Patent Grant
11492601
The present invention relates to a modified bacteriophage, uses thereof, and compositions containing the modified bacteriophage.
This application is a U.S. National Phase application of International Application No. PCT/EP2015/073294, filed Oct. 8, 2015, which claims priority to United Kingdom Application No. 1417805.7 GB, filed Oct. 8, 2014, each of which is incorporated herein by reference.
This application includes as part of its disclosure a biological sequence listing which is being concurrently submitted through EFS-Web. Said biological sequence listing is contained in a file named “43297o3001.txt” which was created on Apr. 6, 2017, and has a size of 126,577 bytes, and is hereby incorporated by reference in its entirety.
The World Health Organisation's 2014 report on global surveillance of antimicrobial resistance reveals that antibiotic resistance is a global problem that is jeopardising the ability to treat common infections in the community and hospitals. Without urgent action, the world is heading towards a post-antibiotic era, in which common infections and minor injuries, which have been treatable for decades, can once again kill (WHO, 2014). Antibiotic resistance complicates patients' recovery from even minor operations and is increasingly causing treatment failures. In fact, there are now strains of some genera of bacteria circulating globally which are resistant to all available antibiotics. Such strains commonly fall within the scope of the so-called ESKAPE pathogens—Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species (Boucher et al., 2009). The term ESKAPE pathogens was coined by Boucher et al., to emphasize that these bacteria currently cause a majority of hospital infections in the US and Europe and can effectively “escape” the majority, if not all, available antibiotics with panantibiotic-resistant infections now occurring. The death rate for patients with serious infections caused by common bacteria treated in hospitals is approximately twice that of patients with infections caused by the same non-resistant bacteria, e.g. people with methicillin-resistant Staphylococcus aureus (MRSA) infections are estimated to be 64% more likely to die than people with a non-resistant form of the infection (WHO, 2014). Of the Gram positive bacteria, methicillin resistant S. aureus continues to be a major cause of morbidity and mortality in hospitals in the US and Europe. However, in more recent years, several highly resistant Gram negative pathogens, including Acinetobacter species, multidrug resistant (MDR) P. aeruginosa, and carbapenem-resistant Klebsiella species and Escherichia coli, have emerged as major pathogens causing serious, and sometimes untreatable, infections. Advances in medicine mean that increasingly complex procedures take place: and these advances are leading to a growing number of elderly patients and patients undergoing surgery, transplantation, and chemotherapy all of which will produce an even greater number of immunocompromised individuals at risk of these infections (Walker et al., 2009). This phenomenon has led to a greater dependence on, and requirement for, effective antibiotics.
P. aeruginosa is one bacterium which is frequently multi-drug resistant (MDR) having intrinsic resistance due to low permeability of its outer membrane limiting drugs getting into the cell, and a multitude of efflux pumps to expel any drugs that successfully manage to enter the cell. P. aeruginosa is also acquiring additional resistance mechanis nce to the “antibiotics of last resort” for Gram negatives, the carbapenems. P. aeruginosa ms, including resista causes approximately 10% of all hospital acquired infections and is the second leading cause of hospital-acquired pneumonia, which accounts for 50% of all hospital-acquired infection prescribing. P. aeruginosa infections in hospitals commonly require intravenous (IV) treatment with current standard of care for P. aeruginosa infections dictating that patients are treated with at least two antibiotics. Unfortunately, resistance frequently develops in patients during therapy. With so few new classes of antibiotic developed and approved for market within the last 30-40 years, there is a critical need for novel, safe and effective antibacterial agents.
As an alternative to conventional antibiotics, one family of proteins which demonstrate broad spectrum antibacterial activity inside bacteria comprises the α/β-type small acid-soluble spore proteins (known henceforth as SASP). Inside bacteria, SASP bind to the bacterial DNA: visualisation of this process, using cryoelectron microscopy, has shown that SspC, the most studied SASP, coats the DNA and forms protruding domains and modifies the DNA structure (Francesconi et al., 1988; Frenkiel-Krispin et al., 2004) from B-like (pitch 3.4 nm) towards A-like (3.18 nm; A-like DNA has a pitch of 2.8 nm). The protruding SspC motifs interact with adjacent DNA-SspC filaments packing the filaments into a tight assembly of nucleo-protein helices. In 2008, Lee et al. reported the crystal structure at 2.1 Å resolution of an α/β-type SASP bound to a 10-bp DNA duplex. In the complex, the α/β-type SASP adopt a helix-turn-helix motif, interact with DNA through minor groove contacts, bind to approximately 6 bp of DNA as a dimer and the DNA is in an A-B type conformation. In this way DNA replication is halted and, where bound, SASP prevent DNA transcription. SASP bind to DNA in a non-sequence specific manner (Nicholson et al., 1990) so that mutations in the bacterial DNA do not affect the binding of SASP. Sequences of α/β-type SASP may be found in appendix 1 of WO02/40678, including SASP-C from Bacillus megaterium which is the preferred a/B-type SASP.
WO02/40678 describes the use as an antimicrobial agent of bacteriophage modified to incorporate a SASP gene. In order to provide effective production of the modified bacteriophage in a bacterial host, WO02/40678 aims to avoid expression of the SASP gene during proliferation of the production host. To this end, the SASP gene was put under the control of an inducible promoter. In one arrangement, the SASP gene was put under the control of a lysis gene promoter which is active only at the end of the bacteriophage life cycle by insertion into the lysis genes of a temperate bacteriophage. In doing so the phage remains viable as a prophage. In another arrangement, the SASP gene could be located elsewhere on the bacteriophage chromosome and placed under the control of a bacteriophage or bacterial promoter whereby the lytic cycle could be left to run its course. In this arrangement, the bacterial promoter would be non-constitutive and could be up-regulated by environmental cues. It was thought that proliferation of the bacterial production host would otherwise be prevented owing to the presence of the SASP gene product, particularly if the SASP gene was under the control of a constitutive promoter.
WO2009019293 describes that effective production of bacteriophage may be achieved where the bacteriophage has been modified to carry a gene encoding a SASP under the control of a promoter which is controlled independently of the bacteriophage, and which is constitutive with no exogenous or in trans regulation necessary or provided. An example is the fbaA promoter from S. aureus which is used to drive expression of the SASP-C gene from Bacillus megaterium and which, when present in multiple copies, for example following infection of target cells, drives toxic levels of SASP expression.
Bacteriophage vectors modified to contain a SASP gene have generally been named SASPject vectors. Once the SASP gene has been delivered to a target bacterium, SASP is produced inside those bacteria where it binds to bacterial DNA and changes the conformation of the DNA from B-like towards A-like. Production of sufficient SASP inside target bacterial cells causes a drop in viability of affected cells.
Bacteriophage have been used as medicines for the treatment of bacterial infections since the 1920s or 30s. Generally, bacteriophage are specific to their bacterial host. Some bacteriophage are temperate and others non-temperate. Temperate phage are able to infect the host cell and integrate into the host cell genome becoming a prophage which is generally harmless to the host cell in this state. Non-temperate or “lytic” phage are only able to replicate in a lytic lifestyle by making new bacteriophage progeny and ending in lysis of the host cell and release of mature phage particles. For useful medicines, the challenge is to provide bacteriophage compositions which can be used to treat infection from a variety of different bacteria in an effective way. It is commonly thought that this is achieved using the most potent bacteriophage compositions available: those with a broadened host range, possibly as a mixture or “cocktail” of bacteriophage, which are obligately lytic and retain viability through replication and release during treatment (Carlton, 1999; Kutateladze and Adamia, 2010). Cocktails of wild type phage have been used to ensure sufficient spectrum of activity against clinical strains of bacteria (Burrowes and Harper, 2012). Such cocktails can consist of up to 20 different and unrelated phage (Abedon 2008). As an alternative to the cocktail approach, E. coli bacteriophage K1-5 has been isolated. This is a naturally-occurring obligately lytic phage which carries more than one host range determinant allowing it to infect and replicate on both K1 and K5 strains of E. coli (Scholl et al, 2001). These phage are considered to be extra potent.
