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Sharifi F, Montaseri M, Yousefi MH, Shekarforoush SS, Berizi E, Wagemans J, Vallino M, Hosseinzadeh S. Isolation and characterization of two Staphylococcus aureus lytic bacteriophages "Huma" and "Simurgh". Virology 2024; 595:110090. [PMID: 38718447 DOI: 10.1016/j.virol.2024.110090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/07/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
Abstract
Nowadays finding the new antimicrobials is necessary due to the emerging of multidrug resistant strains. The present study aimed to isolate and characterize bacteriophages against S. aureus. Strains Huma and Simurgh were the two podovirus morphology phages which isolated and then characterized. Huma and Simurgh had a genome size of 16,853 and 17,245 bp, respectively and both were Rosenblumvirus with G + C content of 29%. No lysogeny-related genes, nor virulence genes were identified in their genomes. They were lytic only against two out of four S. aureus strains. They also were able to inhibit S. aureus for 8 h in-vitro. Both showed a rapid adsorption. Huma and Simurgh had the latent period of 80 and 60 m and the burst sizes of 45 and 40 PFU/ml and also, they showed very low cell toxicity of 1.23%-1.79% on HT-29 cells, respectively. Thus, they can be considered potential candidates for biocontrol applications.
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Affiliation(s)
- Fatemeh Sharifi
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Maryam Montaseri
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Mohammad Hashem Yousefi
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Seyed Shahram Shekarforoush
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Enayat Berizi
- Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Marta Vallino
- Institute of Sustainable Plant Protection, National Research Council of Italy, 10135, Turin, Italy
| | - Saeid Hosseinzadeh
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran.
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2
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Lossouarn J, Beurrier E, Bouteau A, Moncaut E, Sir Silmane M, Portalier H, Zouari A, Cattoir V, Serror P, Petit MA. The virtue of training: extending phage host spectra against vancomycin-resistant Enterococcus faecium strains using the Appelmans method. Antimicrob Agents Chemother 2024; 68:e0143923. [PMID: 38591854 PMCID: PMC11210271 DOI: 10.1128/aac.01439-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/14/2024] [Indexed: 04/10/2024] Open
Abstract
Phage therapy has (re)emerged as a serious possibility for combating multidrug-resistant bacterial infections, including those caused by vancomycin-resistant Enterococcus faecium strains. These opportunistic pathogens belong to a specific clonal complex 17, against which relatively few phages have been screened. We isolated a collection of 21 virulent phages growing on these vancomycin-resistant isolates. Each of these phages harbored a typical narrow plaquing host range, lysing at most 5 strains and covering together 10 strains of our panel of 14 clinical isolates. To enlarge the host spectrum of our phages, the Appelmans protocol was used. We mixed four out of our most complementary phages in a cocktail that we iteratively grew on eight naive strains from our panel, of which six were initially refractory to at least three of the combined phages. Fifteen successive passages permitted to significantly improve the lytic activity of the cocktail, from which phages with extended host ranges within the E. faecium species could be isolated. A single evolved phage able to kill up to 10 of the 14 initial E. faecium strains was obtained, and it barely infected nearby species. All evolved phages had acquired point mutations or a recombination event in the tail fiber genetic region, suggesting these genes might have driven phage evolution by contributing to their extended host spectra.
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Affiliation(s)
- Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Elsa Beurrier
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Astrid Bouteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Elisabeth Moncaut
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Maria Sir Silmane
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Heïdi Portalier
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Asma Zouari
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière et CNR de la Résistance aux Antibiotiques (laboratoire associé "Entérocoques"), Rennes, France
| | - Vincent Cattoir
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière et CNR de la Résistance aux Antibiotiques (laboratoire associé "Entérocoques"), Rennes, France
- Université de Rennes, INSERM, UMR_S1230 BRM, Rennes, France
| | - Pascale Serror
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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3
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Wang R, Yeh YJ, An YN, Virly. Engineering pH-sensitive erodible chitosan hydrogel composite containing bacteriophage: An interplay between hydrogel and bacteriophage against Staphylococcus aureus. Int J Biol Macromol 2023; 253:127371. [PMID: 37827407 DOI: 10.1016/j.ijbiomac.2023.127371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/25/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
Encapsulation of phages represents a key approach for improving phage stability and controlling phage delivery dosage. The hydrogel made from positively charged quaternized chitosan (QCS) and multivalent crosslinker, aldehyde-modified poly(xylitol sebacate)-co-poly(ethylene glycol) (APP) was introduced for the first time for drug (phage 44AHJD) delivery. The freeze-thawing (FT) treatment enhanced the porous structure and the stress resistance of native hydrogel with increased compression stress (stiffness) from 10 to 20 kPa. The stiffness of the phage-loaded hydrogel (FTP) was suitable for the proper release of phage particles and polymer chains, both working synergistically against bacterial growth. The FTP followed the Korsmeyer-Peppas model's anomalous diffusion of phage particles at different temperatures (30-45 °C) and pH (6.6-8.5) conditions. FTP was sensitive to pH, which released more phage particles at pH-neutral conditions, while the release under acidic and alkaline conditions was more based on gel degradation. The high biocompatibility of FTP hydrogel at its working concentration of 30 mg mL-1 was demonstrated through a hemolysis ratio of <2 %. Sixty percent of the total encapsulated phages and 6 mg mL-1 of hydrogel debris were released after 10 h of hydrogel submerge treatment, which can fight the growing bacteria and the emergence of phage-resistant bacteria.
