WO2022261360A1

WO2022261360A1 - Plyss2 lysins and variants thereof for use against multidrug resistant gram-positive bacteria

Info

Publication number: WO2022261360A1
Application number: PCT/US2022/032883
Authority: WO
Inventors: Raymond Schuch; Jane Ambler
Original assignee: Contrafect Corporation
Priority date: 2021-06-09
Filing date: 2022-06-09
Publication date: 2022-12-15

Abstract

Disclosed herein are methods of inhibiting the growth, reducing the population, or killing multidrug-resistant Gram-positive bacteria, the method comprising contacting the multidrug-resistant Gram-positive bacteria with a lysin polypeptide comprising the amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 18 or a variant thereof having at least 80% identity to SEQ ID NO: 1 or SEQ ID NO: 18, wherein the variant inhibits the growth, reduces the population, or kills the multidrug-resistant Gram-positive bacteria, wherein the multidrug- resistant Gram-positive bacteria are resistant and/or non-susceptible to, for example, at least three antibiotics each from a different class. Methods of preventing or treating a bacterial infection caused by multidrug-resistant Gram-positive bacteria are also disclosed as well as methods of augmenting the efficacy of an antibiotic. Combinations of lysin polypeptides and antibiotics, which are capable of synergistically inhibiting the growth, reducing the population, or killing multidrug-resistant Gram-positive bacteria are also disclosed.

Description

PlvSs2 LYSINS AND VARIANTS THEREOF FOR USE AGAINST MULTIDRUG RESISTANT GRAM-POSITIVE BACTERIA

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of, and relies on the filing date of, U.S. provisional patent application number 63/208,959, filed 9 June 2021 and U.S. provisional patent application number 63/247,068, filed 22 September 2021, the entire disclosures of which are incorporated herein by reference.

SEQUENCE LISTING

[0002] The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on 8 June 2022 is named 0341_0031-00-304_ST25.txt and is 38 kilobytes in size.

FIELD OF THE DISCLOSURE

[0003] The present disclosure relates generally to antibacterial agents and more specifically to PlySs2 and to modified, non-naturally occurring lysin polypeptides, notably, modified PlySs2 lytic enzymes, and the use of these polypeptides alone or in combination with antibiotics in killing multidrug-resistant Gram-positive bacteria and combating bacterial infection and contamination·

BACKGROUND OF THE INVENTION

[0004] Antibiotic resistance is one of the biggest public health challenges of our time. Each year in the U.S. at least 2.8 million people get an antibiotic -resistant infection, and more than 35,000 people die. Accordingly, there is an ongoing need in the art for agents and methods that are capable of effectively treating bacterial infections including those caused by antibiotic- resistant bacteria, particularly multidrug-resistant bacteria. SUMMARY OF THE DISCLOSURE

[0005] In one aspect, the disclosure provides a method for inhibiting the growth, reducing the population, or killing at least one species of multi-drug resistant Gram-positive bacteria, comprising contacting the bacteria with a lysin polypeptide comprising SEQ ID NO: 1 (wild type PlySs2) or SEQ ID NO: 18 (having a deletion of the N terminal methionine of SEQ ID NO: 1), and/or a variant thereof having at least 80% identity, such as 90% identity, such as 95% identity, such as 99%, such as 99.5% identity to SEQ ID NO: 1 or SEQ ID NO: 18, wherein the variant inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria, such as multidrug-resistant Gram-positive bacteria. In one embodiment, a method is provided for inhibiting the growth, reducing the population, or killing at least one species of multi-drug resistant Gram-positive bacteria, comprising contacting the bacteria with a lysin polypeptide, particularly PlySs2 and/or a modified lysin polypeptide having at least one amino acid substitution relative to a counterpart wild-type PlySs2 lysin disclosed herein.

[0006] In some embodiments, the method further comprises contacting the bacteria with one or more antibiotic(s).

[0007] In another aspect, a method is provided for preventing or treating a bacterial infection, including bloodstream infection such as bacteremia or infective endocarditis, caused by at least one species of multi-drug resistant Gram-positive bacteria, the method comprising administering a therapeutically effective amount of a lysin polypeptide to a subject comprising the amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 18 or a variant thereof having at least 80% identity, such as 90% identity, such as 95% identity, such as 99%, such as 99.5% identity, to SEQ ID NO: 1 or SEQ ID NO: 18, wherein the variant inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria, such as a multidrug-resistant Gram-positive bacteria. In an embodiment, the method comprising administering to a subject diagnosed with, at risk for, or exhibiting symptoms of the bacterial infection an amount of PlySs2 and/or a modified lysin polypeptide having at least one amino acid substitution relative to a counterpart wild-type PlySs2 lysin. In a further embodiment, the method further comprises co-administering to said subject, an amount of an antibiotic suitable for the treatment of a Gram positive bacterial infection. In some embodiments, the subject is diagnosed with, at risk for, or exhibits symptoms of a bacterial infection, such as bacteremia or infective endocarditis, bone and/or joint infection, and/or other bacterial infections disclosed herein. [0008] In another aspect, a method is provided for augmenting the efficacy of an antibiotic suitable for the treatment of a multi-drug resistant Gram-positive bacteria or bacterial infection, comprising co- administering the antibiotic with a lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof having at least 80% identity, such as 90% identity, such as 95% identity, such as 99%, such as 99.5% identity, to SEQ ID NO: 1 or SEQ ID NO: 18, wherein co-administration is more effective in inhibiting the growth, or reducing the population, or killing the multidrug-resistant Gram-positive bacteria, than administration of either the one or more antibiotic(s) or the variant thereof individually. In another embodiment, a method is provided for augmenting the efficacy of an antibiotic suitable for the treatment of a multi-drug resistant Gram-positive bacterial infection, comprising co-administering the antibiotic in combination with PlySs2 and/or a modified lysin polypeptide having at least one amino acid substitution relative to a counterpart wild-type PlySs2 lysin, wherein co-administration is more effective in inhibiting the growth, or reducing the population, or killing the multi-drug resistant Gram-positive bacteria than administration of either the antibiotic or the modified lysin polypeptide individually.

[0009] In another aspect, a combination is provided, wherein the combination comprises a lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18, and/or a variant thereof having at least 80% identity, such as 90% identity, such as 95% identity, such as 99%, such as 99.5% identity to SEQ ID NO: 1 or SEQ ID NO: 18, wherein the variant inhibits growth, reduces a population, or kills at least one species of multidrug-resistant Gram-positive bacteria and one or more antibiotic(s), wherein the combination is capable of synergistically inhibiting the growth, reducing the population, or killing at least one species of multidrug-resistant Gram positive bacteria. In some embodiments of all aspects of the disclosure, the amount of lysin polypeptide or the variant thereof used in the foregoing methods may be below that which would result in a concentration equal to the minimal inhibitory concentration (MIC) of SEQ ID NO: 1, SEQ ID NO: 18 or a variant thereof when used in the absence of antibiotic (/._<?., a “sub- MIC lysin amount”); alternatively or additionally, the amount of antibiotic used in the foregoing methods may be below that which corresponds to the MIC for the antibiotic when used in the absence of SEQ ID NO: 1, SEQ ID NO: 18 or a variant thereof (/._<?., a “sub-MIC antibiotic amount”).

[0010] In another embodiment, a combination is provided, wherein the combination comprises PlySs2 or a modified lysin polypeptide and an antibiotic. In certain embodiments, the minimum amount of the modified lysin polypeptide, the antibiotic, or both or PlySs2, the antibiotic or both that is effective in the combination is below the respective MIC amount of the modified lysin polypeptide and/or the antibiotic or PlySs2 and/or the antibiotics. In some embodiments, the PlySs2 and the antibiotic or the modified lysin polypeptide and the antibiotic are provided in the same composition, and in certain embodiments, the PlySs2 and the antibiotic or the modified lysin polypeptide and the antibiotic are provided in different compositions [0011] In some embodiments of all aspects of the disclosure, the one or more antibiotic(s) is one or more of a beta-lactam including penicillins (e.g. methicillin, oxacillin), a cephalosporin (e.g. ceftaroline, cefalexin and cefactor), a monobactam (e.g. aztreonanl) and a carbapenem (e.g. imipenem and entapenem); a macrolide (e.g. erythromycin, azithromycin), an aminoglycoside (e.g. gentamicin, tobramycin, amikacin), ketolides (e.g., telithromycin), a glycopeptide (e.g., vancomycin, teicoplanin), oxazolidinones (e.g., linezolid and tedizolid), a fluoroquinolone (e.g., levofloxacin), a lipopeptide, such as cyclic lipopeptides (e.g. daptomycin, mupirocin, and lysostaphin), a lincomycin (e.g., clindamycin), a tetracycline (e.g., tetracycline, doxycycline ) a sulfonamide (e.g. sulfamethoxazole), trimethoprim and/or combinations thereof, e.g. trimethoprim/sulfamethoxazole. In certain embodiments, the antibiotic is one or more of vancomycin and daptomycin. In other embodiments, the antibiotic is oxacillin.

[0012] In certain embodiments, the multidrug-resistant Gram-positive bacteria comprise Staphylococcus aureus, such as methicillin-resistant Staphylococcus aureus (MRSA) or methicillin sensitive Staphylococcus aureus (MSSA).

[0013] In certain embodiments, the multidrug-resistant bacteria are resistant to at least two antibiotics, such as at least three antibiotics, optionally in addition to oxacillin, selected from a beta-lactam, a cephalosporin, a monobactam, a carbapenem, a macrolide, an aminoglycoside, a glycopeptide, an oxazolidinone a fluoroquinolone, a ketolide, a lipopeptide, a lincomycin, a tetracycline, a sulfonamide, a trimethoprim and a sulfonamide/trimethoprim.

[0014] In certain embodiments, the multidrug -resistant bacteria comprise at least one isolate or strain of at least one species of Gram-positive bacteria that are resistant and/or non-susceptible to at least two antibiotics, such as at least three antibiotics, optionally in addition to oxacillin and/or methicillin, selected from a beta-lactam, a cephalosporin, a monobactam, a carbapenem, a macrolide, an aminoglycoside, a glycopeptide, an oxazolidinone a fluoroquinolone, a ketolide, a lipopeptide, a lincomycin, a tetracycline, a sulfonamide, a trimethoprim and/or a sulfonamide/trimethoprim. [0015] In some embodiments of all aspects of the disclosure, the multidrug -resistant Gram positive bacteria comprise at least one isolate or strain of at least one species of Gram-positive bacteria, are resistant and/or non-susceptible to at least two, such as at least three, such as at least four antibiotics, wherein the at least two, such as the at least three, such as the at least four antibiotics, are each from a different antibiotic class.

[0016] In certain embodiments of all aspects of the disclosure, the multidrug-resistant Gram positive bacteria comprise at least one isolate or strain of at least one species of Gram-positive bacteria that are resistant and/or non-susceptible to at least two antibiotics, such as at least three antibiotics, wherein each antibiotic is from at least two different antibiotic classes, such as at least three different antibiotic classes, selected from a macrolide, an aminoglycoside, a glycopeptide, an oxazolidinone, a fluoroquinolone, a ketolide, a lipopeptide, a lincomycin, a tetracycline, a sulfonamide, a trimethoprim and/or a sulfonamide/trimethoprim.

[0017] In certain embodiments of all aspects of the disclosure, the multidrug-resistant Gram positive bacteria comprise at least one isolate or strain of at least one species of Gram-positive bacteria that are resistant and/or non-susceptible to at least three antibiotics, wherein each antibiotic is from at least three different antibiotic classes selected from a macrolide, an aminoglycoside, a glycopeptide, an oxazolidinone, a fluoroquinolone, a ketolide, a lipopeptide, a lincomycin, a tetracycline, a sulfonamide, a trimethoprim and/or a sulfonamide/trimethoprim. [0018] In certain embodiments of all aspects of the disclosure, the multidrug-resistant Gram positive bacteria comprise at least one isolate or strain of at least one species of Gram-positive bacteria, are resistant and/or non-susceptible to at least four antibiotics, wherein each antibiotic is from a different class selected from a macrolide, an aminoglycoside, a glycopeptide, an oxazolidinone, a fluoroquinolone, a ketolide, a lipopeptide, a lincomycin, a tetracycline, a sulfonamide, a trimethoprim and/or a sulfonamide/trimethoprim.

[0019] In certain embodiments of all aspects of the disclosure, the multidrug-resistant Gram positive bacteria are resistant and/or non-susceptible to at least two antibiotics, such as at least three antibiotics, wherein each antibiotic is from a different antibiotic class selected from a macrolide, an aminoglycoside, a fluoroquinolone, a ketolide, a lincomycin, a tetracycline, a sulfonamide, a trimethoprim and/or a sulfonamide/trimethoprim.

[0020] In certain embodiments, the multidrug-resistant bacteria are resistant to at least two antibiotics, such as at least three antibiotics, optionally in addition to oxacillin and/or methicillin, selected from ceftaroline, clindamycin, daptomycin, doxycycline, erythromycin, gentamicin, levofloxacin, linezolid, trimethoprim/sulfamethoxazole and/or vancomycin. [0021] In certain embodiments, the multidrug-resistant bacteria comprise at least one isolate or strain of at least one species of Gram-positive bacteria that are resistant and/or non-susceptible to at least two antibiotics, such as at least three antibiotics, optionally in addition to a beta lactam, such as oxacillin and/or methicillin, selected from ceftaroline, clindamycin, daptomycin, doxycycline, erythromycin, gentamicin, levofloxacin, linezolid, trimethoprim/sulfamethoxazole and/or vancomycin.

[0022] In certain embodiments, the multidrug-resistant bacteria comprise at least one isolate or strain of at least one species of Gram-positive bacteria that are resistant and/or non-susceptible to at least two antibiotics, such as at least three antibiotics, optionally in addition to a beta lactam, such as oxacillin and/or methicillin, selected from ceftaroline, clindamycin, doxycycline, erythromycin, gentamicin, levofloxacin, and/or trimethoprim/sulfamethoxazole. [0023] In certain embodiment of all aspects of the disclosure, the multidrug-resistant bacteria, such as at least one isolate or strain of at least one species of Gram-positive bacteria, are resistant and/or non-susceptible to all beta lactams including penicillins, carbapenems and first to fourth generation cephalosporins, but not to the fifth generation anti-MRSA cephalosporins (for example ceftaroline).

[0024] In certain embodiments, the multidrug-resistant bacteria are resistant to at least two antibiotics, such as at least three antibiotics, optionally in addition to oxacillin, selected from erythoromycin, levofloxacin, ceftaroline, linezolid and vancomycin. In certain embodiments, the multidrug-resistant bacteria are resistant to at least two antibiotics, such as at least three antibiotics, optionally in addition to oxacillin, selected erythromycin, levofloxacin and ceftaroline.

[0025] In certain embodiments of all aspects of the disclosure, the multidrug-resistant bacteriacomprise at least one isolate or strain of at least one species of Gram-positive bacteria that are resistant and/or non-susceptible to at least two antibiotics, such as at least three antibiotics, optionally in addition to oxacillin, selected from erythoromycin, levofloxacin, ceftaroline, linezolid and/or vancomycin.

[0026] In certain embodiments of all aspects of the disclosure, the multidrug-resistant bacteriacomprise at least one isolate or strain of at least one species of Gram-positive bacteria that are resistant and/or non-susceptible to at least two antibiotics, such as at least three antibiotics, optionally in addition to oxacillin and/or oxacillin, selected from erythromycin, levofloxacin and/or ceftaroline. In certain embodiments of all aspects of the disclosure, the multidrug-resistant bacteria comprise at least one isolate or strain of at least one species of Gram-positive bacteria that are resistant to methicillin and are non-susceptible to oxacillin and at least two antibiotics, such as at least three antibiotics selected from ceftaroline, erythromycin, clindamycin, doxycycline, levofloxacin, gentamicin, linezolid, trimethoprim- sulfamethoxazole, daptomycin and vancomycin.

[0027] In certain embodiments of all aspects of the disclosure, the multidrug-resistant bacteria comprise at least one isolate or strain of at least one species of Gram-positive bacteria that are resistant to methicillin and are non-susceptible to oxacillin and at least two or three antibiotics selected from erythromycin, levofloxacin, clindamycin, ceftarolin and doxycycline, in another embodiment, erythromycin, levofloxacin and clindamycin, in still another embodiment, erythromycin, levofloxacin and clindamycin and in still another embodiment, erythromycin and levofloxacin.

[0028] In another embodiments of all aspects of the disclosure, the multidrug-resistant bacteria comprise at least one isolate or strain of at least one species of Gram-positive bacteria that are resistant and/or non-susceptible to at least three antibiotics from at least three different antibiotic classes wherein at least one of the three antibiotics is selected from a cephalosporin (e.g. ceftaroline, cefalexin and cefactor), a monobactam (e.g. aztreonanl) a carbapenem (e.g. imipenem and entapenem); an aminoglycoside (e.g. gentamicin, tobramycin, amikacin), a ketolide (e.g., telithromycin), a fluoroquinolone (e.g., levofloxacin), a lincomycin (e.g., clindamycin), a tetracycline (e.g., tetracycline, doxycycline), a sulfonamide (e.g. sulfamethoxazole), trimethoprim and combinations thereof (e.g. trimethoprim/sulfamethoxazole). In a further embodiment, the multidrug resistant bacteria are also resistant and/or non-susceptible to methicillin, oxacillin, daptomycin and/or vancomycin. [0029] In some embodiments of all aspects of the disclosure, the amount of PlySs2 or the modified lysin polypeptide used in the foregoing methods may be below that which would result in a concentration equal to the MIC of the PlySs2 or the modified lysin polypeptide when used in the absence of antibiotic (/.<?., a “sub-MIC lysin amount”); alternatively or additionally, the amount of antibiotic used in the foregoing methods may be below that which corresponds, /._<?., which would result in, a concentration equal to the MIC for the antibiotic when used in the absence of PlySs2 or the modified lysin polypeptide (/._<?., a “sub-MIC antibiotic amount”). [0030] In another embodiment, the variant of SEQ ID NO: 1 or SEQ ID NO: 18 (/._<?., a “sub- MIC antibiotic amount”), such as the modified lysin polypeptide has reduced immunogenicity as compared to the counterpart wild-type PlySs2 lysin. The wild-type PlySs2 lysin (SEQ ID NO: 1) or SEQ ID NO: 18 has a cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) endopeptidase domain, which is the enzymatically active domain (EAD) of the PlySs2 polypeptide, and a C-terminal SH3b_5 (SH3b) cell wall-binding domain (CBD). In certain embodiments of all aspects of the disclosure, the variant of SEQ ID NO: 1 or SEQ ID NO: 18 such as the modified lysin polypeptides comprise at least one amino acid substitutions in the CHAP and/or one or more amino acid substitutions in the SH3b domain(s), wherein the variant inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria.

