Patent Application
20160097044
1. Field of the Invention
This invention relates to a pathogen-specific triple fusion construct comprising three antimicrobial domains each having a unique lytic activity: a LysK endopeptidase domain, a LysK amidase domain, and a lysostaphin glycyl-glycine endopeptidase domain. The constructs further comprise a cell wall binding domain and a protein transduction domain (PTD). Triple Fusion-PTD constructs are refractory to resistance development and can be used to kill antibiotic-resistant staphylococcal strains, to treat extracellular and intracellular S. aureus infections, and to eradicate biofilms.
2. Description of the Relevant Art
Staphylococcus aureus is an opportunistic bacterial pathogen responsible for a diverse spectrum of animal and human diseases including mastitis, osteomyelitis, and endocarditis (Lowy, F. D. 1998. New England J. Med. 339:520-532). S. aureus rapidly develops resistance to antibiotics, as illustrated by multi-drug resistant (MDR), methicillin-resistant S. aureus (MRSA) and the reduced susceptibility to vancomycin (vancomycin-intermediate strains) (Appelbaum, P. C. 2007. Clin. Infect. Dis. 45 Suppl. 3:S165-170). The number of hospitalizations due to MRSA infection continues to increase with 9.7 billion dollar increased health care costs in 2005 (Klein et al. 2007. Emerg. Infect. Dis. 13:1840-1846; Klein et al. 2013. Am. J. Epidemiol. 177(7):666-674).
S. aureus, including MRSA, can asymptomatically colonize the anterior nares of healthy humans and from these reservoirs opportunistically infect the host. During an infection, S. aureus has also been reported to reside intracellularly in some host cells, e.g., human nasal epithelial cells (Plouin-Gaudon et al. 2006. Rhinology 44:249-254), bovine mammary cells (Herbert et al. 2000. FEMS Microbiol. Lett. 193:57-62; Peton and Le Loir. 2014. Infect. Genet. Evol. 21:602-615), and avian osteoblasts (Reilly et al. 2000. Bone 26:63-70). Intracellular bacteria evade most antibiotics and the host immune system, allowing them to re-emerge after treatment and infect surrounding cells and tissues (Ellington et al. 2006. J. Orthop. Res. 24:87-93). For example, S. aureus is the most common infective agent associated with reoccurring osteomyelitis (53%) in war zone blast wounds and 60% of these strains were antibiotic-resistant (Yun et al. 2008. J. Trauma 64:S163-S168). There is a need for antimicrobials that can kill both MDR and intracellular bacteria.
Peptidoglycan hydrolases (PGHs) are candidate antimicrobials with properties that are ideal for treatment of MDR infections (Donovan et al. 2009. Biotech International 21:6-10). Peptidoglycan hydrolases digest the bacterial cell wall peptidoglycan (PG) causing osmolysis and death (Becker et al. 2008. FEMS Microbiol. Lett. 287:185-191). The Gram-positive bacterial peptidoglycan structure is highly divergent (Schleifer and Kandler. 1972. Bacteriol. Rev. 36:407-477) and peptidoglycan hydrolase domains target unique bonds in the peptidoglycan and lyse target bacteria often with near-species or serovar-specificity (Schmelcher et al. 2010. Appl. Environ. Microbiol. 76:5745-5756), thus avoiding the adverse effects of antibiotic selection on unrelated commensal strains. Peptidoglycan hydrolases have been shown to be versatile in their applications (for reviews see, Schmelcher et al. 2012. Future Microbiol. 7:1147-1171; Nelson et al. 2012. Adv. Virus Res. 83:299-365; Shen et al. 2012. In: Bacteriophages in Health and Disease, eds. S. Abedon & P. Hyman, CAD Press, pp. 217-239).
The frequency of multi-drug resistant S. aureus is approaching epidemic proportions globally. There is a need to develop pathogen-specific agents that can target the bacterial cell surface, kill antibiotic-resistant strains, treat chronic intracellular and extracellular S. aureus infections and avoid resistant strain development.
We have discovered that a triple fusion antimicrobial protein comprising three different peptidoglycan hydrolase domains each of which specifically attacks the peptidoglycan cell wall of live, untreated S. aureus from without, and further comprising a protein transduction domain, can circumvent the development of resistance and can effectively treat intracellular and extracellular S. aureus as well as planktonic and biofilm colonizations.
In accordance with this discovery, it is an object of the invention to provide a triple fusion antimicrobial protein comprising three different peptidoglycan hydrolase domains together each of which specifically targets and attacks unique bonds of the peptidoglycan cell wall of live, untreated S. aureus when exposed externally and further comprising a protein transduction domain making possible eradication of intracellular S. aureus.
It is also an object of the invention to provide a recombinant nucleic acid encoding a triple fusion antimicrobial protein comprising three different peptidoglycan hydrolase domains (1) a LysK CHAP endopeptidase, (2) a LysK amidase, and (3) a lysostaphin glycyl-glycine endopeptidase domain, a cell wall binding domain, and a protein transduction domain.
An added object of the invention is to provide a pharmaceutical composition comprising triple fusion polypeptides, a cell wall binding domain and a protein transduction domain.
An added object of the invention is to provide compositions useful for the treatment of diseases and infections caused by the extracellular and intracellular bacteria for which the LysK endolysin and lysostaphin are specific where the composition comprises a triple fusion polypeptide having three peptidoglycan hydrolase domains each of which retains its property of effectively lysing said bacteria.
An added object of the invention is method of treating diseases and infections with the triple fusion polypeptide of the invention, wherein said diseases and infections are caused by the bacteria for which the three peptidoglycan hydrolases of the triple fusion protein are highly specific.
A further object of the invention is a method of using the triple fusion polypeptide of the invention to kill S. aureus in biofilms.
Also part of this invention is a kit, comprising a composition for treatment of disease caused by the bacteria for which the LysK endolysin and lysostaphin are highly specific.
Other objects and advantages of this invention will become readily apparent from the ensuing description.
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the U.S. Patent and Trademark Office upon request and payment of the necessary fee.
In response to the critical need for novel antimicrobials with reduced resistance development for treating multi-drug resistant (MDR) S. aureus, we have engineered staphylolytic peptidoglycan hydrolases that degrade Gram-positive peptidoglycan. Many peptidoglycan hydrolases are modular in structure with enzymatic and cell wall binding domains (CBDs) separated by a flexible linker (Nelson et al., supra), allowing for recombinant manipulation and generation of chimeric molecules (Schmelcher et al. 2012, supra; Mao et al. 2013. FEMS Microbiol. Lett. 342:30-36; Becker et al. 2009. Gene 443:32-41). On the premise that a bacterium is unlikely to evade three simultaneous peptidoglycan hydrolase activities, we engineered fusion proteins with three unique lytic activities and determined the impact of these chimeras on resistance development. We further modified these triple-acting fusion peptidoglycan hydrolases with protein transduction domains (PTDs) to facilitate entry into mammalian cells and demonstrated their ability to enhance the eradication of intracellular staphylococci in multiple ex vivo and in vivo models.