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Affiliation(s)
- Reuben Wang
- Institute of Food Safety and Health, National Taiwan University, Taipei City, Taiwan; Master of Public Health (MPH) Program, National Taiwan University, Taipei City, Taiwan; GIP-TRIAD Master's Degree in Agro-Biomedical Science, National Taiwan University, Taipei City, Taiwan.
| | - Yu-Jia Yeh
- Institute of Food Safety and Health, National Taiwan University, Taipei City, Taiwan
| | - Yu-Ning An
- Institute of Food Safety and Health, National Taiwan University, Taipei City, Taiwan
| | - Virly
- Global Health Program, College of Public Health, National Taiwan University, Taipei City, Taiwan; Department of Food Technology, Faculty of Agricultural Technology, Widya Mandala Surabaya Catholic University, Surabaya, Indonesia
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4
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Manoharadas S, Al-Rayes BF, Almuzaini MAM, Almohammadi YM. Resensitisation of Methicillin-Resistant Staphylococcus aureus to Conventional Antibiotics in the Presence of an Engineered Enzybiotic. Pharmaceutics 2023; 15:2511. [PMID: 37896271 PMCID: PMC10610342 DOI: 10.3390/pharmaceutics15102511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most dreadful pathogens relevant in community and nosocomial-related infections around the world. Resensitising MRSA to antibiotics, once it became resistant, was a tough choice due to the high adaptability of this bacteria to savage conditions. This study aimed to create a chimeric enzybiotic against MRSA and test its efficiency, either individually or in combination with antibiotics. The novel enzybiotic BAC100 was constructed by fusing the catalytic domain from the bacteriocin BacL1 from Enterococcus faecalis with the cell-wall-binding domain from protein P17 of Staphylococcus aureus bacteriophage ϕ44AHJD. Apart from its partial lone activity, BAC100 was found to resensitise the MRSA strain to traditional antibiotics, including ampicillin and tetracycline. Both drugs were able to reduce live MRSA cells by 85 and 90%, respectively, within 60 min of treatment together with BAC100. However, no significant activity was observed against MRSA when these drugs were tested independently, pointing to the inherent resistance of MRSA against these conventional antibiotics. To our knowledge, this is one of the first instances where an engineered enzybiotic was found to resensitise MRSA to conventional antibiotics. This study will pave the way for the development of similar peptides that can be used together with antibiotics against gruesome pathogens of clinical importance.
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Affiliation(s)
- Salim Manoharadas
- Central Laboratory, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia; (B.F.A.-R.); (M.A.M.A.); (Y.M.A.)
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Manoharadas S, Ahmad N, Altaf M, Alrefaei AF, Al-Rayes BF. An Enzybiotic Cocktail Effectively Disrupts Preformed Dual Biofilm of Staphylococcus aureus and Enterococcus faecalis. Pharmaceuticals (Basel) 2023; 16:ph16040564. [PMID: 37111322 PMCID: PMC10145859 DOI: 10.3390/ph16040564] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/05/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Multidrug-resistant bacterial infections are on the rise around the world. Chronic infections caused by these pathogens through biofilm mediation often complicate the situation. In natural settings, biofilms are often formed with different species of bacteria existing synergistically or antagonistically. Biofilms on diabetic foot ulcers are formed predominantly by two opportunistic pathogens, Staphylococcus aureus and Enterococcus faecalis. Bacteriophages and phage-based proteins, including endolysins, have been found to be active against biofilms. In this study, we evaluated the activity of two engineered enzybiotics either by themselves or as a combination against a dual biofilm formed by S. aureus and E. faecalis in an inert glass surface. An additive effect in rapidly disrupting the preformed dual biofilm was observed with the cocktail of proteins, in comparison with mono treatment. The cocktail-treated biofilms were dispersed by more than 90% within 3 h of treatment. Apart from biofilm disruption, bacterial cells embedded in the biofilm matrix were also effectively reduced by more than 90% within 3 h of treatment. This is the first instance where a cocktail of engineered enzybiotics has been effectively used to impede the structural integrity of a dual biofilm.
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Affiliation(s)
- Salim Manoharadas
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia
- Central Laboratory RM 63AA, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia
| | - Naushad Ahmad
- Central Laboratory RM 63AA, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia
| | - Mohammad Altaf
- Central Laboratory RM 63AA, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia
| | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia
| | - Basel F Al-Rayes
- Central Laboratory RM 63AA, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia
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Hawkins NC, Kizziah JL, Hatoum-Aslan A, Dokland T. Structure and host specificity of Staphylococcus epidermidis bacteriophage Andhra. SCIENCE ADVANCES 2022; 8:eade0459. [PMID: 36449623 PMCID: PMC9710869 DOI: 10.1126/sciadv.ade0459] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/14/2022] [Indexed: 05/28/2023]
Abstract
Staphylococcus epidermidis is an opportunistic pathogen of the human skin, often associated with infections of implanted medical devices. Staphylococcal picoviruses are a group of strictly lytic, short-tailed bacteriophages with compact genomes that are attractive candidates for therapeutic use. Here, we report the structure of the complete virion of S. epidermidis-infecting phage Andhra, determined using high-resolution cryo-electron microscopy, allowing atomic modeling of 11 capsid and tail proteins. The capsid is a T = 4 icosahedron containing a unique stabilizing capsid lining protein. The tail includes 12 trimers of a unique receptor binding protein (RBP), a lytic protein that also serves to anchor the RBPs to the tail stem, and a hexameric tail knob that acts as a gatekeeper for DNA ejection. Using structure prediction with AlphaFold, we identified the two proteins that comprise the tail tip heterooctamer. Our findings elucidate critical features for virion assembly, host recognition, and penetration.