[0031] In certain embodiments of all aspects of the disclosure, the modified lysin polypeptide comprises at least one amino acid substitution as compared to a wild-type PlySs2 lysin polypeptide, wherein the wild-type PlySs2 lysin polypeptide has an amino acid sequence of SEQ ID NO: 1, a cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domain, and a cell wall binding (SH3b) domain, and wherein the at least one amino acid substitution is in the CHAP domain and/or the SH3b domain, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria. [0032] In certain embodiments of all aspects of the disclosure, the variant lysin polypeptide comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: L92W, V104S, V128T, Y137S, Y164K, N184D, and S198Q (pp296).

[0033] Also disclosed are active fragments of PlySs2 (SEQ ID NO: 1 or SEQ ID NO: 18, e.g., the CHAP domain and the SH3b domain as well as active fragments of the lysin polypeptide variants disclosed herein, wherein the active fragments of the variants include one or more amino acid substitutions in the CHAP domain and/or the SH3b domain.

[0034] In certain embodiments of all aspects of the disclosure, the PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, such as the PlySs2 lysin polypeptide comprising SEQ ID NO: 18, is uniformly active against contemporary Staphylococcus aureus isolates responsible for bloodstream infections in the United States (in 2020). Typically, the activity of the PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, such as the PlySs2 lysin polypeptide comprising SEQ ID NO: 18, is consistent, regardless of resistance phenotype (methicillin- sensitive Staphylococcus aureus (MSSA), methicillin-resistant Staphylococcus aureus (MRSA), including multidrug-resistant (MDR) isolates). As described herein, a PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, such as the PlySs2 lysin polypeptide comprising SEQ ID NO: 18, may be used for the treatment of Staphylococcus aureus bacteremia, including those caused by MDR MRSA isolates

[0035] In certain embodiments of all aspects of the disclosure, the PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure is administered or formulated as a one-time intravenous infusion.

[0036] In certain embodiments of all aspects of the disclosure, the PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, is administered or formulated in an effective amount of 0.25 mg/kg administered or formulated as a one-time intravenous infusion.

[0037] In certain embodiments of all aspects of the disclosure, the PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, is administered or formulated in an effective amount of 18 mg and administered or formulated as a one-time intravenous infusion.

[0038] In certain embodiments of any of the foregoing methods, the subject has normal renal function (e.g., creatinine clearance [CrCl*] >60 mL/minute) or mild renal impairment, and the effective amount of the PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, is 18 mg administered as a one-time intravenous infusion.

[0039] In certain embodiments of any of the foregoing methods, the subject has moderate or severe renal impairment (e.g., creatinine clearance [CrCl*] of 15 to <60 mL/minute) and the effective amount of the PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, is 12 mg administered as a one-time intravenous infusion.

[0040] In certain embodiments of any of the foregoing methods, the subject has end-stage renal disease (ESRD; e.g. CrCl* <15 mL/minute) and/or is on hemodialysis, and the effective amount of the PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, is 18 mg administered as a one-time intravenous infusion.In certain embodiments of all aspects of the disclosure, the PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, such as the PlySs2 lysin polypeptide comprising SEQ ID NO: 18, is uniformly active against contemporary Staphylococcus aureus isolates responsible for bloodstream infections in the United States in 2020. Typically, the activity of the PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, such as the PlySs2 lysin polypeptide comprising SEQ ID NO: 18, is consistent, regardless of resistance phenotype (methicillin-sensitive Staphylococcus aureus (MSSA), methicillin- resistant Staphylococcus aureus (MRSA), including multidrug-resistant (MDR) isolates). [0041] As described herein, a PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, such as the PlySs2 lysin polypeptide comprising SEQ ID NO: 18, may be used for the treatment of Staphylococcus aureus bacteremia, including those caused by MDR MRSA isolatesln certain embodiments of all aspects of the disclosure, the PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, such as the PlySs2 lysin polypeptide comprising SEQ ID NO: 18, is uniformly active against contemporary Staphylococcus aureus isolates responsible for bloodstream infections in the United States in 2020. Typically, the activity of the PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, such as the PlySs2 lysin polypeptide comprising SEQ ID NO: 18, is consistent, regardless of resistance phenotype (methicillin- sensitive Staphylococcus aureus (MSSA), methicillin-resistant Staphylococcus aureus (MRSA), including multidrug-resistant (MDR) isolates). As described herein, a PlySs2 lysin polypeptide comprising SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof, such as the modified lysin polypeptide of the present disclosure, such as the PlySs2 lysin polypeptide comprising SEQ ID NO: 18, may be used for the treatment of Staphylococcus aureus bacteremia, including those caused by MDR MRSA isolates

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts the prevalence of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA) among all causative pathogens of blood stream infections in U.S. hospitals over a 5-year period as described in the Examples.

FIG. 2 depicts the proportion of a methicillin-resistant phenotype among Staphylococcus aureus isolates from patients with blood stream infections, including infective endocarditis, in U.S. hospitals over a 5-year period as described in the Examples. DETAILED DESCRIPTION

Definitions

[0042] As used herein, the following terms and cognates thereof shall have the following meanings unless the context clearly indicates otherwise:

[0043] “Carrier,” refers to a solvent, additive, excipient, dispersion medium, solubilizing agent, coating, preservative, isotonic and absorption delaying agent, surfactant, propellant, diluent, vehicle and the like with which an active compound is administered. Such carriers can be sterile liquids, such as water, saline solutions, aqueous dextrose solutions, aqueous glycerol solutions, and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil, and the like.

[0044] “Pharmaceutically acceptable carrier” refers to any and all solvents, additives, excipients, dispersion media, solubilizing agents, coatings, preservatives, isotonic and absorption delaying agents, surfactants, propellants, diluents, vehicles and the like that are physiologically compatible. The carrier(s) must be “acceptable” in the sense of not being deleterious to the subject to be treated in amounts typically used in medicaments. Pharmaceutically acceptable carriers are compatible with the other ingredients of the composition without rendering the composition unsuitable for its intended purpose. Furthermore, pharmaceutically acceptable carriers are suitable for use with subjects as provided herein without undue adverse side effects (such as toxicity, irritation, and allergic response). Side effects are “undue” when their risk outweighs the benefit provided by the composition. Non-limiting examples of pharmaceutically acceptable carriers or excipients include any of the standard pharmaceutical carriers such as phosphate buffered saline solutions, water, and emulsions such as oil/water emulsions and microemulsions. Suitable pharmaceutical carriers are described, for example, in Remington's Pharmaceutical Sciences by E.W. Martin, 18th Edition.

[0045] “Bactericidal” refers to the property of causing the death of bacteria or capable of killing bacteria to an extent of at least a 3-log 10 (99.9%) or better reduction among an initial population of bacteria over an 18-24 hour period.

[0046] “Bacteriostatic” refer to the property of inhibiting bacterial growth, including inhibiting growing bacterial cells, thus causing a 2-loglO (99%) or better and up to just under a 3-log reduction among an initial population of bacteria over an 18-24 hour period.

[0047] “Antibacterial” refers to both bacteriostatic and bactericidal agents. [0048] “Antibiotic” refers to a compound having properties that have a negative effect on bacteria, such as lethality or reduction of growth. An antibiotic can have a negative effect on Gram-positive bacteria, Gram-negative bacteria, or both. By way of example, an antibiotic can affect cell wall peptidoglycan biosynthesis, cell membrane integrity, or DNA or protein synthesis in bacteria. Nonlimiting examples of antibiotics active against Gram-positive bacteria include methicillin, oxacillin, vancomycin, daptomycin, mupirocin, lysostaphin, penicillins, cloxacillin, erythromycin, carbapenems, cephalosporins, gly copeptides, lincosamides, azithromycin, clarithromycin, roxithromycin, telithromycin, spiramycin, and fidaxomicin. [0049] “Drug resistant” generally refers to a bacterium that is resistant to the antibacterial activity of a drug. When used in certain ways, drug resistance may specifically refer to antibiotic resistance. In some cases, a bacterium that is generally susceptible to a particular antibiotic can develop resistance to the antibiotic, thereby becoming a drug resistant microbe or strain.

[0050] “Effective amount” refers to an amount which, when applied or administered in an appropriate frequency or dosing regimen, is sufficient to prevent, reduce, inhibit, or eliminate bacterial growth or bacterial burden or to prevent, reduce, or ameliorate the onset, severity, duration, or progression of the disorder being treated (for example, bacterial pathogen growth or infection), prevent the advancement of the disorder being treated, cause the regression of the disorder being treated, or enhance or improve the prophylactic or therapeutic effect(s) of another therapy, such as antibiotic or bacteriostatic therapy.

[0051] “Co-administer” is intended to embrace separate administration of two agents, such as a lysin polypeptide and an antibiotic or any other antibacterial agent in a sequential manner as well as administration of these agents in a substantially simultaneous manner, such as in a single mixture/composition or in doses given separately, but nonetheless administered substantially simultaneously to the subject, for example at different times in the same day or 24-hour period. Such co-administration of lysin polypeptides with one or more additional antibacterial agents can be provided as a continuous treatment lasting up to days, weeks, or months. Additionally, depending on the use, the co-administration need not be continuous or coextensive. For example, if the use were as a topical antibacterial agent to treat, e.g., a bacterial ulcer or an infected diabetic ulcer, the lysin polypeptide could be administered only initially within 24 hours of the first antibiotic use, and then the antibiotic use may continue without further administration of the lysin polypeptide.

[0052] “Subject” refers to a mammal, a plant, a lower animal, a single cell organism, or a cell culture. For example, the term “subject” is intended to include organisms, e.g., prokaryotes and eukaryotes, which are susceptible to or afflicted with bacterial infections, for example Gram positive or Gram-negative bacterial infections. Examples of subjects include mammals, e.g., humans, dogs, cows, horses, pigs, sheep, goats, cats, mice, rabbits, rats, and transgenic non human animals. In certain embodiments, the subject is a human, e.g., a human suffering from, at risk of suffering from, or susceptible to infection by Gram-positive bacteria, whether such infection be systemic, topical or otherwise concentrated or confined to a particular organ or tissue.

[0053] “Polypeptide” is used interchangeably with the term “protein,” “peptide,” and refers to a polymer made from amino acid residues. In certain embodiments, the polypeptide has at least about 30 amino acid residues. The term may include not only polypeptides in isolated form, but also active fragments and derivatives thereof. The term “polypeptide” also encompasses fusion proteins or fusion polypeptides comprising PlySs2, an active fragment thereof, and a modified lysin polypeptide as described herein, which maintains the lysin function. Depending on context, a polypeptide can be a naturally-occurring polypeptide or a recombinant, engineered, or synthetically-produced polypeptide. A particular lysin polypeptide can be, for example, derived or removed from a native protein by enzymatic or chemical cleavage, or can be prepared using conventional peptide synthesis techniques (e.g., solid phase synthesis) or molecular biology techniques (such as those disclosed in Sambrook, J. et ak, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989)) or can be strategically truncated or segmented yielding active fragments, maintaining lytic activity against the same or at least one common target bacterium.

[0054] “Fusion polypeptide” refers to an expression product resulting from the fusion of two or more nucleic acid segments, resulting in a fused expression product typically having two or more domains or segments with different properties or functionality. In certain embodiments, the term “fusion polypeptide” also refers to a polypeptide or peptide comprising two or more heterologous polypeptides or peptides covalently linked, either directly or via an amino acid or peptide linker. The polypeptides forming the fusion polypeptide are typically linked C-terminus to N-terminus, although they can also be linked C-terminus to C-terminus, N-terminus to N- terminus, or N-terminus to C-terminus. The term “fusion polypeptide” can be used interchangeably with the term “fusion protein.” Thus, the open-ended expression “a polypeptide comprising” a certain structure includes larger molecules than the recited structure such as fusion polypeptides or constructs. The constructs referred to herein can be made as fusion polypeptides or as conjugates (by linking two or more moieties). [0055] “Heterologous” refers to nucleotide, peptide, or polypeptide sequences that are not naturally contiguous. For example, in the context of the present disclosure, the term “heterologous” can be used to describe a combination or fusion of two or more peptides and/or polypeptides wherein the fusion peptide or polypeptide is not normally found in nature, such as for example a modified lysin polypeptide and a cationic and/or a polycationic peptide, an amphipathic peptide, a sushi peptide (Ding et al. Cell Mol Life Sci., 65(7-8): 1202-19 (2008)), a defensin peptide (Ganz, T. Nature Reviews Immunology 3, 710-720 (2003)), a hydrophobic peptide, and/or an antimicrobial peptide which may have enhanced lytic activity or fusion polypeptide comprising a PlySs2 CHAP and/or Sh3b domain fused to another lysins. Included in this definition are two or more lysin polypeptides or active fragments thereof. These can be used to make a fusion polypeptide with lytic activity.

[0056] “Active fragment” refers to a portion of a polypeptide that retains one or more functions or biological activities of the isolated polypeptide from which the fragment was taken. As used herein, an active fragment of a modified lysin polypeptide or PlySs2 inhibits the growth, or reduces the population, or kills at least one Gram-positive bacterial species, such as S. aureus. [0057] “Amphipathic peptide” refers to a peptide having both hydrophilic and hydrophobic functional groups. In certain embodiments, secondary structure places hydrophobic and hydrophilic amino acid residues at opposite sides (e.g. , inner side vs outer side when the peptide is in a solvent, such as water) of an amphipathic peptide. These peptides may in certain embodiments adopt a helical secondary structure, such as an alpha-helical secondary structure. [0058] “Cationic peptide” refers to a peptide having a high percentage of positively charged amino acid residues. In certain embodiments, a cationic peptide has a pKa-value of 8.0 or greater. The term “cationic peptide” in the context of the present disclosure also encompasses polycationic peptides which are synthetically produced peptides composed of mostly positively charged amino acid residues, such as lysine and/or arginine residues. The amino acid residues that are not positively charged can be neutrally charged amino acid residues, negatively charged amino acid residues, and/or hydrophobic amino acid residues.

[0059] “Hydrophobic group” refers to a chemical group such as an amino acid side chain which has low or no affinity for water molecules but higher affinity for oil molecules. Hydrophobic substances tend to have low or no solubility in water or aqueous phases and are typically apolar but tend to have higher solubility in oil phases. Examples of hydrophobic amino acids include glycine (Gly), alanine (Ala), valine (Val), Leucine (Leu), isoleucine (lie), proline (Pro), phenylalanine (Phe), methionine (Met), and tryptophan (Trp). [0060] “Augmenting” as used herein refers to a degree of activity of an agent, such as antimicrobial activity, that is higher than it would be otherwise. “Augmenting” encompasses additive as well as synergistic (superadditive) effects.

[0061] “Synergistic” or “superadditive” refers to a beneficial effect brought about by two substances in combination that exceeds the sum of the effects of the two agents working independently. In certain embodiments the synergistic or superadditive effect significantly, /._<?., statistically significantly, exceeds the sum of the effects of the two agents working independently. One or both active ingredients may be employed at a subthreshold level, /._<?., a level at which if the active substance is employed individually produces no or a very limited effect. The effect can be measured by assays such as a checkerboard assay, described here. [0062] “Treatment” refers to any process, action, application, therapy, or the like, wherein a subject, including a human being, is subjected to medical aid with the object of curing a disorder, eradicating a pathogen, or improving the subject's condition, directly or indirectly. Treatment also refers to reducing incidence, alleviating symptoms, eliminating recurrence, preventing recurrence, preventing incidence, reducing the risk of incidence, improving symptoms, improving prognosis, or combinations thereof. “Treatment” may further encompass reducing the population, growth rate, or virulence of the bacteria in the subject and thereby controlling or reducing a bacterial infection in a subject or bacterial contamination of an organ, tissue, or environment. Thus “treatment” that reduces incidence is effective to inhibit growth of at least one Gram-positive bacterium in a particular milieu, whether it be a subject or an environment. On the other hand, “treatment” of an already established infection refers to reducing the population, killing, inhibiting the growth, and/or eradicating the Gram-positive bacteria responsible for an infection or contamination·

[0063] The term “preventing” and includes the prevention of the incidence, recurrence, spread, onset, or establishment of a disorder such as a bacterial infection. It is not intended that the present disclosure be limited to complete prevention or to prevention of establishment of an infection. In some embodiments, the onset is delayed, or the severity of a subsequently contracted disease or the chance of contracting it is reduced, and such constitute examples of prevention. With specific reference to biofilm prevention, the term includes prevention of the formation of biofilm, for example by interfering with the adherence of bacteria on a surface of interest, such as the surface of a medical device (e.g., inhaler, catheter, intubation, valve, or other prosthesis). [0064] “Contracted disease” refers to a disease manifesting with clinical or subclinical symptoms, such as the detection of fever, sepsis, or bacteremia, as well as disease that may be detected by growth of a bacterial pathogen (e.g., in culture) when symptoms associated with such pathology are not yet manifest. With respect to medical devices, in particular, a contracted disease shall include a biofilm containing bacteria, such as Staphylococcus or Streptococcus bacteria, and forming when such a device is in use.