Peptidoglycan hydrolases derived from bacteriophage endolysins have the added advantage of co-evolution with the bacteria allowing them to target bonds that the host cell can not readily modify, yielding enzymes that are in theory inherently refractory to resistance development (resistance data for endolysins reviewed in Fischetti, V. A. 2005. Trends Microbiol. 13:491-496). A primary advantage conferred by the peptidoglycan hydrolase attack at the pathogen cell wall is the avoidance of most intracellular resistance mechanisms (e.g. efflux pumps). With multiple peptidoglycan-glycosidase, -endopeptidase, and -amidase domains, there is considerable diversity and often near species-specificity of these activities, ensuring low selective pressure on unrelated, co-resident commensal strains, further reducing the potential for resistance development in non-targeted species. These peptidoglycan hydrolases have additional favorable qualities: non-toxic (Nelson et al. 2001. Proc. Natl. Acad. Sci. U.S.A 98:4107-4112), biodegradable, effective on biofilms (Sass and Bierbaum. 2007. Appl. Environ. Microbiol. 73:347-352) and multi-drug resistant strains (O'Flaherty et al. 2005. J. Bacteriol. 187:7161-7164), and synergistic with antibiotics (Daniel et al. 2010. Antimicrob. Agents Chemother. 54:1603-1612) thereby holding great potential for treating MDR bacteria.
LysK was not as refractory to resistance development (measured by its MIC) as previously reported for Streptococcus and Bacillus endolysins (Fischetti, supra) and a staphylolytic fusion construct (Pastagia et al. 2011. Antimicrob. Agents Chemother. 55:738-744) (in serial dilution plating assays). However, our strategy to reduce resistant strain development by creating triple-acting staphylolytic fusions was successful with very little resistance development for triple fusion L-K in vitro, reflecting at least an order of magnitude improvement over either parental enzyme (alone or in combination). Triple fusion L-K also reduced the bacterial load 5-10 fold better than either parental enzyme in a rat nasal decolonization model, with no in vivo resistance development detected. The observed 98% reduction in nasal bacterial load was virtually identical to the 98% CFU reduction achieved by mupirocin. Despite these successes, as proteins, the peptidoglycan hydrolases must overcome a unique set of therapeutic hurdles.
Peptidoglycan hydrolases are potentially antigenic and engender host immune responses in a manner similar to that seen in phage-based therapies (Gorski et al. 2012. Adv. Virus Res. 83:41-71). However, peptidoglycan hydrolases show minimal immunogenicity in mammals, and adverse responses have not been reported. Bovine intramammary infusions of lysostaphin resulted in detectable levels of specific antibodies only after 18-21 treatments. The antibodies were not neutralizing, nor did they elicit observable effects on the host animal or eliminate the antimicrobial properties of lysostaphin (Daley and Oldham. 1992. Vet. Immunol. Immunopathol. 31:301-312). Serum antibodies raised to phage endolysins specific to Bacillus anthracis, Streptococcus pyogenes, or Streptococcus pneumoniae slowed, but did not inhibit microbial killing in vitro (Fischetti, supra; Loeffler and Fischetti. 2003. Antimicrob. Agents Chemother. 47:375-377). There is also a concern for proinflammatory components released from lysed bacteria (Borysowski et al. 2006. Exp. Biol. Med. (Maywood) 231:366-377). However, adverse immune responses have not been observed in mouse models for an array of systemically delivered staphylolytic enzyme constructs. In fact, seven out of nine endolysins provided 100% protection from MRSA bacteremia versus 20% survival at 48 hours post infection in buffer or oxacillin treated animals. Furthermore, a reduced TNFα response (to near baseline) when mice with mastitis were treated with our triple-acting fusion peptidoglycan hydrolases indicates a reduced inflammatory response compared to untreated controls.
A separate therapeutic hurdle is created by systemic infections of S. aureus during which the pathogen can evade the host immune system (and most antibiotics) through intracellular localization and sequestration of the pathogen. Intracellular invasion has been reported for bovine mastitis [where S. aureus has been identified within mammary alveolar cells and macrophages isolated from milk (Hebert et al., supra; Peton and Le Loir, supra)] and is implicated by the high frequency of MDR S. aureus in recurring osteomyelitis in “cured” blast wound victims from Middle Eastern war zones (Yun et al., supra). Toxic levels of conventional antibiotics are often required to treat classic intracellular pathogens (Gaspar et al. 2008. Curr. Top. Med. Chem. 8:579-591). To address this concern, we engineered our peptidoglycan hydrolase constructs with 11 different protein transduction domains (PTDs) and identified the optimal PTD domain(s) to facilitate import of the peptidoglycan hydrolases into cultured cells. Initial data with lysostaphin indicated that a PTD was essential for eradication of intracellular S. aureus within both the cultured bovine mammary epithelial cell line (MAC-T, Nexia Biotechnologies, Quebec, Canada) and human brain microvascular endothelial cells (hBMECs). In contrast, triple fusion K-L did not require a PTD to invade cultured bovine mammary cells or murine osteoblasts and showed a similar efficacy with or without a PTD in bone infection models. Both LysK and triple fusion L-K were ineffective at intracellular eradication when fused to any of the eleven PTDs. Despite equivalent intracellular efficacy with either triple fusion K-L or construct K-L-PTD1 in cultured mammary cells, the latter construct showed almost 3 orders of magnitude greater CFU reduction in vivo in the mastitis model. These inconsistencies underline the complexity of PTDs, cargo proteins, and cellular uptake mechanisms to achieve intracellular localization as well as the vagaries of ex vivo versus in vivo experiments (e.g. physiology of infection; monoculture vs. live tissue). Triple fusions K-L and L-K both harbor virtually identical sequences, with only the order of the domains being rearranged, suggesting that an alternative tertiary structure likely contributes to their differential efficacy.
The ability of peptidoglycan hydrolases to reduce or eradicate static biofilms (Sass and Bierbaum. 2007. Appl. Environ. Microbiol. 73:347-352) is an important advantage over conventional antibiotics, since biofilms are proposed to play a critical role in infectious disease (Biel, M. A. 2010. Methods Mol. Biol. 635:175-194). There was an apparent benefit conferred by adding a PTD to the engineered triple fusion K-L in our dynamic S. aureus biofilm eradication experiments.
The ability to engineer a peptidoglycan hydrolase antimicrobial with qualities not readily achievable with conventional antibiotics (refractory to resistance development, biofilm eradication, treatment of intracellular and MDR pathogens) offers the possibility that other desirable traits could be engineered into peptidoglycan hydrolase antimicrobials. Engineered peptidoglycan hydrolases comprise a much needed class of antibacterials for treating multiple-drug resistant pathogens.
According to the present invention, the terms “nucleic acid molecule”, “nucleic acid sequence”, “polynucleotide”, “polynucleotide sequence”, “nucleic acid fragment”, “isolated nucleic acid fragment” are used interchangeably herein. These terms encompass nucleotide sequences and the like. A polynucleotide may be a polymer of RNA or DNA that is single- or double-stranded and that optionally contains synthetic, non-natural or altered nucleotide bases. A polynucleotide in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA, synthetic DNA, or mixtures thereof. This will also include a DNA sequence for which the codons encoding, for example, the LysK-lysostaphin fusion protein according to the invention will have been optimized according to the host organism in which it will be expressed, these optimization methods being well known to those skilled in the art.