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Affiliation(s)
- N’Toia C. Hawkins
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - James L. Kizziah
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Asma Hatoum-Aslan
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Terje Dokland
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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7
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Samir S, El-Far A, Okasha H, Mahdy R, Samir F, Nasr S. Isolation and characterization of lytic bacteriophages from sewage at an egyptian tertiary care hospital against methicillin-resistant Staphylococcus aureus clinical isolates. Saudi J Biol Sci 2022; 29:3097-3106. [PMID: 35360502 PMCID: PMC8961222 DOI: 10.1016/j.sjbs.2022.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 01/25/2022] [Accepted: 03/15/2022] [Indexed: 12/03/2022] Open
Abstract
Background Methicillin resistant Staphylococcus aureus (MRSA) is a pathogen to humans causing life-threatening infections. MRSA have the capability to grow resistance to many antibiotics, and phage therapy is one treatment option for this infection. Objectives The aim of the present study was to isolate and characterize the lytic bacteriophages specific to MRSA from domestic sewage water at a tertiary care hospital in Egypt. Methods Thirty MRSA strains were isolated from different clinical samples admitted to the microbiology lab at Theodor Bilharz Research institute (TBRI) hospital, Giza, Egypt. They were confirmed to be MRSA through phenotypic detection and conventional PCR for mecA gene. They were used for the isolation of phages from sewage water of TBRI hospital. Plaque assay was applied to purify and quantify the titer of the isolated phages. The host range of the isolated phages was detected using the spot test assay. The morphology of phages was confirmed using transmission electron microscope (TEM). Digestion of DNA extracted from phages with endonuclease enzymes including EcoRI and SmaI was performed. SDS-PAGE was performed to analyze MRSA specific phage proteins. As a positive control prophages were isolated from a mitomycin C (MitC) treated culture of S. aureus strain ATCC25923. Further characterization using conventional polymerase chain reaction (PCR) was used to select three known Staphylophages by detecting the endolysin gene of phage K, the polymerase gene of phage 44AHJD, and the minor tail gene of phage P68. Results Isolated phages in this research displayed a wide host range against MRSA using the spot test, out of thirty tested MRSA isolates 24 were sensitive and got lysed (80%). The titer of the phages was estimated to be 1.04 × 106 pfu/ml using plaque test. Identification of head and tail morphology of the phages was achieved using TEM and they were designated to tailed phages of order Caudovirales, they composed an icosahedral capsid. Prophages were isolated through MitC induction. DNA of phages was digested by endonuclease enzymes. Conventional PCR yielded 341 bp of phage K endolysin gene and phage P68 minor tail protein gene 501 bp. Protein analysis using SDS-PAGE showed 4 proteins of sizes between 42 kDa and 140 kDa. Conclusion Phages isolated here are alike to others mentioned in previous studies. The high broad host range of the isolated phages is promising to control MRSA and can be in the future commercially suitable for treatment as lysate preparations. Animal models of phage-bacterial interaction will be our next step that may help in resolving the multidrug resistant crisis of MRSA in Egypt.
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Key Words
- AMR, antimicrobial resistance
- CLSI, clinical and laboratory standards institute
- Caudovirales
- ESKAPE, (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species)
- FOX, Cefoxitin
- ITS, Internal transcribed spacer
- LB, Luria-Bertani
- Lytic bacteriophages
- MDR, Multidrug-resistant
- MRSA
- MRSA, Methicillin Resistant Staphylococcus aureus
- MitC, mitomycin C
- Mitomycin C
- NGS, double-stranded, ds, next generation sequencing
- OX, Oxacillin
- PCR, Polymerase chain reaction
- PFU, Plaque forming unit
- PTA, phosphotungstic acid
- Polymerase chain reaction
- Restriction digestion
- S. aureus, Staphylococcus aureus
- SDS-polyacrylamide gel electrophoresis
- Sewage
- TBRI, Theodor Bilharz research Institute
- TEM, Transmission electron microscopy
- Transmission electron microscopy
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Affiliation(s)
- Safia Samir
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
| | - Amira El-Far
- Microbiology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
| | - Hend Okasha
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
| | - Rania Mahdy
- Microbiology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
| | - Fatima Samir
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
| | - Sami Nasr
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute (TBRI), Giza, Egypt
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Bari SMN, Chou-Zheng L, Howell O, Hossain M, Hill CM, Boyle TA, Cater K, Dandu VS, Thomas A, Aslan B, Hatoum-Aslan A. A unique mode of nucleic acid immunity performed by a multifunctional bacterial enzyme. Cell Host Microbe 2022; 30:570-582.e7. [PMID: 35421352 DOI: 10.1016/j.chom.2022.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/10/2021] [Accepted: 03/01/2022] [Indexed: 11/24/2022]
Abstract
The perpetual arms race between bacteria and their viruses (phages) has given rise to diverse immune systems, including restriction-modification and CRISPR-Cas, which sense and degrade phage-derived nucleic acids. These complex systems rely upon production and maintenance of multiple components to achieve antiphage defense. However, the prevalence and effectiveness of minimal, single-component systems that cleave DNA remain unknown. Here, we describe a unique mode of nucleic acid immunity mediated by a single enzyme with nuclease and helicase activities, herein referred to as Nhi (nuclease-helicase immunity). This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses. Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates. Importantly, Nhi homologs are distributed in diverse bacteria and exhibit functional conservation, highlighting the versatility of such compact weapons as major players in antiphage defense.
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Affiliation(s)
- S M Nayeemul Bari
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Lucy Chou-Zheng
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Olivia Howell
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Motaher Hossain
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Courtney M Hill
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Tori A Boyle
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Katie Cater
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Vidya Sree Dandu
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Alexander Thomas
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Barbaros Aslan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA
| | - Asma Hatoum-Aslan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61821, USA.
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Manoharadas S, Altaf M, Alrefaei AF, Ahmad N, Althaf Hussain S, Al-Rayes BF. An Engineered Multimodular Enzybiotic against Methicillin-Resistant Staphylococcus aureus. Life (Basel) 2021; 11:1384. [PMID: 34947915 PMCID: PMC8705753 DOI: 10.3390/life11121384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022] Open
Abstract
Development of multidrug antibiotic resistance in bacteria is a predicament encountered worldwide. Researchers are in a constant hunt to develop effective antimicrobial agents to counter these dreadful pathogenic bacteria. Here we describe a chimerically engineered multimodular enzybiotic to treat a clinical isolate of methicillin-resistant Staphylococcus aureus (S. aureus). The cell wall binding domain of phage ϕ11 endolysin was replaced with a truncated and more potent cell wall binding domain from a completely unrelated protein from a different phage. The engineered enzybiotic showed strong activity against clinically relevant methicillin-resistant Staphylococcus aureus. In spite of a multimodular peptidoglycan cleaving catalytic domain, the engineered enzybiotic could not exhibit its activity against a veterinary isolate of S. aureus. Our studies point out that novel antimicrobial proteins can be genetically engineered. Moreover, the cell wall binding domain of the engineered protein is indispensable for a strong binding and stability of the proteins.
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Affiliation(s)
- Salim Manoharadas
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia
- Central Laboratory RM 63AA, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia; (M.A.); (N.A.); (S.A.H.); (B.F.A.-R.)
| | - Mohammad Altaf
- Central Laboratory RM 63AA, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia; (M.A.); (N.A.); (S.A.H.); (B.F.A.-R.)
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia
| | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia;
| | - Naushad Ahmad
- Central Laboratory RM 63AA, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia; (M.A.); (N.A.); (S.A.H.); (B.F.A.-R.)