[0065] The term “derivative” in the context of a peptide or polypeptide (which as stated herein includes an active fragment) is intended to encompass, for example, a polypeptide modified to contain one or more chemical moieties other than an amino acid that do not substantially adversely impact or destroy the polypeptides ’s activity, such as lytic activity. The chemical moiety can be linked covalently to the peptide, e.g., via an amino terminal amino acid residue, a carboxy terminal amino acid residue, or at an internal amino acid residue. Such modifications may be natural or non-natural. In certain embodiments, a non-natural modification may include the addition of a protective or capping group on a reactive moiety, addition of a detectable label, such as antibody and/or fluorescent label, addition or modification of glycosylation, or addition of a bulking group such as PEG (pegylation) and other changes known to those skilled in the art. In certain embodiments, the non-natural modification may be a capping modification, such as N-terminal acetylations and C-terminal amidations. Exemplary protective groups that may be added to lysin polypeptides include, but are not limited to, t-Boc and Fmoc. Commonly used fluorescent label proteins such as, but not limited to, green fluorescent protein (GFP), red fluorescent protein (RFP), cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and mCherry, are compact proteins that can be bound covalently or noncovalently to a lysin polypeptide or fused to a lysin polypeptide without interfering with normal functions of cellular proteins. In certain embodiments, a polynucleotide encoding a fluorescent protein is inserted upstream or downstream of the lysin polynucleotide sequence. This will produce a fusion protein (e.g., Lysin Polypeptide:: GFP) that does not interfere with cellular function or function of a lysin polypeptide to which it is attached. Polyethylene glycol (PEG) conjugation to proteins has been used as a method for extending the circulating half-life of many pharmaceutical proteins. Thus, in the context of lysin polypeptide derivatives, the term “derivative” encompasses lysin polypeptides chemically modified by covalent attachment of one or more PEG molecules. It is anticipated that pegylated lysin polypeptides will exhibit prolonged circulation half-life compared to the unpegylated lysin polypeptides, while retaining biological and therapeutic activity. Another example is the use of “artilysins”, whereby a short polycationic and amphipathic alpha helices are appended to the N- or C-termini of a lysin polypeptide to improve in vitro antibacterial activity, such as a streptococcal lysin to improve in vitro anti-streptococcal activity.

[0066] “Percent amino acid sequence identity” refers to the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the reference polypeptide sequence, such as a lysin polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as a part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for example, using publicly available software such as BLAST or software available commercially for example from DNASTAR. Two or more polypeptide sequences can be anywhere from 0-100% identical, or any integer value there between. In the context of the present disclosure, two polypeptides are “substantially identical” when at least 80% of the amino acid residues (preferably at least about 85%, at least about 90%, and preferably at least about 95%, at least about 98%, or at least 99%) are identical. The term “percent (%) amino acid sequence identity” as described herein applies to peptides as well. Thus, the term “Substantially identical” will encompass mutated, truncated, fused, or otherwise sequence-modified variants of isolated polypeptides and peptides, such as those described herein, and active fragments thereof, as well as polypeptides with substantial sequence identity (e.g., at least 80%, at least 85%, at least 90%, at least 95% identity, at least 98% identity, or at least 99% identity as measured for example by one or more methods referenced above) as compared to the reference (wild type or other intact) polypeptide. Two amino acid sequences are “substantially homologous” when at least about 80% of the amino acid residues (preferably at least about 85%, at least about 90%, at least about 95%, at least about 98% identity, or at least about 99% identity) are identical, or represent conservative substitutions. The sequences of polypeptides of the present disclosure, are substantially homologous when one or more, or several, or up to 10%, or up to 15%, or up to 20% of the amino acids of the polypeptide, such as the lysin and/or fusion polypeptides described herein, are substituted with a similar or conservative amino acid substitution, and wherein the resulting polypeptide, such as the lysin and/or fusion polypeptides described herein, have at least one activity, antibacterial effects, and/or bacterial specificities of the reference polypeptide, such as the lysin and/or fusion polypeptides described herein. [0067] As used herein, a “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a side chain with a similar charge. Families of amino acid residues having side chains with similar charges have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta- branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).

[0068] “Inhalable composition” refers to pharmaceutical compositions of the present disclosure that are formulated for direct delivery to the respiratory tract during or in conjunction with routine or assisted respiration (e.g., by intratracheobronchial, pulmonary, and/or nasal administration), including, but not limited to, atomized, nebulized, dry powder, and/or aerosolized formulations.

[0069] “Biofilm” refers to bacteria that attach to surfaces and aggregate in a hydrated polymeric matrix that may be comprised of bacterial- and/or host-derived components. A biofilm is an aggregate of microorganisms in which cells adhere to each other on a biotic or abiotic surface. These adherent cells are frequently embedded within a matrix comprised of, but not limited to, extracellular polymeric substance (EPS). Biofilm EPS, which is also referred to as slime (although not everything described as slime is a biofilm) or plaque, is a polymeric conglomeration generally composed of extracellular DNA, proteins, and polysaccharides. In certain embodiments, the biofilm may contain Staphylococcus and/or Streptococcus bacteria. [0070] “Suitable” in the context of an antibiotic being suitable for use against certain bacteria refers to an antibiotic that was found to be effective against those bacteria even if resistance subsequently developed.

[0071] “Wild -type PlySs2 lysin” and “PlySs2 lysin,” refer to a polypeptide having the amino acid sequence:

[0072] MTTVNE ALNN VR AQ V GS G VS VGNGEC Y AL AS W YERMIS PD ATV GLG AG V G WV S G AIGDTIS AKNIGS S YNW QAN GWT VSTS GPFKAGQIVTLG ATPGNPY GH WIVE AVDGDRLTILEQNYGGKRYPVRNYYSAASYRQQVVHYITPPGTVAQSAPNLAGSRS YRETGTMTVTVDALNVRRAPNTSGEIVAVYKRGESFDYDTVIIDVNGYVWVSYIGGS GKRNYVATGATKDGKRFGNAWGTFK (SEQ ID NO: 1; 245 amino acid residues including the initial methionine residue which is removed during post-translational processing, leaving a 244-amino acid peptide as set forth in SEQ ID NO: 18). Accordingly, “Wild-type PlySs2 lysin” and “PlySs2 lysin,”refers to a polypeptide having the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO: 18.

[0073] “Modified lysin polypeptide” or “variant” in reference to SEQ ID NO: 1 or SEQ ID NO: 18 as used herein are used interchangeably to refer to a non-naturally occurring variant (or active fragment thereof) of the wild-type PlySs2 lysin (SEQ ID NO: 1) or the wild-type PlySs2 lysin, wherein the initial methionine residue is removed (SEQ ID NO: 18). The modified lysin polypeptide or variant of SEQ ID NO: 1 or SEQ ID NO: 18 has at least one amino acid substitution in the CHAP domain and/or the SH3b domain, and inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria, such as S. aureus. In some embodiments, the modified lysin polypeptide or variant has at least 80% identity, such as 90%, such as 95%, such as 99%, such as 99.5% identity to SEQ ID NO: 1 or SEQ ID NO: 18.

[0074] “Immunogenic” or “immunogenicity” means predicted to be immunogenic or to have immunogenicity by establishing (for example, through computationally guided in silico methods) the existence of one or more T-cell epitopes. Immunogenicity of a modified lysin polypeptide as disclosed herein can be measured by TCE score, using any available in silico computationally guided method for obtaining such score and compared to the similarly derived TCE score of a wild-type PlySs2 lysin having the amino acid sequence of SEQ ID NO: 1. Alternatively, immunogenicity of a modified lysin polypeptide as disclosed herein can be measured by an in vitro T cell response. By extension, “less immunogenic,” “reduced immunogenicity,” or the like means predicted to be less immunogenic or to have reduced immunogenicity by depletion (which includes elimination or attenuation by amino acid replacement) of one or more T-cell epitopes (i.e., have a lower TCE score as compared to a reference polypeptide) or that the modified lysin polypeptide as disclosed herein elicits a reduced T cell response. Therefore, as used herein, a modified lysin polypeptide is “less immunogenic,” or has “reduced immunogenicity,” or the like if the modified lysin polypeptide has either 1) a lower TCE score than a wild-type PlySs2 lysin having the amino acid sequence of SEQ ID NO: 1 or 2) a reduced T cell response.

[0075] “Reduced T cell response” means that the modified lysin polypeptide induces less T cell activation than a wild-type PlySs2 lysin having the amino acid sequence of SEQ ID NO: 1, as measured by an in vitro T cell proliferation (³{H] -thymidine incorporation) assay using CD8+ depleted, human peripheral blood mononuclear cells in which the human peripheral blood mononuclear cells are exposed to fluorescein isothiocyanate-labeled anti-cytokine antibodies and the response measured.

[0076] “Substantially” used in the context of lytic activity (antimicrobial activity) of a modified lysin polypeptide of the present disclosure means at least a considerable portion of the antibacterial activity of the wild-type PlySs2 lysin, such that, on the basis of such activity, the modified lysin polypeptide would be useful alone or together with other antimicrobial agents, such as one or more antibiotics and/or lysostaphin, to inhibit, combat, or eliminate Staphylococcal or Streptococcal bacterial infection by killing these bacteria. Nonlimiting examples of such substantial activity compared to the wild-type PlySs2 lysin include no more than about 5, such as no more than about 4, no more than about 3, or no more than about 2, times the MIC of the wild-type lysin. Other measures of activity can be, for example, minimum biofilm eliminating concentration (MBEC) or in vivo efficacy using, for example, an animal model, such as the mouse neutropenic thigh infection model (MNTI). Still other measures can be the ability to synergize with antibiotics, such as vancomycin, daptomycin or oxacillin, or the ability to ameliorate, prevent, or delay development of, bacterial resistance of antibiotics, such as vancomycin, daptomycin or oxacillin, similar to the wild-type PlySs2 lysin. The same term “substantially” used in the context of reduced immunogenicity means having at most 65%, such as at most 50%, at most 40%, at most 30%, or at most 25% of the immunogenicity of the wild- type PlySs2 lysin, as measured for example by a TCE score [19].

Multi-drug resistant bacteria

[0077] In some embodiments, the lysin polypeptides as described herein comprising the PlySs2 lysins of SEQ ID NO: 1 or SEQ ID NO: 18 or a variant thereof) are capable of inhibiting the growth, reducing the population, or killing a multidrug -resistant MDR pathogen, such as at least one species, e,g„ at least one strain or isolate of at least one species, of a Gram-positive bacteria, which is multidrug-resistant. As used herein, a “multidrug-resistant” (“MDR”) pathogen, such as multidrug-resistant Gram-positive bacteria, is one that has developed resistance or become non-susceptible to at least two antimicrobial drugs (in some embodiment, of different class), each used as a monotherapy.

[0078] Typically, susceptibility, non-susceptibility and resistance are determined by breakpoints (interpretive criteria). Drugs, such as antibiotics, may have susceptible only breakpoints (S); resistance only breakpoints (R); S, intermediate (I) and R breakpoints; or more typically, S and R breakpoints. [0079] Generally, susceptibility may be determined using Antimicrobial susceptibility testing (AST), which involves laboratory testing on microbes, including bacteria, to determine susceptibility or resistance to one or more drugs. Results of antimicrobial susceptibility testing show if, e.g., bacteria are susceptible (can be treated with drug), intermediate (may be treatable with drug, but may require a higher dosage), or resistant (cannot be treated with drug). The term “non-susceptible” includes both resistant and intermediate isolates.

[0080] For example, certain strains of S. aureus have been found to be resistant to several antibiotics including methicillin and/or vancomycin (Antibiotic Resistant Threats in the United States, 2013, U.S. Department of Health and Services, Centers for Disease Control and Prevention). One skilled in the art can readily determine if a bacterium is drug resistant and/or non-susceptible using routine laboratory techniques that determine the susceptibility or resistance of a bacterium to a drug or antibiotic, such as described in the Examples.

[0081] In some embodiments, multidrug-resistant Gram-positive bacteria are those that have a developed resistance or become non-susceptible to at least two, such as at least three, antimicrobial drugs, optionally in addition to oxacillin and/or methicillin, typically in addition to oxacillin.

[0082] In some embodiments, the multidrug-resistant Gram-positive bacteria, such as at least one isolate or strain of at least one species of Gram-positive bacteria, are resistant and/or non- susceptible to at least two, such as at least three, such as at least four, such as at least five antibiotics, wherein each of the at least two, at least three or at least four antibiotics are from different antibiotic classes, such as those selected from a beta-lactam, a cephalosporin, a monobactam, a carbapenem, a macrolide, an aminoglycoside, a glycopeptide, an oxazolidinone a fluoroquinolone, a ketolide, a lipopeptide, a lincomycin, a tetracycline, a sulfonamide, a trimethoprim and a sulfonamide/trimethoprim.

[0083] More typically, the multidrug-resistant Gram-positive bacteria of the present disclosure are resistant and/or non-susceptible to at least two, such as at least three antibiotics, wherein each antibiotic is from a different antibiotic class, such as an antibiotic class selected from a macrolide, an aminoglycoside, a fluoroquinolone, a ketolide, a lincomycin, a tetracycline, a sulfonamide, a trimethoprim and/or a sulfonamide/trimethoprim.

[0084] In certain embodiments, the multidrug-resistant bacteria, such as at least one isolate or strain of at least one species of Gram-positive bacteria, are resistant and/or non-susceptible to at least two antibiotics, such as at least three antibiotics, optionally in addition to a beta lactam, such as oxacillin and/or methicillin, selected from ceftaroline, clindamycin, daptomycin, doxycycline, erythromycin, gentamicin, levofloxacin, linezolid, trimethoprim/sulfamethoxazole and/or vancomycin.

[0085] In certain embodiments of all aspects of the disclosure, the multidrug-resistant bacteria, such as at least one isolate or strain of at least one species of Gram-positive bacteria, are resistant and/or non-susceptible to all beta lactams including penicillins, carbapenems and first to fourth generation cephalosporins, but not to the fifth generation anti-MRSA cephalosporins (for example ceftaroline).

[0086] In certain embodiments, the multidrug-resistant bacteria are resistant to at least two antibiotics, such as at least three antibiotics, optionally in addition to oxacillin and/or methicillin, selected from erythoromycin, levofloxacin, ceftaroline, linezolid and vancomycin. In certain embodiments, the multidrug-resistant bacteria are resistant to at least two antibiotics, such as at least three antibiotics, optionally in addition to oxacillin and methicillin, selected from erythromycin, levofloxacin and ceftaroline.

[0087] In some embodiments the multidrug-resistant Gram-positive bacteria of the present disclosure are bacteria that have developed resistance or became non-susceptible to antimicrobial drugs, such as a Staphylococcus aureus, that is resistant and/or non-susceptible to two or more, in some embodiments, three or more antibiotics, selected from ceftaroline, clindamycin, daptomycin, doxycycline, erythromycin, gentamicin, levofloxacin, linezolid, trimethoprim/sulfamethoxazole and/or vancomycin. In specific embodiments, the multidrug- resistant Gram-positive bacteria is Staphylococcus aureus resistant and/or non-susceptible to three or more antibiotics, e.g., selected from ceftaroline, clindamycin, doxycycline, erythromycin, levofloxacin. In some embodiments, the multidrug-resistant Gram-positive bacteria of the present disclosure have additionally developed resistance or are non-susceptible to oxacillin.

[0088] In some embodiments, the multidrug-resistant bacteria are MSSA. In some embodiments, the multidrug-resistant bacteria are MRSA. In some embodiments of all aspects of the disclosure, the multidrug-resistant bacteria do not include MRSA. In other embodiments of all aspects of the disclosure, the multidrug-resistant bacteria include MRSA strain that are also resistant and/or non-susceptible to two or more, in some embodiments, three or more antibiotics, selected from ceftaroline, clindamycin, daptomycin, doxycycline, erythromycin, gentamicin, levofloxacin, linezolid, trimethoprim/sulfamethoxazole and/or vancomycin. PlySs2

[0089] The present disclosure is directed to methods of using PlySs2. In certain embodiments, PlySs2 or a fragment or variant thereof thereof inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria, such as multidrug-resistant bacteria, such as at least one isolate or at least one strain of at least one species of Gram-positive bacteria, which multidrug-resistant as described herein.

[0090] As used herein, the terms “PlySs2”, “PlySs2 lysin”, “PlySs2 lysins”, “PlySs2” “CF- 301” and “exebacase” are used interchangeably and encompass PlySs2, set forth herein as SEQ ID NO: 1 (with or without the initial methionine residue or SEQ ID NO: 18). PlySs2, which was identified as an anti-staphylococcal lysin encoded within a prophage of the Streptococcus suis genome, exhibits bacteriocidal and bacteriostatic activity against the following exemplified bacteria.

[0091] PlySs2, i.e., exebacase, as described in the Examples, was uniformly active against contemporary Staphylococcus aureus isolates responsible for bloodstream infections in the US in 2020. PlySs2, i.e., exebacase, activity was consistent, regardless of resistance phenotype (MSSA, MRSA, including MDR isolates). Surveillance data as presented herein further support PlySs2, i.e., exebacase, as an option for the treatment of Staphylococcus aureus, including those caused by MDR MRSA isolates.

Table i. Reduction in Growth of Different Bacteria and Relative kill with a lysin, PlySs2 (partial listing)

[0092] The PlySs2 lysin of SEQ ID NO: 1 has a domain arrangement characteristic of most bacteriophage lysins, defined by a catalytic N-terminal domain linked to a cell wall-binding C-terminal domain. The N-terminal domain belongs to the cysteine-histidine-dependent amidohydrolases/peptidases (CHAP) family common among lysins and other bacterial cell wall-modifying enzymes. The C-terminal domain belongs to the SH3b family that typically forms the cell wall-binding element of lysins. The italicized amino acids indicate the CHAP domain (amino acids 1 to 146) and the dotted underline indicates the SH3b domain (amino acids 157 to 245). The naturally occurring linker between the two domains is PPGTVAQSAP (SEQ ID NO: 2).

MTTVNEALNNVRAQVGSGVSVGNGECYALASWYERMISPDATVGLGAGVGWVSGAI GDTISAKNIGSSYNWQANGWTVSTSGPFKAGQIVTLGATPGNPYGHVVIVEAVDGDR LTILEQNYGGKR YPVRNYYSAA SYRQQWHYITPPGTV AQS A PN L AGS RS Y RETGTMT YTyDALNVRRAPNTS_GEIVAVYKRGES_FDYpTVIIDyNGYYWyS_YIGGSGKRNYVA TGATKDGKRFGNAWGTPK (SEQ ID NO: 1).

[0093] In some embodiments, PlySs2 or a fragment or variant thereof suitable for use with the present methods includes an isolated polypeptide sequence having at least 70%, such as at least 80%, such as at least 85%, such as at least 90%, such as at least 95%, such as at least 98%, such as at least 99% sequence, such as at least 99.5% identity with SEQ ID NO: 1 or SEQ ID NO: 18, wherein the PlySs2 or a fragment or variant thereof retains one or more biological activities, e.g., catalytic activity, ability to bind to bacterial cell walls, such as Staphylococcus or Streptococcus, bacteriocidal or bacteriostatic activity, including the ability to kill Gram-positive bacteria in biofilm, such as Staphylococcus and/or Streptococcus of the PlySs2 lysin having the amino acid sequence of SEQ ID NO: 1 described herein.

[0094] A modified lysin polypeptide may be formed by any method known in the art as described herein and as described in WO 2013/170015, which is herein incorporated by reference in its entirety, e.g., by modifying the PlySs2 lysin of SEQ ID NO: 1 or SEQ ID NO: 18 through site-directed mutagenesis or via mutations in hosts that produce the PlySs2 lysin of SEQ ID NO: 1 or SEQ ID NO: 18, and which retain one or more of the biological functions as described herein. For example, one of skill in the art can reasonably make and test substitutions or replacements to, e.g., the CHAP domain and/or the SH3b domain of the PlySs2 lysin of SEQ ID NO: 1. Sequence comparisons to the Genbank database can be made with either or both of the CHAP and/or SH3b domain sequences or with the PlySs2 lysin full amino acid sequence of SEQ ID NO: 1, for instance, to identify amino acids for substitution. For example, a mutant or variant having an alanine replaced for valine at valine amino acid residue 19 in the PlySs2 amino acid sequence of SEQ ID NO: 1 is active and capable of killing Gram-positive bacteria in a manner similar to and as effective as the SEQ ID NO: 1 PlySs2 lysin.

[0095] Further, the CHAP domain contains conserved cysteine and histidine amino acid sequences (the first cysteine and histidine in the CHAP domain) which are characteristic and conserved in CHAP domains of different polypeptides. It is reasonable to predict, for example, that the conserved cysteine and histidine residues should be maintained in a mutant or variant of PlySs2 so as to maintain activity or capability. Accordingly, particularly desirable residues to retain in a lysin variant of the present disclosure include active-site residues Cys26, Hisl02, Glull8, and Asnl20 in the CHAP domain of SEQ ID NO: 1. Particularly desirable substitutions include: Lys for Arg and vice versa such that a positive charge may be maintained, Glu for Asp and vice versa such that a negative charge may be maintained, Ser for Thr such that a free -OH can be maintained and Gin for Asn such that a free NH2 can be maintained. Other suitable variants include substitutions in SEQ ID NO: 1 in the CHAP and/or SH3 domain regions that are not shared between other known lysins, such as between the CHAP domain of instant SEQ ID NO: 1 and the CHAP domain of PlyC as shown in for example, in Schmitz, 2011, “Expanding the Horizons of Enzybiotic Identification” Student Theses and Dissertations, paper 138, which is herein incorporated by reference in its entirety. Suitable modified lysins are also described herein.

[0096] In some embodiments, the present method includes administering an active fragment of a lysin to a subject in need thereof. Suitable active fragments include those that retain a biologically active portion of a protein or peptide fragment of the embodiments, as described herein. Such modified lysin polypeptides include polypeptides comprising amino acid sequences that include fewer amino acids than the full length protein of the lysin protein and exhibit at least one activity of the corresponding full-length protein. Typically, biologically active portions comprise a domain or motif with at least one activity of the corresponding protein. An exemplary domain sequence for the N-terminal CHAP domain of the PlySs2 lysin described above. An exemplary domain sequence for the C terminal SH3b domain of the PlySs2 lysin is also described above. A biologically active portion of a protein or protein fragment of the disclosure can be a polypeptide which is, for example, 10, 25, 50, 100 amino acids in length. Other biologically active portions, in which other regions of the protein are deleted can be prepared by recombinant techniques and evaluated for one or more of the functional activities of the native form of a polypeptide of the embodiments.

[0097] In some embodiments, suitable active fragments include those having at least 70%, such as at least 80%, such as at least 85%, such as at least 90%, such as at least 95%, such as at least 98% or such as at least 99% sequence identity with the active fragments described herein including the CHAP and/or the SH3b domain, wherein the active fragment thereof retains at least one activity of CHAP and/or the SH3b domain.

[0098] A lysin or active fragment thereof or modified lysin polypeptide as described herein for use in the present method may be produced by a bacterial organism after being infected with a particular bacteriophage or may be produced or prepared recombinantly or synthetically, e.g., chemically synthesized or prepared using a cell free synthesis system. In as much as the lysin polypeptide sequences and nucleic acids encoding the lysin polypeptides are described and referenced herein, the present lysins may be produced via the isolated gene for the lysin from the phage genome, putting the gene into a transfer vector, and cloning said transfer vector into an expression system, using standard methods of the art, as described for example in WO 2013/170015, which is herein incorporated by reference in its entirety. The present modified lysin polypeptides may be truncated, chimeric, shuffled or “natural,” and may be in combination as described, for example, in U. S. Patent No. 5,604,109, which is incorporated herein in its entirety by reference.

[0099] Mutations can be made in the amino acid sequences, or in the nucleic acid sequences encoding the polypeptides and lysins described herein, including in the lysin sequence set forth in SEQ ID NO: 1, SEQ ID NO: 18 or in active fragments or truncations thereof, such that a particular codon is changed to a codon which codes for a different amino acid to obtain a sequence with a substituted amino acid, or one or more amino acids are deleted or added. [00100] Such a mutation is generally made by making the fewest nucleotide changes possible. A substitution mutation of this sort can be made to change an amino acid in the resulting protein in a non-conservative manner (for example, by changing the codon from an amino acid belonging to a grouping of amino acids having a particular size or characteristic to an amino acid belonging to another grouping) or in a conservative manner (for example, by changing the codon from an amino acid belonging to a grouping of amino acids having a particular size or characteristic to an amino acid belonging to the same grouping). Such a conservative change generally leads to less change in the structure and function of the resulting protein. A non-conservative change is more likely to alter the structure, activity or function of the resulting protein. The present disclosure should be considered to include sequences containing conservative changes which do not significantly alter the activity or binding characteristics of the resulting protein. Thus, one of skill in the art, based on a review of the sequence of the PlySs2 lysin polypeptide provided herein and on their knowledge and the public information available for other lysin polypeptides, can make amino acid changes or substitutions in the lysin polypeptide sequence. Amino acid changes can be made to replace or substitute one or more, one or a few, one or several, one to five, one to ten, or such other number of amino acids in the sequence of the lysin(s) provided herein to generate mutants or modified lysin polypeptides thereof. Such mutants or modified lysin polypeptide thereof may be predicted for function or tested for function or capability for anti-bacterial activity as described herein against, e.g., Staphylococcal, Streptococcal, or Enterococcal bacteria, and/or for having comparable activity to the lysin(s) as described and particularly provided herein. Thus, changes made to the sequence of lysin, and mutants or modified lysin polypeptide described herein can be tested using the assays and methods known in the art and described herein. One of skill in the art, on the basis of the domain structure of the lysin(s) hereof can predict one or more, one or several amino acids suitable for substitution or replacement and/or one or more amino acids which are not suitable for substitution or replacement, including reasonable conservative or non-conservative substitutions.

Modified Lysin Polypeptides

[00101] The present disclosure is directed to methods of using a modified lysin polypeptide having lytic activity and reduced immunogenicity as compared to a wild-type PlySs2 lysin against multidrug-resistant Gram-positive bacteria. As used herein “lytic activity” encompasses the ability of a lysin to kill bacteria, reduce the population of bacteria or inhibit bacterial growth. Lytic activity also encompasses the ability to remove or reduce a biofilm and/or the ability to reduce the minimum inhibitory concentration (MIC) of an antibiotic. [00102] Typically, the present modified lysin polypeptides are capable of degrading peptidoglycan, a major structural component of the bacterial cell wall, resulting in cell lysis. The modified lysin polypeptides are further capable of reducing immunogenicity and/or reducing inflammatory response-related toxicity compared to a wild-type PlySs2 lysin.

[00103] Suitable methods for assessing the activity of a modified lysin polypeptide as disclosed herein are well known in the art and described in the examples. Briefly, a MIC value (i.e., the minimum concentration of peptide sufficient to suppress at least 80% of the bacterial growth compared to control) may be determined for a modified lysin polypeptide and compared to, e.g., a wild-type PlySs2 lysin or inactive compound. For example, MIC values for a modified lysin polypeptide may be determined against e.g., laboratory Staphylococcus aureus strains, in e.g., Mueller- Hinton broth or Mueller-Hinton broth supplemented with serum, such as horse serum.

[00104] In some embodiments, the present modified lysin polypeptides are capable of reducing a biofilm. Methods for assessing the Minimal Biofilm Eradicating Concentration (MBEC) of a modified lysin polypeptide may be determined using a variation of the broth microdilution MIC method with modifications (See Ceri et al. 1999. J. Clin Microbial. 37 : 1771- 1776, which is herein incorporated by reference in its entirety and Schuch et al., 2017, Antimicrob. Agents Chemother. 61, pages 1-18, which is herein incorporated by reference in its entirety.) In this method, colonies of bacteria, e.g., Staphylococcus aureus such as methicillin- resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA), are suspended in medium, e.g., phosphate buffer solution (PBS) diluted e.g., 1:100 in TSBg (tryptic soy broth supplemented with 0.2% glucose), added as e.g., 0.15 ml aliquots, to a Calgary Biofilm Device (96-well plate with a lid bearing 96 polycarbonate pegs; lnnovotech Inc.) and incubated e.g., 24 hours at 37°C. Biofilms are then washed and treated with e.g., a 2-fold dilution series of the lysin in TSBg at e.g., 37°C for 24 hours. After treatment, wells are washed, air-dried at e.g., 37°C and stained with e.g., 0.05% crystal violet for 10 minutes. After staining, the biofilms are destained in e.g., 33% acetic acid and the OD600 of e.g., extracted crystal violet is determined. The MB EC of each sample is the minimum lysin concentration required to remove >95% of the biofilm biomass assessed by crystal violet quantitation.

[00105] In some embodiments, the present modified lysin polypeptides reduce the minimum inhibitory concentration (MIC) of an antibiotic. Any known method to assess MIC may be used. In some embodiments, a checkerboard assay is used to determine the effect of a lysin on antibiotic concentration. The checkerboard assay is based on a modification of the CLSI method for MIC determination by broth microdilution (See Clinical and Laboratory Standards Institute (CLSI), CLSI. 2015. Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria That Grow Aerobically; Approved Standard-lOth Edition. Clinical and Laboratory Standards Institute, Wayne, PA, which is herein incorporated by reference in its entirety and Ceri et al. 1999. J. Clin. Microbiol. 37: 1771-1776, which is also herein incorporated by reference in its entirety).

[00106] Checkerboards are constructed by first preparing columns of e.g., a 96-well polypropylene microtiter plate, wherein each well has the same amount of antibiotic diluted 2- fold along the horizontal axis. In a separate plate, comparable rows are prepared in which each well has the same amount of lysin diluted e.g., 2-fold along the vertical axis. The lysin and antibiotic dilutions are then combined, so that each column has a constant amount of antibiotic and doubling dilutions of lysin, while each row has a constant amount of lysin and doubling dilutions of antibiotic. Each well thus has a unique combination of lysin and antibiotic. Bacteria are added to the drug combinations at a given concentration. The MIC of each drug, alone and in combination, is then recorded after e.g., 16 hours at 37°C in ambient air. Summation fractional inhibitory concentrations (åFICs) are calculated for each drug and the minimum åLIC value (åFICmin) is used to determine the effect of the lysin/antibiotic combination.

[00107] In some embodiments, the lysin polypeptides disclosed herein have been modified from a wild-type PlySs2 lysin. As disclosed herein, wild-type PlySs2 comprises both a CHAP domain and a SH3b domain, each of which in turn comprises multiple T-cell epitopes (TCE). TCE 1, TCE 2, TCE 3, and TCE 4 are located in the CHAP domain, while TCE 5, TCE 6, TCE 7, and TCE 8 are located in the SH3b domain. TCE 1 corresponds to amino acid residues 32-45 of SEQ ID NO: 1. TCE 2 corresponds to amino acid residues 84-98 of SEQ ID NO: 1. TCE 3 corresponds to amino acid residues 100-112 of SEQ ID NO: 1. TCE 4 corresponds to amino acid residues 128-145 of SEQ ID NO: 1. TCE 5 corresponds to amino acid residues 164-170 of SEQ ID NO: 1. TCE 6 corresponds to amino acid residues 172-187 of SEQ ID NO: 1. TCE 7 corresponds to amino acid residues 189-201 of SEQ ID NO: 1, and TCE 8 corresponds to amino acid residues 204-221 of SEQ ID NO: 1.

[00108] In certain embodiments, the modified lysin polypeptide comprises at least one substitution as compared to the wild-type PlySs2 polypeptide (SEQ ID NO: 1), wherein the at least one substitution is in one or more of TCE 1, TCE 2, TCE 3, or TCE 4, wherein the modified lysin polypeptide or fragment thereof inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria. In certain embodiments, the modified lysin polypeptide comprises at least one substitution as compared to the wild-type PlySs2 polypeptide (SEQ ID NO: 1), wherein the at least one substitution is in one or more of TCE 5, TCE 6, TCE 7, or TCE 8, wherein the modified lysin polypeptide or fragment thereof inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria. In certain embodiments, the modified lysin polypeptide comprises at least a first substitution and at least a second substitution as compared to the wild-type PlySs2 polypeptide (SEQ ID NO: 1), wherein the at least the first substitution is in one or more of TCE 1, TCE 2, TCE 3, or TCE 4 and at least the second substitution is in one or more of TCE 5, TCE 6, TCE 7, or TCE 8, wherein the modified lysin polypeptide or fragment thereof inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria. Typically, the modified lysin polypeptide has reduced immunogenicity as compared to a wild-type PlySs2 having the amino acid sequence of SEQ ID NO: 1.

[00109] In certain embodiments, the modified lysin polypeptide comprises at least two substitutions as compared to the wild-type PlySs2 polypeptide (SEQ ID NO: 1) or SEQ ID NO: 18, wherein the at least two substitutions are in TCE 4. In certain embodiments, the modified lysin polypeptide comprises at least four substitutions as compared to the wild-type PlySs2 polypeptide (SEQ ID NO: 1) or SEQ ID NO: 18, wherein at least one substitution is in TCE 2, at least one substitution is in TCE 3, and at least two substitutions are in TCE 4.

[00110] In certain embodiments, a modified lysin polypeptide as disclosed herein may result from modifying the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO: 18 by an amino acid substitution in the CHAP domain in at least one position selected from amino acid residue 35, 92, 104, 128, and 137 and/or an amino acid substitution in the SH3b domain in at least one position selected from amino acid residue 164, 184, 195, 198, 204, 206, 212, and 214. Accordingly, in certain embodiments, disclosed herein is a modified lysin polypeptide having at least one amino acid substitution as compared to the wild-type PlySs2 polypeptide (SEQ ID NO: 1), wherein the modified lysin polypeptide comprises at least one amino acid substitution in the CHAP domain in at least one position selected from amino acid residue 35, 92, 104, 128, and 137 of SEQ ID NO: 1 or SEQ ID NO: 18 and/or at least one amino acid substitution in SH3b domain in at least one position selected from amino acid residue 164, 184, 195, 198, 204, 206, 212, and 214 of SEQ ID NO: 1 or SEQ ID NO: 18, wherein the modified lysin polypeptide or fragment thereof inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria. In certain embodiments, the modified lysin polypeptide comprises an amino acid substitution in amino acid residues of 92, 104, 128, and 137 of SEQ ID NO: 1 or SEQ ID NO: 18. In certain embodiments, the modified lysin polypeptide comprises an amino acid substitution in amino acid residues 92, 104, 128, 137, 164, 184, and 198 of SEQ ID NO: 1 or SEQ ID NO: 18. Typically, the modified lysin polypeptide has reduced immunogenicity as compared to a wild-type PlySs2 having the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO: 18.

[00111] In certain embodiments, the modified lysin polypeptide may contain at least 3 amino acid substitutions, such as at least 4, at least 5, at least 6, at least 7, at least 8, or at least 9 amino acid substitutions. In certain embodiments, the modified lysin polypeptide may contain 3-9 amino acid substitutions, such as 4-9, 5-9, 6-9, 7-9, 8-9, or 9 amino acid substitutions relative to SEQ ID NO: 1 or SEQ ID NO: 18. In certain embodiments, the modified lysin polypeptide may comprise at least two, such as at least three or at least four, amino acid substitutions relative to SEQ ID NO: 1 or SEQ ID NO: 18 in the CHAP domain, and in certain embodiments, the modified lysin polypeptide may comprise at least two, such as at least three or at least four, amino acid substitutions relative to SEQ ID NO: 1 or SEQ ID NO: 18in the SH3b domain. In certain embodiments, the modified lysin polypeptide may consist of two, three or four amino acid substitutions relative to SEQ ID NO: 1 or SEQ ID NO: 18 in the CHAP domain, and in certain embodiments, the modified lysin polypeptide may consist of two, three, or four amino acid substitutions relative to SEQ ID NO: 1 or SEQ ID NO: 18in the SH3b domain.

[00112] In certain embodiments, the modified lysin polypeptide comprises one or more of the following amino acid substitutions relative to SEQ ID NO: 1: R35E, L92W, V104S, V128T, Y137S, Y164N, Y164K, N184D, R195E, S198H, S198Q, V204K, V204A, 1206E, V212E, V212A, and V214G. In certain embodiments, the modified lysin polypeptide comprises one or more of the following amino acid substitutions located in the CHAP domain: R35E, L92W, V104S, V128T and Y137S, and/or one or more of the following amino acid substitutions located in the SH3b domain: Y164N, Y164K, N184D, R195E, S198H, S198Q, V204K, V204A, I206E, V212A, V212E, and V214G, wherein the modified lysin polypeptide or fragment thereof inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria. In some embodiments, corresponding modifications are obtained in reference to SEQ ID NO: 18.