There remains a need to provide improved bacteriophage for use in treating bacterial infections in medicine as well as inhibiting or preventing bacterial cell growth in medical and non-medical situations.
In a first aspect, the present invention provides a modified bacteriophage capable of infecting a plurality of different target bacteria, which bacteriophage includes an α/β small acid-soluble spore protein (SASP) gene encoding a SASP which is toxic to the target bacteria; wherein the bacteriophage is non-lytic; and wherein the bacteriophage expresses a hybrid host range determinant (HRD) which comprises an amino acid sequence from a plurality of different bacteriophages. The bacterial host specificity of the HRD is advantageously within the same bacterial species.
It has surprisingly been found that a modified bacteriophage may be produced which is capable of infecting a variety of different target bacteria and which is effective for use in medicine even though the bacteriophage is non-lytic. The bacteriophage has an enhanced host range because it expresses a hybrid HRD protein. The hybrid HRD comprises an amino acid sequence from a plurality of different bacteriophages. Bacteriophages according to the invention may be produced by genetic engineering, for example by selecting HRD from closely related phage. Having created such an extra-potent phage, it can then be rendered non-lytic, and hence non-viable and yet still be suitable as a SASPject vector.
The modified bacteriophage may be non-lytic because it comprises an inactivated lysis gene. Insertion of sequence into the lysis gene or removal of the lysis gene would render this gene inactive. The lysis gene may conveniently be inactivated by insertion of the SASP gene.
In one aspect, the term ‘SASP’ as used in the specification refers to a protein with α/β-type SASP activity, that is, the ability to bind to DNA and modify its structure from its B-like form towards A-like form, and not only covers the proteins listed in appendix 1 of WO02/40678, but also any homologues thereof, as well as any other protein also having α/β-type SASP activity. In an alternative aspect, the term ‘SASP’ as used in the specification refers to any protein listed in appendix 1 of WO02/40678, or any homologue having at least 70%, 75%, 80%, 85%, 90%, 92%, 94%, 95%, 96%, 98% or 99% sequence identity with any one of the proteins. listed in appendix 1 of WO02/40678. In another alternative aspect, the term ‘SASP’ as used in the specification refers to any protein listed in appendix 1 of WO02/40678.
The SASP gene may be chosen from any one of the genes encoding the SASP disclosed in Appendix 1 of WO02/40678. In a preferred arrangement the SASP is SASP-C. The SASP-C may be from Bacillus megaterium.
It is preferred that the SASP gene is under the control of a constitutive promoter which is advantageously sufficiently strong to drive production of toxic levels of SASP when the modified bacteria phage is present in multiple copies in the target bacterium. Useful constitutive promoters include pdhA for pyruvate dehydrogenase E1 component alpha sub units, rpsB for the 30S ribosomal protein S2, pgi for glucose-6-phosphate isomerase and the fructose bisphosphate aldolase gene promoter fda. Preferred regulated promoters, active during infection, are lasB for elastase. These promoters are typically from P. aeruginosa. Promoters having a sequence showing at least 90% sequence identity to these promoter sequences may also be used.
The present invention is generally applicable to bacteriophage infecting a variety of different target bacteria. In one arrangement at least one of the target bacteria is Pseudomonas. Advantageously, the plurality of different target of bacteria is a plurality of different Pseudomonas bacteria. An important target is Pseudomonas aeruginosa.
It was not previously considered obvious that use of an obligate lytic phage would be suitable as a SASPject vector, since a requirement of a SASPject vector is that it is specifically not lytic for optimal therapeutic use, giving an increased time window for SASP expression and enabling prevention of rapid lysis upon treatment in vivo, thus limiting the potential release of antibiotic resistance genes and toxic cell wall components which can lead to a dangerous inflammatory response.
The approach described in the present invention is advantageous as compared to the cocktail approach described previously. Mixtures of modified bacteriophage, such as SASPject vectors are identical in structure and genome sequence, other than carrying a different HRD or hybrid HRD. One advantage is that control of the manufacturing process for the mix of SASPjects will be straightforward, which is an important aspect of a pharmaceutical preparation: the process will be materially the same for phage modified to carry a heterologous HRD as they share identical or near-identical biophysical properties. Another advantage is that the in vivo characteristics of the SASPject vectors are likely to be similar, e.g. pharmacokinetics/pharmacodynamics, as each vector is structurally the same or similar.
In the present invention it has been found that phage can be created which are extra-potent obligately-lytic bacteriophage carrying a hybrid HRD. Surprisingly, such phage can be used to make enhanced SASPject vectors by rendering these phage non-lytic and non-viable, by insertion or replacement of a lytic gene(s) with a gene for a SASP. Phage suitable for such modification may be isolated by screening for phage capable of infecting a chosen bacterial species. For instance, phage may be isolated which infect Pseudomonas aeruginosa, by screening for phage from environmental sources which are able to form plaques on representative P. aeruginosa strains (Gill and Hyman, 2010). Isolated phage may have their whole genomes sequenced and annotated. HRD may be tail fibre proteins, which are commonly found to be proteins responsible for the initial recognition/binding to the host bacterium, for instance in phage T4, T5 and T7 (Rakhuba et al., 2010). Alternatively other HRD may be baseplate proteins. Phage genomes may be searched for potential HRD sequences by assessing the homology of all proteins in the phage genome to known sequences, using BLAST searches.
According to the present invention it is preferred that each HRD has a broad host range. This may be defined as the ability to infect >50% of a diverse collection or clinical isolates, totalling at least 35, preferably at least 40, more preferably at least 44, and most preferably >50 in number. Such isolates should be from a range of geographical locations, including Europe, the Americas, and Asia, should carry a diverse range of antibiotic resistance phenotypes, including multi-drug resistant (MDR) strains, and should be from a diverse range of infection sites, such as strains cultured from blood, lung and skin infections. Such isolates can be obtained from public strain collections such as the American Type Culture Collection (ATCC) and the National Collection of Type Cultures (NCTC). Generally, each tail fibre protein comprises a C-terminal receptor binding region for binding to the target bacteria and an N-terminal region linking the C-terminal receptor binding region to the body of the bacteriophage. Each of the C-terminal and N-terminal regions may be from different bacteriophage. In one arrangement, the N-terminal region comprises amino acids 1 to 628 of the tail fibre protein and the C-terminal region comprises the amino acids 629 to 964 of the tail fibre protein.
The C-terminal region may have no more than 96% amino acid sequence identity with the C-terminal region of bacteriophage Phi33 and may be from any one of the bacteriophage Phi33, LBL3, SPM-1, F8, PB1, KPP12, LMA2, SN, 14-1, JG024, NH-4, PTP47, C36, PTP92 and PTP93. Lower amino acid sequence identities in the C-terminal region are preferred. Advantageously the sequence identity is less than 90%, more advantageously less than 80%, preferably less than 70%, more preferably less than 60%, still more preferably less than 50%, particularly preferably less than 40%, more particularly preferably less than 30%. The N-terminal region may have at least 90% and advantageously at least 95% amino acid sequence identity with the N-terminal region of bacteriophage Phi33 and may be from any one of bacteriophage Phi33, LBL3, SPM-1, F8, PB1, KPP12, LMA2, SN, 14-1, JG024, NH-4, PTP47, C36, PTP92 and PTP93. The N-terminal region and the C-terminal region may be from different bacteriophage tail fibre proteins to provide a heterologous tail fibre protein.