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia
| | - Shaik Althaf Hussain
- Central Laboratory RM 63AA, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia; (M.A.); (N.A.); (S.A.H.); (B.F.A.-R.)
- Department of Zoology, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia;
| | - Basel F. Al-Rayes
- Central Laboratory RM 63AA, College of Science, King Saud University, P.O. Box 2454, Riyadh 11451, Saudi Arabia; (M.A.); (N.A.); (S.A.H.); (B.F.A.-R.)
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10
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Hatoum-Aslan A. The phages of staphylococci: critical catalysts in health and disease. Trends Microbiol 2021; 29:1117-1129. [PMID: 34030968 PMCID: PMC8578144 DOI: 10.1016/j.tim.2021.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/21/2023]
Abstract
The phages that infect Staphylococcus species are dominant residents of the skin microbiome that play critical roles in health and disease. While temperate phages, which can integrate into the host genome, have the potential to promote staphylococcal pathogenesis, the strictly lytic variety are powerful antimicrobials that are being exploited for therapeutic applications. This article reviews recent insights into the diversity of staphylococcal phages and newly described mechanisms by which they influence host pathogenicity. The latest efforts to harness these viruses to eradicate staphylococcal infections are also highlighted. Decades of research has focused on the temperate phages of Staphylococcus aureus as model systems, thus underscoring the need to broaden basic research efforts to include diverse phages that infect other clinically relevant Staphylococcus species.
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Affiliation(s)
- Asma Hatoum-Aslan
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, IL, 61801, USA.
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Sáez Moreno D, Visram Z, Mutti M, Restrepo-Córdoba M, Hartmann S, Kremers AI, Tišáková L, Schertler S, Wittmann J, Kalali B, Monecke S, Ehricht R, Resch G, Corsini L. ε 2-Phages Are Naturally Bred and Have a Vastly Improved Host Range in Staphylococcus aureus over Wild Type Phages. Pharmaceuticals (Basel) 2021; 14:325. [PMID: 33918287 PMCID: PMC8065394 DOI: 10.3390/ph14040325] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/24/2022] Open
Abstract
Due to the rapid spread of antibiotic resistance, and the difficulties of treating biofilm-associated infections, alternative treatments for S. aureus infections are urgently needed. We tested the lytic activity of several wild type phages against a panel of 110 S. aureus strains (MRSA/MSSA) composed to reflect the prevalence of S. aureus clonal complexes in human infections. The plaquing host ranges (PHR) of the wild type phages were in the range of 51% to 60%. We also measured what we called the kinetic host range (KHR), i.e., the percentage of strains for which growth in suspension was suppressed for 24 h. The KHR of the wild type phages ranged from 2% to 49%, substantially lower than the PHRs. To improve the KHR and other key pharmaceutical properties, we bred the phages by mixing and propagating cocktails on a subset of S. aureus strains. These bred phages, which we termed evolution-squared (ε2) phages, have broader KHRs up to 64% and increased virulence compared to the ancestors. The ε2-phages with the broadest KHR have genomes intercrossed from up to three different ancestors. We composed a cocktail of three ε2-phages with an overall KHR of 92% and PHR of 96% on 110 S. aureus strains and called it PM-399. PM-399 has a lower propensity to resistance formation than the standard of care antibiotics vancomycin, rifampicin, or their combination, and no resistance was observed in laboratory settings (detection limit: 1 cell in 1011). In summary, ε2-phages and, in particular PM-399, are promising candidates for an alternative treatment of S. aureus infections.
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Affiliation(s)
- David Sáez Moreno
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
| | - Zehra Visram
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
| | - Michele Mutti
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
| | - Marcela Restrepo-Córdoba
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
| | - Susana Hartmann
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
| | - Ana Isabel Kremers
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
| | - Lenka Tišáková
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (S.S.); (J.W.)
| | - Susanne Schertler
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (S.S.); (J.W.)
| | - Johannes Wittmann
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (S.S.); (J.W.)
| | - Benham Kalali
- Bactrace Biotec AG, Neherstr. 1, 81675 Munich, Germany;
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (S.M.); (R.E.)
- Institute of Medical Microbiologye and Hygiene, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, Fiedlerstr. 42, D-01307 Dresden, Germany
- InfectoGnostics Research Campus Jena, 07743 Jena, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (S.M.); (R.E.)
- InfectoGnostics Research Campus Jena, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich-Schiller University, 07743 Jena, Germany
| | - Grégory Resch
- Department of Fundamental Microbiology, University Lausanne, CH-1015 Lausanne, Switzerland;
| | - Lorenzo Corsini
- PhagoMed Biopharma GmbH, Leberstrasse 20, A-1110 Vienna, Austria; (D.S.M.); (Z.V.); (M.M.); (M.R.-C.); (S.H.); (A.I.K.); (L.T.)