The term “isolated” polynucleotide refers to a polynucleotide that is substantially free from other nucleic acid sequences, such as other chromosomal and extrachromosomal DNA and RNA, that normally accompany or interact with it as found in its naturally occurring environment. However, isolated polynucleotides may contain polynucleotide sequences which may have originally existed as extrachromosomal DNA but exist as a nucleotide insertion within the isolated polynucleotide. Isolated polynucleotides may be purified from a host cell in which they naturally occur. Conventional nucleic acid purification methods known to skilled artisans may be used to obtain isolated polynucleotides. The term also embraces recombinant polynucleotides and chemically synthesized polynucleotides.
The term “construct” refers to a recombinant nucleic acid, generally recombinant DNA, that has been generated for the purpose of the expression of a specific nucleotide sequence(s), or is to be used in the construction of other recombinant nucleotide sequences. A “construct” or “chimeric gene construct” refers to a nucleic acid sequence encoding a protein, operably linked to a promoter and/or other regulatory sequences.
The term “operably linked” refers to the association of two or more nucleic acid fragments on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter) or a DNA sequence and a regulatory sequence(s) are connected in such a way as to permit gene expression when the appropriate molecules (e.g., transcriptional activator proteins) are bound to the regulatory sequence(s).
“Regulatory sequences” refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence.
“Promoter” refers to a nucleotide sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3′ to a promoter sequence. The promoter sequence consists of proximal and more distal upstream elements, the latter elements often referred to as enhancers. Accordingly, an “enhancer” is a nucleotide sequence that can stimulate promoter activity and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue-specificity of a promoter.
The term “cDNA” refers to all nucleic acids that share the arrangement of sequence elements found in native mature mRNA species, where sequence elements are exons and 3′ and 5′ non-coding regions. Normally mRNA species have contiguous exons, with the intervening introns removed by nuclear RNA splicing, to create a continuous open reading frame encoding the protein. “cDNA” refers to a DNA that is complementary to and derived from an mRNA template.
As used herein, “recombinant” refers to a nucleic acid molecule which has been obtained by manipulation of genetic material using restriction enzymes, ligases, and similar genetic engineering techniques as described by, for example, Sambrook et al. 1989. Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. or DNA Cloning: A Practical Approach, Vol. I and II (Ed. D. N. Glover), IRL Press, Oxford, 1985. “Recombinant,” as used herein, does not refer to naturally occurring genetic recombinations.
As used herein, the terms “encoding”, “coding”, or “encoded” when used in the context of a specified nucleic acid mean that the nucleic acid comprises the requisite information to guide translation of the nucleotide sequence into a specified protein. The information by which a protein is encoded is specified by the use of codons. A nucleic acid encoding a protein may comprise non-translated sequences (e.g., introns) within translated regions of the nucleic acid or may lack such intervening non-translated sequences (e.g., as in cDNA).
A “protein” or “polypeptide” is a chain of amino acids arranged in a specific order determined by the coding sequence in a polynucleotide encoding the polypeptide. Each protein or polypeptide has a unique function.
The invention includes, as depicted in
The characteristic of the three different peptidoglycan hydrolase domains described as “specifically targets and attacks” means that each of the three different domains cuts the peptidoglycan cell wall at a different, unique covalent bond of the peptidoglycan cell wall of live, untreated S. aureus from without.
Modifications of the primary amino acid sequence of the lytic domains of the invention may result in further mutant or variant proteins having substantially equivalent activity to the fusion polypeptides described herein. Such modifications may be deliberate, as by site-directed mutagenesis, or may occur by spontaneous changes in amino acid sequences where these changes produce modified polypeptides having substantially equivalent activity to the endolysin polypeptides of the triple fusion polypeptide. Any polypeptides produced by minor modifications of the endolysin primary amino acid sequence are included herein as long as the biological activity endolysin is present; e.g., having a role in pathways leading to lysis of staphylococcal bacteria.
As used herein, “substantially similar” refers to nucleic acid fragments wherein changes in one or more nucleotide bases results in substitution of one or more amino acids, but do not affect the functional properties of the polypeptide encoded by the nucleotide sequence. “Substantially similar” also refers to modifications of the nucleic acid fragments of the instant invention such as deletion or insertion of nucleotides that do not substantially affect the functional properties of the resulting transcript. It is therefore understood that the invention encompasses more than the specific exemplary nucleotide or amino acid sequences and includes functional equivalents thereof. Alterations in a nucleic acid fragment that result in the production of a chemically equivalent amino acid at a given site, but do not affect the functional properties of the encoded polypeptide, are well known in the art. Thus, a codon for the amino acid alanine, a hydrophobic amino acid, may be substituted by a codon encoding another less hydrophobic residue, such as glycine, or a more hydrophobic residue, such as valine, leucine, or isoleucine. Similarly, changes which result in substitution of one negatively charged residue for another, such as aspartic acid for glutamic acid, or one positively charged residue for another, such as lysine for arginine, can also be expected to produce a functionally equivalent product. Nucleotide changes which result in alteration of the N-terminal and C-terminal portions of the polypeptide molecule would also not be expected to alter the activity of the polypeptide. Each of the proposed modifications is well within the routine skill in the art, as is determination of retention of biological activity of the encoded products.
Moreover, substantially similar nucleic acid fragments may also be characterized by their ability to hybridize. Estimates of such homology are provided by either DNA-DNA or DNA-RNA hybridization under conditions of stringency as is well understood by those skilled in the art (1985. Nucleic Acid Hybridization, Hames and Higgins, Eds., IRL Press, Oxford, U.K.). Stringency conditions can be adjusted to screen for moderately similar fragments, such as homologous sequences from distantly related organisms, to highly similar fragments, such as genes that duplicate functional enzymes from closely related organisms. An indication that nucleotide sequences are substantially identical is if two molecules hybridize to each other under stringent conditions. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. However, stringent conditions encompass temperatures in the range of about 1° C. to about 20° C., depending upon the desired degree of stringency as otherwise qualified herein. Thus, isolated sequences that encode a LysK-Lyso-CBD and/or Lyso-Lysk-CBD fusion polypeptide sequences disclosed herein, or to fragments thereof, are encompassed by the present invention.
Substantially similar nucleic acid fragments of the instant invention may also be characterized by the percent identity of the amino acid sequences that they encode to the amino acid sequences disclosed herein, as determined by algorithms commonly employed by those skilled in this art. Methods of alignment of sequences for comparison are well known in the art. Thus, the determination of percent identity between any two sequences can be accomplished using a mathematical algorithm. Non-limiting examples of such mathematical algorithms are the algorithm of Myers and Miller (1988. CABIOS 4:11-17), the local homology algorithm of Smith et al. (1981. Adv. Appl. Math. 2:482); the homology alignment algorithm of Needleman and Wunsch (1970. J. Mol. Biol. 48:443-453); the search-for-similarity-method of Pearson and Lipman (1988. Proc. Natl. Acad. Sci. 85:2444-2448; the algorithm of Karlin and Altschul (1990. Proc. Natl. Acad. Sci. USA 87:2264), modified as in Karlin and Altschul (1993. Proc. Natl. Acad. Sci. USA 90:5873-5877).
Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, Calif.); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Version 8 (available from Genetics Computer Group (GCG), 575 Science Drive, Madison, Wis., USA). Alignments using these programs can be performed using the default parameters.