[00113] Typically, the modified lysin polypeptide has reduced immunogenicity as compared to a wild-type PlySs2 having the amino acid sequence of SEQ ID NO: 1.

[00114] The substitutions herein are designated using the one-letter amino acid code of the original amino acid in SEQ ID NO: 1 that is replaced, followed by the amino acid position in SEQ ID NO: 1, followed by the amino acid that is substituted into the sequence to result in the modified lysin polypeptide. Accordingly, by way of example, R35E indicates a substitution wherein the arginine at amino acid number 35 of SEQ ID NO: 1 is replaced with glutamic acid. [00115] Exemplary modified lysin polypeptides are disclosed herein as pp55, pp61, pp65, pp296, pp324, pp325, pp341, pp338, pp388, pp400, pp616, pp619, pp628, pp632, and pp642.

[00116] The exemplary modified lysin polypeptides comprise the amino acid substitutions relative to the amino acid sequence of SEQ ID NO:l as shown below in Table 1.

Table 1

[00117] In certain embodiments disclosed herein, the modified lysin polypeptide is pp55 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQID NO: 1: L92W, V104S, V128T, and Y137S. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 3. In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 3, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild-type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 3. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 3. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 3. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 3. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 3.

[00118] In certain embodiments disclosed herein, the modified lysin polypeptide is pp61 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: L92W, V104S, V128T, Y137S, S198H, and I206E. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 4, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild-type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 4. In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 4. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 4. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 4. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 4. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 4.

[00119] In certain embodiments disclosed herein, the modified lysin polypeptide thereof is pp65 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: L92W, V104S, V128T, Y137S, S198Q, V204A, and V212A. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 5. In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 5, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild-type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 5. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 5. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 5. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 5. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 5.1n certain embodiments disclosed herein, the modified lysin polypeptide is pp296 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: L92W, V104S, V128T, Y137S, Y164K, N184D, and S198Q, such that the amino acid sequence is

MTTVNE ALNN VR AQ V GS G V S V GN GEC Y AL AS WYERMIS PD ATV GLGAG V GWV S G AIGDTIS AKNIGS S YN W Q ANG WT V S TS GPFKAGQIVTW G ATPGNPY GH V S IVE A VDG DRLTILEQNY GGKRYPTRNYY S AASSRQQVVHYITPPGTVAQS APNLAGSRSKRETG TMTVT VD ALN VRRAPDTS GEIV A V YKRGEQFD YDT VIID VN G Y VW V S YIGGS GKRN YV ATG ATKDGKRFGNAW GTFK (SEQ ID NO: 6). In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 6. In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 6, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild-type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 6. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 6. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 6. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 6. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 6.

[00120] In certain embodiments disclosed herein, the modified lysin polypeptide is pp324 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: L92W, V104S, V128T, Y137S, Y164K, and N184D. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 7. In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 7, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild- type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 7. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 7. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 7. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 7. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 7.

[00121] In certain embodiments disclosed herein, the modified lysin polypeptide is pp325 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: L92W, V104S, V128T, Y137S, Y164N, and R195E. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 8. In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 8, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild- type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 8. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 8. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 8. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 8. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 8.

[00122] In certain embodiments disclosed herein, the modified lysin polypeptide is pp381 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: L92W, V104S, V128T, Y137S, N184D, and S198H. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 9. In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 9, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild- type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 9. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 9. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 9. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 9. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 9. [00123] In certain embodiments disclosed herein, the modified lysin polypeptide is pp341 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: L92W, V104S, V128T, Y137S, N184D, V204A, and V212A. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 10, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild-type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 10. In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 10. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 10. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 10. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 10. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 10.

[00124] In certain embodiments disclosed herein, the modified lysin polypeptide is pp388 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: Y164N, N184D, R195E, V204K, and V212E. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 11. In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 11, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild-type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 11. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 11. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 11. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 11. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 11.

[00125] In certain embodiments disclosed herein, the modified lysin polypeptide is pp400 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: R35E, L92W, V104S, V128T, and Y137S. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 12. In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 12, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild-type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 12. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 12. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 12. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 12. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 12.

[00126] In certain embodiments disclosed herein, the modified lysin polypeptide is pp616 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: V128T, Y137S, and Y164K. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 13. In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 13, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild-type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 13. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 13. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 13. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 13. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 13. [00127] In certain embodiments disclosed herein, the modified lysin polypeptide is pp619 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: L92W, V104S, V128T, Y137S, and Y164K. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 14. In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 14, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild-type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 14. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 14. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 14. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 14. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 14.

[00128] In certain embodiments disclosed herein, the modified lysin polypeptide is pp628 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: L92W, V104S, V128T, Y137S, Y164K, V204K, and V212E. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 15. In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 15, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild- type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 15. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 15. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 15. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 15. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 15.

[00129] In certain embodiments disclosed herein, the modified lysin polypeptide is pp632 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: L92W, V104S, V128T, Y137S, Y164K, N184D, S198Q, V204K, and V212E. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 16. In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 16, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild-type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 16. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 16. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 16. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 16. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 16.

[00130] In certain embodiments disclosed herein, the modified lysin polypeptide is pp642 and comprises the following amino acid substitutions relative to the amino acid sequence of SEQ ID NO: 1: L92W, V104S, V128T, Y137S, Y164K, I206E, and V214G. In certain embodiments, the modified lysin polypeptide comprises the amino acid sequence of SEQ ID NO: 17. In certain embodiments, the modified lysin polypeptide has at least 80% sequence identity with SEQ ID NO: 17, wherein the modified lysin polypeptide inhibits the growth, reduces the population, or kills at least one species of Gram-positive bacteria and optionally wherein the modified lysin polypeptide has reduced immunogenicity as compared to the wild- type PlySs2 (SEQ ID NO: 1). In certain embodiments, the modified lysin polypeptide has at least 85% sequence identity with SEQ ID NO: 17. In certain embodiments, the modified lysin polypeptide has at least 90% sequence identity with SEQ ID NO: 17. In certain embodiments, the modified lysin polypeptide has at least 95% sequence identity with SEQ ID NO: 17. In certain embodiments, the modified lysin polypeptide has at least 98% sequence identity with SEQ ID NO: 17. In certain embodiments, the modified lysin polypeptide has at least 99% sequence identity with SEQ ID NO: 17.

[00131] In some embodiments, corresponding modifications are obtained in reference to SEQ ID NO: 18.

[00132] In addition to the at least one substitution in the CHAP and/or Sh3b domains, the modified lysin polypeptides can also include one or more amino acid insertions and/or deletions, provided those modifications do not interfere with the lytic activity and/or reduced immunogenicity of the modified lysin polypeptide.

[00133] Also disclosed are chimeric lysin polypeptides. Chimeric lysin polypeptides are known in the art. For example, ClyF is a chimeric lysin that combines the catalytic domain of Plyl87 lysin (the N-terminal 157 amino acid residues) with the binding domain of PlySs2 (the C-terminal 99 residues) [10]. In certain embodiments, the chimeric lysin polypeptide comprises a modified PlySs2 CHAP domain, as disclosed herein, and the binding domain of another lysin. In certain embodiments, the chimeric lysin polypeptide comprises the catalytic domain of another lysin and a modified PlySs2 SH3b domain, as disclosed herein. [00134] In some embodiments, an active fragment of the modified lysin polypeptide is obtained. The term “active fragment” refers to a portion of a full-length lysin, which retains one or more biological activities of the reference lysin. Thus, as used herein, an active fragment of a modified lysin polypeptides inhibits the growth, or reduces the population, or kills at least one Gram-positive bacterial species.

Vectors and Host Cells

[00135] Nucleic acids encoding PlySs2 or the modified lysin polypeptides disclosed herein can be introduced into an appropriate vector for expressing the modified lysin polypeptides. Generally, any system or vector suitable to maintain, propagate or express a polypeptide in a host may be used for expression of the modified lysin polypeptides disclosed herein or fragments thereof or PlySs2 or fragments thereof. For example, “recombinant expression vectors” or “expression vectors,” can direct the expression of genes to which they are operatively linked. The appropriate DNA/polynucleotide sequence may be inserted into the expression system by any of a variety of well-known and routine techniques, such as, for example, those set forth in Sambrook et al., eds., Molecular Cloning: A Laboratory Manual (3rd Ed.), Vols. 1-3, Cold Spring Harbor Laboratory (2001). Additionally, tags can also be added to the modified lysin polypeptides of the present disclosure or PlySs2 to provide convenient methods of isolation, e.g., c-myc, biotin, poly-His, etc. Kits for such expression systems are commercially available.

[00136] A wide variety of host/expression vector combinations may be employed in expressing the polynucleotide sequences encoding the present modified lysin polypeptides or PlySs2. Large numbers of suitable vectors are known to those of skill in the art, and are commercially available. Examples of suitable vectors are provided, e.g., in Sambrook et al, eds., Molecular Cloning: A Laboratory Manual (3rd Ed.), Vols. 1-3, Cold Spring Harbor Laboratory (2001). Such vectors include, among others, chromosomal, episomal and vims derived vectors, e.g., vectors derived from bacterial plasmids, from bacteriophage, from transposons, from yeast episomes, from insertion elements, from yeast chromosomal elements, from viruses such as baculoviruses, papova viruses, such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and retroviruses, and vectors derived from combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, such as cosmids and phagemids. [00137] Furthermore, the vectors may provide for the constitutive or inducible expression of PlySs2 or the modified lysin polypeptides of the present disclosure. Suitable vectors include but are not limited to derivatives of SV40 and known bacterial plasmids, e.g., E. coli plasmids colEl, pCRl, pBR322, pMB9 and their derivatives, plasmids such as RP4, pBAD24 and pBAD- TOPO; phage DNAS, e.g., the numerous derivatives of phage A, e.g., NM989, and other phage DNA, e.g., M13 and filamentous single stranded phage DNA; yeast plasmids such as the 2 D plasmid or derivatives thereof; vectors useful in eukaryotic cells, such as vectors useful in insect or mammalian cells; vectors derived from combinations of plasmids and phage DNAs, such as plasmids that have been modified to employ phage DNA or other expression control sequences; and the like. Many of the vectors mentioned above are commercially available from vendors such as New England Biolabs Inc., Addgene, Takara Bio Inc., ThermoFisher Scientific Inc., etc.

[00138] Additionally, vectors may comprise various regulatory elements (including promoter, ribosome binding site, terminator, enhancer, various cis-elements for controlling the expression level) wherein the vector is constructed in accordance with the host cell. Any of a wide variety of expression control sequences (sequences that control the expression of a polynucleotide sequence operatively linked to it) may be used in these vectors to express the polynucleotide sequences encoding PlySs2 or the modified lysin polypeptides of the present disclosure. Useful control sequences include, but are not limited to: the early or late promoters of SV40, CMV, vaccinia, polyoma or adenovirus, the lac system, the trp system, the TAC system, the TRC system, the LTR system, the major operator and promoter regions of phage A, the control regions of fd coat protein, the promoter for 3-phosphoglycerate kinase or other glycolytic enzymes, the promoters of acid phosphatase (e.g., Pho5), the promoters of the yeast mating factors, E. coli promoter for expression in bacteria, and other promoter sequences known to control the expression of genes of prokaryotic or eukaryotic cells or their viruses, and various combinations thereof. Typically, the polynucleotide sequences encoding the or PlySs2 polypeptides are operatively linked to a heterologous promoter or regulatory element. A polynucleotide sequence is “operatively linked” when it is placed into a functional relationship with another nucleotide sequence. For example, a promoter or regulatory DNA sequence is said to be “operatively linked” to a DNA sequence that codes for an RNA and/or a protein if the two sequences are operatively linked, or situated such that the promoter or regulatory DNA sequence affects the expression level of the coding or structural DNA sequence. Operatively linked DNA sequences are typically, but not necessarily, contiguous. [00139] A wide variety of host cells are useful in expressing the present polypeptides. Non-limiting examples of host cells suitable for expression of the present polypeptides include well known eukaryotic and prokaryotic hosts, such as strains of E. coli, Pseudomonas, Bacillus, Streptomyces, fungi such as yeasts, and animal cells, such as CHO, Rl.l, B-W and L-M cells, African Green Monkey kidney cells (e.g., COS 1, COS 7, BSC1, BSC40, and BMT10), insect cells (e.g., Sf9), and human cells and plant cells in tissue culture.

[00140] While the expression host may be any known expression host cell, in a typical embodiment the expression host is one of the strains of E. coli. These include, but are not limited to commercially available E. coli strains such as ToplO (ThermoFisher Scientific, Inc.), DH5a (Thermo Fisher Scientific, Inc.), XLI-Blue (Agilent Technologies, Inc.), SCSllO (Agilent Technologies, Inc.), JM109 (Promega, Inc.), LMG194 (ATCC), and BL21 (Thermo Fisher Scientific, Inc.). There are several advantages of using E. coli as a host system including: fast growth kinetics, where under the optimal environmental conditions, its doubling time is about 20 min (Sezonov et ah, J. Bacterial. 1898746-8749 (2007)), easily achieved high density cultures, easy and fast transformation with exogenous DNA, etc. Details regarding protein expression in E. coli, including plasmid selection as well as strain selection are discussed in details by Rosano, G. and Ceccarelli, E., Front Microbial., 5: 172 (2014).

[00141] Efficient expression of the present modified lysin polypeptides or PlySs2 depends on a variety of factors such as optimal expression signals (both at the level of transcription and translation), correct protein folding, and cell growth characteristics. Regarding methods for constructing the vector and methods for transducing the constructed recombinant vector into the host cell, conventional methods known in the art can be utilized. While it is understood that not all vectors, expression control sequences, and hosts will function equally well to express the polynucleotide sequences encoding the modified lysin polypeptides of the present disclosure or PlySs2, one skilled in the art will be able to select the proper vectors, expression control sequences, and hosts without undue experimentation to accomplish the desired expression without departing from the scope of this disclosure.

[00142] PlySs2 and the modified lysin polypeptides of the present disclosure can be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography, and lectin chromatography. High performance liquid chromatography can also employed for lysin polypeptide purification. [00143] Alternatively, the vector system used for the production of the modified lysin polypeptides of the present disclosure or PlySs2 may be a cell-free expression system. Various cell-free expression systems are commercially available, including, but are not limited to those available from Promega, LifeTechnologies, Clonetech, etc.

Compositions Comprising PlySs2 or the Modified Lysin Polypeptides

[00144] PlySs2 and/or the modified lysin polypeptides disclosed herein may be incorporated into antimicrobial and bactericidal compositions and unit dosage forms thereof alone or with one or more conventional antibiotics and other bactericidal agents.

[00145] Typically, the compositions contain PlySs2 and/or the modified lysin polypeptide as disclosed herein in an amount effective for killing Gram-positive bacteria selected from the group consisting of Staphylococcus aureus, Listeria monocytogenes, a coagulase negative staphylococcus such as from the Staphylococcus epidermidis group, the Staphylococcus saprophyticus group, the Staphylococcus simulans group, the Staphylococcus intermedius group, the Staphylococcus sciuri group, and the Staphylococcus hyicus group; Streptococcus suis, Streptococcus pyogenes, Streptococcus agalactiac, Streptococcus dysgalactiae, Streptococcus pneumoniae, species included in the viridans streptococci group such as the Streptococcus anginosis group, Streptococcus mitis group, Streptococcus sanguinis group, Streptococcus bovis group, Streptococcus salivarius group, and Streptococcus mutans group; Enterococcus faecalis, and Enterococcus faecium.

[00146] The compositions disclosed herein can take the form of solutions, suspensions, emulsions, tablets, pills, pellets, capsules, capsules containing liquids, powders, sustained- release formulations, suppositories, tampon applications, aerosols, sprays, lozenges, troches, candies, injectables, chewing gums, ointments, smears, time-release patches, liquid- absorbed wipes, and combinations thereof. Hence, the compositions can be employed as solids, such as tablets, lyophilized powders for reconstitution, liposomes or micelles, or the compositions can be employed as liquids, such as solutions, suspensions, gargles, emulsions, or capsules filled solids or liquids, such as for oral use. In certain embodiments, the compositions can be in the form of suppositories or capsules for rectal administration or in the form of sterile injectable or inhalable solutions or suspensions for parenteral (including, for example, intravenous or subcutaneous) or topical, such as dermal, nasal, pharyngeal or pulmonary, use. Such compositions include pharmaceutical compositions, and unit dosage forms thereof may comprise conventional or new ingredients in conventional or special proportions, with or without additional active compounds or principles. Such unit dosage forms may contain any suitable effective amount of the active ingredient commensurate with the intended daily dosage range to be employed.

[00147] Carriers and excipients can be selected from a great variety of substances acceptable for human or veterinary use. Non-limiting examples of pharmaceutically acceptable carriers or excipients include any of the standard pharmaceutical carriers, such as phosphate buffered saline solutions, water, polyols, disaccharides or polysaccharides, and emulsions such as oil/water emulsions and microemulsions. Other stabilizing excipients include proprietary blends of stabilizing and protecting solutions (SPS), cyclodextrins and recombinant human albumin (rHSA). Other excipients may include bulking agents, buffering agents, tonicity modifiers (e.g. , salts and amino acids), surfactants, preservatives, antioxidants, and co-solvents. For solid oral compositions comprising PlySs2 or a modified lysin polypeptide disclosed herein, suitable pharmaceutically acceptable excipients include, but are not limited to, starches, sugars, diluents, granulating agents, lubricants, binders, disintegrating agents, and the like. For liquid oral compositions, suitable pharmaceutically acceptable excipients may include, but are not limited to, water, glycols, oils, alcohols, flavoring agents, preservatives, and the like. For topical solid compositions such as creams, gels, foams, ointments, or sprays, suitable excipients may include, but are not limited to a cream, a cellulosic, or an oily base, emulsifying agents, stiffening agents, rheology modifiers or thickeners, surfactants, emollients, preservatives, humectants, alkalizing or buffering agents, and solvents.