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12
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Manoharadas S, Altaf M, Alrefaei AF, Devasia RM, Badjah Hadj AYM, Abuhasil MSA. Concerted dispersion of Staphylococcus aureus biofilm by bacteriophage and 'green synthesized' silver nanoparticles. RSC Adv 2021; 11:1420-1429. [PMID: 35424119 PMCID: PMC8693614 DOI: 10.1039/d0ra09725j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022] Open
Abstract
Staphylococcal biofilms predominantly cause persistent nosocomial infections. The widespread antibiotic resistance followed by its ability to form biofilm in biological and inert surfaces often contributes to major complications in patients and veterinary animals. Strategic importance of bacteriophage therapy against critical staphylococcal infections had been predicted ever since the advent of antibiotic resistant staphylococcal strains. The significance of metal nanoparticles in quenching biofilm associated bacteria was previously reported. In this study, we demonstrate a concerted action of ‘green synthesized’ silver nanoparticles and bacteriophages in removing pre-formed Staphylococcus aureus biofilms from an inert glass surface in a time dependent manner. Our results demonstrate, for the first time, the rapid co-operative dispersion of the bacterial biofilm. In addition, the synergistic activity of the nanoparticles and bacteriophages causes the loss of viability of the biofilm entrapped bacterial cells thus preventing establishment of a new infection and subsequent colonization. This work further opens up a platform for the combinational therapeutic approach with a variety of nanoparticles and bacteriophages against mono or poly bacterial biofilm in environmental, industrial or clinical settings. Formation of biofilm by Staphylococcus aureus ‘Rumba’ on untreated glass surface and a concerted disruption of the biofilm by silver nanoparticle and phage ϕ44AHJD.![]()
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Affiliation(s)
- Salim Manoharadas
- King Saud University, Department of Botany and Microbiology, Central Laboratory RM 55A College of Science Building 5, P.O. Box. 2454 Riyadh 11451 Saudi Arabia +966-14699665 +966-114689170
| | - Mohammad Altaf
- King Saud University, Department of Botany and Microbiology, Central Laboratory RM 55A College of Science Building 5, P.O. Box. 2454 Riyadh 11451 Saudi Arabia +966-14699665 +966-114689170.,King Saud University, Department of Chemistry, College of Science P.O. Box. 2454 Riyadh 11451 Saudi Arabia
| | - Abdulwahed Fahad Alrefaei
- King Saud University, Department of Zoology, College of Science P.O. Box. 2454 Riyadh 11451 Saudi Arabia
| | | | - Ahmed Yacine M Badjah Hadj
- King Saud University, Department of Chemistry, College of Science P.O. Box. 2454 Riyadh 11451 Saudi Arabia
| | - Mohammed Saeed Ali Abuhasil
- King Saud University, Department of Food Science and Nutrition, College of Agriculture and Food Science P.O. Box. 2454 Riyadh 11451 Saudi Arabia
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13
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Pedersen JS, Kot W, Plöger M, Lametsh R, Neve H, Franz CM, Hansen LH. A Rare, Virulent Clostridium perfringens Bacteriophage Susfortuna Is the First Isolated Bacteriophage in a New Viral Genus. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:230-236. [PMID: 36147286 PMCID: PMC9041476 DOI: 10.1089/phage.2020.0038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background: Clostridium perfringens is a well known swine pathogen. C. perfringens type A is considered the causative agent of enteric diseases in neonatal and weaned piglets. Phage therapy using C. perfringens phages in vivo has previously proved effective. Materials and Methods: Pig fecal samples were used to isolate phages, with Clostridium perfringens type A as host. Complete genome sequencing, comparative genomics, a proteome analysis and electron microscopy were used to characterize the phage. Results: Clostridium phage Susfortuna has a double-stranded DNA genome of 19,046 bp with a G+C% content of 29.2, inverted terminal repeats and 28 predicted coding sequences (CDSs). Putative functions could not be assigned to most of the CDSs (64.3%). Transmission electron microscopy of phage Susfortuna revealed an isometric head and a short protruding tail stub resembling the structure of the Podoviridae family. A proteome analysis of phage Susfortuna identified seven structural proteins, but only one could be assigned with a putative function. Conclusions: Based on the morphology, the inverted terminal repeats and the small genome size, phage Susfortuna belongs to subfamily Picovirinae within the Podoviridae family in the order Caudovirales. Together with C. perfringens bacteriophage CPD7, phage Susfortuna represent a new genus of bacteriophages with very limited DNA sequence similarity to other known C. perfringens phages. Despite the limited DNA sequence similarity, the gene synteny among putative structural genes of phage Susfortuna is conserved among several C. perfringens bacteriophages belonging to the Podoviridae family indicating a common ancestor.
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Affiliation(s)
- Julie Stenberg Pedersen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Maja Plöger
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Réne Lametsh
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Charles M.A.P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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14
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Titze I, Lehnherr T, Lehnherr H, Krömker V. Efficacy of Bacteriophages Against Staphylococcus aureus Isolates from Bovine Mastitis. Pharmaceuticals (Basel) 2020; 13:ph13030035. [PMID: 32110980 PMCID: PMC7151712 DOI: 10.3390/ph13030035] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 02/05/2020] [Accepted: 02/24/2020] [Indexed: 01/16/2023] Open
Abstract
The lytic efficacy of bacteriophages against Staphylococcus aureus isolates from bovine milk was investigated in vitro, regarding possible applications in the therapy of udder inflammation caused by bacterial infections (mastitis). The host range of sequenced, lytic bacteriophages was determined against a collection of 92 Staphylococcus (S.) aureus isolates. The isolates originated from quarter foremilk samples of clinical and subclinical mastitis cases. A spot test and a subsequent plaque assay were used to determine the phage host range. According to their host range, propagation and storage properties, three phages, STA1.ST29, EB1.ST11, and EB1.ST27, were selected for preparing a bacteriophage mixture (1:1:1), which was examined for its lytic activity against S. aureus in pasteurized and raw milk. It was found that almost two thirds of the isolates could be lysed by at least one of the tested phages. The bacteriophage mixture was able to reduce the S. aureus germ density in pasteurized milk and its reduction ability was maintained in raw milk, with only a moderate decrease compared to the results in pasteurized milk. The significant reduction ability of the phage mixture in raw milk promotes further in vivo investigation.
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Affiliation(s)
- Isabel Titze
- Department of Bioprocess Engineering and Microbiology, University of Applied Sciences and Arts Hannover, D-30453 Hannover, Germany;
| | - Tatiana Lehnherr
- Phage Technology Center GmbH, D-59199 Bönen, Germany; (T.L.); (H.L.)
| | - Hansjörg Lehnherr
- Phage Technology Center GmbH, D-59199 Bönen, Germany; (T.L.); (H.L.)
| | - Volker Krömker
- Department of Bioprocess Engineering and Microbiology, University of Applied Sciences and Arts Hannover, D-30453 Hannover, Germany;
- Section for Production, Nutrition and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark
- Correspondence:
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15
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Cha Y, Son B, Ryu S. Effective removal of staphylococcal biofilms on various food contact surfaces by Staphylococcus aureus phage endolysin LysCSA13. Food Microbiol 2019; 84:103245. [DOI: 10.1016/j.fm.2019.103245] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/14/2019] [Accepted: 06/16/2019] [Indexed: 10/26/2022]
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16
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Coding-Complete Genome Sequence of Staphylococcus aureus Podophage Portland. Microbiol Resour Announc 2019; 8:8/47/e01337-19. [PMID: 31753959 PMCID: PMC6872901 DOI: 10.1128/mra.01337-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus bacteria, especially the multidrug resistance strains, are responsible for a wide range of clinical infections. Here, we announce the genome sequence of S. aureus podophage Portland, which is closely related to a group of phi29‐like S. aureus podophages, including phages phi44AHJD and phiP68. The exact genome sequence ends of phage Portland were not determined and may be obscured by terminal proteins. Staphylococcus aureus bacteria, especially the multidrug resistance strains, are responsible for a wide range of clinical infections. Here, we announce the genome sequence of S. aureus podophage Portland, which is closely related to a group of phi29‐like S. aureus podophages, including phages phi44AHJD and phiP68. The exact genome sequence ends of phage Portland were not determined and may be obscured by terminal proteins.
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17
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Hrebík D, Štveráková D, Škubník K, Füzik T, Pantůček R, Plevka P. Structure and genome ejection mechanism of Staphylococcus aureus phage P68. SCIENCE ADVANCES 2019; 5:eaaw7414. [PMID: 31663016 PMCID: PMC6795507 DOI: 10.1126/sciadv.aaw7414] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/23/2019] [Indexed: 06/01/2023]
Abstract
Phages infecting Staphylococcus aureus can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect Gram-positive bacteria. Here, we present the structures of native S. aureus phage P68, genome ejection intermediate, and empty particle. The P68 head contains 72 subunits of inner core protein, 15 of which bind to and alter the structure of adjacent major capsid proteins and thus specify attachment sites for head fibers. Unlike in the previously studied phages, the head fibers of P68 enable its virion to position itself at the cell surface for genome delivery. The unique interaction of one end of P68 DNA with one of the 12 portal protein subunits is disrupted before the genome ejection. The inner core proteins are released together with the DNA and enable the translocation of phage genome across the bacterial membrane into the cytoplasm.
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Affiliation(s)
- Dominik Hrebík
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Dana Štveráková
- Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Karel Škubník
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tibor Füzik
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Roman Pantůček
- Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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18
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Głowacka-Rutkowska A, Gozdek A, Empel J, Gawor J, Żuchniewicz K, Kozińska A, Dębski J, Gromadka R, Łobocka M. The Ability of Lytic Staphylococcal Podovirus vB_SauP_phiAGO1.3 to Coexist in Equilibrium With Its Host Facilitates the Selection of Host Mutants of Attenuated Virulence but Does Not Preclude the Phage Antistaphylococcal Activity in a Nematode Infection Model. Front Microbiol 2019; 9:3227. [PMID: 30713528 PMCID: PMC6346686 DOI: 10.3389/fmicb.2018.03227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/12/2018] [Indexed: 12/22/2022] Open
Abstract
Phage vB_SauP_phiAGO1.3 (phiAGO1.3) is a polyvalent Staphylococcus lytic podovirus with a 17.6-kb genome (Gozdek et al., 2018). It can infect most of the Staphylococcus aureus human isolates of dominant clonal complexes. We show that a major factor contributing to the wide host range of phiAGO1.3 is a lack or sparcity of target sites for certain restriction-modification systems of types I and II in its genome. Phage phiAGO1.3 requires for adsorption β-O-GlcNAcylated cell wall teichoic acid, which is also essential for the expression of methicillin resistance. Under certain conditions an exposure of S. aureus to phiAGO1.3 can lead to the establishment of a mixed population in which the bacteria and phages remain in equilibrium over multiple generations. This is reminiscent of the so called phage carrier state enabling the co-existence of phage-resistant and phage-sensitive cells supporting a continuous growth of the bacterial and phage populations. The stable co-existence of bacteria and phage favors the emergence of phage-resistant variants of the bacterium. All phiAGO1.3-resistant cells isolated from the phage-carrier-state cultures contained a mutation inactivating the two-component regulatory system ArlRS, essential for efficient expression of numerous S. aureus virulence-associated traits. Moreover, the mutants were unaffected in their susceptibility to infection with an unrelated, polyvalent S. aureus phage of the genus Kayvirus. The ability of phiAGO1.3 to establish phage-carrier-state cultures did not preclude its antistaphylococcal activity in vivo in an S. aureus nematode infection model. Taken together our results suggest that phiAGO1.3 could be suitable for the therapeutic application in humans and animals, alone or in cocktails with Kayvirus phages. It might be especially useful in the treatment of infections with the majority of methicillin-resistant S. aureus strains.
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Affiliation(s)
- Aleksandra Głowacka-Rutkowska
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Gozdek
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Empel
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Jan Gawor
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Karolina Żuchniewicz
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Aleksandra Kozińska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Janusz Dębski
- Laboratory of Mass Spectrometry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Robert Gromadka
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Małgorzata Łobocka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
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19
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Drilling AJ, Ooi ML, Miljkovic D, James C, Speck P, Vreugde S, Clark J, Wormald PJ. Long-Term Safety of Topical Bacteriophage Application to the Frontal Sinus Region. Front Cell Infect Microbiol 2017; 7:49. [PMID: 28286740 PMCID: PMC5323412 DOI: 10.3389/fcimb.2017.00049] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/08/2017] [Indexed: 12/13/2022] Open
Abstract
Background:Staphylococcus aureus biofilms contribute negatively to a number of chronic conditions, including chronic rhinosinusitis (CRS). With the inherent tolerance of biofilm-bound bacteria to antibiotics and the global problem of bacterial antibiotic resistance, the need to develop novel therapeutics is paramount. Phage therapy has previously shown promise in treating sinonasal S. aureus biofilms. Methods: This study investigates the long term (20 days) safety of topical sinonasal flushes with bacteriophage suspensions. The bacteriophage cocktail NOV012 against S. aureus selected for this work contains two highly characterized and different phages, P68 and K710. Host range was assessed against S. aureus strains isolated from CRS patients using agar spot tests. NOV012 was applied topically to the frontal sinus region of sheep, twice daily for 20 days. General sheep wellbeing, mucosal structural changes and inflammatory load were assessed to determine safety of NOV012 application. Results: NOV012 could lyse 52/61 (85%) of a panel of locally derived CRS clinical isolates. Application of NOV012 to the frontal sinuses of sheep for 20 days was found to be safe, with no observed inflammatory infiltration or tissue damage within the sinus mucosa. Conclusion: NOV012 cocktail appears safe to apply for extended periods to sheep sinuses and it could infect and lyse a wide range of S. aureus CRS clinical isolates. This indicates that phage therapy has strong potential as a treatment for chronic bacterial rhinosinusitis.