It is advantageous to identify phage tail fibre proteins which share sequence identity of greater than 90% in the N-terminal region. For example several phage—Phi33, PTP47, PTP92 and C36—with a broad host range for P. aeruginosa strains (all of these phage infect >60%, when analysed against 260 strains), have been isolated/identified and their genomes sequenced. Analysis of the genome sequences of Phi33, PTP47, PTP92 and C36 reveals that they contain genes encoding putative tail fibre proteins with a high level of sequence identity in the N-terminal region (>95% amino acid sequence identity), following a 2 sequence BLAST alignment, compared to the Phi33 tail fibre amino acids 1-628 (amino acid identity in parentheses): C36 (96%), PTP47 (98%), PTP92 (97%). BLAST searches have shown that these 4 phages are related to 10 other deposited phage genome sequences which, together, form the family of PB1-like phage: PB1, SPM1, F8, LBL3, KPP12, LMA2, SN, JG024, NH-4, 14-1 (Ceyssens et al., 2009). The homology of these putative tail fibre proteins was assessed. Following a 2 sequence BLAST alignment, compared to the Phi33 tail fibre protein (amino acid identity in parentheses): LBL3 (96%), SPM-1 (95%), F8 (95%), PB1 (95%), KPP12 (94%), LMA2 (94%), SN (87%), 14-1 (86%), JG024 (83%), NH-4 (83%), C36 (96%), PTP47 (86%), PTP92 (83%). An alignment of all 14 of the aforementioned phage is shown in
Analysis of the annotated tail fibre protein sequences from these 14 phages reveals that the N-terminal region of the proteins—equivalent to Phi33 tail fibre amino acids 1-628—show an even higher level of sequence identity at the amino acid level than the sequence identity of these proteins over their entire length, in the range of 96-100% for all 14 proteins. Following a 2 sequence BLAST alignment, compared to the N-terminal amino acids 1-628 of the Phi33 tail fibre protein (amino acid identity in parentheses): LBL3 (96%), SPM-1 (96%), F8 (96%), PB1 (96%), KPP12 (98%), LMA2 (99%), SN (99%), 14-1 (97%), JG024 (97%), NH-4 (97%), PTP47 (98%), C36 (96%), PTP92 (97%). However, the C-terminal region of the protein—equivalent to Phi33 tail fibre amino acids 629-964—is not as conserved as the N-terminal region in some of the proteins, the range of sequence identity being typically 57-96%. Following a 2 sequence BLAST alignment, compared to the C-terminal 629-964 amino acids of the Phi33 tail fibre protein (amino acid identity in parentheses): LBL3 (94%), SPM-1 (93%), F8 (93%), PB1 (94%), KPP12 (87%), LMA2 (85%), SN (65%), 14-1 (65%), JG024 (57%), NH-4 (57%), PTP47 (64%), C36 (96%), PTP92 (57%). Analysis of phage tail fibres from other, well characterised, phage has shown that they possess an N-terminal tail base plate binding region and a C-terminal receptor binding region (Veesler and Cambillau, 2011). In experimental analysis of their bacterial strain host range, using plaque assay or growth inhibition tests, the phage Phi33, PTP47, PTP92 and C36 have overlapping but non-identical host range (Table 1). Taken together with the established evidence for the role of the C-terminal region of phage tail fibres being involved in bacterial host receptor binding, and the sequence variation in the C-terminal region of these 4 phage, and their similar but non-identical host range, it is postulated that the C-terminal variation is associated with host range in the phage assessed.
It is further provided, according to this invention, that the genes for a homologous tail fibre protein can be taken from one phage and added to another, replacing the resident tail fibre, based upon their high level of sequence identity in the N-terminal region. The N-terminal region is thought to be involved in the binding of the tail fibre to the phage tail (Veesler and Cambillau, 2011), allowing the formation of viable phage with the host range associated with donor phage's tail fibre. Hybrid tail fibre genes may be made, carrying the conserved N-terminal tail attachment region of the tail fibre from a recipient phage, together with the variable C-terminal receptor-binding region from a homologous donor phage tail fibre protein, using tail fibres genes such as those described herein. Such tail fibre hybrid genes could be used to replace the tail fibres of the phage. This provides an N-terminal region of the hybrid tail fibre (from the recipient phage) and allows the formation of viable phage with the host range associated with donor phage's tail fibre C-terminal receptor-binding region. Transplantation of engineered tail fibre hybrid genes into a recipient phage has been demonstrated in the present invention. Using standard molecular genetic techniques, Phi33 has been modified to carry heterologous tail fibre hybrids from the following phage: PTP92, PTP47, LBL3, SPM-1, F8, PB1, KPP12, LMA2, SN, 14-1, NH-4. All modified phage have been shown to be viable and able to plaque on P. aeruginosa. (The nomenclature of tail fibre hybrids is as follows: As an example, a hybrid gene such that the N-terminal tail attachment region of Phi33 is hybridised with the C-terminal receptor binding region of PTP47 is Phi33(N)PTP47(C).)
In one such modified phage, Phi33 was engineered such that its tail fibre gene carries the C-terminal receptor binding region of PTP92, creating PTP93 (Phi33(N)PTP92(C)). This was assessed in more detail, by testing the host range against 35 diverse P. aeruginosa clinical isolates. Comparing host range of the progenitor phage (Phi33), the tail fibre donor (PTP92) and the hybrid phage (PTP93), the host range of the PTP93 hybrid phage is equivalent to that of the tail fibre donor phage (PTP92) rather than Phi33, but it was surprisingly found that in some instances PTP93 possesses the host range of Phi33 on strains that PTP92 cannot infect, thus PTP93 inherits the host range of both phages (Table 2). PTP93 possesses a broader host range (92%) than either Phi33 (74%) or PTP92 (66%) (Table 2). PTP93 is an example of an obligately lytic bacteriophage which can be considered as “extra-potent” as it possesses a characteristic above and beyond those exhibited in their unmodified state. Such extra potent phage are suitable for further modification to make SASPject vectors.
Phi33, through assessment of sequence homology by one skilled in the art, can be placed in the group of PB1-like phage (Ceyssens et al., 2009), and may be considered a broad host range phage by the definition given earlier. Such a phage could be isolated by the methods described earlier. Phi33 is suitable for genetic modification to introduce a gene for SASP under the control of a promoter. Such a modified phage would be suitable for use in treating infections caused by susceptible P. aeruginosa bacteria, either on its own or in combination with other modified bacteriophage.
A preferred approach according to the present invention is to use one or more obligately lytic phage, each engineered to carry a SASP gene expressed from a constitutive promoter, each phage being genetically identical other than their tail fibre or tail fibre hybrid gene, and whereby a lytic gene(s) is inactivated. Such phage may be propagated in strains carrying the deleted lytic gene in trans. Preferred obligately lytic phage for modification and for provision of tail fibre genes to create tail fibre genes or tail fibre hybrid genes are phages carrying tail fibre genes which encode predicted proteins that possess >90% amino acid sequence identity in their N-terminal regions compared to N-terminal regions of the tail fibre of other isolated or identified phage. Preferred obligate lytic phage meeting this criterion are Phi33, PTP92, PTP47, LBL3, SPM-1, F8, PB1, KPP12, LMA2, SN, 14-1, NH-4, PTP93, JG024, PTP47 and C36. Such phage can be identified by a simple PCR assay, by subjecting plaques of isolated phage to PCR with primers specific to highly conserved regions in the N-terminal region of the tail genes. In such a way, suitable phage can be identified without whole genome sequencing. Phage PB1 can be obtained from a public strain collection. Phages need not be isolated or provided in order to generate tail fibre sequences as such sequences may be identified in DNA sequence databases, or other sources of DNA sequences, which may provide the information necessary in order to synthesise and clone, by standard methods, such sequences, or to create hybrid tail fibre sequences.