[00148] For example, PlySs2 and/or the modified lysin polypeptides disclosed herein can be combined with buffers that maintain the pH of a liquid suspension, solution, or emulsion within a range that does not substantially affect the activity of the PlySs2 or modified lysin polypeptide. For example, a desirable pH range of the composition or of the environment wherein the active ingredient is found upon administration may be between about 4.0 and about 9.0, for example between about 4.5 and about 8.5.

[00149] A stabilizing buffer may be optionally included to permit the modified lysin polypeptide or PlySs2 to exert its activity in an optimized fashion. The buffer may contain a reducing reagent, such as dithiothreitol. The stabilizing buffer may also be or include a metal chelating reagent, such as ethylenediaminetetracetic acid disodium salt, or it may contain a phosphate or citrate-phosphate buffer, or any other buffering agent, such as Tris or succinate. [00150] A mild surfactant can be included in a pharmaceutical composition in an amount effective to potentiate the therapeutic effect of the modified lysin polypeptides or PlySs2 used in the composition. Suitable mild surfactants may include, inter alia, esters of polyoxyethylene sorbitan and fatty acids (such as the Tween series), octylphenoxy polyethoxy ethanol (such as the Triton-X series), n-Octyl-fl-D-glucopyranoside, n-Octyl-fl-D-thioglucopyranoside, n- Decyl-f3-D-glucopyranoside, n-Dodecyl-f3-D-glucopyranoside, poloxamer, polysorbate 20, polysorbate 80, polyethylene glycol, and biologically occurring surfactants, e.g., fatty acids, glycerides, monoglycerides, deoxycholate, and esters of deoxycholate.

[00151] Preservatives may also be used in the compositions disclosed herein, and may, for example, comprise about 0.05% to about 0.5% by weight of the total composition. The use of preservatives may assure that if the product is microbially-contaminated, the formulation will prevent or diminish microorganism growth (or attenuate the potency of the formulation). Exemplary preservatives include methylparaben, propylparaben, butylparaben, chloroxylenol, sodium benzoate, DMDM Hydantoin, 3-Iodo-2-Propylbutyl carbamate, potassium sorbate, chlorhexidine digluconate, or a combination thereof.

[00152] For oral administration, Plyss2 and/or the modified lysin polypeptides disclosed herein can be formulated into solid or liquid preparations, for example tablets, capsules, powders, solutions, suspensions, and dispersions. For oral administration in the form of a tablet or capsule, the active ingredient may be combined with one or more pharmaceutically acceptable excipients such as binding agents (e.g., pregelatinized maize starch, polyvinylpyrrolidone, or hydroxypropyl methylcellulose); fillers (e.g., lactose, sucrose, glucose, mannitol, sorbitol, other reducing and non-reducing sugars, microcrystalline cellulose, calcium sulfate, or calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc, silica, steric acid, sodium stearyl fumarate, glyceryl behenate, calcium stearate, and the like); disintegrants (e.g. , potato starch or sodium starch glycolate); wetting agents (e.g. , sodium lauryl sulphate), coloring and flavoring agents, gelatin, sweeteners, natural and synthetic gums (such as acacia, tragacanth or alginates), buffer salts, carboxymethylcellulose, polyethyleneglycol, waxes, and the like. For oral administration in liquid form, the drug components can be combined with non-toxic, pharmaceutically acceptable inert carriers (e.g., ethanol, glycerol, water), suspending agents (e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible fats), emulsifying agents (e.g., lecithin or acacia), non-aqueous vehicles (e.g., almond oil, oily esters, ethyl alcohol or fractionated vegetable oils), preservatives (e.g., methyl or propyl-p- hydroxybenzoates or sorbic acid), and the like. Stabilizing agents such as antioxidants (e.g., BHA, BHT, propyl gallate, sodium ascorbate, or citric acid) can also be added to stabilize the dosage forms.

[00153] In certain embodiments, the tablets can be coated by methods well-known in the art. The compositions disclosed herein can be also introduced in microspheres or microcapsules, e.g. , fabricated from poly glycolic acid/lactic acid (PGLA). Liquid preparations for oral administration can take the form of, for example, solutions, syrups, emulsions, or suspensions, or they can be presented as a dry product for reconstitution with water or other suitable vehicle before use. Preparations for oral administration can be suitably formulated to give controlled or postponed release of the active compound.

[00154] The active agents can also be administered in the form of liposome delivery systems, such as small unilamellar vesicles, large unilamellar vesicles, and multilamellar vesicles. Liposomes can be formed from a variety of phospholipids, such as cholesterol, stearylamine, or phosphatidylcholines, as is well known.

[00155] For preparing solid compositions such as tablets and pills, a modified lysin polypeptide as disclosed herein or PlySs2 as also herein disclosed may be mixed with a pharmaceutical excipient to form a solid preformulation composition. If desired, tablets may be sugar coated or enteric coated by standard techniques. The tablets or pills may be coated or otherwise compounded to provide a dosage form affording the advantage of prolonged or delayed action. For example, the tablet or pill can include an inner dosage and an outer dosage component, the latter being in the form of an envelope over the former. The two components can be separated by an enteric layer, which serves to resist disintegration in the stomach and permit the inner component to pass intact into the duodenum or to be further delayed in release. A variety of materials can be used for such enteric layers or coatings, such materials including a number of polymeric acids and mixtures of polymeric acids with such materials as shellac, cetyl alcohol, and cellulose acetate. Similarly, the orally-administered medicaments may be administered in the form of a time-controlled release vehicle, including diffusion-controlled systems, osmotic devices, dissolution-controlled matrices, and erodible/degradable matrices. [00156] Topical compositions as disclosed herein may further comprise a pharmaceutically or physiologically acceptable carrier, such as a dermatologically or an otically acceptable carrier. Such carriers, in the case of dermatologically acceptable carriers, may be compatible with skin, nails, mucous membranes, tissues, and/or hair, and can include any conventionally used dermatological carrier meeting these requirements. In the case of otically acceptable carriers, the carrier may be compatible with all parts of the ear. Such carriers can be readily selected by one of ordinary skill in the art. Carriers for topical administration of the compounds disclosed herein include, but are not limited to, mineral oil, liquid petroleum, white petroleum, propylene glycol, polyoxyethylene and/or polyoxypropylene compounds, emulsifying wax, sorbitan monostearate, polysorbate 60, cetyl esters wax, cetearyl alcohol, 2- octyldodecanol, benzyl alcohol, and water. In formulating skin ointments, the active components of the present disclosure may be formulated in an oleaginous hydrocarbon base, an anhydrous absorption base, a water-in-oil absorption base, an oil-in-water water-removable base, and/or a water-soluble base. In formulating otic compositions, the active components of the present disclosure may be formulated in an aqueous polymeric suspension including such carriers as dextrans, polyethylene glycols, polyvinylpyrrolidone, polysaccharide gels, Gelrite®, cellulosic polymers like hydroxypropyl methylcellulose, and carboxy-containing polymers such as polymers or copolymers of acrylic acid, as well as other polymeric demulcents. The topical compositions as disclosed herein may be in any form suitable for topical application, including aqueous, aqueous-alcoholic or oily solutions; lotion or serum dispersions; aqueous, anhydrous or oily gels; emulsions obtained by dispersion of a fatty phase in an aqueous phase (O/W or oil in water) or, conversely, dispersion of an aqueous phase in a fatty phase (W/O or water in oil), microemulsions or alternatively microcapsules, microparticles or lipid vesicle dispersions of ionic and/or nonionic type, creams, lotions, gels, foams (which may use a pressurized canister, a suitable applicator, an emulsifier, and an inert propellant), essences, milks, suspensions, or patches. Topical compositions disclosed herein may also contain adjuvants such as hydrophilic or lipophilic gelling agents, hydrophilic or lipophilic active agents, preserving agents, antioxidants, solvents, fragrances, fillers, sunscreens, odor- absorbers, and dyestuffs. In a further aspect, the topical compositions disclosed herein may be administered in conjunction with devices such as transdermal patches, dressings, pads, wraps, matrices and bandages capable of being adhered or otherwise associated with the skin or other tissue or organ of a subject, being capable of delivering a therapeutically-effective amount of one or more modified lysin polypeptides and/or PlySs2 as disclosed herein.

[00157] In some embodiments, the topical compositions disclosed herein additionally comprise one or more components used to treat topical bums. Such components may include, but are not limited to, a propylene glycol hydrogel; a combination of a glycol, a cellulose derivative and a water-soluble aluminum salt; an antiseptic; an antibiotic; and a corticosteroid. Humectants (such as solid or liquid wax esters), absorption promoters (such as hydrophilic clays, or starches), viscosity building agents, and skin-protecting agents may also be added. Topical formulations may be in the form of rinses such as mouthwash. See, e.g. ,W02004/004650.

[00158] PlySs2 and/or the modified lysin polypeptides disclosed herein may also be administered by injection of a therapeutic agent comprising the appropriate amount of a PlySs2 or modified lysin polypeptide and a carrier. For example, the PlySs2 or modified lysin polypeptides can be administered intramuscularly, intracerebrovetricularly, intrathecally, subdermally, subcutaneously, intreaperitoneally, intravenously, or by direct injection or continuous infusion to treat infections by bacteria, such as gram-positive bacteria. The carrier may be comprised of distilled water, a saline solution, albumin, a serum, or any combinations thereof. Additionally, pharmaceutical compositions of parenteral injections can comprise pharmaceutically-acceptable aqueous or nonaqueous solutions of plySs2 or modified lysin polypeptides in addition to one or more of the following: pH buffered solutions, adjuvants (e.g. , preservatives, wetting agents, emulsifying agents, stabilizing agents, and dispersing agents), liposomal formulations, nanoparticles, dispersions, suspensions, and emulsions, as well as sterile powders for reconstitution into sterile injectable solutions or dispersions just prior to use. [00159] In certain embodiments, formulations for injection can be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, and in certain embodiments may include an added preservative. The compositions can take such forms as excipients, suspensions, solutions, or emulsions in oily or aqueous vehicles, and can contain formulatory agents such as suspending, stabilizing, bulking, and/or dispersing agents. The active ingredient can be in powder form for reconstitution with a suitable vehicle, e.g. , sterile pyrogen-free water, before use. Examples of buffering agents may include histidine, Tris, phosphate, succinate citrate, methionine, cystine, glycine, mild surfactants, calcium, and magnesium. A reducing agent such as dithiothreitol can also be included.

[00160] In cases where parenteral injection is the chosen mode of administration, an isotonic formulation may be used. Generally, additives for isotonicity can include sodium chloride, dextrose, sucrose, glucose, trehalose, mannitol, sorbitol, and lactose. In some cases, isotonic solutions such as phosphate buffered saline may be used. Stabilizers can include histidine, methionine, glycine, arginine, gelatin, and albumin, such as human or bovine serum albumin. A person of ordinary skill will readily appreciate that many of the foregoing excipients can also be used in compositions for injection.

[00161] A vasoconstriction agent can be added to the compositions disclosed herein. In certain embodiments, the compositions may be provided sterile and pyrogen-free. [00162] In another embodiment, the compositions disclosed herein may be dry inhalable powders or other inhalable compositions, such as aerosols or sprays. The inhalable compositions disclosed herein can further comprise a pharmaceutically acceptable carrier. For administration by inhalation, PlySs2 and/or the modified lysin polypeptides may be conveniently delivered in the form of an aerosol spray presentation from such devices as inhalers, pressurized aerosol dispensers, or nebulizers, with the use of a suitable propellant, e.g. , dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide, or other suitable gas. In the case of a pressurized aerosol, the dosage unit can be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, e.g., gelatin for use in an inhaler or insufflator can be formulated containing a powder mix of the active ingredient and a suitable powder base such as lactose or starch.

[00163] In one embodiment, PlySs2 and/or the modified lysin polypeptides disclosed herein may be formulated as a dry, inhalable powder or as an aerosol or spray. In specific embodiments, PlySs2 and/or the modified lysin polypeptide inhalation solution may further be formulated with a propellant for aerosol delivery. In certain embodiments, solutions may be nebulized. Many dispensing devices are available in the art for delivery of pharmaceutical compositions, including polypeptides, by inhalation. These include nebulizers, pressurized aerosol dispensers, and inhalers.

[00164] A surfactant can be added to an inhalable pharmaceutical composition as disclosed herein in order to lower the surface and interfacial tension between the medicaments and the propellant. Where the medicaments, propellant, and excipient are to form a suspension, a surfactant may or may not be required. Where the medicaments, propellant, and excipient are to form a solution, a surfactant may or may not be necessary, depending in part on the solubility of the particular medicament and excipient. The surfactant may be any suitable, non-toxic compound that is non-reactive with the medicament and that reduces the surface tension between the medicament, the excipient, and the propellant and/or acts as a valve lubricant. [00165] Examples of suitable surfactants include, but are not limited to: oleic acid; sorbitan trioleate; cetyl pyridinium chloride; soya lecithin; polyoxyethylene(20) sorbitan monolaurate; polyoxyethylene (10) stearyl ether; polyoxyethylene (2) oleyl ether; poly oxypropylene-polyoxy ethylene ethylene diamine block copolymers; polyoxyethylene(20) sorbitan monostearate; polyoxyethylene(20) sorbitan monooleate; polyoxypropylene- polyoxy ethylene block copolymers; castor oil ethoxylate; and combinations thereof. [00166] Examples of suitable propellants include, but are not limited to: dichlorodifluoromethane, trichlorofluoromethane, dichloro-tetrafluoroethane, and carbon dioxide.

[00167] Examples of suitable excipients for use in inhalable compositions include, but are not limited to: lactose, starch, propylene glycol diesters of medium chain fatty acids; triglyceride esters of medium chain fatty acids, short chains, or long chains, or any combination thereof; perfluorodimethylcyclobutane; perfluorocyclobutane; polyethylene glycol; menthol; lauroglycol; diethylene glycol monoethylether; polyglycolized glycerides of medium chain fatty acids; alcohols; eucalyptus oil; short chain fatty acids; and combinations thereof.

[00168] In some embodiments, the compositions disclosed herein comprise nasal applications. Nasal applications include, for instance, nasal sprays, nasal drops, nasal ointments, nasal washes, nasal injections, nasal packings, bronchial sprays and inhalers, or indirectly through use of throat lozenges, mouthwashes or gargles, or through the use of ointments applied to the nasal nares, or the face or any combination of these and similar methods of application. [00169] Compositions disclosed herein can also be formulated for rectal administration, e.g., as suppositories or retention enemas (e.g. , containing conventional suppository bases such as cocoa butter or other glycerides).

[00170] In certain embodiments, the compositions disclosed herein may further comprise at least one antibiotic, such as at least one antibiotic effective to inhibit the growth, reduce the population, or kill at least one species of Gram-positive bacteria. In certain embodiments, the at least one antibiotic is effective against one or more of Staphylococcus aureus, Listeria monocytogenes, a coagulase negative staphylococcus such as from the Staphylococcus epidermidis group, the Staphylococcus saprophyticus group, the Staphylococcus simulans group, the Staphylococcus intermedius group, the Staphylococcus sciuri group, and the Staphylococcus hyicus group; Streptococcus suis, Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus dysgalactiac, Streptococcus pneumoniae, species included in the viridans streptococci group such as the Streptococcus anginosis group, Streptococcus mitis group, Streptococcus sanguinis group, Streptococcus bovis group, Streptococcus salivarius group, and Streptococcus mutans group; Enterococcus faecalis, and Enterococcus faecium. [00171] In certain embodiments of the compositions disclosed herein, the PlySs2 and/or the modified lysin polypeptide in combination with the at least one antibiotic may exhibit synergism, for example synergism in the PlySs2 and/or the modified lysin polypeptide’s or the antibiotic’s ability to inhibit the growth, reduce the population, or kill at least one species of Gram-positive bacteria. Synergy may refer to the inhibitory activity of a combination of two active agents, wherein the fractional inhibitory concentration (FIC) index for the combination is less than 1, and for strong synergy, less than or equal to 0.5. The FIC of an agent is the minimum concentration of that agent that kills bacteria when used in combination with another agent divided by the concentration of the first agent that has the same effect when the first agent is used alone. The FIC index for the combination of A and B is the sum of their individual FIC values.

[00172] Synergy may be evaluated in a checkerboard assay (and can be validated by time-kill curves). Each checkerboard assay generates many different combinations, and, by convention, the FIC values of the most effective combination are used in calculating the FIC index. The FIC index defines the nature of the interaction. Antimicrobial agents with additive interactions have a FIC index of 1; an FIC index of <1 defines synergistic interactions; combinations with an FIC index >1 are antagonistic. The lower the FIC index, the more synergistic a combination. See, e.g., Singh, P.K. et al, Am J Physiol Lung Cell Mol Physiol 279: L799-L805, 2000. Synergy has implications for an efficacious, new general anti-infective strategy based on the co-administration of PlySs2 and/or modified lysin polypeptides and antibiotics. In particular each and both PlySs2 and/or modified lysin polypeptides and antibiotics may be administered at reduced doses and amounts, with enhanced bactericidal and bacteriostatic activity and with reduced risk of resistance development. In other words, the benefits of synergy are not only realized when one or both agents are used at sub-MIC concentrations, although the existence of synergy may be revealed by testing with sub-MIC concentrations of each agent.

Methods

[00173] Due to their high degree of activity and their low toxicity, together presenting a favorable therapeutic index, PlySs2 and/or a modified lysin polypeptide as disclosed herein may be administered to a subject in need thereof, e.g., a living animal (including a human) for the treatment, alleviation, or amelioration, palliation, or elimination of an indication or condition which is susceptible thereto.

[00174] In one aspect, the present disclosure is directed to a method of preventing or treating a multidrug-resistant bacterial infection caused by a multi-drug resistant bacteria as described herein comprising co-administering to a subject diagnosed with, at risk for, or exhibiting symptoms of a bacterial infection, a combination of a first effective amount of the composition containing an effective amount of PlySs2 and/or a modified lysin polypeptide as described herein, and a second effective amount of an antibiotic suitable for the treatment of Gram-positive bacterial infection.