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Affiliation(s)
- Amanda J Drilling
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide Adelaide, SA, Australia
| | - Mian L Ooi
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide Adelaide, SA, Australia
| | - Dijana Miljkovic
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide Adelaide, SA, Australia
| | - Craig James
- Adelaide Pathology Partners Adelaide, SA, Australia
| | - Peter Speck
- School of Biological Sciences, Flinders University Bedford Park, SA, Australia
| | - Sarah Vreugde
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide Adelaide, SA, Australia
| | | | - Peter-John Wormald
- Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide Adelaide, SA, Australia
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20
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Verstappen KM, Tulinski P, Duim B, Fluit AC, Carney J, van Nes A, Wagenaar JA. The Effectiveness of Bacteriophages against Methicillin-Resistant Staphylococcus aureus ST398 Nasal Colonization in Pigs. PLoS One 2016; 11:e0160242. [PMID: 27487020 PMCID: PMC4972443 DOI: 10.1371/journal.pone.0160242] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/15/2016] [Indexed: 12/02/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an important colonizer in animals and an opportunistic pathogen in humans. In humans, MRSA can cause infections that might be difficult to treat because of antimicrobial resistance. The use of bacteriophages has been suggested as a potential approach for the control of MRSA colonization to minimize the—often occupational—exposure of humans. The aim of this study was to assess the efficacy of bacteriophage treatment on porcine nasal colonization with MRSA in vitro, in vivo, and ex vivo. The effectiveness of a bacteriophage combination of phage K*710 and P68 was assessed in vitro by incubating them with MRSA V0608892/1 (ST398) measuring the OD600 hourly. To study the in vivo effect, bacteriophages were administered in a gel developed for human application, which contain 109 plaque-forming units (pfu)/mL (K and P68 in a 19.25:1 ratio) for 5 days to piglets (N = 8) that were experimentally colonized with the MRSA strain. Eight piglets experimentally colonized were used as a negative control. The MRSA strain was also used to colonize porcine nasal mucosa explants and bacteriophages were applied to assess the ex vivo efficacy of treatment. Bacteriophages were effective in vitro. In vivo, sixteen piglets were colonized with MRSA but the number of CFU recovered after the application of the bacteriophages in 8 piglets was not reduced compared to the control animals (approx. 105 CFU/swab). In the ex vivo model, 108 CFU were used to establish colonization with MRSA; a reduction of colonization was not observed after application of bacteriophages. However, application of mupirocin both in vivo and ex vivo resulted in a near eradication of MRSA. In conclusion: i) The MRSA strain was killed in the presence of the bacteriophages phage K*710 and P68 in vitro. ii) Bacteriophages did not reduce porcine nasal colonization in vivo or ex vivo. Physiological in vivo and ex vivo conditions may explain these observations. Efficacy in the ex vivo model matched that of the in vivo system.
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Affiliation(s)
- Koen M Verstappen
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Pawel Tulinski
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- * E-mail:
| | - Ad C Fluit
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, the Netherlands
| | | | - Arie van Nes
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Central Veterinary Institute of Wageningen UR, Lelystad, the Netherlands
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21
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Li X, Gerlach D, Du X, Larsen J, Stegger M, Kühner P, Peschel A, Xia G, Winstel V. An accessory wall teichoic acid glycosyltransferase protects Staphylococcus aureus from the lytic activity of Podoviridae. Sci Rep 2015; 5:17219. [PMID: 26596631 PMCID: PMC4667565 DOI: 10.1038/srep17219] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/27/2015] [Indexed: 01/10/2023] Open
Abstract
Many Staphylococcus aureus have lost a major genetic barrier against phage infection, termed clustered regularly interspaced palindromic repeats (CRISPR/cas). Hence, S. aureus strains frequently exchange genetic material via phage-mediated horizontal gene transfer events, but, in turn, are vulnerable in particular to lytic phages. Here, a novel strategy of S. aureus is described, which protects S. aureus against the lytic activity of Podoviridae, a unique family of staphylococcal lytic phages with short, non-contractile tails. Unlike most staphylococcal phages, Podoviridae require a precise wall teichoic acid (WTA) glycosylation pattern for infection. Notably, TarM-mediated WTA α-O-GlcNAcylation prevents infection of Podoviridae while TarS-mediated WTA β-O-GlcNAcylation is required for S. aureus susceptibility to podoviruses. Tracking the evolution of TarM revealed an ancient origin in other staphylococci and vertical inheritance during S. aureus evolution. However, certain phylogenetic branches have lost tarM during evolution, which rendered them podovirus-susceptible. Accordingly, lack of tarM correlates with podovirus susceptibility and can be converted into a podovirus-resistant phenotype upon ectopic expression of tarM indicating that a "glyco-switch" of WTA O-GlcNAcylation can prevent the infection by certain staphylococcal phages. Since lytic staphylococcal phages are considered as anti-S. aureus agents, these data may help to establish valuable strategies for treatment of infections.
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Affiliation(s)
- Xuehua Li
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - David Gerlach
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - Xin Du
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - Jesper Larsen
- Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Marc Stegger
- Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark.,Pathogen Genomics Division, Translational Genomics Research Institute, 3051 W Shamrell Blvd, Flagstaff, 86001 Arizona, USA
| | - Petra Kühner
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - Andreas Peschel
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
| | - Guoqing Xia
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany.,Institute of Inflammation &Repair, The University of Manchester, Manchester, United Kingdom
| | - Volker Winstel
- Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, 72076 Tübingen, Germany
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El Haddad L, Roy JP, Khalil GE, St-Gelais D, Champagne CP, Labrie S, Moineau S. Efficacy of two Staphylococcus aureus phage cocktails in cheese production. Int J Food Microbiol 2015; 217:7-13. [PMID: 26476571 DOI: 10.1016/j.ijfoodmicro.2015.10.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 09/19/2015] [Accepted: 10/01/2015] [Indexed: 12/18/2022]
Abstract
Staphylococcus aureus is one of the most prevalent pathogenic bacteria contaminating dairy products. In an effort to reduce food safety risks, virulent phages are investigated as antibacterial agents to control foodborne pathogens. The aim of this study was to compare sets of virulent phages, design phage cocktails, and use them in a cocktail to control pathogenic staphylococci in cheese. Six selected phages belonging to the three Caudovirales families (Myoviridae, Siphoviridae, Podoviridae) were strictly lytic, had a broad host range, and did not carry genes coding for virulence traits in their genomes. However, they were sensitive to pasteurization. At MOI levels of 15, 45, and 150, two anti-S. aureus phage cocktails, each containing three phages, one from each of the three phage families, eradicated a 10(6)CFU/g S. aureus population after 14 days of Cheddar cheese curd ripening at 4°C. The use of these phages did not trigger over-production of S. aureus enterotoxin C. The use of phage cocktails and their rotation may prevent the emergence of phage resistant bacterial strains.