Particularly preferred phage for modification are PTP93, Phi33, PTP92, PTP47 and C36. Particularly preferred extra-potent obligate lytic phage are: Phi33, modified to carry the tail fibre hybrid Phi33(N)PTP92(C) in place of the resident tail fibre; Phi33 modified to carry the tail fibre hybrid Phi33(N)PTP47(C) in place of the resident tail fibre. In one aspect of the present invention, preferred extra-potent non-lytic SASPject derivatives of Phi33 include: Phi33, modified to carry the tail fibre hybrid Phi33(N)PTP92(C) in place of the resident tail fibre and carrying SASP-C from Bacillus megaterium under the control of the P. aeruginosa ribosomal subunit protein S2 (rpsB) gene promoter in place of the endolysin gene; Phi33 modified to carry the tail fibre hybrid Phi33(N)PTP47(C) in place of the resident tail fibre and carrying SASP-C from Bacillus megaterium under the control of the P. aeruginosa ribosomal subunit protein S2 (rpsB) gene promoter in place of the endolysin gene; Phi33 modified to carry SASP-C from Bacillus megaterium under the control of the P. aeruginosa ribosomal subunit protein S2 (rpsB) gene promoter in place of the endolysin gene. In one preferred aspect, the present invention provides a preferred mixture of SASPject comprising or consisting of the 3 aforementioned SASPjects formulated together.
In a particularly preferred aspect of the present invention, extra-potent non-lytic SASPject derivatives of Phi33 include: Phi33, modified to carry the tail fibre hybrid Phi33(N)PTP92(C) in place of the resident tail fibre and carrying SASP-C from Bacillus megaterium, codon-optimised for expression in P. aeruginosa, under the control of the P. aeruginosa fructose bisphosphate aldolase (fda) gene promoter in place of the endolysin gene; Phi33 modified to carry the tail fibre hybrid Phi33(N)PTP47(C) in place of the resident tail fibre and carrying SASP-C from Bacillus megaterium, codon-optimised for expression in P. aeruginosa, under the control of the P. aeruginosa fructose bisphosphate aldolase (fda) gene promoter in place of the endolysin gene; Phi33 modified to carry SASP-C from Bacillus megaterium, codon-optimised for expression in P. aeruginosa, under the control of the P. aeruginosa fructose bisphosphate aldolase (fda) gene promoter in place of the endolysin gene. In a particularly preferred aspect the present invention provides a mixture of SASPject comprising or consisting of the 3 aforementioned SASPjects formulated together.
The efficacy of Phi33 carrying the 33(N)92(C) tail fibre, modified to carry an rpsB-SASP-C cassette (PTP110), together with Phi33 modified to carry an rpsB-SASP-C cassette (PTP114) as a mixture, compared to the 2 unmodified bacteriophage, is shown in
A mixture of three modified bacteriophage, designated PT3.8, was constructed and its efficacy in killing P. aeruginosa tested. The mixture consists of: Phi33 carrying the Phi33(N)PTP92(C) tail fibre, modified to carry the fda-SASP-C (P. aeruginosa codon optimised sequence) in place of the endolysin lysis gene (PTP384); Phi33 carrying the Phi33(N)PTP47(C) tail fibre, modified to carry the fda-SASP-C (P. aeruginosa codon optimised sequence) in place of the endolysin lysis gene (PTP385); Phi33 carrying the Phi33(N)Phi33(C) tail fibre, modified to carry the fda-SASP-C (P. aeruginosa codon optimised sequence) in place of the endolysin lysis gene (PTP284).
The efficacy of PT3.8 was tested in a 24 hour time-kill curve experiment against a multi-drug resistant (MDR) clinical isolate (trachea isolation site, antibiotic resistance to ceftazidime, piperacillin-tazobactam and imipenem) of P. aeruginosa, strain 3503 and reference strain ATCC 27853. Briefly, cultures were set up in Luria Bertani (LB) broth supplemented with 5 mM calcium chloride, 5 mM magnesium sulphate and 0.1% glucose (LC broth), and grown at 37° C. 5×105 colony forming units per millilitre (cfu/ml) of P. aeruginosa was incubated with 3×109 plaque forming units per ml (pfu/ml) of PT3.8, or extra LC broth as a control (untreated culture). Samples were removed at 0, 1, 2, 4, 6 and 24 hours for serial dilution and plating on LC agar plates and then overnight incubation at 32° C. For both strains, the viable cell count was reduced from 5×105 cfu/ml to below the limit of detection (102 cfu/ml) within 1 hour of treatment, and no viable cells were detected after 24 hours (
In another time-kill curve experiment, performed as above but over 1 hour, 5×105 cfu/ml of strain 3503 was incubated with 3×109 pfu/ml of PT3.8, or extra LC broth as a control (untreated culture). No viable cells could be detected (limit of detection=1×102 cfu/ml) from 2 minutes onwards, whilst the untreated control culture was at 1×106 cfu/ml by 1 hour, thus demonstrating rapid activity of PT3.8 compared to marketed antibiotics (
PT3.8 was tested in a murine lung infection model. Briefly, animals were anaesthetised and then administered an inoculum of 7.5 log10 cfu of P. aeruginosa strain ATCC 27853 by nasal inhalation. At 2 hours post infection, the mice were treated either with PT3.8 (3×1010 pfu) or a vehicle (buffer) control by intravenous injection. At 2 and 22 hours post treatment, mice were euthanised by carbon dioxide asphyxiation, and the thoracic cavities opened and the lungs removed and weighed. Lung tissue was homogenised in tryptone soya broth (TSB) and the number of viable cells in the lung tissue was enumerated by serial dilution and plating on Cetrimide agar plates. A control (not treated) group of mice was euthanised at 2 hours post infection and the viable cells in the lung tissue enumerated, to assess the viable cell count in the lung tissue at the time of treatment. There was a rapid reduction in cfu/gram (cfu/g) of lung tissue in the PT3.8 treated mice, reducing by 5-logs at 2 hours post treatment compared to viable cell levels at the time at which the mice were treated (
In another embodiment, an obligately lytic phage may be modified to create a SASPject by replacing or inactivating the lytic gene(s) with SASP under the control of a constitutive promoter, and the tail fibre gene could be deleted altogether. Such phage must be propagated in a strain in which a tail fibre gene or tail fibre hybrid gene is expressed in trans, and the lytic gene is expressed in trans. In such an instance, the SASPject progeny from such a strain would carry a single tail fibre, derived from the propagation strain, yet would lack in their genomes any tail fibre or tail fibre hybrid gene(s). Several such propagation strains could be constructed and the same tail fibre deleted SASPject expressed in each. In this way several different SASPject derivatives could be made, each carrying a different tail fibre or tail fibre hybrid protein. These SASPjects could be used to formulate a mixture.
In another embodiment, an obligately-lytic phage engineered to carry a SASP gene expressed from a constitutive promoter, in place of or inactivating a lytic gene, may be propagated in a host strain carrying the gene(s) for hybrid tail fibre protein(s) in trans under the control of a suitable promoter, and the lytic gene in trans expressed from a suitable promoter. Suitable promoters for the tail fibre hydrid gene(s) may be a phage promoter, particularly the promoter which drives expression of the tail fibre gene in the engineered, obligately-lytic phage. Other suitable promoters are inducible promoters, such as lac, and trp, together with their cognate regulatory proteins. Suitable promoters for the lytic gene may be a phage promoter, particularly the promoter which usually drives expression of the lytic gene in the engineered obligately-lytic phage. Other suitable promoters are inducible promoters, such as lac, and trp, together with their cognate regulatory proteins. The SASPject progeny obtained from such strains are extra-potent and non-lytic, carrying the tail fibre hybrid(s) expressed from the strain in trans as well as their own. Alternatively, the tail fibre gene from the obligately lytic phage may be deleted altogether, providing that a strain is used for propagation in which tail fibre gene(s) or tail fibre hybrid gene(s) are expressed in trans, and the lytic gene is expressed in trans, allowing for the formation of derivative SASPjects. In such an instance, the SASPject progeny from such a strain would carry multiple tail fibres, yet would lack in their genomes any tail fibre or tail fibre hybrid gene(s).
In a further aspect, the present invention provides a composition for inhibiting or preventing bacterial cell growth, which comprises a modified bacteriophage or mixtures thereof as defined herein and a carrier therefor. The modified bacteriophage may be provided in admixture with at least one other modified bacteriophage which is capable of infecting target bacteria, which includes a SASP gene encoding a SASP which is toxic to the target bacteria and which is non-lytic. The at least one other modified bacteriophage may or may not express a plurality of different HRDs. Such compositions may have a wide range of uses and are therefore to be formulated according to the intended use. The composition may be formulated as a medicament, especially for human treatment and may treat various conditions, including bacterial infections. Among those infections treatable according to the present invention are localised tissue and organ infections, or multi-organ infections, including blood-stream infections, topical infections, oral infections including dental carries, respiratory infections and eye infections. The carrier may be a pharmaceutically-acceptable recipient or diluent. The exact nature and quantities of the components of such compositions may be determined empirically and will depend in part upon the routes of administration of the composition.
Routes of administration to recipients include intravenous, intra-arterial, oral, buccal, sublingual, intranasal, by inhalation, topical (including ophthalmic), intra-muscular, subcutaneous and intra-articular. For convenience of use, dosages according to the invention will depend on the site and type of infection to be treated or prevented. Respiratory infections may be treated by inhalation administration and eye infections may be treated using eye drops. Oral hygiene products containing the modified bacteriophage are also provided; a mouthwash or toothpaste may be used which contains modified bacteriophage according to the invention formulated to eliminate bacteria associated with dental plaque formation.
A modified bacteriophage, or mixture thereof, according to the invention may be used as a bacterial decontaminant, for example in the treatment of surface bacterial contamination as well as land remediation or water treatment. The bacteriophage may be used in the treatment of medical personnel and/or patients as a decontaminating agent, for example in a handwash. Treatment of work surfaces and equipment is also provided, especially that used in hospital procedures or in food preparation. One particular embodiment comprises a composition formulated for topical use for preventing, eliminating or reducing carriage of bacteria and contamination from one individual to another. This is important to limit the transmission of microbial infections, particularly in a hospital environment where bacteria resistant to conventional antibiotics are prevalent. For such a use the modified bacteriophage may be contained in Tris buffered saline or phosphate buffered saline or may be formulated within a gel or cream. For multiple use a preservative may be added. Alternatively the product may be lyophilised and excipients, for example a sugar such as sucrose, may be added.
This invention will now be described in more detail, by way of example only, and with reference to the accompanying drawings, in which:
Summary of the genetic modification of a lytic bacteriophage to render it non-lytic, and such that it carries one of a number of possible tail fibre variants, in addition to SASP-C under the control of a promoter that usually controls expression of the 30S ribosomal subunit protein S2 gene (rpsB).
Genes can be removed and added to the phage genome using homologous recombination. There are several ways in which phages carrying foreign genes and promoters can be constructed and the following is an example of such methods.
For the construction of a Phi33 derivative it is shown how, using an E. coli/P. aeruginosa broad host range vector, as an example only, the existing tail fibre, or a section of the tail fibre, in the bacteriophage genome may be replaced by an alternative tail fibre or tail fibre section from a different bacteriophage, via homologous recombination. It is also shown as an example only, how the resulting phage may be rendered non-lytic, and how additional DNA sequences, such as the SASP-C gene from B. megaterium under the control of a P. aeruginosa rpsB promoter, or the SASP-C gene from B. megaterium, codon optimised for expression in P. aeruginosa, under the control of a P. aeruginosa fda promoter may be added to the bacteriophage genome via homologous recombination.
A tail fibre gene, or section of a tail fibre gene, from an alternative phage may be cloned between two regions of Phi33 DNA that flank the native tail fibre, or section thereof, along with a lacZα genetic marker, in a broad host range E. coli/P. aeruginosa vector. This plasmid may be introduced into P. aeruginosa, and the resulting strain infected with Phi33. Following harvesting of progeny phage, double recombinants in which the native Phi33 tail fibre or tail fibre section, has been replaced by the new tail fibre or tail fibre section and lacZα, may be isolated by plaquing on a suitable P. aeruginosa (lacZΔM15+) host strain using medium containing a chromogenic substrate that detects the action of β-galactosidase.
In a subsequent step, the lacZα marker may be removed from the bacteriophage genomes by making versions of the previously described tail fibre region recombination plasmids that do not contain the lacZα marker, introducing the new plasmids into suitable P. aeruginosa host strains and infecting with the previously modified bacteriophage derivatives of Phi33 carrying the corresponding alternative tail fibre gene, or section thereof, along with the lacZα marker. Recombinants that retain the new tail fibre or tail fibre section, but from which lacZα has been removed, may be isolated by plaquing on a suitable P. aeruginosa (lacZΔM15+) host strain using medium containing a chromogenic substrate that detects the action of β-galactosidase.
In a subsequent step, a similar homologous recombination may be used to replace the endolysin gene of Phi33, or of any of the previously described Phi33 derivatives, or similar bacteriophage or similar derivatives, with the gene for SASP-C, under the control of a P. aeruginosa rpsB promoter, while simultaneously adding an E. coli lacZα reporter gene for the identification of recombinant phage. A region consisting of SASP-C controlled by the rpsB promoter, and the E. coli lacZα allele, may be cloned between two regions of Phi33 that flank the endolysin gene, in a broad host range E. coli/P. aeruginosa vector. This plasmid may be transferred to a suitable P. aeruginosa (endolysin+ lacZΔM15+) strain, and the resulting strain infected by Phi33 or the previously constructed Phi33 derivative (from which the initial lacZα marker has been removed). Progeny phage may be harvested and double recombinants identified by plaquing on P. aeruginosa (endolysin+ lacZΔM15+), looking for acquisition of the new lacZα reporter on medium containing a chromogenic substrate that detects the action of β-galactosidase.
In an alternative subsequent step, a similar homologous recombination may be used to replace the endolysin gene of Phi33, or of any of the previously described Phi33 derivatives, or similar bacteriophage or similar derivatives, with the gene for SASP-C that has been codon optimised for expression in P. aeruginosa, under the control of a P. aeruginosa fda promoter, while simultaneously adding an E. coli lacZα reporter gene for the identification of recombinant phage. A region consisting of codon optimised SASP-C controlled by the fda promoter, and the E. coli lacZα allele, may be cloned between two regions of Phi33 that flank the endolysin gene, in a broad host range E. coli/P. aeruginosa vector. This plasmid may be transferred to a suitable P. aeruginosa (endolysin+ lacZΔM15+) strain, and the resulting strain infected by Phi33 or the previously constructed Phi33 derivative (from which the initial lacZα marker has been removed). Progeny phage may be harvested and double recombinants identified by plaquing on P. aeruginosa (endolysin+ lacZΔM15+), looking for acquisition of the new lacZα reporter on medium containing a chromogenic substrate that detects the action of β-galactosidase.
Since these bacteriophage to be modified are lytic (rather than temperate), another requirement for these described steps of bacteriophage construction is the construction of a suitable host P. aeruginosa strain that carries either the E. coli lacZΔM15 gene at a suitable location in the bacterial genome, or both the Phi33 endolysin gene and the E. coli lacZΔM15 at a suitable location in the bacterial genome, to complement the lacZα or Δendolysin, lacZαphenotypes of the desired recombinant bacteriophage. As an example, the construction of these P. aeruginosa strains may be achieved via homologous recombination using an E. coli vector that is unable to replicate in P. aeruginosa. The genomic location for insertion of the endolysin and lacZΔM15 transgenes should be chosen such that no essential genes are affected and no unwanted phenotypes are generated through polar effects on the expression of adjacent genes. As an example, one such location may be immediately downstream of the P. aeruginosa strain PAO1 phoA homologue.
The E. coli lacZΔM15 allele may be cloned into an E. coli vector that is unable to replicate in P. aeruginosa, between two regions of P. aeruginosa strain PAO1 genomic DNA that flank the 3′ end of phoA. This plasmid may be introduced into P. aeruginosa and isolates having undergone a single homologous recombination to integrate the whole plasmid into the genome selected according to the acquisition of tetracycline (50 μg/ml) resistance. Isolates (lacZΔM15+) which have undergone a second homologous recombination event may then be isolated on medium containing 10% sucrose (utilising the sacB counter-selectable marker present on the plasmid backbone).
The Phi33 endolysin gene and the E. coli lacZΔM15 allele may be cloned into an E. coli vector that is unable to replicate in P. aeruginosa, between two regions of P. aeruginosa strain PAO1 genomic DNA that flank the 3′ end of phoA. This plasmid may be introduced into P. aeruginosa and isolates having undergone a single homologous recombination to integrate the whole plasmid into the genome selected according to the acquisition of tetracycline (50 μg/ml) resistance. Isolates (endolysin+, lacZΔM15+) which have undergone a second homologous recombination event may then be isolated on medium containing 10% sucrose (utilising the sacB counter-selectable marker present on the plasmid backbone).
In a subsequent step, a similar homologous recombination may be used to remove the lacZα marker from the previously described, (lacZα+) Phi33 derivatives that have been modified to replace the endolysin gene with the gene for SASP-C, under the control of a P. aeruginosa rpsB promoter. A region consisting of SASP-C controlled by the rpsB promoter, may be cloned between two regions of Phi33 that flank the endolysin gene, in a broad host range E. coli/P. aeruginosa vector. This plasmid may be transferred to a suitable P. aeruginosa (endolysin+ lacZΔM15k) strain, and the resulting strain infected by the previously described (lacZα+) Phi33 derivatives that have been modified to replace the endolysin gene with the gene for SASP-C, under the control of a P. aeruginosa rpsB promoter. Progeny phage may be harvested and double recombinants identified by plaquing on P. aeruginosa (endolysin+ lacZΔM15+), looking for loss of the lacZα reporter on medium containing a chromogenic substrate that detects the action of β-galactosidase.
In an alternative subsequent step, a similar homologous recombination may be used to remove the lacZα marker from the previously described, (lacZα+) Phi33 derivatives that have been modified to replace the endolysin gene with the gene for SASP-C, codon optimised for expression in P. aeruginosa, under the control of a P. aeruginosa fda promoter. A region consisting of SASP-C, codon optimised for expression in P. aeruginosa, controlled by the fda promoter, may be cloned between two regions of Phi33 that flank the endolysin gene, in a broad host range E. coli/P. aeruginosa vector. This plasmid may be transferred to a suitable P. aeruginosa (endolysin+ lacZΔM15+) strain, and the resulting strain infected by the previously described (lacZα+) Phi33 derivatives that have been modified to replace the endolysin gene with the gene for SASP-C, codon optimised for expression in P. aeruginosa, under the control of a P. aeruginosa fda promoter. Progeny phage may be harvested and double recombinants identified by plaquing on P. aeruginosa (endolysin+ lacZΔM15+), looking for loss of the lacZα reporter on medium containing a chromogenic substrate that detects the action of β-galactosidase.
Experimental Procedures
PCR reactions to generate DNA for cloning purposes may be carried out using Herculase II Fusion DNA polymerase (Agilent Technologies), depending upon the melting temperatures (Tm) of the primers, according to manufacturers instructions. PCR reactions for screening purposes may be carried out using Taq DNA polymerase (NEB), depending upon the Tm of the primers, according to manufacturers instructions. Unless otherwise stated, general molecular biology techniques, such as restriction enzyme digestion, agarose gel electrophoresis, T4 DNA ligase-dependent ligations, competent cell preparation and transformation may be based upon methods described in Sambrook et al., (1989). Enzymes may be purchased from New England Biolabs or Thermo Scientific. DNA may be purified from enzyme reactions and prepared from cells using Qiagen DNA purification kits. Plasmids may be transferred from E. coli strains to P. aeruginosa strains by conjugation, mediated by the conjugation helper strain E. coli HB101 (pRK2013). A chromogenic substrate for β-galactosidase, S-gal, that upon digestion by β-galactosidase forms a black precipitate when chelated with ferric iron, may be purchased from Sigma (S9811).
Primers may be obtained from Sigma Life Science. Where primers include recognition sequences for restriction enzymes, additional 2-6 nucleotides may be added at the 5′ end to ensure digestion of the PCR-amplified DNA.
All clonings, unless otherwise stated, may be achieved by ligating DNAs overnight with T4 DNA ligase and then transforming them into E. coli cloning strains, such as DH5α or TOP10, with isolation on selective medium, as described elsewhere (Sambrook et al., 1989).
An E. coli/P. aeruginosa broad host range vector, such as pSM1080, may be used to transfer genes between E. coli and P. aeruginosa. pSM1080 was previously produced by combining the broad host-range origin of replication from a P. aeruginosa plasmid, oriT from pRK2, the tetAR selectable marker for use in both E. coli and P. aeruginosa, from plasmid pRK415, and the high-copy-number, E. coli origin of replication, oriV, from plasmid pUC19.
An E. coli vector that is unable to replicate in P. aeruginosa, pSM1104, may be used to generate P. aeruginosa mutants by allelic exchange. pSM1104 was previously produced by combining oriT from pRK2, the tetAR selectable marker for use in both E. coli and P. aeruginosa, from plasmid pRK415, the high-copy-number, E. coli origin of replication, oriV, from plasmid pUC19, and the sacB gene from Bacillus subtilis strain 168, under the control of a strong promoter, for use as a counter-selectable marker.
Detection of Phi33-Like Phage (PB1-Like Phage Family) Conserved N-Terminal Tail Fibre Regions by PCR
1. Primers for the detection of Phi33-like phage-like tail fibre genes in experimental phage samples may be designed as follows:
The DNA sequences of the tail fibre genes from all sequenced Phi33-like phage (including Phi33, PB1, NH-4, 14-1, LMA2, KPP12, JG024, F8, SPM-1, LBL3, PTP47, C36, PTP92 and SN) may be aligned using Clustal Omega, which is available on the EBI website, and the approximately 2 kb-long highly conserved region mapping to the gene's 5′ sequence may be thus identified (positions 31680-33557 in the PB1 genome sequence, Acc. EU716414). Sections of 100% identity among the 11 tail fibre gene sequences may be identified by visual inspection. Three pairs of PCR primers targeting selected absolutely conserved regions, and amplifying PCR products no longer than 1 kb may be chosen as follows: pair B4500 and B4501, defining a 194 bp-long region; pair B4502 and B4503, defining a 774 bp-long region; and pair B4504 and B4505, defining a 365 bp-long region.
Primer B4500 consists of sequence of PB1 phage genome (Acc. EU716414) ranging from position 31680 to 31697. Primer B4501 consists of sequence of PB1 phage genome (Acc. EU716414) ranging from position 31851 to 31872. Primer B4502 consists of sequence of PB1 phage genome (Acc. EU716414) ranging from position 31785 to 31804. Primer B4503 consists of sequence of PB1 phage genome (Acc. EU716414) ranging from position 32541 to 32558. Primer B4504 consists of sequence of PB1 phage genome (Acc. EU716414) ranging from position 32868 to 32888. Primer B4505 consists of sequence of PB1 phage genome (Acc. EU716414) ranging from position 33213 to 33232.
2. Phi33-like tail fibre genes may be detected in experimental phage samples as follows:
Plaques of isolated phage of environmental origin may be picked from agar plates and added to water and incubated for 30 minutes, making plaque soak outs. The plaque soak outs may be diluted and a portion added to PCR reactions containing one or all of the above primer pairs, and PCR may be performed according to a standard protocol. PCR products may be visualised on a 1.5% agarose gel with ethidium bromide staining, and evaluated for their size. PCR products of the correct size for the primer pair used may be gel-extracted and submitted to an external facility for sequencing. Sequencing results may be compared with the available tail fibre gene sequences in order to confirm the identity of the PCR product.
Construction of Plasmids to Generate Pseudomonas aeruginosa Strains Carrying Either the Escherichia coli lacZΔM15 Gene, or Both the Phi33 Endolysin Gene and the Escherichia coli lacZΔM15 Gene, Immediately Downstream of the phoA Locus of the Bacterial Genome
1. Plasmid pSMX200 (
A region comprising the terminal approximately 1 kb of the phoA gene from P. aeruginosa may be amplified by PCR using primers B4200 and B4201 (
Primer B4200 consists of a 5′ SpeI restriction site (underlined), followed by sequence located approximately 1 kb upstream of the stop codon of phoA from P. aeruginosa strain PAO1 (
Primer B4200
5′-GATAACTAGTCCTGGTCCACCGGGGTCAAG-3′ (SEQ ID NO: 7)
Primer B4201
5′-GCTCAGATCTTCCTTAAGtcaGTCGCGCAGGTTCAG-3′ (SEQ ID NO: 8)
Primer B4202
5′-AGGAAGATCTGAGCTAGCTCGGACCAGAACGAAAAAG-3′ (SEQ ID NO: 9)
Primer B4203
5′-GATACTCGAGGCGGATGAACATTGAGGTG-3′ (SEQ ID NO: 10)
2. Plasmid pSMX201 (
The endolysin promoter may be amplified by PCR from Phi33 using primers B4204 and B4205 (
Primer B4204 consists of a 5′ AflII restriction site (underlined), followed by a bi-directional transcriptional terminator (soxR terminator, 60-96 bases of Genbank accession number DQ058714), and sequence of the beginning of the Phi33 endolysin promoter region (underlined, in bold) (
3. Plasmid pSMX202 (
The lacZΔM15 gene under the control of a lac promoter may be amplified by PCR from Escherichia coli strain DH10B using primers B4208 and B4209 (
Primer B4208 consists of a 5′ BglII restriction site (underlined), followed by sequence of the lac promoter (
TTTGACACCAGACCAAC
-3′
4. Plasmid pSMX203 (
The lacZΔM15 gene under the control of a lac promoter may be amplified by PCR from Escherichia coli strain DH10B using primers B4208 and B4209 (
Primer B4208 consists of a 5′ BglII restriction site (underlined), followed by sequence of the lac promoter (
TTTGACACCAGACCAAC
-3′
Genetic Modification of Pseudomonas aeruginosa to Introduce the Phi33 Endolysin Gene and Escherichia coli lacZΔM15 Immediately Downstream of the phoA Locus of the Bacterial Genome
1. Plasmid pSMX202 (
2. Double recombinants may then be selected via sacB-mediated counterselection, by plating onto medium containing 10% sucrose.
3. Isolates growing on 10% sucrose may then be screened by PCR to confirm that the endolysin gene and lacZΔM15 have been introduced downstream of the P. aeruginosa phoA gene.
4. Following verification of an isolate (PAX20), this strain may then be used as a host for further modification of Phi33-related bacteriophage, where complementation of both an endolysin mutation and a lacZα reporter are required.
Genetic Modification of Pseudomonas aeruginosa to Introduce the Escherichia coli lacZΔM15 Gene Immediately Downstream of the phoA Locus of the Bacterial Genome
1. Plasmid pSMX203 (
2. Double recombinants may then be selected via sacB-mediated counterselection, by plating onto medium containing 10% sucrose.
3. Isolates growing on 10% sucrose may then be screened by PCR to confirm that lacZΔM15 has been introduced downstream of the P. aeruginosa phoA gene.
4. Following verification of an isolate (PAX21), this strain may then be used as a host for further modification of bacteriophage, where complementation of a lacZα reporter is required.
Construction of a Plasmid to Replace the 3′ Section of the Phi33 Tail Fibre with that of PTP92, Utilising a lacZα Screening Process
1. pSMX204 (
A 1 kb region of Phi33 sequence covering the terminal 20 bases of the Phi33 tail fibre, and the adjacent downstream region, may be amplified by PCR using primers B4222 and B4249 (
Primer B4222 consists of a 5′ NheI restriction site (underlined), followed by sequence from Phi33, approximately 1 kb downstream of the end of the Phi33 tail fibre gene (
2. pSMX205 (
The lacZα open reading frame may be amplified by PCR from pUC19 using primers B4250 and B4252 (
Primer B4250 consists of a 5′ AvrII restriction site, followed by sequence complementary to the 3′ end of the lacZα open reading frame (
Genetic Modification of Phi33 to Replace the 3′ Section of the Tail Fibre Gene with that of PTP92
1. Plasmid pSMX205 (
2. Strain PTA20 may be infected with phage Phi33, and the progeny phage harvested.
3. Recombinant phage in which the 3′ end of the Phi33 tail fibre gene has been replaced by that of PTP92, and to which lacZα has been added, may be identified by plaquing the lysate from step (2) on P. aeruginosa strain PAX21, onto medium containing S-gal, looking for black plaques, which are indicative of β-galactosidase activity.
4. PCR may be carried out to check that the tail fibre gene has been replaced, and that lacZα is present.
5. Following identification of a verified isolate (PTPX21;
Construction of a Plasmid to Replace the 3′ Section of the Phi33 Tail Fibre with that of PTP47, Utilising a lacZα Screening Process
1. pSMX206 (
The lacZα open reading frame may be amplified by PCR from pUC19 using primers B4250 and B4258 (
Primer B4250 consists of a 5′ AvrII restriction site, followed by sequence complementary to the 3′ end of the lacZα open reading frame (
Genetic Modification of Phi33 to Replace the 3′ Section of the Tail Fibre Gene with that of PTP47
1. Plasmid pSMX206 (
2. Strain PTA21 may be infected with phage Phi33, and the progeny phage harvested.
3. Recombinant phage in which the 3′ end of the Phi33 tail fibre gene has been replaced by that of PTP47, and to which lacZα has been added, may be identified by plaquing the lysate from step (2) on P. aeruginosa strain PAX21, onto medium containing S-gal, looking for black plaques, which are indicative of β-galactosidase activity.
4. PCR may be carried out to check that the tail fibre gene has been replaced, and that lacZα is present.
5. Following identification of a verified isolate (PTPX22;
Construction of a Plasmid to Remove the lacZα Marker from PTPX21
1. pSMX207 (
The region of Phi33 sequence located immediately downstream of the Phi33 tail fibre may be amplified by PCR using primers B4222 and B4255 (
Primer B4255 consists of a 5′ section of the end of the PTP92 tail fibre gene (underlined), followed by sequence immediately downstream of the Phi33 tail fibre gene (
Genetic Modification of PTPX21 to Remove the lacZα Marker
1. Plasmid pSMX207 (
2. Strain PTA22 may be infected with phage PTPX21, and the progeny phage harvested.
3. Recombinant phage in which the lacZα marker has been removed may be identified by plaquing the lysate from step (2) on P. aeruginosa strain PAX21, onto medium containing S-gal, looking for white plaques, which are indicative of loss of β-galactosidase activity.