[00175] PlySs2 and/or the modified lysin polypeptides of the present disclosure can be co-administered with standard care antibiotics or with antibiotics of last resort, individually or in various combinations as within the skill of the art. Traditional antibiotics used against Gram positive bacteria are described herein and may include, for example, antibiotics of different types and classes, such a beta-lactam including penicillins (e.g. methicillin, oxacillin), a cephalosporin (e.g. ceftaroline, cefalexin and cefactor), a monobactam (e.g. aztreonanl) and a carbapenem (e.g. imipenem and entapenem); a macrolide (e.g. erythromycin, azithromycin), an aminoglycoside (e.g. gentamicin, tobramycin, amikacin), a glycopeptide (e.g., vancomycin, teicoplanin), oxazolidinones (e.g., linezolid and tedizolid), a fluoroquinolone (e.g., levofloxacin), ketolides (e.g., telithromycin), a lipopeptide, such as cyclic lipopeptides (e.g. daptomycin, mupirocin, and lysostaphin), a lincomycin (e.g., clindamycin), a tetracycline (e.g., tetracycline, doxycycline ) a sulfonamide (e.g. sulfamethoxazole), trimethoprim and combinations thereof, e.g. trimethoprim/sulfamethoxazole. In certain embodiments of all aspects of the disclosure, the antibiotic is daptomycin. In certain embodiments of all aspects of the disclosure, the antibiotic is vancomycin and daptomycin. In certain embodiments of all aspects of the disclosure, the antibiotic is oxacillin.

[00176] Combining PlySs2 and/or the modified lysin polypeptides of the present disclosure with antibiotics provides an efficacious antibacterial regimen. In some embodiments, co-administration of PlySs2 and/or the modified lysin polypeptides of the present disclosure with one or more antibiotics may be carried out at reduced doses and amounts of either PlySs2 and/or the modified lysin polypeptides or the antibiotic or both, and/or reduced frequency and/or duration of treatment with augmented bactericidal and bacteriostatic activity, reduced risk of antibiotic resistance and with reduced risk of deleterious neurological or renal side effects (such as those associated with colistin or polymyxin B use). As used herein the term “reduced dose” refers to the dose of one active ingredient in the combination compared to monotherapy with the same active ingredient. In some embodiments, the dose of PlySs2 and/or the modified lysin polypeptide or the antibiotic in a combination may be suboptimal or even subthreshold compared to the respective monotherapy.

[00177] In some embodiments, the present disclosure provides a method of augmenting antibiotic activity of one or more antibiotics against Gram-positive bacteria including multidrug-resistant Gram-positive bacteria as described herein compared to the activity of said antibiotics used alone by administering to a subject one or more modified lysin polypeptides and/or PlySs2 disclosed herein together with an antibiotic of interest. The combination is effective against the bacteria and permits resistance against the antibiotic to be overcome and/or the antibiotic to be employed at lower doses, decreasing undesirable side effects.

[00178] In some embodiments, the present disclosure provides any methods disclosed herein wherein:

(a) the PlySs2-type lysin, e.g. exebacase, is administered as a one-time intravenous infusion;

(b) the effective amount of the PlySs2-type lysin, e.g. exebacase, is 0.25 mg/kg administered as a one-time intravenous infusion;

(c) the effective amount of the PlySs2-type lysin, e.g. exebacase, is 18 mg administered as a one-time intravenous infusion;

(d) the patient has normal renal function (e.g., creatinine clearance [CrCl*] >60 mL/min) or mild renal impairment, and the effective amount of the PlySs2-type lysin, e.g. exebacase, is 18 mg administered as a one-time intravenous infusion;

(e) the patient has moderate or severe renal impairment (e.g., CrCl* of 15 to <60 mL/min), and the effective amount of the PlySs2-type lysin, e.g. exebacase, is 12 mg administered as a one-time intravenous infusion;

(f) the patient has end-stage renal disease (ESRD; e.g. CrCl* <15 mL/min) and/or is on hemodialysis, and the effective amount of the PlySs2-type lysin, e.g. exebacase, is 8 mg administered as a one-time intravenous infusion; or

(g) the patient is a child less than two years of age and the effective amount of the PlySs2- type lysin, e.g. exebacase, is 0.5 mg/kg to 1.5 mg/kg, e.g., about 1 mg/kg, administered as a one-time intravenous infusion.

[00179] The terms “infection” and “bacterial infection” are meant to include respiratory tract infections (RTIs), such as respiratory tract infections in patients having cystic fibrosis (CF), lower respiratory tract infections, such as acute exacerbation of chronic bronchitis (ACEB), acute sinusitis, community- acquired pneumonia (CAP), hospital- acquired pneumonia (HAP) and nosocomial respiratory tract infections; sexually transmitted diseases, such as gonococcal cervicitis and gonococcal urethritis; urinary tract infections; acute otitis media; sepsis including neonatal septisemia and catheter-related sepsis; and osteomyelitis including acute, chronic and haematogenous osteomyelitis. Infections caused by drug-resistant bacteria and multidrug-resistant bacteria are also contemplated.

[00180] Non- limiting examples of infections caused by Gram-positive bacterial may include: A) Nosocomial infections: 1. Respiratory tract infections especially in cystic fibrosis patients and mechanically-ventilated patients; 2. bacteremia and sepsis; 3. Wound infections, particularly those of burn victims; 4. Urinary tract infections; 5. Post-surgery infections on invasive devises; 6. Endocarditis including prosthetic valve endocarditis, cardiac device infection and right-sided endocarditis and endocarditis due to intravenous administration of contaminated drug solutions; 7. Infections in patients with acquired immunodeficiency syndrome, cancer chemotherapy, steroid therapy, hematological malignancies, organ transplantation, renal replacement therapy, and other conditions with severe neutropenia. B) Community- acquired infections: 1. Community- acquired respiratory tract infections; 2. Meningitis; 3. Folliculitis and infections of the ear canal caused by contaminated water; 4. Malignant otitis externa in the elderly and diabetics; 5. Osteomyelitis of the caleaneus in children; 6. Eye infections commonly associated with contaminated contact lens; 7. Skin infections such as nail infections in people whose hands are frequently exposed to water; 8. Gastrointestinal tract infections; and 9. Muscoskeletal system infections.

[00181] In other embodiments, the lysins of the present methods are used to treat a joint infection. Infected joints may include infected hip, knee, ankle, shoulder, elbow or wrist joints. Typically, the infected joint is a knee joint or a hip joint.

[00182] In some embodiments, the infected joint is a native joint. Infection of a native joint (also referred to herein as septic arthritis of a native joint) may occur when a penetrating injury, such as a puncture wound, occurs near or above a joint, allowing bacteria to directly enter the joint. In other embodiments, the joint infection occurs when bacteria from a distant infection spreads through the bloodstream to the native joint.

[00183] In other embodiments, the infected joint is a prosthetic joint, including, for example, septic arthritis of a prosthetic joint). The prosthetic joints may include hip, knee, shoulder, elbow, and ankle prostheses. Typically, the prosthetic joint is a prosthetic hip or knee. [00184] The one or more species of Gram-positive bacteria of the present methods may include any of the species of Gram-positive bacteria as described herein or known in the art. Typically, the species of Gram-positive bacteria may include Listeria monocytogenes, Staphylococcus aureus, coagulase negative staphylococci (including at least 40 recognized species including, but not limited to, the Staphylococcus epidermidis group, the Staphylococcus saprophyticus group, the Staphylococcus simulans group, the Staphylococcus intermedius group, the Staphylococcus sciuri group, the Staphylococcus hyicus group, and any isolates referred to as from the “unspecified species group”), Streptococcus suis, Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus pneumoniae, any additional species included in the viridans streptococci group (including, but not limited to, all species and strains included in the Streptococcus anginosis group, Streptococcus mitis group, Streptococcus sanguinis group, Streptococcus bovis (now gallolyticus ) group, Streptococcus salivarius group, and Streptococcus mutans group), Enterococcus faecalis, and Enterococcus faecium. Other examples of Gram-positive bacteria include but are not limited to the genera Actinomyces, Bacillus, Lactococcus, Mycobacterium, Corynebacterium, and Clostridium. [00185] In some embodiments of all aspects of the disclosure, co-administering the PlySs2 and/or the present modified lysin polypeptides and an antibiotic of interest may be used for the prevention, control, disruption, and treatment of bacterial biofilm formed by Gram positive bacteria. Biofilm formation occurs when microbial cells adhere to each other and are embedded in a matrix of extracellular polymeric substance (EPS) on a surface. The growth of microbes in such a protected environment that is enriched with biomacromolecules (e.g. polysaccharides, nucleic acids and proteins) and nutrients allow for enhanced microbial cross talk and increased virulence. Biofilm may develop in any supporting environment including living and nonliving surfaces such as the mucus plugs of the CF lung, contaminated catheters, implants, contact lenses, etc (Sharma et al. Biologicals, 42(1): 1-7 (2014), which is herein incorporated by reference in its entirety). Because biofilms protect the bacteria, they are often more resistant to traditional antimicrobial treatments, making them a serious health risk, which is evidenced by more than one million cases of catheter-associated urinary tract infections (CAUTI) reported each year, many of which can be attributed to biofilm-associated bacteria (Donlan, RM (2001) Emerg Infect DA7(2):277-281; Maki D and Tambyah P (2001) Emerg Infect Dis 7(2):342-347).

[00186] Thus, in one embodiment of all aspects of the disclosure, PlySs2 and/or the modified lysin polypeptides of the present disclosure are co-administered with an antibiotic of interest and used for the prevention, control, disruption, and treatment of bacterial infections due to Gram-positive bacteria when the Gram-positive bacteria are protected by a bacterial biofilm.

[00187] In some embodiments of all aspects of the disclosure, inhibiting the growth, or reducing the population, or killing at least one species of Gram-positive bacteria comprises contacting bacteria with PlySs2 and/or the modified lysin polypeptides as described herein and an antibiotic of interest, wherein the bacteria are present on a surface of e.g., medical devices, floors, stairs, walls and countertops in hospitals and other health related or public use buildings and surfaces of equipment in operating rooms, emergency rooms, hospital rooms, clinics, and bathrooms and the like.

[00188] Examples of medical devices that can be protected using PlySs2 and/or the modified lysin polypeptides described herein include but are not limited to tubing and other surface medical devices, such as urinary catheters, mucous extraction catheters, suction catheters, umbilical cannulae, contact lenses, intrauterine devices, intravaginal and intraintestinal devices, endotracheal tubes, bronchoscopes, dental prostheses and orthodontic devices, surgical instruments, dental instruments, tubings, dental water lines, fabrics, paper, indicator strips (e.g., paper indicator strips or plastic indicator strips), adhesives (e.g., hydrogel adhesives, hot-melt adhesives, or solvent-based adhesives), bandages, tissue dressings or healing devices and occlusive patches, and any other surface devices used in the medical field. The devices may include electrodes, external prostheses, fixation tapes, compression bandages, and monitors of various types. Medical devices can also include any device which can be placed at the insertion or implantation site such as the skin near the insertion or implantation site, and which can include at least one surface which is susceptible to colonization by Gram-positive bacteria.

[00189] In some embodiments and all aspects of the disclosure, inhibiting the growth, or reducing the population, or killing at least one species of Gram-positive bacteria comprises contacting bacteria with PlySs2 and/or the modified lysin polypeptides as described herein and optionally an antibiotic of interest, wherein the Gram-positive bacteria is a multidrug-resistant bacteria. In some embodiments, the Gram-positive bacteria is resistant to at least two antibiotics, such as at least three antibiotics, such as at least four antibiotics. In some embodiments, the Gram-positive bacteria comprises Staphylococcus aureus, such as MRSA or MSSA, typically MRSA. In some embodiments, the at least two, such as the at least three, such as the at least four antibiotics to which the Gram-positive bacteria are resistant are selected from two or more, such as three or more, such as four or more of a beta-lactam including penicillins (e.g. methicillin, oxacillin), a cephalosporin (e.g. ceftaroline, cefalexin and cefactor), a monobactam (e.g. aztreonanl) and a carbapenem (e.g. imipenem and entapenem); a macrolide (e.g. erythromycin, azithromycin), an aminoglycoside (e.g. gentamicin, tobramycin, amikacin), a glycopeptide (e.g., vancomycin, teicoplanin), oxazolidinones (e.g., linezolid and tedizolid), a fluoroquinolone (e.g., levofloxacin), ketolides (e.g., telithromycin), a lipopeptide, such as cyclic lipopeptides (e.g. daptomycin, mupirocin, and lysostaphin), a lincomycin (e.g., clindamycin), a tetracycline (e.g., tetracycline, doxycycline ) a sulfonamide (e.g. sulfamethoxazole), trimethoprim and combinations thereof, e.g. trimethoprim/sulfamethoxazole.

Dosage and Administration

[00190] Dosages administered depend on a number of factors such as the activity of infection being treated; the age, health and general physical condition of the subject to be treated; the activity of PlySs2 or a particular modified lysin polypeptide; the nature and activity of the antibiotic if any with which a PlySs2 or a modified lysin polypeptide according to the present disclosure is being paired; and the combined effect of such pairing. In certain embodiments, effective amounts of the PlySs2 or the modified lysin polypeptide to be administered may fall within the range of about 0.1-100 mg/kg (or 1 to 100 mcg/ml), such as from 0.5 mg/kg to 30 mg/kg. In certain embodiments, the PlySs2 or the modified lysin polypeptide may be administered 1-4 times daily for a period ranging from 1 to 14 days. The antibiotic, if one is also used, may be administered at standard dosing regimens or in lower amounts in view of any synergism. All such dosages and regimens, however, (whether of PlySs2, the modified lysin polypeptide or any antibiotic administered in conjunction therewith) are subject to optimization. Optimal dosages can be determined by performing in vitro and in vivo pilot efficacy experiments as is within the skill of the art but taking the present disclosure into account.

[00191] It is contemplated that PlySs2 and/or the modified lysin polypeptides disclosed herein may provide a rapid bactericidal and, when used in sub-MIC amounts, may provide a bacteriostatic effect. It is further contemplated that PlySs2 and/or the modified lysin polypeptides disclosed herein may be active against a range of antibiotic -resistant bacteria or multidrug resistant bacteria. Based on the present disclosure, in a clinical setting, PlySs2 and the present modified lysin polypeptides may be a potent alternative (or additive) for treating infections arising from drug- and multidrug-resistant bacteria alone or together with antibiotics (including antibiotics to which resistance has developed).

[00192] In some embodiments, time exposure to PlySs2 and/or the modified lysin polypeptides disclosed herein may influence the desired concentration of active polypeptide units per ml. Carriers that are classified as “long” or “slow” release carriers (such as, for example, certain nasal sprays or lozenges) may possess or provide a lower concentration of polypeptide units per ml but over a longer period of time, whereas a “short” or “fast” release carrier (such as, for example, a gargle) may possess or provide a high concentration of polypeptide units (meg) per ml but over a shorter period of time. There are circumstances where it may be desirable to have a higher unit/ml dosage or a lower unit/ml dosage.

[00193] For the wild-type PlySs2 or the modified lysin polypeptides of the present disclosure, the therapeutically effective dose may be estimated initially either in cell culture assays or in animal models, usually mice, rabbits, dogs, or pigs. The animal model can also be used to achieve a desirable concentration range and route of administration· Obtained information can then be used to determine the effective doses, as well as routes of administration, in humans. Dosage and administration can be further adjusted to provide sufficient levels of the active ingredient or to maintain the desired effect. Additional factors that may be taken into account include the severity of the disease state; age, weight and gender of the patient; diet; desired duration of treatment; method of administration; time and frequency of administration; drug combinations; reaction sensitivities; tolerance/response to therapy; and the judgment of a treating physician.

[00194] A treatment regimen can entail daily administration (e.g. , once, twice, thrice, etc. daily), every other day (e.g., once, twice, thrice, etc. every other day), semi- weekly, weekly, once every two weeks, once a month, etc. In one embodiment, treatment can be given as a continuous infusion. Unit doses can be administered on multiple occasions. Intervals can also be irregular as indicated by monitoring clinical symptoms. Alternatively, the unit dose can be administered as a sustained release formulation, in which case less frequent administration may be used. Dosage and frequency may vary depending on the patient. It will be understood by one of skill in the art that such guidelines will be adjusted for localized administration, e.g., intranasal, inhalation, rectal, etc., or for systemic administration, e.g., oral, rectal (e.g., via enema), intramuscular (i.m.), intraperitoneal (i.p.), intravenous (i.v.), subcutaneous (s.c.), transurethral, and the like.The PlySs2 or the modified lysin polypeptides described herein and their preparation, characterization, and use will be better understood in connection with the following examples, which are intended as an illustration of and not a limitation upon the scope of the present disclosure.

[00195] The present disclosure is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described herein will become apparent to those skilled in the art from the foregoing description. All patents, applications, publications, test methods, literature, and other materials cited herein are hereby incorporated by reference.

EXAMPLE 1. MATERIALS AND METHODS

IA. Bacterial Isolates

[00196] The in vitro activity of PlySs2 and 12 comparator antibiotics, i.e., ceftaroline, clindamycin, daptomycin, doxycycline, erythromycin, gentamicin, levofloxacin, linezolid, oxacillin, tetracycline, trimethoprim/sulfamethoxazole and vancomycin, were evaluated against Staphylococcus aureus isolates recovered from the blood of bacteremia patients (3% with infective endocarditis). The patients were hospitalized during 2020 in 29 U.S. medical centers located in 9 Census regions (20 states) as part of the SENTRY Antimicrobial Surveillance Program. A total of 2,849 pathogens (1 patient infection episode) were consecutively recovered from blood cultures of the patients. Among the 2,849 pathogens, 666 (23.4%) were identified as S. aureus isolates (FIG. 1). The isolates were confirmed at the species level using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF, Bruker Daltonics, Inc., Bremen, Germany). 38.6% of the S. aureus isolates were MRSA isolates (FIG. 2). Twenty (20) of the S. aureus isolates were the causative pathogen in those patients with infective endocarditis, eight of which were MRSA.

IB. Susceptibility Testing

[00197] Minimal inhibitory concentrations (MICs) of PlySs2 against Staphylococcus aureus were determined by broth microdilution (BMD) using a nonstandard antimicrobial susceptibility testing (AST) medium comprised of cation-adjusted Mueller Hinton broth (caMHB) supplemented with donor herd horse serum and DL-dithiothreitol to final concentrations of 25% and 0.5 mM, respectively. This medium, referred to as caMHB-HSD, is approved for use with PlySs2 by the Clinical and Laboratory Standards Institute (CLSI). See Performance Standards for Antimicrobial Susceptibility Testing, 31st Edition. CLSI guideline M100. Wayne, PA: Clinical and Laboratory Standards Institute; 2021).

[00198] Frozen-form broth microdilution panels containing cation-adjusted Mueller- Hinton broth (CA-MHB)) for the 12 comparator antibiotics were manufactured (JMO Laboratories (North Liberty, IA)). The comparator antibiotics were tested following the reference BMD method for each. (Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria that Grow Aerobically. 11^th Edition. CLSI guideline M07. Wayne, PA: Clinical and Laboratory Standards Institute; 2018). CLSI M100 (2021) criteria were used for categorical MIC interpretations of the comparator agents. Quality assurance was performed by sterility checks, colony counts, and testing of CLSI-recornmended quality control reference strains.

1C. Multidrug-Resistance determination

[00199] MRS A isolates were defined as methicillin-resistant based on an oxacillin- resistant phenotype. Such isolates are usually defined as multidrug-resistant (MDR) using standard phenotypic classifications. Here, the MRSA isolates were further characterized as MDR, when, in addition to oxacillin, the non-susceptible phenotypes were observed for two or more of ceftaroline, clindamycin, daptomycin, doxycycline, erythromycin, gentamicin, levofloxacin, linezolid, trimethoprim/sulfamethoxazole and/or vancomycin.

EXAMPLE 2. RESULTS

[00200] As shown in FIG. 1, the predominant causative pathogen of blood stream infections (BSI) in U.S. hospitals during the last five years of surveillance was Staphylococcus aureus (24.2%). The annual prevalence of MRSA among all organisms responsible for BSI remained between 9% and 11% (FIG. 1). The second most common species was Escherichia coli (20.8%), followed by Klebsiella pneumonia (8.7%), coagulase-negative staphylococci (6.6%) and other pathogens (5.5% or less). Data not shown. The annual occurrence of a methicillin-resistant phenotype among Staphylococcus aureus was between 43.1% and 38.6% (FIG. 2).

[00201] COVID-19 appeared to have minimal impact on the etiology of blood stream infections in the United States, as Staphylococcus aureus continued to represent the main pathogen responsible for blood stream infections during the SENTRY Antimicrobial Surveillance Program for 2020. Similar to the previous 4 years, Staphylococcus aureus accounted for approximately 25% of all pathogens recovered from blood specimens, although the occurrence of a methicillin-resistant phenotype within Staphylococcus aureus causing blood stream infections in the United States were slightly lower in 2020 (38.6%) compared to the previous 4 years (39.5-43.1%).

[00202] As shown below in Tables 1 and 2, PlySs2 inhibited all Staphylococcus aureus isolates at MIC values of < 1 pg/mL (MIC range 0.06-1 pg/mL). MICso, MIC90 and modal MIC values were 0.5 pg/mL. MIC50/90 values against methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) were 0.5/0.5 pg/mL. Accordingly, the PlySs2 in vitro activity was uniform when tested against Staphylococcus aureus clinical isolates responsible for BSI, including infective endocarditis, isolated from patients in the United States in 2020. Further, the PlySs2 activity was consistent, regardless of resistance phenotype (MSSA, MRSA, including MDR isolates).

[00203] As shown in Table 3, while most of the comparators were active against MSSA (91.7%-100% susceptible), many comparators exhibited reduced susceptibility against MRSA, including ceftaroline (88.3% susceptible). However, among the drugs that are indicated for treating Staphylococcus aureus bacteremia due to MRSA, daptomycin and vancomycin were active against all isolates (100% susceptible). Tables 1 and 3.

[00204] In addition, a total of 62.3% of all MRSA isolates were categorized as MDR isolates. PlySs2 demonstrated equal MIC₅₀ and MIC₉₀ results against the MDR isolates (MIC_50/90, 0.5/0.5 pg/mL) and non-MDR isolates (0.5/0.5 pg/mL). Daptomycin and vancomycin also were active (100% susceptible) against MDR MRSA isolates. Tables 1 and 3.

[00205] Accordingly, the data presented here support the use of PlySs2 for the treatment of bacterial infections, such as bacteremia and infective endocarditis, including those caused by multidrug-resistant MRSA isolates.

Table 1

MIC50/MIC90 in mg/L (% susceptible by CLSI

S. aureusfPhenotype Ml 00 criteria) (No. tested)

CF-301 VAN DAP

All (666) 0.5/0.5 (-) 1/1 (100) 0.25/0.5 (100)

Table 2. MIC distribution of exebacase against S. aureus isolated from patients with BSI, including IE, in U.S. hospitals in 2020.

No. and cumulative % of isolates inhibited at MIC ^g/mL)

S. aureus / of:

Subset (no. of isolates) - MIC50 MIC90

<0.03 0.06 0.12 0.25 0.5 1 2

1 0 43 577 45

All^a (666) 0.5 0.5

0.2 0.2 6.6 93.2 100.0

0 29 352 28

Methicillin-susceptible (409) 0.5 0.5

0.0 7.1 93.2 100.0

1 0 14 225 17 Methicillin-resistant (257) 0.5 0.5

0.4 0.4 5.8 93.4 100.0

1 0 10 137 12 MDR (160) 0.5 0.5

(0.6) (0.6) (6.9) (92.5) (100.0)

4 88 5

Non-MDR (97) 0.5 0.5

(4.1) (94.8) (100.0)

Isolates were defined as methicillin-resistant based on an oxacillin resistance phenotype. A multi-drug resistance (MDR) phenotype was defined among methecillin-resistant Staphylococcus aureus (MRSA) isolates when non-susceptible phenotypes were observed for oxacillin and 2 or more of the following agents: ceftarolne, erythromycin, clindamycin, doxycycline, levofloxacin, gentamicin, linezolid, trimethoprim-sulfamethoxazole, daptomycin and vancomycin.

Table 3. Antimicrobial activity of exebacase and comparator agents against S. aureus isolated from patients with BSI, including IE, in U.S. hospitals in 2020

Antimicrobial agent CLSP

MIC50 MIC90 MIC range %S^C %\ %R

All^b (666)

Execabase 0.5 0.5 0.06 to 1

Erythromycin 8 >8 <_0.06 to >8 46.8 2.3 50.9

Levofloxacin 0.25 >4 <_0.06 to >4 69.5 0.6 29.9

Oxacillin 0.5 >8 0.12 to >8 61.4 - 38.6

Clindamycin 0.06 >2 < 0.03 to >2 87.4 0.2 12.5

Ceftaroline 0.25 1 <_0.06 to 2 95.5 4.5^d 0.0

Daptomycin 0.25 0.5 <_.0.12 to 1 100.0

Doxycycline <^0.06 0.5 < 0.06 to >8 98.2 1.5 0.3

Gentamicin <_1 <_1 <_1 to >8 98.0 0.2 1.8

Linezolid 1 2 <_.0.12 to 4 100.0 0.0

Trimethoprim- sulfamethoxazole <_0.5 <_0.5 <_0.5 to >16 97.9 - 2.1 Vancomycin 1 1 0.25 to 2 100.0 0.0 0.0 MSSA^e (409)

Execabase 0.5 0.5 0.25 to 1

Erythromycin 0.25 >8 <_0.06 to >8 67.2 3.2 29.6

Levofloxacin 0.25 0.5 <_0.06 to >4 91.7 0.2 8.1

Oxacillin 0.5 1 0.12 to 2 100.0 0.0

Clindamycin 0.06 0.12 < 0.03 to >2 95.8 0.0 4.2

Ceftaroline 0.25 0.5 < 0.06 to 1 100.0 0.0 0.0

Daptomycin 0.25 0.5 <_.0.12 to 1 100.0

Doxycycline <_0.06 0.12 <_0.06 to >8 99.5 0.2 0.2

Gentamicin <_1 <_1 <_1 to >8 98.5 0.0 1.5

Linezolid 1 2 < 0.12 to 4 100.0 0.0

Trimethoprim- sulfamethoxazole <_0.5 <_0.5 <_0.5 to >16 99.8 0.2 Vancomycin 1 1 0.25 to 2 100.0 0.0 0.0 MRSA^e (257)

Execabase 0.5 0.5 0.06 to 1

Erythromycin >8 >8 < 0.06 to >8 14.4 0.8 84.8

Levofloxacin 4 >4 <_0.06 to >4 34.2 1.2 65.6

Oxacillin >8 >8 4 to >8 0.0 100.0

Clindamycin 0.06 >2 < 0.03 to >2 73.9 0.4 25.7

Ceftaroline 1 2 0.12 to 2 88.3 11.7^d 0.0

Daptomycin 0.25 0.5 < 0.12 to 1 100.0

Doxycycline <_0.06 1 <_0.06 to >8 96.1 3.5 0.4

Gentamicin <_1 <1 <_1 to >8 97.3 0.4 2.3

Linezolid 1 2 < 0.12 to 2 100.0 0.0

Trimethoprim- sulfamethoxazole <_0.5 <_0.5 <_0.5 to >16 94.9 5.1 Vancomycin 1 1 0.5 to 2 100.0 0.0 0.0 MDR^e (160)

Execabase 0.5 0.5 0.06 to 1

Erythromycin >8 >8 0.25 to >8 1.9 0.6 97.5

Levofloxacin >4 >4 0.25 to >4 3.1 1.9 95.0

Oxacillin >8 >8 8 to >8 0.0 100.0

Clindamycin 0.06 >2 < 0.03 to >2 58.1 0.6 41.2

Ceftaroline 1 2 0.25 to 2 81.2 18.8^d 0.0

Daptomycin 0.25 0.5 < 0.12 to 0.5 100.0

Doxycycline <_0.06 1 <_0.06 to >8 94.4 5.0 0.6

Gentamicin <_1 <1 <_1 to >8 96.2 0.6 3.1

Linezolid 1 2 0.25 to 2 100.0 0.0

Trimethoprim- sulfamethoxazole <_0.5 <_0.5 < 0.5 to >16 91.9 8.1

Vancomycin 1 1 0.5 to 2 100.0 0.0 0.0 aCriteria as published by CLSI (2021); breakpoint not available. b Data for tetracycline not shown c “S” sensitive; “I” intermediate; “R” resistant d Intermediate may be interpreted as susceptible-dose dependent. e Isolates were defined as methicillin-resistant based on an oxacillin resistance phenotype. Multi-drug resistance (MDR) phenotype was defined among MRS A isolates when non-susceptible phenotypes were observed for oxacillin and 2 or more of the following agents: ceftaroline, erythromycin, clindamycin, doxycycline, levofloxacin, gentamicin, linezolid, trimethoprim-sulfamethoxazole, daptomycin and vancomycin.

Claims

CLAIMS We claim:

1. A method of inhibiting the growth, reducing the population, or killing multidrug- resistant Gram-positive bacteria, the method comprising contacting the multidrug-resistant Gram-positive bacteria with a lysin polypeptide comprising the amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 18 or a variant thereof having at least 80% identity to SEQ ID NO: 1 or SEQ ID NO: 18, wherein the variant inhibits the growth, reduces the population, or kills the multidrug-resistant Gram-positive bacteria, wherein the multidrug-resistant Gram-positive bacteria are resistant and/or non-susceptible to at least three antibiotics, wherein each antibiotic is from a different antibiotic class.

2. A method of preventing or treating a bacterial infection caused by a multidrug-resistant Gram-positive bacteria, the method comprising administering a therapeutically effective amount of a lysin polypeptide to a subject comprising the amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 18 or a variant thereof having at least 80% identity to SEQ ID NO: 2 or SEQ ID NO: 18, wherein the variant inhibits the growth, reduces the population, or kills the multidrug-resistant Gram-positive bacteria, wherein the multidrug-resistant Gram-positive bacteria are resistant and/or non-susceptible to at least three antibiotics, wherein each antibiotic is from a different antibiotic class.

3. The method of claim 1 or claim 2, wherein the variant of SEQ ID NO: 1 or SEQ ID NO: 18 comprises at least one amino acid substitution as compared to a lysin polypeptide having the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO: 18, a cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domain, and a cell wall binding (SH3b) domain, wherein the at least one amino acid substitution is in the CHAP domain and/or the SH3b domain, and wherein the variant inhibits the growth, reduces the population, or kills the Gram-positive bacteria.

4. The method of claim 1 , wherein the method further comprises contacting the bacteria with one or more antibiotic(s).

5. The method of any one of claims 2 or 3, wherein the method further comprises co administering one or more antibiotic(s) to the subject.

6. The method of any one of claims 3-5, wherein the at least one amino acid substitution comprises L92W, V104S, V128T, Y137S, Y164K, N184D, and S198Q.

7. The method of any one of claims 3-6, wherein the variant comprises the amino acid sequence of SEQ ID NO: 6.

8. The method of any one of claims 4 or 5, wherein the one or more antibiotic(s) comprises a beta-lactam antibiotic including penicillins (e.g. methicillin, oxacillin), a cephalosporin (e.g. ceftaroline, cefalexin and cefactor), a monobactam (e.g. aztreonanl) a carbapenem (e.g. imipenem and entapenem); a macrolide (e.g. erythromycin, azithromycin), an aminoglycoside (e.g. gentamicin, tobramycin, amikacin), a ketolide (e.g., telithromycin), a glycopeptide (e.g., vancomycin, teicoplanin), oxazolidinones (e.g., linezolid and tedizolid), a fluoroquinolone (e.g., levofloxacin), a lipopeptide, such as cyclic lipopeptides (e.g. daptomycin, mupirocin), a lincomycin (e.g., clindamycin), a tetracycline (e.g., tetracycline, doxycycline ), a sulfonamide (e.g. sulfamethoxazole), trimethoprim and combinations thereof (e.g. trimethoprim/sulfamethoxazole) .

9. The method of any one of claims 4 or 5, wherein the antibiotic is vancomycin, daptomycin or oxacillin.

10. The method of any one of claims 1-9, wherein the lysin polypeptide or the variant thereof is administered in an amount corresponding to a concentration below the minimal inhibitory concentration (MIC) of the lysin polypeptide or variant thereof.

11. The method of any one of claims 4-10, wherein the antibiotic is administered in an amount corresponding to a concentration below the minimal inhibitory concentration (MIC) of the antibiotic.

12. The method of any one of the preceding claims, wherein the multidrug-resistant Gram positive bacteria comprise Staphylococcus aureus.

13. The method of any one of the preceding claims, wherein the multidrug-resistant bacteria comprise methicillin-resistant Staphylococcus aureus or methicillin-sensitive Staphylococcus aureus.

14. The method of any one of the preceding claims, wherein the multidrug-resistant bacteria comprise methicillin-resistant Staphylococcus aureus.

15. The method of any one of the preceding claims, wherein the multidrug-resistant bacteria are resistant and/or non-susceptible to at least three antibiotics each selected from different antibiotic class, selected from a beta-lactam, a cephalosporin, a monobactam, a carbapenem, a macrolide, an aminoglycoside, a glycopeptide, an oxazolidinone, a fluoroquinolone, a ketolide, a lipopeptide, a lincomycin, a tetracycline, a sulfonamide, a trimethoprim and sulfonamide/trimethoprim.

16. The method of any one of the preceding claims, wherein the multidrug-resistant bacteria are resistant and/or non-susceptible to at least three antibiotics selected from ceftaroline, clindamycin, daptomycin, doxycycline, erythromycin, gentamicin, levofloxacin, linezolid, trimethoprim/sulfamethoxazole and/or vancomycin.

17. The method of claim 15, wherein the at least three antibiotic classes are in addition to a beta-lactam antibiotic, such as oxacillin.

18. The method of any one of claims 2-18, wherein the bacterial infection comprises bacteremia and/or infective endocarditis.

19. The method of any one of claims 1-14 or 18, wherein the multidrug-resistant Gram positive bacteria are resistant and/or non-susceptible to at least three antibiotics, wherein each antibiotic is from a different class selected from a macrolide, an aminoglycoside, a glycopeptide, an oxazolidinone, a fluoroquinolone, a ketolide, a lipopeptide, a lincomycin, a tetracycline, a sulfonamide, a trimethoprim and sulfonamide/trimethoprim.

20. The method of any one of claims 1-14 or 18, wherein the multidrug-resistant Gram positive bacteria are resistant and/or non-susceptible to at least three antibiotics, wherein each antibiotic is from a different class selected from a macrolide, an aminoglycoside, a fluoroquinolone, a ketolide, a lincomycin, a tetracycline, a sulfonamide, a trimethoprim and sulfonamide/trimethoprim.

21. A method of inhibiting the growth, reducing the population, or killing multidrug- resistant Gram-positive bacteria, the method comprising contacting the multidrug-resistant Gram-positive bacteria with a lysin polypeptide comprising the amino acid sequence of SEQ ID NO: 18, wherein the multidrug -resistant Gram-positive bacteria are resistant to methicillin and/or oxacillin and are non-susceptible to at least two antibiotics selected from a cephalosporin (e.g. ceftaroline, cefalexin and cefactor), a monobactam (e.g. aztreonanl) a carbapenem (e.g. imipenem and entapenem); an aminoglycoside (e.g. gentamicin, tobramycin, amikacin), a ketolide (e.g., telithromycin), a fluoroquinolone (e.g., levofloxacin), a lincomycin (e.g., clindamycin), a tetracycline (e.g., tetracycline, doxycycline ), a sulfonamide (e.g. sulfamethoxazole), trimethoprim and combinations thereof (e.g. trimethoprim/sulfamethoxazole) .

22. Any of the foregoing methods, wherein the lysin polypeptide is administered or formulated as a one-time intravenous infusion in an effective amount of 18mg, 12mg or 8mg.