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Affiliation(s)
- Lynn El Haddad
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec G1V 0A6, Canada
| | - Jean-Pierre Roy
- Techniques de santé animale, Cégep de Sherbrooke, 475 rue du Cégep, Sherbrooke, Québec J1E 4K1, Canada
| | - Georges E Khalil
- Department of Behavioral Science, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Daniel St-Gelais
- Food Research and Development Centre, Agriculture and Agri-Food, 3600 Casavant Blvd West, Saint-Hyacinthe, Québec J2S 8E3, Canada; Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec G1V 0A6, Canada
| | - Claude P Champagne
- Food Research and Development Centre, Agriculture and Agri-Food, 3600 Casavant Blvd West, Saint-Hyacinthe, Québec J2S 8E3, Canada; Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec G1V 0A6, Canada
| | - Steve Labrie
- Département des sciences des aliments, Faculté des sciences de l'agriculture et de l'alimentation, STELA, Université Laval, Québec G1V 0A6, Canada; Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec G1V 0A6, Canada.
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23
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Ghasemi SM, Bouzari M, Yoon BH, Chang HI. Comparative genomic analysis of Lactococcus garvieae phage WP-2, a new member of Picovirinae subfamily of Podoviridae. Gene 2014; 551:222-9. [DOI: 10.1016/j.gene.2014.08.060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 08/10/2014] [Accepted: 08/29/2014] [Indexed: 10/24/2022]
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24
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Insights into new bacteriophages of Lactococcus garvieae belonging to the family Podoviridae. Arch Virol 2014; 159:2909-15. [PMID: 24928734 DOI: 10.1007/s00705-014-2142-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 05/31/2014] [Indexed: 10/25/2022]
Abstract
Lactococcus garvieae is an emerging pathogen responsible for lactococcosis, a serious disease in trout aquaculture. The identification of new bacteriophages against L. garvieae strains may be an effective way to fight this disease and to study the pathogen's biology. Three L. garvieae phages, termed WP-1, WWP-2 and SP-2, were isolated from different environments, and their morphological features, genome restriction profiles and structural protein patterns were studied. Random cloning of HindIII-cut fragments was performed, and the fragments were partially sequenced for each phage. Although slight differences were observed by transmission electron microscopy, all of the phages had hexagonal heads and short non-contractile tails and were classified as members of the family Podoviridae. Restriction digestion analysis of the nucleic acids of the different phages revealed that the HindIII and AseI digests produced similar DNA fragment patterns. Additionally, SDS-PAGE analysis indicated that the isolated phages have similar structural proteins. The sequence BLAST results did not show any significant similarity with other previously identified phages. To the best of our knowledge, this study provides the first molecular characterization of L. garvieae phages.
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25
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Uchiyama J, Takemura-Uchiyama I, Kato SI, Sato M, Ujihara T, Matsui H, Hanaki H, Daibata M, Matsuzaki S. In silico analysis of AHJD-like viruses, Staphylococcus aureus phages S24-1 and S13', and study of phage S24-1 adsorption. Microbiologyopen 2014; 3:257-70. [PMID: 24591378 PMCID: PMC3996573 DOI: 10.1002/mbo3.166] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 12/27/2013] [Accepted: 01/18/2014] [Indexed: 11/24/2022] Open
Abstract
Staphylococcus aureus is a clinically important bacterium that is commensal in both humans and animals. Bacteriophage (phage) attachment to the host bacterial surface is an important process during phage infection, which involves interactions between phage receptor-binding proteins and host receptor molecules. However, little information is available on the receptor-binding protein of S. aureus phages. S. aureus virulent phages S24-1 and S13' (family Podoviridae, genus AHJD-like viruses) were isolated from sewage. In the present study, we investigated the receptor-binding protein of AHJD-like viruses using phage S24-1. First, based on a comparative genomic analysis of phages S24-1 and S13', open reading frame 16 (ORF16) of phage S24-1 was speculated to be the receptor-binding protein, which possibly determines the host range. Second, we demonstrated that this was the receptor-binding protein of phage S24-1. Third, our study suggested that wall teichoic acids in the cell walls of S. aureus are the main receptor molecules for ORF16 and phage S24-1. Finally, the C-terminal region of ORF16 may be essential for binding to S. aureus. These results strongly suggest that ORF16 of phage S24-1 and its homologs may be the receptor-binding proteins of AHJD-like viruses.
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Affiliation(s)
- Jumpei Uchiyama
- Department of Microbiology and Infection, Faculty of Medicine, Kochi UniversityNankoku City, Kochi, Japan
- Center for Innovative and Translational Medicine, Faculty of Medicine, Kochi UniversityNankoku City, Kochi, Japan
| | - Iyo Takemura-Uchiyama
- Department of Microbiology and Infection, Faculty of Medicine, Kochi UniversityNankoku City, Kochi, Japan
| | - Shin-ichiro Kato
- Research Institute of Molecular Genetics, Kochi UniversityNankoku City, Kochi, Japan
| | - Miho Sato
- Science Research Center, Kochi UniversityNankoku City, Kochi, Japan
| | - Takako Ujihara
- Science Research Center, Kochi UniversityNankoku City, Kochi, Japan
| | - Hidehito Matsui
- Research Center for Infections and Antimicrobials, Kitasato Institute for Life Sciences, Kitasato UniversityTokyo, Japan
| | - