators are operably linked to the nucleic acid sequence disclosed herein.
In some embodiments, an expression cassette includes a nucleotide sequence for a selectable marker. In some embodiments, the nucleotide sequence encodes either a selectable or a screenable marker, depending on whether the marker confers a trait that is selected for by chemical means, such as by using a selective agent (e.g. an antibiotic), or on whether the marker is simply a trait that one identifies through observation or testing, such as by screening (e.g., fluorescence).
In addition to expression cassettes, the nucleic acid sequences disclosed herein (e.g. nucleic acid sequence comprising a CRISPR array) are used in connection with vectors. A vector comprises a nucleic acid molecule comprising the nucleotide sequence(s) to be transferred, delivered or introduced. Non-limiting examples of general classes of vectors include, but are not limited to, a viral vector, a plasmid vector, a phage vector, a phagemid vector, a cosmid vector, a fosmid vector, a bacteriophage, an artificial chromosome, or an agrobacterium binary vector in double or single stranded linear or circular form which may or may not be self-transmissible or mobilizable. A vector transforms prokaryotic or eukaryotic host either by integration into the cellular genome or exist extrachromosomally (e.g. autonomous replicating plasmid with an origin of replication). Additionally, included are shuttle vectors by which is meant a DNA vehicle capable, naturally or by design, of replication in two different host organisms. In some embodiments, a shuttle vector replicates in actinomycetes and bacteria and/or eukaryotes. In some embodiments, the nucleic acid in the vector are under the control of, and operably linked to, an appropriate promoter or other regulatory elements for transcription in a host cell. In some embodiments, the vector is a bi-functional expression vector which functions in multiple hosts.
In some embodiments, the nucleic acid sequence is codon optimized for expression in any species of interest. Codon optimization involves modification of a nucleotide sequence for codon usage bias using species-specific codon usage tables. The codon usage tables are generated based on a sequence analysis of the most highly expressed genes for the species of interest. When the nucleotide sequences are to be expressed in the nucleus, the codon usage tables are generated based on a sequence analysis of highly expressed nuclear genes for the species of interest. The modifications of the nucleotide sequences are determined by comparing the species-specific codon usage table with the codons present in the native polynucleotide sequences. Codon optimization of a nucleotide sequence results in a nucleotide sequence having less than 100% identity (e.g., 50%, 60%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and the like) to the native nucleotide sequence but which still encodes a polypeptide having the same function as that encoded by the original nucleotide sequence. In some embodiments, the nucleic acid sequences of this disclosure are codon optimized for expression in the organism/species of interest.
In some embodiments, the nucleic acid sequence, and/or expression cassettes disclosed herein are expressed transiently and/or stably incorporated into the genome of a host organism. In some embodiments, a the nucleic acid sequence and/or expression cassettes disclosed herein is introduced into a cell by any method known to those of skill in the art. Exemplary methods of transformation include transformation via electroporation of competent cells, passive uptake by competent cells, chemical transformation of competent cells, as well as any other electrical, chemical, physical (mechanical) and/or biological mechanism that results in the introduction of nucleic acid into a cell, including any combination thereof. In some embodiments, transformation of a cell comprises nuclear transformation. In some embodiments, transformation of a cell comprises plasmid transformation and conjugation.
In some embodiments, when more than one nucleic acid sequence is introduced, the nucleotide sequences are assembled as part of a single nucleic acid construct, or as separate nucleic acid constructs, and are located on the same or different nucleic acid constructs. In some embodiments, nucleotide sequences are introduced into the cell of interest in a single transformation event, or in separate transformation events.
In some embodiments, a bacteriophage disclosed herein is further genetically modified to express an antibacterial peptide, a functional fragment of an antibacterial peptide or a lytic gene. In some embodiments, a bacteriophage disclosed herein express at least one antimicrobial agent or peptide disclosed herein. In some embodiments, a bacteriophage disclosed herein comprises a nucleic acid sequence that encodes an enzybiotic where the protein product of the nucleic acid sequence targets phage resistant bacteria. In some embodiments, the bacteriophage comprises nucleic acids which encode enzymes which assist in breaking down or degrading biofilm matrix. In some embodiments, a bacteriophage disclosed herein comprises nucleic acids encoding Dispersin D aminopeptidase, amylase, carbohydrase, carboxypeptidase, catalase, cellulase, chitinase, cutinase, cyclodextrin glycosyltransferase, deoxyribonuclease, esterase, alpha-galactosidase, beta-galactosidase, glucoamylase, alpha-glucosidase, beta-glucosidase, haloperoxidase, invertase, laccase, lipase, mannosidase, oxidase, pectinolytic enzyme, peptidoglutaminase, peroxidase, phytase, polyphenoloxidase, proteolytic enzyme, ribonuclease, transglutaminase, xylanase or lyase. In some embodiments, the enzyme is selected from the group consisting of cellulases, such as glycosyl hydroxylase family of cellulases, such as glycosyl hydroxylase 5 family of enzymes also called cellulase A; polyglucosamine (PGA) depolymerases; and colonic acid depolymerases, such as 1,4-L-fucodise hydrolase, colanic acid, depolymerazing alginase, DNase I, or combinations thereof. In some embodiments, a bacteriophage disclosed herein secretes an enzyme disclosed herein.
In some embodiments, an antimicrobial agent or peptide is expressed and/or secreted by a bacteriophage disclosed herein. In some embodiments, a bacteriophage disclosed herein secretes and expresses an antibiotic such as ampicillin, penicillin, penicillin derivatives, cephalosporins, monobactams, carbapenems, ofloxacin, ciproflaxacin, levofloxacin, gatifloxacin, norfloxacin, lomefloxacin, trovafloxacin, moxifloxacin, sparfloxacin, gemifloxacin, pazufloxacin or any antibiotic disclosed herein. In some embodiments, a bacteriophage disclosed herein comprises a nucleic acid sequence encoding an antibacterial peptide, expresses an antibacterial peptide, or secretes a peptide that aids or enhances killing of a Pseudomonas species. In some embodiments, a bacteriophage disclosed herein comprises a nucleic acid sequence encoding a peptide, a nucleic acid sequence encoding an antibacterial peptide, expresses an antibacterial peptide, or secretes a peptide that aids or enhances the activity of the first and/or the second Type I CRISPR-Cas system.
Disclosed herein, in certain embodiments, are methods of killing a Pseudomonas species comprising introducing into a Pseudomonas species any of the bacteriophages disclosed herein.
Further disclosed herein, in certain embodiments, are methods of modifying a mixed population of bacterial cells having a first bacterial species that comprises a target nucleotide sequence in the essential gene and a second bacterial species that does not comprise a target nucleotide sequence in the essential gene, the method comprising introducing into the mixed population of bacterial cells any of the bacteriophages disclosed herein.
Also disclosed herein, in certain embodiments, are methods of treating a disease or condition in an individual in need thereof, the method comprising administering to the individual any of the bacteriophages disclosed herein.
In some embodiments, the Pseudomonas species is killed solely by lytic activity of the bacteriophage. In some embodiments, the Pseudomonas species is killed solely by activity of the CRISPR-Cas system. In some embodiments, the Pseudomonas species is killed by the processing of the CRISPR array by a CRISPR-Cas system to produce a processed crRNA capable of directing CRISPR-Cas based endonuclease activity and/or cleavage at the target nucleotide sequence in the target gene of the bacterium.
In some embodiments, the Pseudomonas species is killed by lytic activity of the bacteriophage in combination with activity of the Type I CRISPR-Cas system. In some embodiments, the Pseudomonas species is killed by the activity of the Type I CRISPR-Cas system, independently of the lytic activity of the bacteriophage. In some embodiments, the activity of the Type I CRISPR-Cas system supplements or enhances the lytic activity of the bacteriophage. In some embodiments, the activity of the Type I CRISPR-Cas system and the lytic activity of the bacteriophage are additive.
In some embodiments, the lytic activity of the bacteriophage and the activity of the Type I CRISPR-Cas system is synergistic. In some embodiments, a synergistic activity is defined as an activity resulting in a greater level of phage kill than the additive combination of the lytic activity of the bacteriophage and the Type I CRISPR-Cas system. In some embodiments, the lytic activity of the bacteriophage is modulated by a concentration of the bacteriophage. In some embodiments, the activity of the Type I CRISPR-Cas system is modulated by a concentration of the bacteriophage.
In some embodiments, the synergistic killing of the bacterium is modulated to favor killing by the lytic activity of the bacteriophage over the activity of the first CRISPR-Cas system by increasing the concentration of bacteriophage administered to the bacterium. In some embodiments, the synergistic killing of the bacterium is modulated to disfavor killing by the lytic activity of the bacteriophage over the activity of the CRISPR-Cas system by decreasing the concentration of bacteriophage administered to the bacterium. In some embodiments, at low concentrations, lytic replication allows for amplification and killing of the target bacteria. In some embodiments, at high concentrations, amplification of a phage is not required. In some embodiments, the synergistic killing of the bacterium is modulated to favor killing by the activity of the CRISPR-Cas system over the lytic activity of the bacteriophage by altering the number, the length, the composition, the identity, or any combination thereof, of the spacers so as to increase the lethality of the CRISPR array. In some embodiments, the synergistic killing of the bacterium is modulated to disfavor killing by the activity of the CRISPR-Cas system over the lytic activity of the bacteriophage by altering the number, the length, the composition, the identity, or any combination thereof, of the spacers so as to decrease the lethality of the CRISPR array.
In one aspect, provided herein is a method of treating a Pseudomonas infection in a subject, the method comprising administering to the subject a composition comprising a bacteriophage, wherein the bacteriophage comprises a nucleic acid sequence encoding a Type I CRISPR-Cas system that causes cell death by targeting and degrading the Pseudomonas bacterial genome. In some embodiments, the CRISPR-Cas system that targets a Pseudomonas bacteria comprises a CRISPR array comprising one or more spacer sequences complementary to target nucleotide sequence in a Pseudomonas species; a Cascade polypeptide; and a Cas3 polypeptide. In some embodiments, the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120. In some embodiments, the CRISPR array further comprises at least one repeat sequence. In some embodiments, the at least one repeat sequence is operably linked to the one or more spacer sequences at either its 5′ end or its 3′ end. In some embodiments, the repeat sequence comprises at least about 90% sequence identity to any one of SEQ ID NOS: 26-30. In some embodiments, the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
In one embodiment, the essential gene is Tsf, acpP, gapA, infA, sect, csrA, trmD, ftsA, fusA, glyQ, eno, nusG, dnaA, dnaS, pheS, rplB, gltX, hisS, rplC, aspS, gyrB, glnS, dnaE, rpoA, rpoB, pheT, infB, rpsC, rplF, alaS, leuS, serS, rplD, gyrA, or metK. In some embodiments, the Cascade polypeptide forms a Cascade complex of a Type I-A CRISPR-Cas system, a Type I-B CRISPR-Cas system, a Type I-C CRISPR-Cas system, a Type I-D CRISPR-Cas system, a Type I-E CRISPR-Cas system, or a Type I-F CRISPR-Cas system. In some embodiments, the Cascade complex comprises: (i) a Cas7 polypeptide, a Cas8a1 polypeptide or a Cas8a2 polypeptide, a Cas5 polypeptide, a Csa5 polypeptide, and a Cas6a polypeptide, wherein the Cas3 polypeptide comprises a Cas3′ polypeptide and a Cas3″ polypeptide having no nuclease activity (Type I-A CRISPR-Cas system); (ii) a Cas6b polypeptide, a Cas8b polypeptide, a Cas7 polypeptide, and a Cas5 polypeptide (Type I-B CRISPR-Cas system); (iii) a Cas5d polypeptide, a Cas8c polypeptide, and a Cas7 polypeptide (Type I-C CRISPR-Cas system); (iv) a Cas10d polypeptide, a Csc2 polypeptide, a Csc1 polypeptide, a Cas6d polypeptide (Type I-D CRISPR-Cas system); (v) a Cse1 polypeptide, a Cse2 polypeptide, a Cas7 polypeptide, a Cas5 polypeptide, and a Cas6e polypeptide (Type I-E CRISPR-Cas system); (vi) a Csy1 polypeptide, a Csy2 polypeptide, a Csy3 polypeptide, and a Csy4 polypeptide (Type I-F CRISPR-Cas system). In some embodiments, the Cascade complex comprises a Cas5d polypeptide (optionally SEQ ID NO: 80), a Cas8c polypeptide (optionally SEQ ID NO: 81), and a Cas7 polypeptide (optionally SEQ ID NO: 82) (Type I-C CRISPR-Cas system). In some embodiments, the nucleic acid sequence further comprises a promoter sequence.
In one embodiment, provided herein is a method for treatment of a selected group of subjects suffering from a Pseudomonas infection. In one embodiment, the subjects are refractory to one or more commonly practiced therapies, e.g. therapy comprising one or more antibiotic compounds.
In one embodiment, the selected group of subjects are identified as subjects that are infected with a MDR strain of a Pseudomonas sp. In one embodiment, the selected group of subjects are identified as subjects that are immunocompromised. In some embodiments, the infection is a nosocomial infection. In some embodiments, the infection is a persistent or recurring infection. In some embodiments, the subject is symptomatic. In some embodiments, the subject suffers from a chronic Pseudomonas induced infection and disease. In one embodiment, the composition is administered to the subject once as a single dose.
In some embodiments, provided herein is a method of treating subjects suffering from a Pseudomonas infection by administering a composition, e.g. a pharmaceutical composition comprising one or more bacteriophages, e.g., a bacteriophage cocktail, wherein the bacteriophage in the composition e.g., the bacteriophage cocktail are from the lineage consisting of a PhiKZvirus, PhiKMV virus, Brunyoghevirus, Samunavirus, Nankokuvirus, Abidjanvirus, Baikalvirus, Beetrevirus, Casadabanvirus, Citexvirus, Cystovirus, Detrevirus, Elvirus, Hollowayvirus, Kochitakasuvirus, Litunavirus, Luzseptimavirus, Nipunavirus, Pakpunavirus, Pamexvirus, Paundecimvirus, Phitrevirus, Primolicivirus, Septimatrevirus, Stubburvirus, Tertilicivirus, Yuavirus, Zicotriavirus or Pbunavirus. In some embodiments, the composition comprises the bacteriophage cocktail 511. In some embodiments, the composition comprises the bacteriophage cocktail PACK512. In some embodiments, provided herein is a pharmaceutical composition wherein the pharmaceutical composition comprises at least six bacteriophage, wherein the bacteriophage are from a group consisting of p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695. In some embodiments, the compositions disclosed herein, such as one or more bacteriophages, engineered bacteriophages or bacteriophage cocktail described herein is used to treat cancer. In some embodiments, the bacteriophage is selected from the Table 1A, Table 5A, and/or from the Table 5B.
In some embodiments, the treatment is administered as an intravenous or intramuscular drug. In some embodiments, the treatment is administered via oral route. In some embodiments, the treatment is administered via a nebulizer. In some embodiments, the treatment is administered via a patient-operable nebulizer. In some embodiments, the treatment is administered via a metered dose nebulizer.
In some embodiments, the treatment is administered in combination with one or more other drugs or therapeutics, e.g., an antibiotic, such as Tobramycin. In some embodiments an exemplary therapeutic co-administered with the composition comprising one or more bacteriophage could also be an antibiotic such as ampicillin, penicillin, penicillin derivatives, cephalosporins, monobactams, carbapenems, ofloxacin, ciproflaxacin, levofloxacin, gatifloxacin, norfloxacin, lomefloxacin, trovafloxacin, moxifloxacin, sparfloxacin, gemifloxacin, pazufloxacin or any antibiotic disclosed herein. In some embodiments, the additional therapeutic comprises a drug for improving airway function. In some embodiments, the additional therapeutic comprises a drug for reducing airway responsiveness. In some embodiments, the additional therapeutic comprises a drug for reducing airway inflammation. In some embodiments, the additional therapeutic comprises a bronchodilator. In some embodiments, the additional therapeutic comprises a drug for improving oxygen availability. In some embodiments, the additional therapeutic comprises a drug for reducing airway mucogenesis. In some embodiments, the additional therapeutic comprises a DNAse. In some embodiments, the additional therapeutic is saline. In some embodiments, the additional therapeutic is a therapeutic method comprising coughing practices, e.g., as used for treating cystic fibrosis.
In one embodiment, the composition is administered to the subject more than once, e.g., multiple doses. In one embodiment, the composition is administered to the subject 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more doses. In one embodiment, the composition is administered to the subject once a day, once in 2 days, once in 3 days, once in 4 days, once in 5 days, once in 6 days, or once a week. In one embodiment, the composition is administered to the subject once in 10 days. In one embodiment, the composition is administered to the subject once in 12 days. In one embodiment, the composition is administered to the subject once in 2 weeks. In one embodiment, the composition is administered to the subject once in 3 weeks. In one embodiment, the composition is administered to the subject once in 1 month.
In one embodiment, the first composition is administered multiple doses to the subject over a period of one month, 2 months, 3 months, 4 months 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months, 13 months, 14 months, 15 months, 16 months. 17 months, 18 months, 19 months, 20 months, 21 months, 22 months, 23 months, 24 months or more.
In one aspect, provided herein is a method of treating a Pseudomonas infection in a subject, the method comprising administering to the subject a first composition comprising a bacteriophage, wherein the bacteriophage comprises a nucleic acid sequence encoding a Type I CRISPR-Cas system that targets a Pseudomonas bacterium; and administering to the subject a second therapeutic. In some embodiments, the second therapeutic is an antibiotic or an antibacterial composition. In one embodiment, the first composition and the second therapeutic are administered on the same day. In one embodiment, the first composition and the second therapeutic are administered on the different days.
Dose and duration of the administration of a composition disclosed herein will depend on a variety of factors, including the subject's age, subject's weight, and tolerance of the phage. In some embodiments, a bacteriophage disclosed herein is administered to a subject intra-arterially, intravenously, intraurethrally, intramuscularly, orally, subcutaneously, by inhalation, or any combination thereof. In some embodiments, a bacteriophage disclosed herein is administered to a subject by oral administration. In some embodiments, a bacteriophage disclosed herein is administered to patients by topical, cutaneous, transdermal, transmucosal, implantation, sublingual, buccal, rectal, vaginal, ocular, otic, or nasal administration. In some embodiments, a bacteriophage disclosed herein is administered to a subject by any combination of the aforementioned routes of administration. In some embodiments, a bacteriophage disclosed herein is administered to a subject by inhalation. In some embodiments, a bacteriophage disclosed herein is administered to a subject by inhalation using a nebulizer.
In some embodiments, the composition and methods described herein are for treatment of a lung infection or a disease. In some embodiments, the lung infection or disease is cystic fibrosis. In some embodiments, administration of the composition comprising the bacteriophage to a patient with cystic fibrosis or cystic fibrosis-associated bronchiectasis is via a nebulizer. In some embodiments, the treatment is administered via a patient-operable nebulizer. In some embodiments, the treatment is administered via a metered dose nebulizer. In some embodiments, the treatment is administered in combination with one or more other drugs or therapeutics, e.g., an antibiotic or bronchodilator. In some embodiments, the treatment is a bacteriophage, a bacteriophage composition, and/or a bacteriophage cocktail as described herein. For instance, a composition comprising p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695. The composition may be in a nebulizable formulation for pulmonary delivery.
In some embodiments, a dose of phage between 103 and 1020 PFU is administered to a subject. In some embodiments, a dose of phage between 103 and 1010 PFU is administered to a subject. In some embodiments, a dose of phage between 106 and 1020 PFU is administered to a subject. In some embodiments, a dose of phage between 106 and 1010 PFU is administered to a subject. For example, in some embodiments, a composition comprising a bacteriophage in an amount between 103 and 1011 PFU is administered to a subject. In some embodiments, a composition comprising a bacteriophage in an amount about 103, 104, 105, 106, 107, 108, 109, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019, 1020, 1021, 1022, 1023, 1024 PFU or more is administered to a subject. In some embodiments, a composition comprising a bacteriophage in an amount of less than 101 PFU is administered to a subject. In some embodiments, a composition comprising a bacteriophage in an amount between 101 and 108, 104 and 109, 105 and 1010, or 107 and 1011 PFU is administered to a subject. In some embodiments, a composition comprising two or more bacteriophage is administered to a subject, wherein each bacteriophage is administered in an amount about 103, 104, 105, 106, 107, 108, 109, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019, 1020, 1021, 1022, 1023, 1024, PFU or more. In some embodiments, a composition comprising two or more bacteriophage is administered to a subject, wherein each bacteriophage is administered in an amount of less than 101 PFU. In some embodiments, a composition comprising two or more bacteriophage is administered to a subject, wherein each bacteriophage is administered in an amount between 101 and 108, 104 and 109, 105 and 1010, or 107 and 1011 PFU.
In some embodiments, a bacteriophage or a mixture is administered to a subject in need thereof 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 times a day. In some embodiments, a bacteriophage or a mixture is administered to a subject in need thereof at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 times a week. In some embodiments, a bacteriophage or a mixture is administered to a subject in need thereof at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, or 90 times a month. In some embodiments, a bacteriophage or a mixture is administered to a subject in need thereof every 2, 4, 6, 8, 10, 12, 14, 18, 20, 22, or 24 hours.
In some embodiments, the compositions (bacteriophage) disclosed herein are administered before, during, or after the occurrence of a disease or condition. In some embodiment, the timing of administering the composition containing the bacteriophage varies. In some embodiments, the pharmaceutical compositions are used as a prophylactic and are administered continuously to subjects with a propensity to conditions or diseases in order to prevent the occurrence of the disease or condition. In some embodiments, pharmaceutical compositions are administered to a subject during or as soon as possible after the onset of the symptoms. In some embodiments, the administration of the compositions is initiated within the first 48 hours of the onset of the symptoms, within the first 24 hours of the onset of the symptoms, within the first 6 hours of the onset of the symptoms, or within 3 hours of the onset of the symptoms. In some embodiments, the initial administration of the composition is via any route practical, such as by any route described herein using any formulation described herein. In some embodiments, the compositions is administered as soon as is practicable after the onset of a disease or condition is detected or suspected, and for a length of time necessary for the treatment of the disease, such as, for example, from about 1 month to about 3 months. In some embodiments, the length of treatment will vary for each subject.
Disclosed herein, in certain embodiments, are methods of treating bacterial infections. In some embodiments, the bacteriophages disclosed herein treat or prevent diseases or conditions mediated or caused by bacteria as disclosed herein in a human or animal subject. In some embodiments, the bacteriophages disclosed herein treat or prevent diseases or conditions caused or exacerbated by bacteria as disclosed herein in a human or animal subject. Such bacteria are typically in contact with tissue of the subject including: gut, oral cavity, lung, armpit, ocular, vaginal, anal, ear, nose or throat tissue. In some embodiments, a bacterial infection is treated by modulating the activity of the bacteria and/or by directly killing of the bacteria.
In some embodiments, the target bacteria is Pseudomonas. In some embodiments, the bacterium is Pseudomonas aeruginosa.
In some embodiments, one or more target bacteria present in a bacterial population are pathogenic. In some embodiments, the pathogenic bacteria are uropathogenic. In some embodiments, the pathogenic bacteria are pulmonary pathogens. In some embodiments, the pathogenic bacteria are bloodstream pathogens.
In some embodiments, the bacteriophages disclosed herein are used to treat an infection, a disease, or a condition, in the pulmonary system of a subject. In some embodiments, the bacteriophages are used to modulate and/or kill target bacteria within the pulmonary microbiome of a subject. In some embodiments, the bacteriophages are used to selectively modulate and/or kill one or more target bacteria from a plurality of bacteria within the pulmonary microbiome of a subject. In some embodiments, the bacteriophages are used to selectively modulate and/or kill one or more target pathogenic bacteria from a plurality of bacteria within the pulmonary microbiome of a subject.
In some embodiments, the bacteriophages disclosed herein are used to treat an infection, a disease, or a condition, in the urinary tract of a subject. In some embodiments, the bacteriophages are used to modulate and/or kill target bacteria within the urinary tract flora of a subject. In some embodiments, the bacteriophages are used to selectively modulate and/or kill one or more target uropathogenic bacteria from a plurality of bacteria within the urinary tract flora of a subject.
In some embodiments, the bacteriophages disclosed herein are used to treat an infection, a disease, or a condition, on the skin of a subject. In some embodiments, the bacteriophages are used to modulate and/or kill target bacteria on the skin of a subject.
In some embodiments, the bacteriophages disclosed herein are used to treat an infection, a disease, or a condition, on a mucosal membrane of a subject. In some embodiments, the bacteriophages are used to modulate and/or kill target bacteria on the mucosal membrane of a subject.
In some embodiments, the pathogenic bacteria are antibiotic resistant.
In some embodiments, the one or more target bacteria present in the bacterial population form a biofilm. In some embodiments, the biofilm comprises pathogenic bacteria. In some embodiments, the bacteriophage disclosed herein is used to treat a biofilm.
In some embodiments, the bacteriophage treats acne and other related skin infections.
In some embodiments, a Pseudomonas species is a multiple drug resistant (MDR) bacteria strain. An MDR strain is a bacteria strain that is resistant to at least one antibiotic. In some embodiments, a bacteria strain is resistant to an antibiotic class such as a cephalosporin, a fluoroquinolone, a carbapenem, a colistin, an aminoglycoside, vancomycin, streptomycin, and methicillin. In some embodiments, a bacteria strain is resistant to an antibiotic such as a Ceftobiprole, Ceftaroline, Clindamycin, Dalbavancin, Daptomycin, Linezolid, Mupirocin, Oritavancin, Tedizolid, Telavancin, Tigecycline, Vancomycin, an Aminoglycoside, a Carbapenem, Ceftazidime, Cefepime, Ceftobiprole, a Fluoroquinolone, Piperacillin, Ticarcillin, Linezolid, a Streptogramin, Tigecycline, Daptomycin, or any combination thereof. In some embodiments, the MDR strain is Pseudomonas aeruginosa.
In some embodiments, the bacterium is a Pseudomonas species. In some embodiments, the bacterium is Pseudomonas aeruginosa. In some embodiments, the methods and compositions disclosed herein are for use in veterinary and medical applications as well as research applications.
In some embodiments, the bacterial infection is present in a subject with cystic fibrosis. In some embodiments the bacterial infection is present in a subject with non-cystic fibrosis bronchiectasis. In some embodiments, the bacterial infection is present in a subject with pneumonia. In some embodiments, the bacterial infection contributes to the pneumonia. As non-limiting examples, the pneumonia is hospital acquired pneumonia, ventilator acquired pneumonia, community acquired pneumonia, or health care acquired pneumonia. In some embodiments, the bacterial infection is a blood system infection (BSI).
In some embodiments, the methods described herein comprise administering an additional therapeutic. In some embodiments, the additional therapeutic is an antibiotic. In some embodiments, the antibiotic comprises tobramycin.
“Microbiome”, “microbiota”, and “microbial habitat” are used interchangeably hereinafter and refer to the ecological community of microorganisms that live on or in a subject's bodily surfaces, cavities, and fluids. Non-limiting examples of habitats of microbiome include: gut, colon, skin, skin surfaces, skin pores, vaginal cavity, umbilical regions, conjunctival regions, intestinal regions, stomach, nasal cavities and passages, gastrointestinal tract, urogenital tracts, saliva, mucus, and feces. In some embodiments, the microbiome comprises microbial material including, but not limited to, bacteria, archaea, protists, fungi, and viruses. In some embodiments, the microbial material comprises a gram-negative bacterium. In some embodiments, the microbial material comprises a gram-positive bacterium. In some embodiments, the microbial material comprises Proteobacteria, Actinobacteria, Bacteroidetes, or Firmicutes.
In some embodiments, the bacteriophages as disclosed herein are used to modulate or kill target bacteria within the microbiome of a subject. In some embodiments, the bacteriophages are used to modulate and/or kill target bacteria within the microbiome by the CRISPR-Cas system, lytic activity, or a combination thereof. In some embodiments, the bacteriophages are used to modulate and/or kill target bacteria within the microbiome of a subject. In some embodiments, the bacteriophages are used to selectively modulate and/or kill one or more target bacteria from a plurality of bacteria within the microbiome of a subject.
In some embodiments, the bacteriophages are used to modulate or kill target single or plurality of bacteria within the pulmonary microbiome of a subject. Modification (e.g., dysbiosis) of the pulmonary microbiome increases the risk for health conditions such as diabetes, mental disorders, ulcerative colitis, colorectal cancer, autoimmune disorders, obesity, diabetes, diseases of the central nervous system and inflammatory bowel disease.
In some embodiments, a bacteriophage disclosed herein is administered to a subject to promote a healthy microbiome. In some embodiments, a bacteriophage disclosed herein is administered to a subject to restore a subject's microbiome to a microbiome composition that promotes health. In some embodiments, a composition comprising a bacteriophage disclosed herein comprises a prebiotic or a third agent. In some embodiment, microbiome related disease or disorder is treated by a bacteriophage disclosed herein.
In some embodiments, bacteriophages disclosed herein are further used for food and agriculture sanitation (including meats, fruits and vegetable sanitation), hospital sanitation, home sanitation, vehicle and equipment sanitation, industrial sanitation, etc. In some embodiments, bacteriophages disclosed herein are used for the removal of antibiotic-resistant or other undesirable pathogens from medical, veterinary, animal husbandry, or any additional environments bacteria are passed to humans or animals.
Environmental applications of phage in health care institutions are for equipment such as endoscopes and environments such as ICUs which are potential sources of nosocomial infection due to pathogens that are difficult or impossible to disinfect. In some embodiments, a phage disclosed herein is used to treat equipment or environments inhabited by bacterial genera which become resistant to commonly used disinfectants. In some embodiments, phage compositions disclosed herein are used to disinfect inanimate objects. In some embodiments, an environment disclosed herein is sprayed, painted, or poured onto with aqueous solutions with phage titers. In some embodiment a solution described herein comprises between 101-1020 plaque forming units (PFU)/ml. In some embodiments, a bacteriophage disclosed herein is applied by aerosolizing agents that include dry dispersants to facilitate distribution of the bacteriophage into the environment. In some embodiments, objects are immersed in a solution containing bacteriophage disclosed herein.
In some embodiments, bacteriophages disclosed herein are used as sanitation agents in a variety of fields. Although the terms “phage” or “bacteriophage” may be used, it should be noted that, where appropriate, this term should be broadly construed to include a single bacteriophage, multiple bacteriophages, such as a bacteriophage mixtures and mixtures of a bacteriophage with an agent, such as a disinfectant, a detergent, a surfactant, water, etc.
In some embodiments, bacteriophages are used to sanitize hospital facilities, including operating rooms, patient rooms, waiting rooms, lab rooms, or other miscellaneous hospital equipment. In some embodiments, this equipment includes electrocardiographs, respirators, cardiovascular assist devices, intraaortic balloon pumps, infusion devices, other patient care devices, televisions, monitors, remote controls, telephones, beds, etc. In some situations, the bacteriophage is applied through an aerosol canister. In some embodiments, bacteriophage is applied by wiping the phage on the object with a transfer vehicle.
In some embodiments, a bacteriophage described herein is used in conjunction with patient care devices. In some embodiment, bacteriophage is used in conjunction with a conventional ventilator or respiratory therapy device to clean the internal and external surfaces between patients. Examples of ventilators include devices to support ventilation during surgery, devices to support ventilation of incapacitated patients, and similar equipment. In some embodiments, the conventional therapy includes automatic or motorized devices, or manual bag-type devices such as are commonly found in emergency rooms and ambulances. In some embodiments, respiratory therapy includes inhalers to introduce medications such as bronchodilators as commonly used with chronic obstructive pulmonary disease or asthma, or devices to maintain airway patency such as continuous positive airway pressure devices.
In some embodiment, a bacteriophage described herein is used to cleanse surfaces and treat colonized people in an area where highly-contagious bacterial diseases, such as meningitis or enteric infections are present.
In some embodiments, water supplies are treated with a composition disclosed herein. In some embodiments, bacteriophage disclosed herein is used to treat contaminated water, water found in cisterns, wells, reservoirs, holding tanks, aqueducts, conduits, and similar water distribution devices. In some embodiments, the bacteriophage is applied to industrial holding tanks where water, oil, cooling fluids, and other liquids accumulate in collection pools. In some embodiments, a bacteriophage disclosed herein is periodically introduced to the industrial holding tanks in order to reduce bacterial growth.
In some embodiments, bacteriophages disclosed herein are used to sanitize a living area, such as a house, apartment, condominium, dormitory, or any living area. In some embodiments, the bacteriophage is used to sanitize public areas, such as theaters, concert halls, museums, train stations, airports, pet areas, such as pet beds, or litter boxes. In this capacity, the bacteriophage is dispensed from conventional devices, including pump sprayers, aerosol containers, squirt bottles, pre-moistened towelettes, etc, applied directly to (e.g., sprayed onto) the area to be sanitized, or be transferred to the area via a transfer vehicle, such as a towel, sponge, etc. In some embodiments, a phage disclosed herein is applied to various rooms of a house, including the kitchen, bedrooms, bathrooms, garage, basement, etc. In some embodiments, a phage disclosed herein is in the same manner as conventional cleaners. In some embodiments, the phage is applied in conjunction with (before, after, or simultaneously with) conventional cleaners provided that the conventional cleaner is formulated so as to preserve adequate bacteriophage biologic activity.
In some embodiments, a bacteriophage disclosed herein is added to a component of paper products, either during processing or after completion of processing of the paper products. Paper products to which a bacteriophage disclosed herein is added include, but are not limited to, paper towels, toilet paper, moist paper wipes.
In some embodiments, a bacteriophage described herein is used in any food product or nutritional supplement, for preventing contamination. Examples for food or pharmaceuticals products are milk, yoghurt, curd, cheese, fermented milks, milk based fermented products, ice-creams, fermented cereal based products, milk based powders, infant formulae or tablets, liquid suspensions, dried oral supplement, wet oral supplement, or dry-tube-feeding.
The broad concept of bacteriophage sanitation is applicable to other agricultural applications and organisms. Produce, including fruits and vegetables, dairy products, and other agricultural products. For example, freshly-cut produce frequently arrive at the processing plant contaminated with pathogenic bacteria. This has led to outbreaks of food-borne illness traceable to produce. In some embodiments, the application of bacteriophage preparations to agricultural produce substantially reduce or eliminate the possibility of food-borne illness through application of a single phage or phage mixture with specificity toward species of bacteria associated with food-borne illness. In some embodiments, bacteriophages are applied at various stages of production and processing to reduce bacterial contamination at that point or to protect against contamination at subsequent points.
In some embodiments, specific bacteriophages are applied to produce in restaurants, grocery stores, produce distribution centers. In some embodiments, bacteriophages disclosed herein are periodically or continuously applied to the fruit and vegetable contents of a salad bar. In some embodiments, the application of bacteriophages to a salad bar or to sanitize the exterior of a food item is a misting or spraying process or a washing process.
In some embodiments, a bacteriophage described herein is used in matrices or support media containing with packaging containing meat, produce, cut fruits and vegetables, and other foodstuffs. In some embodiments, polymers that are suitable for packaging are impregnated with a bacteriophage preparation.
In some embodiments, a bacteriophage described herein is used in farm houses and livestock feed. In some embodiments, on a farm raising livestock, the livestock is provided with bacteriophage in their drinking water, food, or both. In some embodiments, a bacteriophage described herein is sprayed onto the carcasses and used to disinfect the slaughter area.
The use of specific bacteriophages as biocontrol agents on produce provides many advantages. For example, bacteriophages are natural, non-toxic products that will not disturb the ecological balance of the natural microflora in the way the common chemical sanitizers do, but will specifically lyse the targeted food-borne pathogens. Because bacteriophages, unlike chemical sanitizers, are natural products that evolve along with their host bacteria, new phages that are active against recently emerged, resistant bacteria are rapidly identified when required, whereas identification of a new effective sanitizer is a much longer process, several years.
Disclosed herein, in certain embodiments, are pharmaceutical compositions comprising (a) the nucleic acid sequences as disclosed herein; and (b) a pharmaceutically acceptable excipient. Also disclosed herein, in certain embodiments, are pharmaceutical compositions comprising (a) the bacteriophages as disclosed herein; and (b) a pharmaceutically acceptable excipient. Further disclosed herein, in certain embodiments, are pharmaceutical compositions comprising (a) the compositions as disclosed herein; and (b) a pharmaceutically acceptable excipient. In some embodiments, the pharmaceutically acceptable excipient comprises a surfactant. In some embodiments, the pharmaceutically acceptable excipient is a buffer.
In some embodiments, the disclosure provides pharmaceutical compositions and methods of administering the same to treat bacterial, archaeal infections or to disinfect an area. In some embodiments, the pharmaceutical composition comprises any of the reagents discussed above in a pharmaceutically acceptable carrier. In some embodiments, a pharmaceutical composition or method disclosed herein treats a Pseudomonas bacterial infection. In some embodiments, the bacterial infection is a P. aeruginosa bloodstream infection. In some embodiments, the bacterial infection is a P. aeruginosa respiratory infection. In some embodiments, a pharmaceutical composition of method disclosed herein treats cystic fibrosis-associated bronchiectasis. In some embodiments, a pharmaceutical composition or method disclosed herein treats non-cystic fibrosis-associated bronchiectasis. In some embodiments, a pharmaceutical composition of method disclosed herein treats malignant external otitis, endophthalmitis, endocarditis, meningitis, pneumonia, or septicemia.
In some embodiments, compositions disclosed herein comprise medicinal agents, pharmaceutical agents, carriers, adjuvants, dispersing agents, diluents, and the like.
In some embodiments, the bacteriophages disclosed herein are formulated for administration in a pharmaceutical carrier in accordance with suitable methods. In some embodiments, the manufacture of a pharmaceutical composition according to the disclosure, the bacteriophage is admixed with, inter alia, an acceptable carrier. In some embodiments, the carrier is a solid (including a powder) or a liquid, or both, and is preferably formulated as a unit-dose composition. In some embodiments, one or more bacteriophages are incorporated in the compositions disclosed herein, which are prepared by any suitable method of a pharmacy.
In some embodiment, a method of treating subject's in-vivo, comprising administering to a subject a pharmaceutical composition comprising a bacteriophage disclosed herein in a pharmaceutically acceptable carrier, wherein the pharmaceutical composition is administered in a therapeutically effective amount. In some embodiments, the administration of the bacteriophage to a human subject or an animal in need thereof are by any means known in the art.
In some embodiment, methods and compositions suitable for administering bacteriophages disclosed herein to a surface of an object or subject includes aqueous solutions. In some embodiments, such aqueous solutions are sprayed onto the surface of an object or subject. In some embodiment, the aqueous solutions are used to irrigate and clean a physical wound of a subject form foreign debris including bacteria.
In some embodiments, methods and compositions suitable for nasal administration or otherwise administered to the lungs of a subject include any suitable means, e.g., administered by an aerosol suspension of respirable particles comprising the bacteriophage compositions, which the subject inhales. In some embodiments, the respirable particles are liquid or solid. As used herein, “aerosol” includes any gas-borne suspended phase, which is capable of being inhaled into the bronchioles or nasal passages. In some embodiments, aerosols of liquid particles are produced by any suitable means, such as with a pressure-driven aerosol nebulizer, an ultrasonic nebulizer, or a mesh nebulizer. In some embodiments, aerosols of solid particles comprising the composition is produced with any solid particulate medicament aerosol generator, by techniques known in the pharmaceutical art.
Nebulizers are liquid aerosol generators that convert bulk liquids, usually aqueous-based compositions, into mists or clouds of small droplets, having diameters less than 5 microns mass median aerodynamic diameter (MMAD), which can be inhaled into the lower respiratory tract. The bulk liquid contains particles of the therapeutic agent(s) or a solution of the therapeutic agent(s) and any necessary excipients. The droplets carry the therapeutic agent(s) into the nose, upper airways or deep lungs when the aerosol cloud is inhaled.
Pneumatic (jet) nebulizers use a pressurized gas supply as a driving force for liquid atomization. Compressed gas is delivered through a nozzle or jet to create a low pressure field which entrains a surrounding bulk liquid and shears it into a thin film or filaments. The film or filaments are unstable and break up into small droplets which are carried by the compressed gas flow into the inspiratory breath. Baffles inserted into the droplet plume screen out the larger droplets and return them to the bulk liquid reservoir. Examples include the PARI LC® Plus®, or Sprint® nebulizers, the Devilbiss PulmoAide® nebulizer and the Boehringer Ingelheim Respimat® inhaler.
Electromechanical nebulizers use electrically generated mechanical force to atomize liquids. The electromechanical driving force is applied by vibrating the bulk liquid at ultrasonic frequencies or by forcing the bulk liquid through small holes in a thin film. The forces generate thin liquid films or filament streams which break up into small droplets to form a slow moving aerosol stream which can be entrained in a respiratory flow.
One form of electromechanical nebulizers is ultrasonic nebulizers, in which the bulk liquid is coupled to a vibrator oscillating at frequencies in the ultrasonic range. The coupling is achieved by placing the liquid in direct contact with the vibrator such as a plate or ring in a holding cup, or by placing large droplets on a solid vibrating projector. The vibrations generate circular standing films which break up into droplets at their edges to atomize the liquid. Examples include the DuroMist® nebulizer, Drive Medical's Beetle Neb® nebulizer, Octive Tech's Densylogic® nebulizer and the John Bunn Nano-Sonic® nebulizer. Another form of an electromechanical nebulizer is a mesh nebulizer, in which the bulk liquid is driven through a mesh or membrane with small holes ranging from 2 to 8 microns in diameter, to generate thin filaments which immediately break up into small droplets. In some designs, the liquid is forced through the mesh by applying pressure with a solenoid piston driver (AERx®) or by sandwiching the liquid between a piezoelectrically vibrated plate and the mesh, which results in an oscillatory pumping action (EFlow®, AerovectRx, TouchSpray™). In a second design type the mesh vibrates back and forth through a standing column of the liquid to pump it through the holes. Examples include the AeroNeb®, AeroNeb Go®, Pro®; PARI EFlow®; Omron 22UE®; and Aradigm AERx®.
In some embodiments, bacteriophages disclosed herein are for oral administration. In some embodiments, the bacteriophages are administered in solid dosage forms, such as capsules, tablets, and powders, or in liquid dosage forms, such as elixirs, syrups, and suspensions. In some embodiments, compositions and methods suitable for buccal (sub-lingual) administration include lozenges comprising the bacteriophages in a flavored base, usually sucrose and acacia or tragacanth; and pastilles comprising the bacteriophages in an inert base such as gelatin and glycerin or sucrose and acacia.
In some embodiments, methods and compositions of the present disclosure are suitable for parenteral administration comprising sterile aqueous and non-aqueous injection solutions of the bacteriophage. In some embodiments, these preparations are isotonic with the blood of the intended recipient. In some embodiments, these preparations comprise antioxidants, buffers, bacteriostals and solutes which render the composition isotonic with the blood of the intended recipient. In some embodiments, aqueous and non-aqueous sterile suspensions include suspending agents and thickening agents. In some embodiments, compositions disclosed herein are presented in unit\dose or multi-dose containers, for example sealed ampoules and vials, and are stored in a freeze-dried(lyophilized) condition requiring only the addition of the sterile liquid carrier, for example, saline or water for injection on immediately prior to use.
In some embodiment, methods and compositions suitable for rectal administration are presented as unit dose suppositories. In some embodiments, these are prepared by admixing the bacteriophage with one or more conventional solid carriers, for example, cocoa butter, and then shaping the resulting mixture. In some embodiments, methods and compositions suitable for topical application to the skin are in the form of an ointment, cream, lotion, paste, gel, spray, aerosol, or oil. In some embodiments, carriers which are used include petroleum jelly, lanoline, polyethylene glycols, alcohols, transdermal enhancers, and combinations of two or more thereof.
In some embodiments, methods and compositions suitable for transdermal administration are presented as discrete patches adapted to remain in intimate contact with the epidermis of the recipient for a prolonged period of time.
In some embodiments, the bacteriophages disclosed herein are administered to the subject in a therapeutically effective amount. In some embodiments, at least one bacteriophage composition disclosed herein is formulated as a pharmaceutical formulation. In some embodiments, a pharmaceutical formulation comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more bacteriophage disclosed herein. In some instances, a pharmaceutical formulation comprises a bacteriophage described herein and at least one of: an excipient, a diluent, or a carrier.
In some embodiments, a pharmaceutical formulation comprises an excipient. Excipients are described in the Handbook of Pharmaceutical Excipients, American Pharmaceutical Association (1986) and includes but are not limited to solvents, dispersion media, diluents, or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, and lubricants.
Non-limiting examples of suitable excipients include but is not limited to a buffering agent, a preservative, a stabilizer, a binder, a compaction agent, a lubricant, a chelator, a dispersion enhancer, a disintegration agent, a flavoring agent, a sweetener, a coloring agent.
In some embodiments, an excipient is a buffering agent. Non-limiting examples of suitable buffering agents include but is not limited to sodium citrate, magnesium carbonate, magnesium bicarbonate, calcium carbonate, and calcium bicarbonate. In some embodiments, a pharmaceutical formulation comprises any one or more buffering agent listed: sodium bicarbonate, potassium bicarbonate, magnesium hydroxide, magnesium lactate, magnesium glucomate, aluminum hydroxide, sodium citrate, sodium tartrate, sodium acetate, sodium carbonate, sodium polyphosphate, potassium polyphosphate, sodium pyrophosphate, potassium pyrophosphate, disodium hydrogen phosphate, dipotassium hydrogen phosphate, trisodium phosphate, tripotassium phosphate, potassium metaphosphate, magnesium oxide, magnesium hydroxide, magnesium carbonate, magnesium silicate, calcium acetate, calcium glycerophosphate, calcium chloride, calcium hydroxide and other calcium salts.
In some embodiments an excipient is a preservative. Non-limiting examples of suitable preservatives include but is not limited to antioxidants, such as alpha-tocopherol and ascorbate, and antimicrobials, such as parabens, chlorobutanol, and phenol. In some embodiments, antioxidants include but not limited to Ethylenediaminetetraacetic acid (EDTA), citric acid, ascorbic acid, butylated hydroxytoluene (BHT), butylated hydroxy anisole (BHA), sodium sulfite, p-amino benzoic acid, glutathione, propyl gallate, cysteine, methionine, ethanol and N-acetyl cysteine. In some embodiments, preservatives include validamycin A, TL-3, sodium ortho vanadate, sodium fluoride, N-a-tosyl-Phe-chloromethylketone, N-a-tosyl-Lys-chloromethylketone, aprotinin, phenylmethylsulfonyl fluoride, diisopropylfluorophosphate, protease inhibitor, reducing agent, alkylating agent, antimicrobial agent, oxidase inhibitor, or other inhibitor.
In some embodiments, a pharmaceutical formulation comprises a binder as an excipient. Non-limiting examples of suitable binders include starches, pregelatinized starches, gelatin, polyvinylpyrolidone, cellulose, methylcellulose, sodium carboxymethylcellulose, ethylcellulose, polyacrylamides, polyvinyloxoazolidone, polyvinylalcohols, C12-C18 fatty acid alcohol, polyethylene glycol, polyols, saccharides, oligosaccharides, and combinations thereof.
In some embodiments, the binders that are used in a pharmaceutical formulation are selected from starches such as potato starch, corn starch, wheat starch; sugars such as sucrose, glucose, dextrose, lactose, maltodextrin; natural and synthetic gums; gelatine; cellulose derivatives such as microcrystalline cellulose, hydroxypropyl cellulose, hydroxyethyl cellulose, hydroxypropyl methyl cellulose, carboxymethyl cellulose, methyl cellulose, ethyl cellulose; polyvinylpyrrolidone (povidone); polyethylene glycol (PEG); waxes; calcium carbonate; calcium phosphate; alcohols such as sorbitol, xylitol, mannitol and water or a combination thereof.
In some embodiments, a pharmaceutical formulation comprises a lubricant as an excipient. Non-limiting examples of suitable lubricants include magnesium stearate, calcium stearate, zinc stearate, hydrogenated vegetable oils, sterotex, polyoxyethylene monostearate, talc, polyethylene glycol, sodium benzoate, sodium lauryl sulfate, magnesium lauryl sulfate, and light mineral oil. In some embodiments, lubricants that are in a pharmaceutical formulation are selected from metallic stearates (such as magnesium stearate, calcium stearate, aluminum stearate), fatty acid esters (such as sodium stearyl fumarate), fatty acids (such as stearic acid), fatty alcohols, glyceryl behenate, mineral oil, paraffins, hydrogenated vegetable oils, leucine, polyethylene glycols (PEG), metallic lauryl sulphates (such as sodium lauryl sulphate, magnesium lauryl sulphate), sodium chloride, sodium benzoate, sodium acetate and talc or a combination thereof.
In some embodiments, an excipient comprises a flavoring agent. In some embodiments, flavoring agents includes natural oils; extracts from plants, leaves, flowers, and fruits; and combinations thereof.
In some embodiments, an excipient comprises a sweetener. Non-limiting examples of suitable sweeteners include glucose (corn syrup), dextrose, invert sugar, fructose, and mixtures thereof (when not used as a carrier); saccharin and its various salts such as a sodium salt; dipeptide sweeteners such as aspartame; dihydrochalcone compounds, glycyrrhizin; Stevia rebaudiana (Stevioside); chloro derivatives of sucrose such as sucralose; and sugar alcohols such as sorbitol, mannitol, sylitol, and the like.
In some instances, a pharmaceutical formulation comprises a coloring agent. Non-limiting examples of suitable color agents include food, drug and cosmetic colors (FD&C), drug and cosmetic colors (D&C), and external drug and cosmetic colors (Ext. D&C).
In some embodiments, the pharmaceutical formulation disclosed herein comprises a chelator. In some embodiments, a chelator includes ethylenediamine-N,N,N′,N′-tetraacetic acid (EDTA); a disodium, trisodium, tetrasodium, dipotassium, tripotassium, dilithium and diammonium salt of EDTA; a barium, calcium, cobalt, copper, dysprosium, europium, iron, indium, lanthanum, magnesium, manganese, nickel, samarium, strontium, or zinc chelate of EDTA.
In some instances, a pharmaceutical formulation comprises a diluent. Non-limiting examples of diluents include water, glycerol, methanol, ethanol, and other similar biocompatible diluents. In some embodiments, a diluent is an aqueous acid such as acetic acid, citric acid, maleic acid, hydrochloric acid, phosphoric acid, nitric acid, sulfuric acid, or similar.
In some embodiments, a pharmaceutical formulation comprises a surfactant. In some embodiments, surfactants are be selected from, but not limited to, polyoxyethylene sorbitan fatty acid esters (polysorbates), sodium lauryl sulphate, sodium stearyl fumarate, polyoxyethylene alkyl ethers, sorbitan fatty acid esters, polyethylene glycols (PEG), polyoxyethylene castor oil derivatives, docusate sodium, quaternary ammonium compounds, amino acids such as L-leucine, sugar esters of fatty acids, glycerides of fatty acids or a combination thereof.
In some instances, a pharmaceutical formulation comprises an additional pharmaceutical agent. In some embodiments, an additional pharmaceutical agent is an antibiotic agent. In some embodiments, an antibiotic agent is of the group consisting of aminoglycosides, ansamycins, carbacephem, carbapenems, cephalosporins (including first, second, third, fourth and fifth generation cephalosporins), lincosamides, macrolides, monobactams, nitrofurans, quinolones, penicillin, sulfonamides, polypeptides or tetracycline.
In some embodiments, an antibiotic agent described herein is an aminoglycoside such as Amikacin, Gentamicin, Kanamycin, Neomycin, Netilmicin, Tobramycin or Paromomycin. In some embodiments, an antibiotic agent described herein is an Ansamycin such as Geldanamycin or Herbimycin.
In some embodiments, an antibiotic agent described herein is a carbacephem such as Loracarbef. In some embodiments, an antibiotic agent described herein is a carbapenem such as Ertapenem, Doripenem, Imipenem/Cilastatin or Meropenem.
In some embodiments, an antibiotic agent described herein is a cephalosporins (first generation) such as Cefadroxil, Cefazolin, Cefalexin, Cefalotin or Cefalothin, or alternatively a Cephalosporins (second generation) such as Cefaclor, Cefamandole, Cefoxitin, Cefprozil or Cefuroxime. In some embodiments, an antibiotic agent is a Cephalosporins (third generation) such as Cefixime, Cefdinir, Cefditoren, Cefoperazone, Cefotaxime, Cefpodoxime, Ceftibuten, Ceftizoxime and Ceftriaxone or a Cephalosporins (fourth generation) such as Cefepime or Ceftobiprole.
In some embodiments, an antibiotic agent described herein is a lincosamide such as Clindamycin and Azithromycin, or a macrolide such as Azithromycin, Clarithromycin, Dirithromycin, Erythromycin, Roxithromycin, Troleandomycin, Telithromycin and Spectinomycin.
In some embodiments, an antibiotic agent described herein is a monobactams such as Aztreonam, or a nitrofuran such as Furazolidone or Nitrofurantoin.
In some embodiments, an antibiotic agent described herein is a penicillin such as Amoxicillin, Ampicillin, Azlocillin, Carbenicillin, Cloxacillin, Dicloxacillin, Flucloxacillin, Mezlocillin, Nafcillin, Oxacillin, Penicillin G or V, Piperacillin, Temocillin and Ticarcillin.
In some embodiments, an antibiotic agent described herein is a sulfonamide such as Mafenide, Sulfonamidochrysoidine, Sulfacetamide, Sulfadiazine, Silver sulfadiazine, Sulfamethizole, Sulfamethoxazole, Sulfanilimide, Sulfasalazine, Sulfisoxazole, Trimethoprim, or Trimethoprim-Sulfamethoxazole (Co-trimoxazole) (TMP-SMX).
In some embodiments, an antibiotic agent described herein is a quinolone such as Ciprofloxacin, Enoxacin, Gatifloxacin, Levofloxacin, Lomefloxacin, Moxifloxacin, Nalidixic acid, Norfloxacin, Ofloxacin, Trovafloxacin, Grepafloxacin, Sparfloxacin and Temafloxacin.
In some embodiments, an antibiotic agent described herein is a polypeptide such as Bacitracin, Colistin or Polymyxin B.
In some embodiments, an antibiotic agent described herein is a tetracycline such as Demeclocycline, Doxycycline, Minocycline or Oxytetracycline.
1. A bacteriophage comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising:
2. The bacteriophage of embodiment 1, wherein the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120.
3. The bacteriophage of any one of embodiments 1-2, wherein the CRISPR array further comprises at least one repeat sequence.
4. The bacteriophage of embodiment 3, wherein the at least one repeat sequence is operably linked to the one or more spacer sequences at either its 5′ end or its 3′ end.
5. The bacteriophage of any one of embodiments 3-4, wherein the repeat sequence comprises at least about 90% sequence identity to any one of SEQ ID NOS: 26-30.
6. The bacteriophage of any one of embodiments 1-5, wherein the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
7. The bacteriophage of any one of embodiments 1-6, wherein the target nucleotide sequence comprises a coding sequence.
8. The bacteriophage of any one of embodiments 1-6, wherein the target nucleotide sequence comprises a non-coding or intergenic sequence.
9. The bacteriophage of any one of embodiments 1-6, wherein the target nucleotide sequence comprises all or a part of a promoter sequence.
10. The bacteriophage of embodiment 9, wherein the promoter sequence comprises at least about 90% sequence identity to any one of SEQ ID NOs: 1-11.
11. The bacteriophage of embodiment 1, wherein the target nucleotide sequence comprises all or a part of a nucleotide sequence located on a coding strand of a transcribed region of an essential gene.
12. The bacteriophage of embodiment 11, wherein the essential gene is Tsf, acpP, gapA, infA, secY, csrA, trmD, ftsA, fusA, glyQ, eno, nusG, dnaA, dnaS, pheS, rplB, gltX, hisS, rplC, aspS, gyrB, glnS, dnaE, rpoA, rpoB, pheT, infB, rpsC, rplF, alaS, leuS, serS, rplD, gyrA, glmS, fus, adk, rpsK, rplR, ctrA, parC, tRNA-Ser, tRNA-Asn, or metK.
13. The bacteriophage of any one of embodiments 1-12, wherein the Cascade polypeptide forms a Cascade complex of a Type I-A CRISPR-Cas system, a Type I-B CRISPR-Cas system, a Type I-C CRISPR-Cas system, a Type I-D CRISPR-Cas system, a Type I-E CRISPR-Cas system, or a Type I-F CRISPR-Cas system.
14. The bacteriophage of embodiment 13, wherein the Cascade complex comprises:
15. The bacteriophage of embodiment 13, wherein the Cascade complex comprises a Cas5d polypeptide (optionally SEQ ID NO: 80), a Cas8c polypeptide (optionally SEQ ID NO: 81), and a Cas7 (optionally SEQ ID NO: 82) polypeptide (Type I-C CRISPR-Cas system).
16. The bacteriophage of any one of embodiments 1-15, wherein the nucleic acid sequence further comprises a promoter sequence.
17. The bacteriophage of any one of embodiments 1-16, wherein the bacteriophage is an obligate lytic bacteriophage.
18. The bacteriophage of any one of embodiments 1-16, wherein the bacteriophage is a temperate bacteriophage that is rendered lytic.
19. The bacteriophage of embodiment 18, wherein the temperate bacteriophage is rendered lytic by the removal, replacement, or inactivation of a lysogeny gene.
The bacteriophage of any one of embodiments 17-19, wherein the Pseudomonas species is killed solely by lytic activity of the bacteriophage.
21. The bacteriophage of any one of embodiments 1-19, wherein the Pseudomonas species is killed solely by activity of the CRISPR-Cas system.
22. The bacteriophage of any one of embodiments 17-19, wherein the Pseudomonas species is killed by lytic activity of the bacteriophage in combination with activity of the CRISPR-Cas system.
23. The bacteriophage of embodiment 22, wherein the Pseudomonas species is killed by the activity of the CRISPR-Cas system, independently of the lytic activity of the bacteriophage.
24. The bacteriophage of embodiment 22, wherein the activity of the CRISPR-Cas system supplements or enhances the lytic activity of the bacteriophage.
25. The bacteriophage of embodiment 22, wherein the lytic activity of the bacteriophage and the activity of the CRISPR-Cas system are synergistic.
26. The bacteriophage of any one of embodiments 17-25, wherein the lytic activity of the bacteriophage, the activity of the CRISPR-Cas system, or both, is modulated by a concentration of the bacteriophage.
27. The bacteriophage of any one of embodiments 1-26, wherein the bacteriophage infects multiple bacterial strains of the Pseudomonas species.
28. The bacteriophage of any one of embodiments 1-27, wherein the bacteriophage comprises a PhiKZvirus, PhiKMV virus, Brunyoghevirus, Samunavirus, Nankokuvirus, Abidjanvirus, Baikalvirus, Beetrevirus, Casadabanvirus, Citexvirus, Cystovirus, Detrevirus, Elvirus, Hollowayvirus, Kochitakasuvirus, Litunavirus, Luzseptimavirus, Nipunavirus, Pakpunavirus, Pamexvirus, Paundecimvirus, Phitrevirus, Primolicivirus, Septimatrevirus, Stubburvirus, Tertilicivirus, Yuavirus, Zicotriavirus or Pbunavirus.
29. The bacteriophage of embodiment 28, wherein the bacteriophage comprises at least 80% sequence identity to a phage selected from p1106, p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1, or two or more phage thereof.
30. The bacteriophage of embodiment 29, wherein the bacteriophage comprises p1106e003, p1106wt, p1194wt, p1587e002, p1587wt, p1695wt, p1772e005, p1772wt, p1835e002, p1835wt, p2037e002, p2037wt, p2131e002, p2131wt, p2132e002, p2132wt, p2167wt, p2363e003, p2363wt, p2421e002, p2421wt, p2973e002, p2973wt, p3278wt, p4430wt, PB1e002, or PB1wt, or two or more phage thereof.
31. The bacteriophage of any one of embodiments 1-30, wherein the nucleic acid sequence is inserted into a non-essential bacteriophage gene.
32. A pharmaceutical composition comprising:
33. The pharmaceutical composition of embodiment 32, wherein the pharmaceutical composition comprises at least two bacteriophage.
34. The pharmaceutical composition of embodiment 33, wherein the bacteriophage are from the lineage consisting of a PhiKZvirus, PhiKMV virus, Brunyoghevirus, Samunavirus, Nankokuvirus, Abidjanvirus, Baikalvirus, Beetrevirus, Casadabanvirus, Citexvirus, Cystovirus, Detrevirus, Elvirus, Hollowayvirus, Kochitakasuvirus, Litunavirus, Luzseptimavirus, Nipunavirus, Pakpunavirus, Pamexvirus, Paundecimvirus, Phitrevirus, Primolicivirus, Septimatrevirus, Stubburvirus, Tertilicivirus, Yuavirus, Zicotriavirus and Pbunavirus.
35. The pharmaceutical composition of embodiment 33, wherein the pharmaceutical composition comprises at least six bacteriophage, wherein the bacteriophage comprise p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695.
36. The pharmaceutical composition of any one of embodiments 32-35, wherein the pharmaceutical composition is in the form of a tablet, a capsule, a liquid, a syrup, an oral formulation, an intravenous formulation, an intranasal formulation, an ocular formulation, an otic formulation, a subcutaneous formulation, a topical formulation, a transdermal formulation, a transmucosal formulation, an inhalable respiratory formulation, a suppository, a lyophilized formulation, a nebulizable formulation, and any combination thereof.
37. A method of killing a Pseudomonas species comprising introducing into the target bacterium a nucleic acid sequence encoding a Type I CRISPR-Cas system from a bacteriophage, the nucleic acid sequence comprising:
38. The method of embodiment 37, wherein the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120.
39. The method of any one of embodiments 37-38, wherein the CRISPR array further comprises at least one repeat sequence.
40. The method of embodiment 39, wherein the at least one repeat sequence is operably linked to the one or more spacer sequences at either its 5′ end or its 3′ end.
41. The method of any one of embodiments 39-40, wherein the repeat sequence comprises at least about 90% sequence identity to any one of SEQ ID NOS: 26-30.
42. The method of any one of embodiments 37-41, wherein the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
43. The method of any one of embodiments 37-42, wherein the target nucleotide sequence comprises a coding sequence.
44. The method of any one of embodiments 37-42, wherein the target nucleotide sequence comprises a non-coding or intergenic sequence.
45. The method of any one of embodiments 37-42, wherein the target nucleotide sequence comprises all or a part of a promoter sequence.
46. The method of embodiment 45, wherein the promoter sequence comprises at least about 90% sequence identity to any one of SEQ ID NOs: 1-11.
47. The method of any one of embodiments 37-43, wherein the target nucleotide sequence comprises all or a part of a nucleotide sequence located on a coding strand of a transcribed region of an essential gene.
48. The method of embodiment 47, wherein the essential gene is Tsf, acpP, gapA, infA, secY, csrA, trmD, ftsA, fusA, glyQ, eno, nusG, dnaA, dnaS, pheS, rplB, gltX, hisS, rplC, aspS, gyrB, glnS, dnaE, rpoA, rpoB, pheT, infB, rpsC, rplF, alaS, leuS, serS, rplD, gyrA, glmS, fus, adk, rpsK, rplR, ctrA, parC, tRNA-Ser, tRNA-Asn, or metK.
49. The method of any one of embodiments 37-48, wherein the Cascade polypeptide forms a Cascade complex of a Type I-A CRISPR-Cas system, a Type I-B CRISPR-Cas system, a Type I-C CRISPR-Cas system, a Type I-D CRISPR-Cas system, a Type I-E CRISPR-Cas system, or a Type I-F CRISPR-Cas system.
50. The method of embodiment 49, wherein the Cascade complex comprises:
51. The method of embodiment 49, wherein the Cascade complex comprises a Cas5d polypeptide (optionally SEQ ID NO: 80), a Cas8c polypeptide (optionally SEQ ID NO: 81), and a Cas7 polypeptide (optionally SEQ ID NO: 82) (Type I-C CRISPR-Cas system).
52. The method of any one of embodiments 37-51, wherein the nucleic acid sequence further comprises a promoter sequence.
53. The method of any one of embodiments 37-52, wherein the bacteriophage is an obligate lytic bacteriophage.
54. The method of any one of embodiments 37-52, wherein the bacteriophage is a temperate bacteriophage that is rendered lytic.
55. The method of embodiment 54, wherein the temperate bacteriophage is rendered lytic by the removal, replacement, or inactivation of a lysogeny gene.
56. The method of any one of embodiments 37-55, wherein the Pseudomonas species is killed solely by activity of the CRISPR-Cas system.
57. The method of any one of embodiments 53-55, wherein the Pseudomonas species is killed by lytic activity of the bacteriophage in combination with activity of the CRISPR-Cas system.
58. The method of embodiment 57, wherein the Pseudomonas species is killed by the activity of the CRISPR-Cas system, independently of the lytic activity of the bacteriophage.
59. The method of embodiment 57, wherein the activity of the CRISPR-Cas system supplements or enhances the lytic activity of the bacteriophage.
60. The method of embodiment 57, wherein the lytic activity of the bacteriophage and the activity of the CRISPR-Cas system are synergistic.
61. The method of any one of embodiments 53-60, wherein the lytic activity of the bacteriophage, the activity of the CRISPR-Cas system, or both, is modulated by a concentration of the bacteriophage.
62. The method of any one of embodiments 37-61, wherein the bacteriophage infects multiple bacterial strains of the Pseudomonas species.
63. The method of any one of embodiments 37-62, wherein the bacteriophage comprises at least 80% identity to p1106, p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB 1, or two or more phage thereof.
64. The method of embodiment 63, wherein the bacteriophage comprises at least 80% identity to p1106e003, p1106wt, p1194wt, p1587e002, p1587wt, p1695wt, p1772e005, p1772wt, p1835e002, p1835wt, p2037e002, p2037wt, p2131e002, p2131wt, p2132e002, p2132wt, p2167wt, p2363e003, p2363wt, p2421e002, p2421wt, p2973e002, p2973wt, p3278wt, p4430wt, PB 1e002, or PB1wt, or two or more phage thereof.
65. The method of any one of embodiments 37-64, wherein the nucleic acid sequence is inserted in place of or adjacent to a non-essential bacteriophage gene.
66. The method of any one of embodiments 37-65, wherein a mixed population of bacterial cells comprises the Pseudomonas species.
67. The method of any one of embodiments 37-66, further comprising administering at least one additional bacteriophage.
68. The method of embodiment 67, comprising administering at least six bacteriophage, wherein the bacteriophage comprise p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695.
69. A method of treating a disease or condition in an individual in need thereof, the method comprising administering to the individual a bacteriophage comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising:
70. The method of embodiment 69, wherein the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120.
71. The method of any one of embodiments 69-70, wherein the CRISPR array further comprises at least one repeat sequence.
72. The method of embodiment 71, wherein the at least one repeat sequence is operably linked to the one or more spacer sequences at either its 5′ end or its 3′ end.
73. The method of any one of embodiments 71-72, wherein the repeat sequence comprises at least about 90% sequence identity to any one of SEQ ID NOS: 26-30.
74. The method of any one of embodiments 69-73, wherein the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
75. The method of any one of embodiments 69-74, wherein the target nucleotide sequence comprises a coding sequence.
76. The method of any one of embodiments 69-74, wherein the target nucleotide sequence comprises a non-coding or intergenic sequence.
77. The method of any one of embodiments 69-74, wherein the target nucleic acid sequence comprises all or a part of a promoter sequence.
78. The method of embodiment 77, wherein the promoter sequence comprises at least about 90% sequence identity to any one of SEQ ID NOs: 1-11.
79. The method of any one of embodiments 69-74, wherein the target nucleotide sequence comprises all or a part of a nucleotide sequence located on a coding strand of a transcribed region of an essential gene.
80. The method of embodiment 79, wherein the essential gene is Tsf, acpP, gapA, infA, secY, csrA, trmD, ftsA, fusA, glyQ, eno, nusG, dnaA, dnaS, pheS, rplB, gltX, hisS, rplC, aspS, gyrB, glnS, dnaE, rpoA, rpoB, pheT, infB, rpsC, rplF, alaS, leuS, serS, rplD, gyrA, glmS, fus, adk, rpsK, rplR, ctrA, parC, tRNA-Ser, tRNA-Asn, or metK.
81. The method of any one of embodiments 69-80, wherein the Cascade polypeptide forms a Cascade complex of a Type I-A CRISPR-Cas system, a Type I-B CRISPR-Cas system, a Type I-C CRISPR-Cas system, a Type I-D CRISPR-Cas system, a Type I-E CRISPR-Cas system, or a Type I-F CRISPR-Cas system.
82. The method of embodiment 81, wherein the Cascade complex comprises:
83. The method of embodiment 82, wherein the Cascade complex comprises a Cas5d polypeptide (optionally SEQ ID NO: 80), a Cas8c polypeptide (optionally SEQ ID NO: 81), and a Cas7 polypeptide (optionally SEQ ID NO: 82) (Type I-C CRISPR-Cas system).
84. The method of any one of embodiments 69-83, wherein the nucleic acid sequence further comprises a promoter sequence.
85. The method of any one of embodiments 69-84, wherein the bacteriophage is an obligate lytic bacteriophage.
86. The method of any one of embodiments 69-84, wherein the bacteriophage is a temperate bacteriophage that is rendered lytic.
87. The method of embodiment 86, wherein the temperate bacteriophage is rendered lytic by the removal, replacement, or inactivation of a lysogeny gene.
88. The method of any one of embodiments 69-87, wherein the Pseudomonas species is killed solely by activity of the CRISPR-Cas system.
89. The method of any one of embodiments 85-87, wherein the Pseudomonas species is killed by lytic activity of the bacteriophage in combination with activity of the CRISPR-Cas system.
90. The method of embodiment 89, wherein the Pseudomonas species is killed by the activity of the CRISPR-Cas system, independently of the lytic activity of the bacteriophage.
91. The method of embodiment 89, wherein the activity of the CRISPR-Cas system supplements or enhances the lytic activity of the bacteriophage.
92. The method of embodiment 89, wherein the lytic activity of the bacteriophage and the activity of the CRISPR-Cas system are synergistic.
93. The method of any one of embodiments 85-92, wherein the lytic activity of the bacteriophage, the activity of the CRISPR-Cas system, or both, is modulated by a concentration of the bacteriophage
94. The method of any one of embodiments 69-93, wherein the bacteriophage infects multiple bacterial strains.
95. The method of any one of embodiments 69-87, wherein the bacteriophage comprises at least 80% identity to p1106, p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1, or two or more phage thereof.
96. The method of embodiment 95, wherein the bacteriophage comprises at least 80% identity to p1106e003, p1106wt, p1194wt, p1587e002, p1587wt, p1695wt, p1772e005, p1772wt, p1835e002, p1835wt, p2037e002, p2037wt, p2131e002, p2131wt, p2132e002, p2132wt, p2167wt, p2363e003, p2363wt, p2421e002, p2421wt, p2973e002, p2973wt, p3278wt, p4430wt, PB 1e002, or PB1wt, or two or more phage thereof.
97. The method of any one of embodiments 69-96, wherein the nucleic acid sequence is inserted in place of or adjacent to a non-essential bacteriophage gene.
98. The method of any one of embodiments 69-97, further comprising administering at least one additional bacteriophage.
99. The method of embodiment 98, comprising administering at least six bacteriophage, wherein the bacteriophage comprise p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695.
100. The method of any one of embodiments 69-99, wherein the disease or condition is a bacterial infection, cystic fibrosis, non-cystic fibrosis bronchiectasis, or pneumonia.
101. The method of embodiment 100, wherein the bacterial infection is associated with cystic fibrosis or non-cystic fibrosis bronchiectasis, or wherein the bacterial infection is a blood stream infection.
102. The method of any one of embodiments 69-101, wherein the Pseudomonas species causing the disease or condition is a drug resistant Pseudomonas species.
103. The method of embodiment 102, wherein the drug resistant Pseudomonas species is resistant to at least one antibiotic.
104. The method of any one of embodiments 69-103, wherein the Pseudomonas species causing the disease or condition is a multidrug resistant Pseudomonas species.
105. The method of embodiment 104, wherein the multi-drug resistant Pseudomonas species is resistant to at least one antibiotic.
106. The method of any one of embodiments 103 or 105, wherein the antibiotic comprises a cephalosporin, a fluoroquinolone, a carbapenem, a colistin, an aminoglycoside, vancomycin, streptomycin, or methicillin.
107. The method of any one of embodiments 69-106, wherein the Pseudomonas species is Pseudomonas aeruginosa.
108. The method of any one of embodiments 69-107, wherein the administering is intra-arterial, intravenous, intraurethral, intramuscular, oral, subcutaneous, inhalation, topical, cutaneous, transdermal, transmucosal, implantation, sublingual, buccal, rectal, vaginal, ocular, otic, or nasal administration or any combination thereof.
109. The method of any one of embodiments 69-108, further comprising administering an additional therapeutic.
110. The method of embodiment 109, wherein the additional therapeutic comprises tobramycin.
111. The method of any one of embodiments 69-110, wherein the individual is a mammal.
112. A bacteriophage comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising:
113. The bacteriophage of embodiment 112, wherein the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120.
114. The bacteriophage of any one of embodiments 112-113, wherein the CRISPR array further comprises at least one repeat sequence.
115. The bacteriophage of embodiment 114, wherein the at least one repeat sequence is operably linked to the one or more spacer sequences at either its 5′ end or its 3′ end.
116. The bacteriophage of any one of embodiments 112-115, wherein the repeat sequence comprises at least about 90% sequence identity to any one of SEQ ID NOS: 26-30.
117. The bacteriophage of any one of embodiments 112-116, wherein the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
118. The bacteriophage of any one of embodiments 112-117, wherein the target nucleotide sequence comprises a coding sequence.
119. The bacteriophage of any one of embodiments 112-117, wherein the target nucleotide sequence comprises a non-coding or intergenic sequence.
120. The bacteriophage of any one of embodiments 112-117, wherein the target nucleotide sequence comprises all or a part of a promoter sequence.
121. The bacteriophage of embodiment 120, wherein the promoter sequence comprises at least about 90% sequence identity to any one of SEQ ID NOs: 1-11.
122. The bacteriophage of any one of embodiments 112-121, wherein the target nucleotide sequence comprises all or a part of a nucleotide sequence located on a coding strand of a transcribed region of an essential gene.
123. The bacteriophage of embodiment 122, wherein the essential gene is Tsf, acpP, gapA, infA, secY, csrA, trmD, ftsA, fusA, glyQ, eno, nusG, dnaA, dnaS, pheS, rplB, gltX, hisS, rplC, aspS, gyrB, glnS, dnaE, rpoA, rpoB, pheT, infB, rpsC, rplF, alaS, leuS, serS, rplD, gyrA, glmS, fus, adk, rpsK, rplR, ctrA, parC, tRNA-Ser, tRNA-Asn, or metK
124. The bacteriophage of any one of embodiments 112-123, wherein the nucleic acid sequence further comprises a promoter sequence.
125. The bacteriophage of any one of embodiments 112-124, wherein the bacteriophage is an obligate lytic bacteriophage.
126. The bacteriophage of any one of embodiments 112-124, wherein the bacteriophage is a temperate bacteriophage that is rendered lytic.
127. The bacteriophage of embodiment 126, wherein the temperate bacteriophage is rendered lytic by the removal, replacement, or inactivation of a lysogeny gene.
128. The bacteriophage of any one of embodiments 125-127, wherein the Pseudomonas species is killed solely by lytic activity of the bacteriophage.
129. The bacteriophage of any one of embodiments 125-127, wherein the Pseudomonas species is killed solely by activity of the CRISPR-Cas system.
130. The bacteriophage of any one of embodiments 125-127, wherein the Pseudomonas species is killed by lytic activity of the bacteriophage in combination with activity of the CRISPR-Cas system.
131. The bacteriophage of embodiment 130, wherein the Pseudomonas species is killed by the activity of the CRISPR-Cas system, independently of the lytic activity of the bacteriophage.
132. The bacteriophage of embodiment 130, wherein the activity of the CRISPR-Cas system supplements or enhances the lytic activity of the bacteriophage.
133. The bacteriophage of embodiment 130, wherein the lytic activity of the bacteriophage and the activity of the CRISPR-Cas system are synergistic.
134. The bacteriophage of any one of embodiments 125-133, wherein the lytic activity of the bacteriophage, the activity of the CRISPR-Cas system, or both, is modulated by a concentration of the bacteriophage
135. The bacteriophage of any one of embodiments 112-134, wherein the bacteriophage infects multiple bacterial strains.
136. The bacteriophage of any one of embodiments 112-135, wherein the bacteriophage comprises at least 80% identity to p1106, p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1, or two or more phage thereof.
137. The bacteriophage of embodiment 136, wherein the bacteriophage comprises at least 80% identity to p1106e003, p1106wt, p1194wt, p1587e002, p1587wt, p1695wt, p1772e005, p1772wt, p1835e002, p1835wt, p2037e002, p2037wt, p2131e002, p2131wt, p2132e002, p2132wt, p2167wt, p2363e003, p2363wt, p2421e002, p2421wt, p2973e002, p2973wt, p3278wt, p4430wt, PB 1e002, or PB1wt, or two or more phage thereof.
138. The bacteriophage of any one of embodiments 112-137, wherein the nucleic acid sequence is inserted into a non-essential bacteriophage gene.
139. A pharmaceutical composition comprising:
140. The pharmaceutical composition of embodiment 139, wherein the pharmaceutical composition comprises at least two bacteriophage.
141. The pharmaceutical composition of embodiment 140, wherein the pharmaceutical composition comprises at least six bacteriophage, wherein the bacteriophage comprise p1106e003, p1835e002, p1772e005, p2131e002, p4430, and p1695.
142. The pharmaceutical composition of any one of embodiments 139-141, wherein the pharmaceutical composition is in the form of a tablet, a capsule, a liquid, a syrup, an oral formulation, an intravenous formulation, an intranasal formulation, an ocular formulation, an otic formulation, a subcutaneous formulation, a topical formulation, a transdermal formulation, a transmucosal formulation, an inhalable respiratory formulation, a suppository, a lyophilized formulation, a nebulizable formulation, and any combination thereof.
143. A method of sanitizing a surface in need thereof, the method comprising administering to the surface a bacteriophage comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising:
144. The method of embodiment 143, wherein the surface is a hospital surface, a vehicle surface, an equipment surface, or an industrial surface.
145. A method of preventing contamination in a food product or a nutritional supplement, the method comprising administering to the food product or the nutritional supplement a bacteriophage comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising:
146. The method of embodiment 145, wherein the food product or nutritional supplement comprises milk, yoghurt, curd, cheese, fermented milks, milk based fermented products, ice-creams, fermented cereal based products, milk based powders, infant formulae or tablets, liquid suspensions, dried oral supplement, wet oral supplement, or dry-tube-feeding.
147. A bacteriophage comprising a nucleic acid sequence encoding a Type I CRISPR-Cas system comprising:
148. A bacteriophage comprising at least 80% sequence identity to a phage selected from p1106, p1194, p1587, p1695, p1772, p1835, p2037, p2131, p2132, p2167, p2363, p2421, p2973, p3278, p4430, or PB1, or two or more phage thereof.
149. The bacteriophage of embodiment 148, wherein the bacteriophage comprises at least 80% identity to p1106e003, p1106wt, p1194wt, p1587e002, p1587wt, p1695wt, p1772e005, p1772wt, p1835e002, p1835wt, p2037e002, p2037wt, p2131e002, p2131wt, p2132e002, p2132wt, p2167wt, p2363e003, p2363wt, p2421e002, p2421wt, p2973e002, p2973wt, p3278wt, p4430wt, PB 1e002, or PB1wt, or two or more phage thereof.
150. The bacteriophage of embodiment 148, further comprising
151. The bacteriophage of embodiment 150, wherein the one or more spacer sequence comprises at least one of SEQ ID NOs: 12-23, 31-74, or 88-120 or at least 90% sequence identity to any one of SEQ ID NOs: 12-23, 31-74, or 88-120.
152. The bacteriophage of any one of embodiments 150-151, wherein the CRISPR array further comprises at least one repeat sequence.
153. The bacteriophage of embodiment 151, wherein the at least one repeat sequence is operably linked to the one or more spacer sequences at either its 5′ end or its 3′ end.
154. The bacteriophage of any one of embodiments 151-153, wherein the repeat sequence comprises at least about 90% sequence identity to any one of SEQ ID NOS: 26-30.
155. The bacteriophage of any one of embodiments 151-154, wherein the CRISPR array comprises at least about 90% sequence identity to a sequence as set forth in
156. The bacteriophage of any one of embodiments 151-155, wherein the target nucleotide sequence comprises a coding sequence.
157. The bacteriophage of any one of embodiments 151-156, wherein the target nucleotide sequence comprises a non-coding or intergenic sequence.
158. The bacteriophage of any one of embodiments 151-157, wherein the target nucleotide sequence comprises all or a part of a promoter sequence.
159. The bacteriophage of embodiment 158, wherein the promoter sequence comprises at least about 90% sequence identity to any one of SEQ ID NOs: 1-11.
160. A composition comprising at least four bacteriophage, comprising:
161. The composition of embodiment 160, further comprising a fifth bacteriophage comprising at least 80% sequence identity with p1194.
162. The composition of embodiment 160, further comprising a fifth bacteriophage comprising at least 80% sequence identity with p1695.
163. The composition of embodiment 160, further comprising a fifth bacteriophage comprising at least 80% sequence identity with p4430.
164. The composition of embodiment 161 or 163, further comprising a sixth bacteriophage comprising at least 80% sequence identity with p1695.
Bacteriophage were engineered to contain a crArray and Cas construct. Table 1A depicts the components of the phage used in the following application. Table 1B depicts the sequences of the promoters used to drive expression of both the crArray and the Cas promoter. Table 1C depicts the sequence of the spacer sequence in the crArray used to target specific sites. Further,
P.
aeruginosa
P.
aeruginosa
P.
aeruginosa
P.
aeruginosa
E. coli
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
Pseudomonas
P. aeruginosa strains with a functional Type I-C Cas operon were transformed with Cas-only or crRNA-containing plasmids. In the presence of an endogenous Type I-C Cas system, the expression of a crRNA causes the bacteria to self-target and degrade its own DNA. The number of transformants was determined by counting the number of colonies that grow on an agar plate with antibiotic selection specific to the plasmid. The only bacteria that can form colonies are those that both acquire the plasmid and survive self-targeting. These data show that exogenous Cas expression improved self-targeting over the endogenous system and functions when the endogenous system is not present, as seen in
The plasmids were transformed into a P. aeruginosa strain that did not contain a functional Type I-C Cas operon. The transformed plasmids expressed either a spacer array alone or the spacer array and the Type I-C Cas operon.
Plasmids containing individual spacers or unique arrays were transformed into P. aeruginosa strain b1121, which has an endogenous Type I-C Cas system, or a Cas operon null mutant of the same strain. Cell death was observed in b1121 transfected cells, but not in the Cas operon null mutant. These data, as depicted in
Phage carrying the CRISPR-Cas3 construct were serially passaged to assess the stability of the repeats contained in the phage genome. p1772e005 was serially amplified on P. aeruginosa strain b1126 (a Type I-F strain). Amplifications one through eight were performed as one step amplifications where 50 uL of a bacterial overnight culture was added to 5 mL of LB in a 15 mL falcon tube followed by the immediate addition of 1 μL of the previous lysate. The mixtures were grown for 10-16 hours at 37° C. in a shaking incubator. Following incubation, phage-bacterial mixtures were centrifuged for 10 min at 5,000 rcf and the supernatants were filtered through 0.45 μm syringe filters and stored at 4° C. For amplification nine, serial ten-fold dilutions of amplification eight were spotted onto soft agar overlays of strain b1121 or b1126. A single plaque from each plate was picked with a pipette into 200 μL of PBS to obtain amplification nine. Ten microliters of amplification nine, were added to 50 μL of b1121 or b1126 overnight and 5 mL of LB, then grown for ˜16 hours followed by centrifugation and filtration. For sanger sequencing, phage DNA was amplified by PCR from lysates using primers flanking the engineering site. Sanger and NGS sequencing confirmed stability and integrity of the CRISPR-Cas3 construct when loaded onto the phage genome (shown in
1.5 mL of crude lysate was centrifuged for 1 hr at 4° C. and 24,000×g. A fraction of the supernatant (approximately 1.4 mL) was gently discarded, and 1 mL of ammonium acetate (0.1 M, pH 7.5) was added to the remaining lysate, which was then centrifuged. This step was performed twice. Washed phage samples were visualized by negative-stain transmission electron microscopy. A glow-discharged formvar/carbon-coated 400 mesh copper grid (Ted Pella, Inc., Redding, CA) was floated on a 25-μL droplet of the sample suspension for five min, transferred quickly to two drops of deionized water followed by a droplet of 2% aqueous uranyl acetate stain for 30 sec. The grid was blotted with filter paper and air-dried. Samples were observed using a JEOL JEM-1230 transmission electron microscope operating at 80 kV and images were taken using a Gatan Orius SC1000 CCD camera with Gatan Microscopy Suite 3.0 software. Results are exemplified in
p1772wt (wild type) and engineered variants p1772e004 (Cas system only) and p1772e005 (targeting crArray 1+Cas system) were mixed with an exponentially growing culture of b1126 at a multiplicity of infection (MOI) of 1. At 0 min, 15 min, 30 min, 1 h, 2 h, 4 h, 7 h 10 min, and 24 h after infection, samples were collected for plaque forming units (PFU) enumeration (
p1772wt, p1772e004, and p1772e005 were diluted to a particle count of 1e6, and each individual phage was used to infect a panel of 34 different bacteria at an MOI of 0.01. Optical Density (OD) readings at a wavelength of 600 nm were captured every hour over a 20 hour time course. The resulting OD readings were used to generate bacterial growth curves in the presence of one of the three phages. Integration was used to calculate the Area Under the Curve (AUC) for each growth curve, where a smaller AUC upon phage addition indicates reduced bacterial load. Host range was determined by monitoring the OD600 (turbidity) of the culture over time to obtain a bacterial growth curve with the starting amount of introduced phage indicated on the bottom of the graph (input phage titer in plaque forming units per milliliter). The AUC for a given strain was compared in the presence and absence of phage.
Table 2 shows data from a representative growth experiment of two unique full construct-containing engineered phages pArray3 (targeting crArray3+Cas system) and pArray4 (targeting crArray4+Cas system). In this assay, an amplification was performed by inoculating LB growth medium with a single colony of bacteria and adding phage as indicated in the “Input PFU/mL” column. Amplifications were incubated overnight. Following incubation, the bacteria were removed by filtration and phage titer in the lysate was quantified by the soft agar overlay method. The titer of the lysate is indicated in the “Output PFU/mL” column. These data indicate that the engineered phages replicated effectively. These data also demonstrate the relative precision of the titration assay.
This example shows that the Cas system and a crArray was successfully expressed from the phage genome.
p1772wt (wild type), which does not contain the Cas operon, was used as a control. For RNA isolation, the samples collected at each time point were added directly to RNAprotect. Samples were incubated for 5 minutes at room temperature, centrifuged for 10 minutes and 5000×g, and the supernatant discarded. Pellets were stored at −80° C. RNA was then isolated using the Qiagen RNeasy Mini Kit. cDNA was synthesized using the BioRad iScript cDNA synthesis kit. qRT-PCR was performed using BioRad SsoAdvanced Universal SYBR Green Supermix. All data was the average of two biological replicates. Fold change was 2−ΔΔCt, using Pseudomonas aeruginosa gene rpsH as the housekeeping gene and comparing each data point to the cells only control at the same time point.
Top agar overlays were prepared by mixing 100 μL of a saturated overnight culture of the p1772 indicator strain b1121 with 6 mL of 0.375% agar in LB containing 10 mM MgCl2 and 10 mM CaCl2). After the top agar solidified, 2 μL drops of serial 10-fold dilution series of p1772wt (wild type) and p1772e004 (Cas system only) and p1772e005 (targeting crArray 1+Cas system) were spotted onto the surface of the top agar. Plates were incubated at 37° C. for −18 h, then imaged using a Keyence BZ-X800 microscope at 4× and 10× magnification.
p1772 wildtype and engineered phage were mixed with bacteria in logarithmic growth and plated immediately in 2 ul spots on LB agar. The ratio of phage to bacteria was altered through the dilution series so that the amount of bacteria stays constant at each dilution but the amount of phage was a 1 to 4 dilution. At the highest dilution, the multiplicity of infection (MOI) was 100, meaning there were approximately 100 phages per bacteria. In
A P. aeruginosa strain (b1121) with an active endogenous Type I-C Cas system was grown to mid-logarithmic phase and infected with phage in liquid culture at the indicated multiplicity of infection (MOI). In all cases, the phage successfully killed the bacteria, as depicted in
p1772 wildtype and engineered phage variants were mixed with mCherry expressing bacteria in logarithmic growth and plated immediately onto LB agar. The ratio of phage to bacteria was altered by performing a dilution series of the phage, so that the amount of bacteria remained constant in each spot but the amount of phage changed. The highest multiplicity of infection (MOI) was 100, meaning there are approximately 100 phages per bacterium. After overnight incubation, bacterial growth was recorded by imaging the plate by brightfield and mCherry fluorescence. Quantification was performed on the samples based on these images.
Five different phage variants were used to determine the effect of lytic phage delivering non-targeting crRNAs with an exogenous Type I-C Cas system (p1772e008), a self-targeting crRNA alone without an exogenous CRISPR-Cas system (p1772e006), two different self-targeting crArrays delivered with an exogenous Type I-C Cas system (pArray3 and pArray4) and the parent wild-type phage (p1772wt). In these assays, a P. aeruginosa strain lacking any endogenous Cas system and the indicated phage were combined at the indicated ratio and immediately plated on LB plates. The host bacterial strain used in these assays was Cas-null and had a chromosomally integrated mCherry gene to facilitate observation and quantification of bacteria through measurement of relative fluorescence. The results are depicted in
p1772 wildtype and engineered phage variants were mixed with mCherry expressing bacteria in logarithmic growth and plated immediately onto LB agar. The ratio of phage to bacteria was altered by performing a dilution series of the phage, so that the amount of bacteria remained constant in each spot but the amount of phage changed. The highest multiplicity of infection (MOI) was 100, meaning there were approximately 100 phages per bacterium. After overnight incubation, bacterial growth was recorded by imaging the plate by brightfield and mCherry fluorescence. Quantification was performed on the samples based on these images.
Wildtype and engineered phage variants were mixed with mCherry expressing bacteria in logarithmic growth and plated immediately onto LB agar. The results shown are from a multiplicity of infection (MOI) of 1.5, meaning there were approximately 1.5 phages per single bacterium. After overnight incubation, bacterial growth was recorded by imaging the plate for mCherry fluorescence. Quantification as depicted in
An assay was performed with p4209wt (wild type) and p4209e002 (targeting crArray1+Cas system) against a panel of Pseudomonas strains. Briefly, early log phase bacterial culture was mixed with phage to obtain the final titers listed in the figure. Samples were plated immediately (t=0 h) and after 3 and 24 h of incubation at 37° C. Plates were imaged and differences between the wild type and full construct variants tabulated. p4209 wildtype and engineered phage variants were mixed with bacteria in logarithmic growth and plated immediately onto LB agar, or incubated in liquid for the indicated amount of time before plating. The ratio of phage to bacteria was altered by performing a dilution series of the phage, so that the amount of bacteria stays constant in each spot but the amount of phage changes. The relative ratio of the phage and bacteria shifted over the course of the experiment as the bacteria replicated and succumbed to the phage. After overnight incubation, bacterial growth was recorded by imaging the plate. The label at the top of each set of images denotes the Cas type of the bacterial strain shown in that image.
p4209wt, p4209e001 (Cas system only), and p4209e002 (targeting crArray1+Cas system) were plagued on multiple bacterial strains to examine the efficiency of plaquing. P. aeruginosa strain b1121 supported all variants equivalently and is provided as a titer reference. On P. aeruginosa strain b2631, the wild type variant plagued at a significantly decreased level, the Cas-only variant did not plaque at all, and the fully engineered variant plagued with no loss of efficiency compared to b1121. On P. aeruginosa strain b2816, neither the wild type nor Cas-only variants showed any evidence of activity, while the fully engineered variant produced zones of clearing. On P. aeruginosa strain b2825, the wild type and Cas only variants had significantly reduced plaquing efficiency, while the fully engineered variant maintained comparable efficiency to b1121. Both b2631 and b2825 show examples of an engineering event (insertion of the Cas system) having detrimental effects—that is, either a decrease in efficiency of plaquing (b2631) or in plaque clarity (b2825). In both cases, addition of the targeting crArray (which enables activity of the Cas system) not only rescued the decreased activity but improved activity beyond that seen in the wild type parent. The label at the bottom of plate image denotes the bacterial strain shown in that image and the type of endogenous Cas system it contains. These results further support that the Cas system and targeting crArray improved the phages ability to replicate and kill various bacterial strains.
Both the bacterial colony forming units (CFU) and phage plaque forming units (PFU) are shown for each experiment.
A culture of b1121 was grown overnight, back diluted into LB+10 mM MgCl2+mM CaCl2 and grown to an OD600 of 0.45. The culture was split and treated with either LB/salts (cells only control), p1772e005 (MOI=0.1), PB1e002 (MOI=0.1), or a cocktail of p1772e005+PB1e002 (MOI=0.1 per phage). All samples were incubated in a microtiter plate at 37° C. with shaking for 24 h and the OD at 630 nm was measured every 10 minutes. Data is presented as a mean of 12 replicates. Error bars represent the standard deviation. The data show that the cocktail of the two full construct phages suppresses culture rebound to a greater extent than either phage by itself.
A culture of P. aeruginosa cultures were transformed with vectors comprising the different repeat sequences. The vectors were either an empty vector pUCP19 (empty vector) or contained an pUCP19 vector comprises a Pseudomonas Type I C Cas system and a spacer targeting the gyrB gene flanked by the repeat sequence listed in Table 3. An aliquot was taken of each test condition, diluted and spotted to enumerated bacterial CFUs.
The results of this assay are depicted in
A spacer sequence is designed using the following protocol. First, suitable search set of representative genomes for the organism/species/target of interest are acquired. Examples of suitable databases include NCBI genbank and the PATRIC (Pathosystems Resource Integration Center) database. The genomes are downloaded in bulk via FTP (File Transfer Protocol) servers, enabling rapid and programmatic dataset acquisition.
The genomes are searched with relevant parameters to locate suitable spacer sequences. The genomes can be read from start to end, in both the forward and reverse complement orientations, to locate contiguous stretches of DNA that contain a PAM (Protospacer Adjacent Motif) site. The spacer sequence will be the N-length DNA sequence 3′ adjacent to the PAM site, where N is specific to the Cas system of interest and is generally known ahead of time. Characterizing the PAM sequence and spacer sequences are generally performed during the discovery and initial research of a Cas system. Every observed PAM-adjacent spacer can be saved to a file and/or database for downstream use.
Next, the quality of a spacer for use in a CRISPR engineered phage is determined using the following process. First, each observed spacer can be evaluated to determine how many of the evaluated genomes they are present in. The observed spacers can additionally be evaluated to see how many times they may occur in each given genome. Spacers that occur in more than one location per genome can be advantageous because the Cas system may not be able to recognize the target site if a mutation occurs, and each additional “backup” site increases the likelihood that a suitable, non-mutated target location will be present. The observed spacers can be evaluated to determine whether they occur in functionally annotated regions of the genome. If such information is available, the functional annotations can be further evaluated to determine whether those regions of the genome are “essential” for the survival and function of the organism. Focusing on spacers that occur in all, or nearly all, evaluated genomes of interest (>=99) ensures broad applicability to justify the spacer selection. Provided a large selection pool of conserved spacers exists, preference may be given to spacers that occur in regions of the genome that have known function, with higher preference given if those genomic regions are “essential” for survival and occur more than 1 time per genome.
The identified spacer sequences can then be validated by completing the following procedure. First, a plasmid that replicates in the organism(s) of interest and has a selectable marker (e.g. an antibiotic-resistance gene) is identified. The genes encoding the Cas system are inserted into the plasmid such that they will be expressed in the organism of interest. Upstream of the Cas system, a promoter is included that is recognized by the organism of interest to drive expression of the Cas system. Between the promoter and the Cas system, a ribosomal binding site (RBS) is included that is recognized by the organism of interest.
Next, genome-targeting spacers that have been identified bioinformatically are inserted into the plasmid that expresses the Cas system. Upstream of the repeat-spacer-repeat, promoter is included that is recognized by the organism of interest to drive expression of the crRNA. Examples of such promoters are listed in Table 1B. This cloning must be performed in an organism or strain that is not targeted by the spacer being cloned.
Next, a non-targeting spacer is inserted into the plasmid that expresses the Cas system. The sequence of this spacer can be randomly generated and then confirmed bioinformatically to not have targeting sites in the genome of the organism of interest. Upstream of the repeat-spacer-repeat, a promoter that is recognized by the organism of interest to drive expression of the crRNA is included.
Next, the killing efficacy of each tested spacer is determined. The plasmids listed in Table 4 are normalized to the same molar concentration. Each plasmid is transferred to the organism of interest by transformation, conjugation, or any other method for introducing a plasmid into a cell. The transformed cells are plated onto the appropriate selective media (e.g. antibiotic-containing agar). Following cell growth into colonies, the colonies that resulted from each different plasmid transfer are enumerated. Plasmids containing targeting spacers with a significantly lower transfer rate than the control plasmid containing the non-targeting spacer are considered to be successful at targeting the bacterial genome.
Data for purified P. aeruginosa phage was acquired, reported was the best result from combined liquid and plaquing host range assays. The final result was the median of the binary hits across both liquid and plaquing host range for a given phage plus strain combination. Liquid host range involved the addition of 5 uL of frozen, OD-controlled, culture material, 5 uL of known titer phage material and 40 uL of growth media into a well of a 364-well plate along with appropriate culture, phage, and media only controls. The plate was incubated for 20 hours at 37 C while shaking and OD600 readings were taken by the liquid handler every hour. The results were calculated by determining the ratio between areas under the cover (AUC) for samples with phage added and their respective controls. Samples with AUC ratios below 0.65 were considered positive (+) hits while AUC ratios greater than or equal to 0.65 were negative (−) hits. For plaquing host range assays, bacterial strains of interest were cultured and screened for prophage. Bacteriophage of interest were serially diluted 50-fold across a microtiter plate from undiluted to 50-3 in 1×PBS. Agar overlays of strains used as titre host were poured and allowed to sit overnight. The following day, lysates for the bacterial strains of interest were spotted. After 15-20 min, the plates were imaged using the Hamilton-STAR-0062 and either counted by hand or run through an internally developed image analysis pipeline for transformation, background subtraction, and counting. Samples with a positive (+) number of plaque forming units were considered hits. The results of this assay involving P. aeruginosa, wildtype Pbunavirus phage subtypes, and engineered Pbunavirus phage subtypes were listed in Table 5A. The results of this assay involving P. aeruginosa, wildtype Samunavirus phage subtypes, engineered Samunavirus phage subtypes, wildtype PhiKZvirus, wildtype PhiKMVvirus, and wildtype Bruynoghevirus were listed in Table 5B. As listed in Table 5A, the wildtype Pbunavirus phage subtypes were p1106, p1587, p1835, p2037, p2363, p2421, and pb1, while the engineered Pbunavirus phage subtypes were p1106e003, p1587e002, p1835e002, p2037e002, p2363e003, and p2421e002. As listed in Table 5B, the wildtype Samunavirus phage subtypes were p1772, p2131, p2132, and p2973, the engineered Samunavirus phage subtypes were pb1e002, p1772e005, p2131e002, p2132e002, and p2973e002, the wildtype PhiKZvirus phage subtypes were p1194, and p4430, the wildtype PhiKMVvirus phage subtype was p2167, and the wildtype Bruynoghevirus phage subtypes were p1695, and p3278.
P. aeruginosa Phage Host Range
P. aeruginosa Phage Host Range
Data for P. aeruginosa cocktail phage was acquired, reported is the best result from combined liquid and plaquing host range assays. The final result was the median of the binary hits across both liquid and plaquing host range for a given phage plus strain combination. Liquid host range involved the addition of 5 uL of frozen, OD-controlled, culture material, 5 uL of known titer phage material and 40 uL of growth media into a well of a 364-well plate along with appropriate culture, phage, and media only controls. The plate was incubated for 20 hours at 37 C while shaking and OD600 readings were taken by the liquid handler every hour. The results were calculated by determining the ratio between areas under the cover (AUC) for samples with phage added and their respective controls. Samples with AUC ratios below 0.65 were considered positive (+) hits while AUC ratios greater than or equal to 0.65 were negative (−) hits. For plaquing host range assays, bacterial strains of interest were cultured and screened for prophage. Bacteriophage of interest were serially diluted 50-fold across a microtiter plate from undiluted to 50-3 in 1×PBS. Agar overlays of strains used as titre host were poured and allowed to sit overnight. The following day, lysates for the bacterial strains of interest were spotted. After 15-20 min, the plates were imaged using the Hamilton-STAR-0062 and either counted by hand or run through an internally developed image analysis pipeline for transformation, background subtraction, and counting. Samples with a positive (+) number of plaque forming units were considered hits. The detailed composition of phage cocktails ck000125, ck000239, ck000240, ck000241, ck000511, and ck000512 (also referred to as PACK512, Cocktail 512, ck00512, CK512) was listed in Table 6A. As listed in Table 6B, phage cocktail ck000125 comprises p1106e003, p1835e002, p1772e005, and p2131e002. As listed in Table 6B, phage cocktail ck000239 comprises p1106e003, p1835e002, p1772e005, p2131e002, and p1194. As listed in Table 6B, phage cocktail ck000240 comprises p1106e003, p1835e002, p1772e005, p2131e002, and p4430. As listed in Table 6B, phage cocktail ck000241 comprises p1106e003, p1835e002, p1772e005, p2131e002, and p1695. As listed in Table 6B, phage cocktail ck000511 comprises p1106e003, p1835e002, p1772e005, p2131e002, p1194 and p1695. As listed in Table 6B, phage cocktail ck000512 comprises p1106e003, p1835e002, p1772e005, p2131e002, p4430 and p1695.
The results of this assay involving P. aeruginosa, and phage cocktails ck000125, ck000239, ck000240, ck000241, ck000511, and ck000512 are listed in Table 6A. Overall, host range was increased in phage cocktail assays as shown by an increase in positive (+) hits listed on Table 6B, as compared to individual phage assays listed in Table 5A and Table 5B. As listed in Table 6B, cocktail ck000512 P. aeruginosa host range data increased consistently.
As shown in Table 6C, the host range of cocktails CK000125 and CK00512 was tested in 284 different Pseudomonas bacterial isolates. 111 isolates were from cystic fibrosis (CF) and 85 isolates were from non-cystic fibrosis bronchiectasis (NCFB). Of the 284 Pseudomonas isolates, 95 were multi-drug resistant, with 49 of those isolates from CF and 9 from NCFB. The host range for both cocktails was greater than 85%, with cocktail CK00512 have a host range of 100% for all MDF isolates.
P. aeruginosa Cocktail Phage Host Range
As shown on Table 7, P. aeruginosa cocktail phage did not exhibit off-target plaquing. P. aeruginosa cocktail phage was plagued on b2631 or b1121 in addition to b1233/PA01 because not all phage infected this bacterial strain. P. aeruginosa cocktails CK000511 and CK000512 (PACK512); constitutive phage p1835e002, p1106e003, p1772e005, p2131e002, p1194, p1695, and p4430; and positive control phage were plagued on off-target ESKAPE species. No off target plaquing was observed from any of the phage tested, as noted by (−). As detailed on Table 7, data acquired showed that phages only hit (+) P. aeruginosa.
S.
K.
P.
E.
E.
A.
S.
aureus
pneumoniae
aeruginosa
faecium
cloacae
baumanii
epidermidis
Comparison of CRISPR-Phage and Wild-Type Phage
Bacterial isolates, tobramycin MICs and challenge inoculum are described in Table 8. Pseudomonas aeruginosa isolate b1121 was used for this study. A loopful of the bacterial stock was scraped from the surface of a frozen vial of culture and streaked for isolation on several TSA plates. After 16 h of growth at 37° C., the inoculum was removed from the plate, and suspended into PBS, pH 7.2 (Gibco 20012027) and adjusted to an OD650nm of 1.0±0.3. Two cohorts of animals were challenged in the same study with independently prepared inocula.
Tobramycin (75 mg/kg/day, HED 6 mg/kg/day) was tested as a comparator. Tobramycin sulfate (Xgen, Lot no. AZ1240B) was prepared in dH2O, and administered subcutaneously in 0.2 mL. Treatment was initiated 1 h post infection and continued twice daily (BID) at 12-hour intervals for a total of 4 doses. Tobramycin was prepared fresh daily and stored at 4° C. between dosing. Individual bacteriophages were diluted to 4.25E+09 PFU/mL in PBS, pH 7.4 such that the final concentration of each individual phage was 10.7 Log10 PFU/dose. Phages were delivered under anesthesia intranasally 2 h post-challenge. Additional doses were administered at 8, 24 and 32 h post-challenge. Animals were randomized at the time of treatment and separated into two treatment groups. In both cohorts, animals were treated with p1772WT or p1772FC. Tobramycin and PBS were included as controls in both groups.
Specific pathogen-free 7-8-week-old female C57BL/6J mice (Jackson Laboratory, Bar Harbor Maine) were anesthetized with 3% isoflurane and maintained with oxygen at 3 liters/min before inoculation into both nares with 0.050 mL of P. aeruginosa suspension b1121. Mice were placed into the cage in a supine position and allowed to recover from anesthesia. At 24 and 48 h post-challenge, animals were euthanized with CO2 asphyxiation, lungs were removed aseptically and placed into homogenizing tubes. Moribund animals were humanely euthanized and counted as a mortality. High dose group determined by MED (max feasible dose; targeting 1010-11 PFU/mL for highest strain). Necropsy for gross observations and standard tissue panel for histopathology; second lung lobe can be used for PD (PCR).
Lungs were harvested into soft tissue homogenizing tubes containing 1.4 mm ceramic beads (VWR 10158-610), and 1 mL PBS, pH7.4 (Gibco 10010023). Tissues were homogenized for 20 s, followed by a 10 s rest, and an additional 20 s homogenization. Homogenates were serially diluted 1:100 into 0.9% sterile saline (BBL, 221819) and plated on trypticase soy agar (TSA) plates for CFU enumeration using spiral plate methodology. CFU were determined following 20-22 h incubation at 37° C. Bacterial counts were expressed as Log10 CFU per gram of tissue and data from both studies were combined for analyses.
Comparison of phage cocktails and individual phage
P. aeruginosa isolates b1121, b2631 or b3144 were used for these studies. P. aeruginosa suspension isolates were prepared for challenge. P. aeruginosa b3144 was diluted 1:3 in PBS, pH 7.2, and P. aeruginosa b2631 was diluted 1:10 in PBS. Isolate b1121 was not diluted after standardizing to OD650 nm=1.0.
Tobramycin treatment was prepared and dosed as described in
Specific pathogen-free 7-8-week-old female C57BL/6J mice (Jackson Laboratory, Bar Harbor Maine) were anesthetized with 3% isoflurane and maintained with oxygen at 3 liters/min before inoculation into both nares with 0.050 mL of the P. aeruginosa suspension. Mice were placed into the cage in a supine position and allowed to recover from anesthesia. During recovery, cages were placed on a heating pad at 105° F. until animals were fully awake and ambulatory.
At 24 and 48 h post-challenge with P. aeruginosa suspension, lungs were harvested as described above, except that following serial dilution, homogenates were plated on Pseudomonas inhibition agar (PIA) plates for CFU enumeration using spiral plate methodology. CFU were determined for each animal following 16-22 h incubation at 37° C. Bacterial counts were expressed as Log10 CFU per gram of tissue, and data were analyzed using t-tests, Mann-Whitney tests, analysis of variance (ANOVA), or log-rank test. All statistical analyses were performed using GraphPad Prism version 8.0. P values of <0.05 were considered statistically significant.
Treatment with the cocktail and the cocktail in combination with tobramycin resulted in levels of Pseudomonas aeruginosa below the level of detection for all 3 strains tested, as depicted in
In similar assays described above, phage cocktail ck00125 was also tested.
Materials and Methods:
Preparation of challenge Inoculum
Pseudomonas aeruginosa isolates b1121, b2631 or b3144 were used for these studies. Isolates were prepared for challenge as described above, with the following modifications. P. aeruginosa b3144 was diluted 1:3 in PBS, pH 7.2, and P. aeruginosa b2631 was diluted 1:10 in PBS. Isolate b1121 was not diluted after standardizing to OD650 nm=1.0.
Tobramycin was prepared and dosed as described above, except that animals were dosed BID at 12-hour intervals for a total of 3 doses. Individual bacteriophages and cocktail 512 (PACK512) were diluted to the maximum concentration available based on phage titer and EU/mL (table 2). The concentration of phage in both individual and cocktails was the same. Phages were delivered under anesthesia intranasally 2 h post-challenge. Additional doses were administered at 8, 24 h post-challenge. Animals were randomized at the time of treatment and separated into two treatment groups. In cohort one, animals were treated with the cocktail and individual phages. In cohort two, animals were treated with PACK512. Tobramycin, tobramycin plus PACK512 and PBS were included in both cohorts, and data from both studies were combined for analyses.
Specific pathogen-free 7-8-week-old female C57BL/6J mice (Jackson Laboratory, Bar Harbor Maine) were anesthetized with 3% isoflurane and maintained with oxygen at 3 liters/min before inoculation into both nares with 0.050 mL of the P. aeruginosa suspension. Mice were placed into the cage in a supine position and allowed to recover from anesthesia. During recovery, cages were placed on a heating pad at 105° F. until animals were fully awake and ambulatory
In an effort to understand the relative benefits of the cocktail PACK512 (also referred to as ck00512) over individual engineered phages, a comparison was performed between the phages p1106FC, p1772FC, P1835FC, p2131FC, p1685WT, p4430WT and cocktail 512 (PACK512), with or without Tobramycin. Experimental set up is shown in
Lungs were harvested as described above, except that following serial dilution, homogenates were plated on Pseudomonas inhibition agar (PIA) plates for CFU enumeration using spiral plate methodology. CFU were determined for each animal following 16-22 h incubation at 37° C. Bacterial counts were expressed as Log10 CFU per gram of tissue.
Data were analyzed using t-tests, Mann-Whitney tests, analysis of variance (ANOVA) or log-rank test were appropriate. All statistical analyses were performed using GraphPad Prism version 8.0. P values of <0.05 were considered statistically significant.
In this example effect of a phage cocktail on Pseudomonas biofilms was tested. The assay setup is represented in
Mucin is a glycoprotein abundant in mucus from healthy as well as diseased human subjects. Cystic fibrosis is characterized by hyperproduction of mucus by airway and lung epithelia which primarily form a barrier for access by therapeutic agents to the cells. In this experiment, airway epithelial tissue derived from healthy human was cultured for 1 month, and mucin was measured prior to subjecting the culture to bacterial infection for 30 minutes and then chasing with phage cocktail. After incubation for 19.5 hours the sample were collected and bacterial and phage loads were determined. As shown in
In an attempt to understand the time course of phage persistence in vivo, phage levels were determined in the LRTI mouse model over time. It was observed that the level of each phage was high despite bacterial clearance. An exemplary result is shown in
Phage genome copy (GC) levels per dose were determined by qPCR, multiplied by number of doses given and divided by GEOMEAN of lung weight within each treatment group.
PFU per dose was estimated based on the PFU/mL titers of NME phage stocks and the expected PFU/dose in formulated cocktail, then divided by GEOMEAN of lung weight within each treatment group.
While preferred embodiments of the present disclosures have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosures. It should be understood that various alternatives to the embodiments of the disclosures described herein may be employed in practicing the disclosures. It is intended that the following claims define the scope of the disclosures and that methods and structures within the scope of these claims and their equivalents be covered thereby.
This application claims the benefit of U.S. Provisional Application No. 63/110,288, filed on Nov. 5, 2020, and U.S. Provisional Application No. 63/184,728, filed on May 5, 2021, both of which are incorporated herein by reference in their entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2021/058123 | 11/4/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63110288 | Nov 2020 | US | |
| 63184728 | May 2021 | US |