As used herein, “sequence identity” or “identity” in the context of two nucleic acid or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window. When percentage of sequence identity is used in reference to proteins, it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule.
As used herein, “percentage of sequence identity” means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue 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, and multiplying the result by 100 to yield the percentage of sequence identity.
As used herein, “reference sequence” is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full-length cDNA or gene sequence, or the complete cDNA or gene sequence.
The term “substantial identity” of polynucleotide sequences means that a polynucleotide comprises a sequence that has at least 80% sequence identity, preferably at least 85%, more preferably at least 90%, most preferably at least 95% sequence identity compared to a reference sequence using one of the alignment programs described using standard parameters. One of skill in the art will recognize that these values can be appropriately adjusted to determine corresponding identity of proteins encoded by two nucleotide sequences by taking into account codon degeneracy, amino acid similarity, reading frame positioning, and the like. Substantial identity of amino acid sequences for these purposes normally means sequence identity of at least 80%, preferably at least 85%, more preferably at least 90%, and most preferably at least 95%. Preferably, optimal alignment is conducted using the homology alignment algorithm of Needleman et al. (1970. J. Mol. Biol. 48:443).
A “substantial portion” of an amino acid or nucleotide sequence comprises an amino acid or a nucleotide sequence that is sufficient to afford putative identification of the protein or gene that the amino acid or nucleotide sequence comprises. Amino acid and nucleotide sequences can be evaluated either manually by one skilled in the art, or by using computer-based sequence comparison and identification tools that employ algorithms such as BLAST. In general, a sequence of ten or more contiguous amino acids or thirty or more contiguous nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene-specific oligonucleotide probes comprising 30 or more contiguous nucleotides may be used in sequence-dependent methods of gene identification and isolation. In addition, short oligonucleotides of 12 or more nucleotides may be use as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a “substantial portion” of a nucleotide sequence comprises a nucleotide sequence that will afford specific identification and/or isolation of a nucleic acid fragment comprising the sequence. The instant specification teaches amino acid and nucleotide sequences encoding polypeptides that comprise a particular plant protein. The skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art. Thus, such a portion represents a “substantial portion” and can be used to establish “substantial identity”, i.e., sequence identity of at least 80%, compared to the reference sequence. Accordingly, the instant invention comprises the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions at those sequences as defined above.
Fragments and variants of the disclosed nucleotide sequences and proteins encoded thereby are also encompassed by the present invention. By “fragment” a portion of the nucleotide sequence or a portion of the amino acid sequence and hence protein encoded thereby is intended. Fragments of a nucleotide sequence may encode protein fragments that retain the biological activity of the native protein and hence have LysK-Lyso-CBD fusion polypeptide- and/or Lyso-LysK-CBD fusion polypeptide-like activity. Alternatively, fragments of a nucleotide sequence that are useful as hybridization probes may not encode fragment proteins retaining biological activity.
By “variants” substantially similar sequences are intended. For nucleotide sequences, conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of one of the LysK-lysostaphin fusion polypeptides, LysK-Lyso-CBD fusion polypeptide- and/or Lyso-LysK-CBD fusion polypeptide of the invention. Naturally occurring allelic variants such as these can be identified with the use of well-known molecular biology techniques, as, for example, with polymerase chain reaction (PCR), a technique used for the amplification of specific DNA segments. Generally, variants of a particular nucleotide sequence of the invention will have generally at least about 90%, preferably at least about 95% and more preferably at least about 98% sequence identity to that particular nucleotide sequence as determined by sequence alignment programs described elsewhere herein.
By “variant protein” a protein derived from the native protein by deletion (so-called truncation) or addition of one or more amino acids to the N-terminal and/or C-terminal end of the native protein; deletion or addition of one or more amino acids at one or more sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein is intended. Variant proteins encompassed by the present invention are biologically active, that is they possess the desired biological activity, that is, LysK-Lyso-CBD fusion polypeptide and/or Lyso-LysK-CBD fusion polypeptide protein activity as described herein. Such variants may result from, for example, genetic polymorphism or from human manipulation. Biologically active variants of a LysK-Lyso-CBD fusion polypeptide and/or Lyso-LysK-CBD fusion polypeptide of the invention will have at least about 90%, preferably at least about 95%, and more preferably at least about 98% sequence identity to the amino acid sequence for the protein of the invention as determined by sequence alignment programs described elsewhere herein. A biologically active variant of a protein of the invention may differ from that protein by as few as 1-15 amino acid residues, or even 1 amino acid residue.
The polypeptides of the invention may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions. Novel proteins having properties of interest may be created by combining elements and fragments of proteins of the present invention, as well as with other proteins. Methods for such manipulations are generally known in the art. Thus, the genes and nucleotide sequences of the invention include both the naturally occurring sequences as well as mutant forms. Likewise, the proteins of the invention encompass naturally occurring proteins as well as variations and modified forms thereof. Such variants will continue to possess the desired LysK-Lyso-CBD fusion polypeptide and/or Lyso-LysK-CBD fusion polypeptide activity. Obviously, the mutations that will be made in the DNA encoding the variant must not place the sequence out of reading frame and preferably will not create complementary regions that could produce secondary mRNA structure.
The deletions, insertions, and substitutions of the protein sequences encompassed herein are not expected to produce radical changes in the characteristics of the protein. However, when it is difficult to predict the exact effect of the substitution, deletion, or insertion in advance of doing so, one skilled in the art will appreciate that the effect will be evaluated by routine screening assays where the effects of LysK-Lyso-CBD fusion polypeptide and/or Lyso-LysK-CBD fusion polypeptide can be observed.
“Codon degeneracy” refers to divergence in the genetic code permitting variation of the nucleotide sequence without affecting the amino acid sequence of an encoded polypeptide. Accordingly, the instant invention relates to any nucleic acid fragment comprising a nucleotide sequence that encodes all or a substantial portion of the amino acid sequences set forth herein.
The staphylococcal control compositions of the invention comprise the antimicrobial composition of the invention dissolved or suspended in an aqueous carrier or medium. The composition may further generally comprise an acidulant or admixture, a rheology modifier or admixture, a film-forming agent or admixture, a buffer system, a hydrotrope or admixture, an emollient or admixture, a surfactant or surfactant admixture, a chromophore or colorant, and optional adjuvants. The preferred compositions of this invention comprise ingredients which are generally regarded as safe, and are not of themselves or in admixture incompatible with milk or milk by-products or human and veterinary applications. Likewise, ingredients may be selected for any given composition which are cooperative in their combined effects whether incorporated for antimicrobial efficacy, physical integrity of the formulation or to facilitate healing and health in medical and veterinary applications, including for example in the case of mastitis, healing and health of the teat or other human or animal body part. Generally, the composition comprises a carrier which functions to dilute the active ingredients and facilitates stability and application to the intended surface. The carrier is generally an aqueous medium such as water, or an organic liquid such as an oil, a surfactant, an alcohol, an ester, an ether, or an organic or aqueous mixture of any of these, or attached to a solid stratum such as colloidal gold. Water is preferred as a carrier or diluent in compositions of this invention because of its universal availability and unquestionable economic advantages over other liquid diluents.
Avoiding the generalized use of broad range antimicrobials and using highly specific antimicrobials for just the target organisms involved, should help reduce the ever-increasing incidence of antibiotic resistance.
Having now generally described this invention, the same will be better understood by reference to certain specific examples, which are included herein only to further illustrate the invention and are not intended to limit the scope of the invention as defined by the claims.
Mastitis isolates S. aureus Newbould 305, Staphylococcus hyicus MP01, Staphylococcus chromogenes MP02, Staphylococcus simulans MP03, Staphylococcus epidermidis MP04, Staphylococcus xylosus MP05, and Staphylococcus warneri MP06 were gifts from Max Paape (USDA, Beltsville). Strain S. aureus SA113 was provided by Andreas Peschel (University of Tübingen, Germany). S. aureus strains Newman (Regev-Yochay et al. 2006. J. Bacteriol. 188:4996-5001); ALR (Regev-Yochay et al., supra; UAMS-1 (Marriott et al. 2005. Bone 37:504-512) and ISP479C (Sheen et al. 2010. J. Mol. Med. (Berl). 88:633-639). (UAMS-1 and ISP479C were described previously.) The remaining strains (designated with NRS numbers) were obtained from Network on Antimicrobial Resistance in S. aureus (NARSA) repository. The antibiotic resistance profiles of the strains are listed in Table 1.
S. aureus Newman
S. aureus ALR
S. aureus Newbould 305
S. chromogenes MP02
S. epidermidis MP04
S. hyicus MP01
S. simulans MP03
S. warneri MP06
S. xylosus MP05
+All NRS strains were obtained from the Network on Antimicrobial Resistance in Staphylococcus aureus (NARSA) collections (Retrieved from the Internet: <URL: niaid.nih.gov/labsandresources/resources/dmid/narsa/Pages/default.aspx).
#Ciprofloxacin (Cp), Clindamycin (Cc), Erythromycin (E), Gentamicin (Gm), Linezolid (Lz), Oxacillin (OX), Penicillin (p), Streptomycin (S), Tetracycline (Te), Trimethoprimsulfamethoxaxole (SXT), Vancomycin (Va).
Peptidoglycan hydrolases harbor one or two lytic domains along with one or more cell wall binding domains. To impede resistance development, we engineered peptidoglycan hydrolase antimicrobial fusion proteins to harbor three unique lytic activities derived from two parental peptidoglycan hydrolases, lysostaphin, a staphylolytic bacteriocin (Browder et al. 1965. Biochem. Biophys. Res. Commun. 19:389) and LysK, a staphylococcal bacteriophage K endolysin (O'Flaherty et al. 2005. J. Bacteriol. 187:7161-7164)(
A plasmid harboring the gene encoding the 247 amino acid mature (secreted) lysostaphin (Construct L) (UniProtKB/Swiss-Prot #: P10547.2) was a gift from David Kerr, University of Vermont. The staphylococcal phage K endolysin cDNA encoding the 495 amino-acid lysK gene product (Construct K) (Genbank AAO47477.2) was provided by Paul Ross (O'Flaherty et al. 2005. J. Bacteriol. 187:7161-7164). All constructs were performed in E. coli DH5α (Invitrogen, Carlsbad, Calif.), via PCR cloning (Becker et al. 2008, supra), or conventional DNA fragment isolation and ligation using standard methods, and were verified by DNA sequencing. All constructs harbor a C-terminal His6 tag derived from pET21a (EMD Biosciences, San Diego, Calif.). All PCR primers and plasmids are listed in Table 2.
We previously described a head-to-tail fusion of LysK-lysostaphin that included two cell wall binding domains (Donovan et al. 2009, supra) and showed weak staphylolytic activity (Rigden et al. 2003, supra). Improvements were made to create two triple acting constructs, each with a single cell wall binding domain (the SH3b domain from lysostaphin). The first triple-acting peptidoglycan hydrolase (K-L) was constructed with both LysK lytic domains fused to the N-terminus of lysostaphin. The second triple-acting construct (L-K) inserted the LysK lytic domains between lysostaphin's M23 endopeptidase domain and SH3b cell wall binding domain (
The cDNA molecules encoding the triple fusion polypeptides K-L, L-K and the triple fusion PTD polypeptides, K-L-PTD1 comprise nucleotides encoding C-terminal LE,HHHHHH residues and are identified by SEQ ID NOs: 5, 7 and 53, respectively. The proteins encoded by these nucleic acid sequences are identified by SEQ ID NOs: 6, 8 and 54, respectively. The expressed proteins are His-tagged with eight additional amino acid residues introduced at the C-terminus corresponding to the XhoI site (Leu-Glu) followed by six His residues.
Triple fusion K-L encoded by expression vector pSB1101 was created from the lysK truncation LysK390′ expression vector pSB0301, previously described (Becker et al. 2009, supra). The lysostaphin fragment fused to the 3′ end of pSB1101 was amplified with primers Lyso SalIF and LysoXhoIR, digested with XhoI and SalI, and introduced into pSB0301 linearized at the XhoI site, generating pSB1101.
Triple fusion L-K encoded by expression vector pSB1801 was created in several steps. The lysostaphin gene from plasmid p5301 was truncated by PCR-amplifying the M23 peptidase domain with the primers LysoAD155XhoIR and LysoAA1 NdeI F and introducing this PCR product into NdeI+XhoI-digested pET21a, thereby generating pSB1701. A second intermediate construct was produced by amplification of the lysostaphin SH3b domain from plasmid template p5301 with the primers LysoSH3b SalIF and pET21a StyIR, digesting with SalI+StyI, and introducing the amplified fragment into XhoI+StyI-digested pSB0301, thereby generating plasmid pSB1001. The final triple fusion L-K construct was generated by introducing the PCR product generated by amplification of the template pSB1001 with the primers LysKaaSaIF and pET21aStyIR (harboring the two lytic domains of LysK) into XhoI+StyI-digested pSB1701, thereby generating pSB1801.
Fusion of peptidoglycan hydrolase to PTD sequences was accomplished by reverse translation of the 12 PTD sequences (Table 3) into nucleotide sequences (with an E. coli codon usage bias), followed by commercial synthesis (Genscript, Piscataway, N.J.). The individual sequences were inserted at the XhoI site of pET21a such that each PTD coding sequence was in frame with the His6 coding sequences of the vector. The four peptidoglycan hydrolase sequences (encoding mature lysostaphin, lysK, and triple fusions K-L and L-K) were introduced into these PTD-His6 encoding vectors via standard procedures following restriction enzyme digests of the parental peptidoglycan hydrolase vectors (described above) at unique sites (XbaI or NdeI and XhoI) to generate DNA fragments harboring the entire peptidoglycan hydrolase coding region, and ligation of these fragments into similarly digested pET21a vectors harboring the 12 individual PTD sequences.
#35. Derossi et al. 1996. J Biol. Chem. 271:18188-18193
Recombinant peptidoglycan hydrolases were expressed in E. coli BL21 (DE3) (Novagen) grown to mid-log phase at 37° C. in modified LB broth (15 g tryptone, 8 g yeast extract, 5 g NaCl per liter, pH 7.8) with shaking, induced with 1 mM IPTG, and expressed for 20 h at 10° C. Cells were disrupted by sonication and purified via nickel affinity chromatography (Ni-NTA-agarose), per the manufacturer's instructions (Qiagen, Carlsbad Calif.) to >95% purity as described previously (Becker et al. 2008, supra). For peptidoglycan hydrolases used in animal and cell culture experiments, endotoxin was removed via Triton X-114 washes of protein on Ni-NTA columns (Reichelt et al. 2006. Protein Expr. Purif. 46:483-488). Representative random samples were evaluated for endotoxin content via the Limulus amoebocyte lysate assay (LAL QCL-1000, Lonza, Walkersville, Md.) and shown to be <5 Units/ml (e.g., for nasal colonization <5 Units/˜40 mg protein) endotoxin after purification.
SDS-PAGE, zymogram, turbidity reduction and plate lysis assays were performed as described previously (Becker et al. 2009, supra) with minor modifications as follows. For SDS-PAGE and zymogram analysis, one μg of the purified peptidoglycan hydrolase proteins and Kaleidoscope protein standards (Invitrogen, Carlsbad, Calif.) were analyzed by 15% SDS-PAGE. SDS-PAGE and zymogram gels were prepared and electrophoresed in parallel. Zymograms incorporated embedded cells equivalent to 300 ml of mid-logarithmic phase (OD600nm 0.4-0.6) S. aureus Newman into the SDS-PAGE matrix. The SDS-PAGE gels were stained with Coomassie blue using standard protocols, and zymograms were washed twice in excess water for 30 min to remove SDS and incubated for <1 h at room temperature in water until cleared zones developed.
For the plate lysis assays, purified enzymes were serially diluted in saline lysis buffer (SLB; 150 mM NaCl 10 mM Tris buffer, pH 7.5) with 15% glycerol, to yield concentrations of 100, 10, 1, and 0.1 pmoles/10 μl. S. aureus Newman was cultivated in tryptic soy broth (TSB) to an OD600 nm=0.4-0.6. The bacterial cells were harvested and diluted to yield a suspension with an OD600 nm of 0.1. Tryptic soy agar (TSA) plates were flooded with 3 ml of the bacterial cell suspension. Excess culture was removed, and the plates were air dried at room temperature for ˜30 min in a laminar flow hood. 10 μl of each peptidoglycan hydrolase dilution was then spotted onto the air-dried lawn, allowed to air dry, and the culture plates incubated overnight at 37° C. The following day, plates were evaluated visually and photographed.
The Minimum Inhibitory Concentrations (MIC) of each protein for multiple S. aureus strains was determined as previously described (Jones et al. 1985. In: Manual of Clinical Microbiology, Eds. Balows et al. American Society of Microbiology, Washington D.C., pp. 972-977) with the following modifications. Enzymes were serially diluted two fold across a 96 well plate, such that after dilution, 50 μl of the enzyme solution in 300 mM NaCl, 50 mM NaH2PO4, 30% glycerol pH 7.5, remained in each well. To each well was added 50 μl of TSB and 100 μl of S. aureus Newman in TSB (diluted to 5×106 cells/ml). The plates were incubated 20 h at 37° C. and read with a 96 well plate reader. MIC determination values were reported as the median of ≧4 replicates (Table 1).
Three lytic peptidoglycan hydrolase enzyme activities were confirmed. LysK is a 495 amino acid protein with a C-terminal SH3b CBD (SH3-5, Pfam PF08460) (Finn et al. 2008. Nucleic Acids Res. 36: D281-D288) and two lytic domains (
Purified S. aureus peptidoglycan was digested by triple fusions created with LysK and lysostaphin and the products examined via Electrospray Ionization Mass Spectrometry (ESI-MS). For all triple fusion constructs examined, the peptidoglycan digestion products yielded peaks at m/z 702, 645, 588, 531, and 474 that are identical to the peaks obtained with a double digestion with both enzymes (including triple fusions described previously (Donovan et al. 2009, supra). Representative peaks are shown in
The LysK-lysostaphin triple-acting peptidoglycan hydrolases demonstrated intermediate activity compared to the parental peptidoglycan hydrolases in both plate lysis (
For the MIC repeated exposure method, MIC determinations were performed with S. aureus strain Newman. 100 μl of S. aureus strain Newman culture that survived at ½ the MIC (the first well with visible growth) for each round was inoculated into 5 ml TSB and cultivated to mid-log phase growth. This culture was used as the inoculum for the next round of MIC exposure (overnight growth), and the cycle was repeated for 10 rounds. Cells recovered from the well that represented the ½ MIC concentration on round 10 were confirmed to be S. aureus by PCR (Martineau et al. 1998. J. Clin. Microbiol. 36:618-623) (data not shown).
In the Plate lysis method, bacterial cells were scraped from a sub-lethal (not fully cleared) spot from a plate lysis assay (described above), and these ‘exposed’ cells were used to inoculate 5 ml of TSB and grown for 4-6 hours to generate a new culture and lawn for subsequent exposure. Bacteria were passaged in this assay for up to 10 consecutive days, at which time the S. aureus were tested in MIC assays. Plate lysis repeated exposure experiments were performed in duplicate.
Development of resistance to the triple-acting fusion enzymes was tested on S. aureus strain Newman and compared to both parental enzymes applied individually or simultaneously. After 10 rounds of sub-lethal exposure, parental LysK (two lytic domains) and lysostaphin (one lytic domain) yielded cultures with 42-fold and 585-fold increases in MICs, respectively. When S. aureus cells were simultaneously exposed to an equimolar concentration of LysK and lysostaphin, the final MIC increased 129-fold (
Protein Transduction Domains (PTDs) are cationic peptide sequences of ˜9-30 amino acids that occur naturally and facilitate protein transduction across eukaryotic cell membranes (Dietz, supra). Parental enzymes (lysostaphin, LysK) and triple fusions K-L and L-K were each modified by addition of 11 different C-terminal PTD sequences (Table 3; schematic
Three similar intracellular S. aureus eradication assays from three different labs were optimized for (A) a cultured bovine mammary epithelial cell line (MAC-T, Nexia Biotechnologies, Quebec, Canada; Almeida, supra), (B) primary C57BL/6 mouse-derived osteoblasts (mOBs) (McCall et al. 2008. J. Bone Miner. Res. 23: 30-40) or (C) human brain microvascular endothelial cells (hBMEC; Stins, supra). MAC-T cells were grown in 24-well dishes, infected with 1.24 to 6.47×107 S. aureus Newbould 305 (a known bovine mastitis causative agent) at an MOI of 28 to 209 for 2 hours at 37° C. in Dulbecco's Modified Eagle's Medium (DMEM) with no antibiotics. Osteoblasts were grown in 6 well plates as described earlier (Chauhan and Marriott. 2010. J. Med. Microbiol. 59:755-762) and infected with the S. aureus strain UAMS-1 at an MOI of 100:1 for 2 hours at 37° C. in osteoblast growth medium in the absence of antibiotics. HBMEC were cultured in the absence of antibiotics and infected with ˜1×106 bacteria (M01=10) S. aureus strain ISP479C (Pattee, P. A. 1981. J. Bacteriol. 145:479-488) in RPMI culture media with 10% fetal bovine serum (FBS), for 2 h at 37° C. as described previously (Sheen, supra). Following 3×PBS washes to remove extracellular S. aureus, the infected eukaryotic cell cultures (A-C, above) were exposed to gentamicin (A) 100 μg/ml, 1 h (B) 50 μg/ml, 15 min, or (C) 100 μg/ml, 30 min to kill extracellular S. aureus. Subsequently, cells (A) and (C) were washed 3× with PBS to remove gentamicin, whereas cells (B) were cultured in the presence of 25 μg/ml gentamicin for 24 h. Purified peptidoglycan hydrolase proteins were added to (A) MAC-T cells at 25 μg in 1 ml DMEM for 2.5 h, to (B) mOBs at 5 μg/ml for 2 h, or to (C) the hBMECs at 5 μg/ml for 1 h. Gentamicin-only controls received (A) 100 μg/ml, (B) 25 μg/ml, or (C) 100 μg/ml gentamicin in place of the peptidoglycan hydrolase construct. The cultures were finally washed 3× with PBS and examined microscopically (to determine if there had been cell lysis), prior to being trypsinized with 0.05% trypsin+0.025% Triton X-100 in (A and C) PBS or (B) water. The cell lysate was subjected to serial dilution plating, and the resultant CFUs were counted and normalized to the gentamicin control for each assay. CFU numbers in the gentamicin only treated group were in the range of (A) 3.26×104 to 6.19×105, (B) 6-10×103 or (C) 2-4×105 per well. All analyses were performed with one factor ANOVA (α=0.05) and T-Test post hoc analysis with {hacek over (S)}idák correction to α, (α=0.05) for multiple comparisons, comparing each peptidoglycan hydrolase treatment to the gentamicin only treatment.
For Confocal Microscopy of MAC-T cells, a 10 ml TSB overnight culture of S. aureus strain Newbould was washed, resuspended in 10 ml DMEM without FBS, vortexed rigorously and pelleted prior to resuspension in fresh 10 ml DMEM without FBS to OD600=0.2. 100 μl of 1 mg/ml AlexaFluor-488 conjugate of wheat germ agglutinin (WGA; Life Technologies) was added to 10 ml S. aureus 305 in DMEM. The cells were incubated at 37° C. for 30 min, then washed 6× and resuspended in DMEM without FBS.
Confocal fluorescent microscopy was performed for in situ detection of internalized S. aureus and peptidoglycan hydrolase particles in bovine MAC-T cells cultivated on uncoated 50 mm glass bottom dishes (MatTek Corporation, Ashland, Mass.) in high-glucose DMEM (HyClone, Logan, Utah) supplemented with 10% (v/v) heat-inactivated FBS (Atlanta Biologicals, Lawrenceville, Ga.) at 37° C. in a humidified 5% CO2 incubator. After 18 h of culture, when MAC-T cells were about 90-95% confluent, the existing medium was removed and replaced with 1 ml DMEM without FBS containing AlexaFluor488-labeled S. aureus cells. Samples were incubated at 37° C. for 30 min, washed 6× with DMEM without FBS, and 1 ml media was added to each well of a 24-well plate. After 2 hours, MAC-T cells were washed 3× in DMEM without FBS, exposed to 200 μg/ml gentamicin in DMEM for 30 min and washed an additional 3×, to remove extracellular S. aureus. MAC-T cells were exposed to 50 μg/ml of construct K-L-PTD 1 labeled with AlexaFluor 610-X per the manufacturer's protocol (Life Technologies Corporation) for 2 h before 3×DMEM washes. DMEM was replaced with TL Hepes (bio.Lonza.com; solution #04-616) and a drop of NucBlue Fixed Cell Stain (Life Technologies Corporation) was applied to the MAC-T cells prior to imaging.
Neither commercial lysostaphin (1-Sigma; Sigma-Aldrich, St. Louis, Mo.) nor the C-terminal His6-tagged lysostaphin (construct 1) were able to decrease the intracellular CFUs of S. aureus in a cultured bovine mammary epithelial cell line (MAC-T) or cultured human brain microvasculature endothelial cells (hBMEC) (
To confirm protein transfer across mammary epithelial cell membranes, cultured MAC-T cells were exposed to fluorescently-labeled K-L-PTD1 (red) and fluorescently-labeled S. aureus strain Newman (green) and monitored in real-time with confocal microscopy. S. aureus strain Newman and the triple fusion K-L-PTD1 were found to co-localize intracellularly in a single z-plane with MAC-T cells (
In the static biofilm reduction model, biofilms were produced as previously described (Gross et al. 2001. Infect. Immun. 69:3423-3426) with the following modifications. S. aureus strains were grown overnight in 5 ml TSB supplemented with 0.25% D(+)-glucose without shaking at 37° C. The culture was diluted 1/200 in fresh culture medium, and 200 μl was added to each well of a 96 well microtiter plate and incubated without shaking for 24 h at 37° C. Biofilms in the wells were washed twice with 200 μl SLB, treated with 50 μl peptidoglycan hydrolase (Lysostaphin, LysK and the triple fusion proteins K-L and L-K) in SLB at concentrations indicated (
All proteins tested (L, K, K-L and L-K) effectively reduced staphylococcal biofilms when compared to buffer treated biofilms (
To determine whether modification with a PTD can impact biofilm clearance, triple fusion K-L, K-L-PTD1 and vancomycin were tested for antimicrobial activity in a dynamic biofilm model with MRSA strain NRS382 (
In order to visualize the viability of S. aureus NRS382 biofilms, each chamber of the flow cell was fluorescently labeled by the Live/Dead BacLight™ staining kit (Invitrogen, Carlsbad, Calif.) for one hour. The flow cells were then treated with either buffer (PBS) control, 100 μg/ml of vancomycin, triple fusion K-L or K-L-PTD1, all in PBS with a flow rate of 0.5 ml/min. At 0, 60, and 120 minutes, z-stacks of horizontal-plane images of biofilms were obtained with a 20×/1.3 objective lens by a Zeiss 710 confocal laser scanning microscope. The total z-stack image series contained 40×1 μm sections. To quantify the viability of S. aureus NRS382 biofilms at various time points in the presence of different treatments, one image at the center of z-series (i.e. center of the biofilm) for each time point was selected to represent each treatment group. Three squares representing 100×100 pixels were drawn in each image and the mean intensity of live (green channel) and dead (red channel) cell populations were calculated by Zen 2010 digital imaging software (Carl Zeiss). Percentage of live cells in the dynamic biofilm was calculated using a calibration “standard” curve that assigned a fluorescence intensity to live S. aureus NRS382 cells, over a range of cell concentrations. This allowed a direct translation of the mean fluorescent intensities to a percentage of live cells. The percentage of live cells remaining in biofilms after various treatments was statistically analyzed by an unpaired t-test.
At equal gram concentrations (100 μg/ml), all three had a pronounced effect on dynamic biofilms at 60 and 120 minutes post-treatment as visualized by Live/Dead™ viability staining (
To determine whether our triple-acting fusion enzymes showed in vivo potency, we tested the parental and chimeric peptidoglycan hydrolases in a robust nasal colonization model. The rat nasal colonization model is an adaptation of the mouse nasal colonization model that we described previously (Schaffer et al. 2006. Infect. Immun. 74:2145-2153). All animal experiments were conducted in accordance with a protocol approved by the appropriate Institutional Animal Care and Use Committees. Wistar rats (5 to 6 wks of age) were obtained from Charles River Laboratories (Wilmington, Mass.) and given food and water ad libitum. The animals were housed two per cage in a modified barrier facility under viral antibody-free conditions. The rats were given drinking water containing streptomycin sulfate (0.5 g/liter; Sigma) 1 day prior to bacterial inoculation and for the course of the experiment. The drinking water and cages were changed three times per week. Rats were restrained briefly for inoculation in a DecapiCone bag (Braintree Scientific, Braintree, Mass.) and inoculated with 10 μl of 107 CFU S. aureus strain ALR (Sm-resistant) on day 0. The rats were treated intranasally twice a day (6-7 h apart) on days 5, 6, and 7 with 200 μg of either lysostaphin (AMBI, Tarrytown, N.Y.) or recombinant peptidoglycan hydrolases in 20-μl buffer. Control rats received buffer alone. On day 10 the rats were euthanized; the area around the nasal region was wiped with 70% isopropyl alcohol, and the nasal tissue was excised and homogenized on ice in 600 μl TSB. Quantitative cultures of the homogenates were prepared by plating duplicate 100 μl aliquots on TSA plates containing 0.5 mg/ml Sm (to recover the S. aureus strain used for inoculation) and one blood agar plate (to evaluate the total nasal flora). The number of S. aureus colonies from quantitative plate counts was used to estimate the CFU/nose for each rat. The results from a three independent experiments were combined. For rat nasal colonization experiments, significant (P<0.05) differences between the median values of quantitative culture results for different rat groups were compared to the control group by the Mann-Whitney test (InStat; Graph Pad Software).
Treatment with triple fusion L-K resulted in a 98% decrease in the CFU/nose compared to rats treated with buffer (
To determine if addition of a PTD domain impacts the ability of a peptidoglycan hydrolase to reduce the bacterial load in a murine model of mastitis, four constructs comprised of two different PTD domains fused to two different peptidoglycan hydrolase constructs (L-PTD1, 1-PTD9 and K-L-PTD1, K-L-PTD9) were chosen based on factors including purification yield, solubility, stability (not shown), and our results in MAC-T cells (
To evaluate the efficacy of purified, individually administered peptidoglycan hydrolases in a murine model of bovine mastitis, female C57BL6/SJL mice were challenged by the intramammary route with 100 CFU S. aureus Newbould 305 in 50 μl buffer. A single 1.25 nmoles intramammary infusion of each desired peptidoglycan hydrolase (50 μl of a 25 μM solution) or 50 μl PBS was given 30 minutes post infection [with up to six glands treated per animal, each gland receiving a unique treatment] as described earlier (Schmelcher et al. 2012. Appl. Environ. Microbiol. 78:2297-2305; Kerr et al. 2001. Nat. Biotechnol. 19:66-70). Dams were euthanized 18 h post infusion, the mammary glands were aseptically dissected, and portions of the gland were used for determination of bacterial load and TNFα concentrations, as described previously (Schmelcher et al., supra).
In vivo, lysostaphin was effective in reducing the bacterial load approximately 4 logs compared to controls (
Statistical analysis: The variables were analyzed as two-factor mixed models with Treatment as the factor and Mouse as random Blocks. This model ignores within mouse correlations. Log(TNFα) was used. The variance grouping technique was used for log CFU and log TNFα to correct for variance heterogeneity. Means comparisons were done with Sidak adjusted p-values so that the experiment-wise error was 0.05. Log(TNFα) is back-transformed to the original units for graphing.
To examine the intracellular uptake and eradication in murine osteoblast-containing tissue samples, both ex vivo calvaria (skull cap), and in vivo femur injury models were tested. Calvaria were isolated from neonatal mice and infected with UAMS-1 strain of S. aureus (1×106 bacteria/calvaria) for 2 h at 37° C. in osteoblast growth medium in the absence of antibiotics. Following 3× washes with PBS, calvaria were exposed to 50 μg/ml of gentamicin for 15 min to kill extracellular bacteria and further cultured in gentamicin containing osteoblast growth media. After 24 h later, calvaria were treated with peptidoglycan hydrolases (5 μg/ml) or gentamicin only control for 2 h. Lysis buffer containing 0.05% trypsin and 0.25% Triton X-100 was used to homogenize the calvaria, the homogenates were quantitatively plated on LB agar plates, and the CFU were enumerated after 24 h. The data represents triplicate determinants of two separate experiments.
Calvaria were isolated, and infected as described above using GFP-tagged UAMS-1 strain of S. aureus. Two hours post-infection, calvaria were washed with PBS followed by a 15 minutes treatment with 50 μg/ml gentamicin to kill extracellular bacteria. 24 hours post-infection, calvaria were treated with 5 μg/ml peptidoglycan hydrolases or gentamicin only control for two hours and embedded in Tissue-Tek O.C.T compound (Sakura, Torrance, Calif.). Tissues were sectioned and nuclei were counter stained with DAPI (Life technologies, Grand Island, N.Y.). GFP and DAPI levels of uninfected and infected sections were visualized under a fluorescent microscope at 20×. Fluorescence intensity from these sections was measured using ImageJ and defined as arbitrary fluorescence intensity units to quantify these results.
Both the triple fusion K-L and its PTD-modified version (K-L-PTD1) were able to eliminate GFP-labeled intracellular S. aureus strain UAMS-1 from murine calvaria (
We utilized a previously described (Marriott, supra) murine model of staphylococcal osteomyelitis that reproduces the clinical and gross pathological phases of inflammatory bone diseases, such as human post-traumatic osteomyelitis. C57BL/6J mice were anesthetized with isoflurane and the femur surgically exposed. A trough was drilled through the bone cortex by use of a high-speed drill with a round burr. Damaged bone sites were inoculated with S. aureus (1×103) in agarose beads. Agarose beads containing S. aureus were prepared as follows: 1.4% low melt agarose (Invitrogen, Carlsbad, Calif.) was cooled to 40-42° C. prior to the addition of bacteria. This mixture was added to mineral oil, vigorously stirred, and cooled rapidly on ice. The resulting agarose beads were washed and stored on ice prior to bone application. This method of application induces local infection in bone tissue but markedly reduces the risk of systemic bacterial infection. The muscle fascia and surgical incision were closed, and the disease was allowed to proceed for 24 hours. Mice were either untreated or treated intramuscularly at the site of infection with peptidoglycan hydrolases (triple fusion K-L and K-L-PTD1) 5 mg/kg) given twice in a 24 hours period. Animals were euthanized, and the femurs were removed, homogenized in lysis buffer (0.05% trypsin and 0.25% Triton X-100 in water) and plated on LB agar plates. The data shown are the average normalized colony counts per ml of lysis buffer and represent the results of two separate experiments (n=6). Asterisks represent statistical significance as determined by one-way ANOVA followed by Tukey's posthoc test.
Both triple fusion K-L (p=0.012) and K-L-PTD1 (p=0.021) significantly reduced bacterial load as compared to no treatment, but the presence or absence of PTD1 had no significant effect (p=0.73) (
All publications and patents mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent was specifically and individually indicated to be incorporated by reference.
The foregoing description and certain representative embodiments and details of the invention have been presented for purposes of illustration and description of the invention. It is not intended to be exhaustive or to limit the invention to the precise forms disclosed. It will be apparent to practitioners skilled in this art that modifications and variations may be made therein without departing from the scope of the invention.