4. PCR may be carried out to check that the tail fibre gene has been retained, and that lacZα has been removed.
5. Following identification of a verified isolate (PTPX23;
Construction of a Plasmid to Remove the lacZα Marker from PTPX22
1. pSMX208 (
The region of Phi33 sequence located immediately downstream of the Phi33 tail fibre may be amplified by PCR using primers B4222 and B4262 (
Primer B4262 consists of a 5′ section of the end of the PTP47 tail fibre gene (underlined), followed by sequence immediately downstream of the Phi33 tail fibre gene (
Genetic Modification of PTPX22 to Remove the lacZα Marker
1. Plasmid pSMX208 (
2. Strain PTA23 may be infected with phage PTPX22, and the progeny phage harvested.
3. Recombinant phage in which the lacZα marker has been removed may be identified by plaquing the lysate from step (2) on P. aeruginosa strain PAX21, onto medium containing S-gal, looking for white plaques, which are indicative of loss of β-galactosidase activity.
4. PCR may be carried out to check that the tail fibre gene has been retained, and that lacZα has been removed.
5. Following identification of a verified isolate (PTPX24;
Construction of a Plasmid to Replace the Endolysin Gene of Phi33, PTPX23, PTPX24, and Similar Phage, by rpsB-SASP-C and lacZα
1. Plasmid pSMX209 (
The region of Phi33 sequence immediately downstream of the endolysin gene may be amplified by PCR using primers B4265 and B4266 (
Primer B4265 consists of a 5′ NheI restriction site (underlined), followed by Phi33 sequence located approximately 340 bp downstream of the Phi33 endolysin gene (
2. Plasmid pSMX210 (
The SASP-C gene from Bacillus megaterium strain KM (ATCC 13632) may be amplified by PCR using primers B4269 and B4270 (
Primer B4269 comprises a 5′ KpnI restriction site, followed by 5 bases, and then a bi-directional transcriptional terminator, and then sequence complementary to the 3′ end of the SASP-C gene from B. megaterium strain KM (ATCC 13632) (underlined, in bold;
TTAGTACTTGCCGCCTAG
-3′
3. pSMX211 (
lacZα may be PCR amplified using primers B4273 and B4274 (
Primer B4273 consists of a 5′ KpnI restriction site (underlined), followed by sequence complementary to the 3′ end of lacZα (
Genetic Modification of Phi33, PTPX23, PTPX24, and Similar Phage, to Replace the Endolysin Gene with rpsB-SASP-C and lacZα
1. Plasmid pSMX211 (
2. Strain PTA24 may be infected in individual experiments with phage Phi33, or PTPX23, or PTPX24, or other similar phage, and the progeny phage harvested.
3. Recombinant phage, in which the endolysin gene has been replaced by rpsB-SASP-C and lacZα, may be identified by plaquing the lysate from step (2) on P. aeruginosa strain PAX20, onto medium containing S-gal, looking for black plaques, which are indicative of β-galactosidase activity.
4. PCR may be carried out to check that the endolysin gene has been replaced, and that rpsB-SASP-C and lacZα are present.
5. Following identification of verified isolates (for example, PTPX25 (
Genetic Modification to Remove the lacZα Marker from PTPX25, PTPX26, PTPX27, and Similar Derivatives of Phi33
1. Plasmid pSMX210 (
2. Strain PTA25 may be infected in individual experiments with phage PTPX25, or PTPX26, or PTPX27, or other similar phage, and the progeny phage harvested.
3. Recombinant phage, in which lacZα marker has been removed, may be identified by plaquing the lysate from step (2) on P. aeruginosa strain PAX20, onto medium containing S-gal, looking for white plaques, which are indicative of loss of β-galactosidase activity.
4. PCR may be carried out to confirm removal of the lacZα marker, while ensuring that rpsB-SASP-C is still present.
5. Following identification of verified isolates (for example, PTP114 (
Construction of a Plasmid to Replace the Endolysin Gene of Phi33, PTPX23, PTPX24, and Similar Phage, by Fda-SASP-C (Codon Optimised) and lacZα
1. Plasmid pSMX212 (
The region of Phi33 sequence immediately downstream of the endolysin gene may be amplified by PCR using primers B4265 and B4310 (
Primer B4265 consists of a 5′ NheI restriction site (underlined), followed by Phi33 sequence located approximately 340 bp downstream of the Phi33 endolysin gene (
2. Plasmid pSMX213 (
The SASP-C gene from Bacillus megaterium strain KM (ATCC 13632) may be codon optimised for expression in P. aeruginosa (
Primer B4312 comprises a 5′ XhoI restriction site, followed by a bi-directional transcriptional terminator, and then sequence complementary to the 3′ end of the SASP-C gene from B. megaterium strain KM (ATCC 13632) that has been codon optimised for expression in P. aeruginosa (underlined, in bold;
ACTTGCCGCCCAG-3′
3. pSMX214 (
lacZα may be PCR amplified using primers B4316 and B4317 (
Primer B4316 consists of a 5′ XhoI restriction site (underlined), followed by sequence complementary to the 3′ end of lacZα (
Genetic Modification of Phi33, PTPX23, PTPX24, and Similar Phage, to Replace the Endolysin Gene with Fda-Codon Optimised SASP-C and lacZα
1. Plasmid pSMX214 (
2. Strain PTA26 may be infected in individual experiments with phage Phi33, or PTPX23, or PTPX24, or other similar phage, and the progeny phage harvested.
3. Recombinant phage, in which the endolysin gene has been replaced by fda-codon optimised SASP-C and lacZα, may be identified by plaquing the lysate from step (2) on P. aeruginosa strain PAX20, onto medium containing S-gal, looking for black plaques, which are indicative of β-galactosidase activity.
4. PCR may be carried out to check that the endolysin gene has been replaced, and that fda-codon optimised SASP-C and lacZα are present.
5. Following identification of verified isolates (for example, PTPX29 (
Genetic Modification to Remove the lacZα Marker from PTPX29, PTPX30, PTPX34, and Similar Derivatives of Phi33
1. Plasmid pSMX213 (
2. Strain PTA27 may be infected in individual experiments with phage PTPX29, or PTPX30, or PTPX34, or other similar phage, and the progeny phage harvested.
3. Recombinant phage, in which lacZα marker has been removed, may be identified by plaquing the lysate from step (2) on P. aeruginosa strain PAX20, onto medium containing S-gal, looking for white plaques, which are indicative of loss of β-galactosidase activity.
4. PCR may be carried out to confirm removal of the lacZα marker, while ensuring that fda-codon optimised SASP-C is still present.
5. Following identification of verified isolates (for example, PTP284 (
| Number | Date | Country | Kind |
|---|---|---|---|
| 1417805 | Oct 2014 | GB | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2015/073294 | 10/8/2015 | WO |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2016/055585 | 4/14/2016 | WO | A |
| Number | Name | Date | Kind |
|---|---|---|---|
| 20030216338 | Merril | Nov 2003 | A1 |
| 20170306298 | Fairhead | Oct 2017 | A1 |
| Number | Date | Country |
|---|---|---|
| 2002007742 | Jan 2002 | WO |
| 2002040678 | May 2002 | WO |
| 2003076583 | Sep 2003 | WO |
| 2004113375 | Dec 2004 | WO |
| 2009019293 | Feb 2009 | WO |
| 2016055585 | Apr 2016 | WO |
| Entry |
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| Number | Date | Country | |
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| 20170313991 A1 | Nov 2017 | US |
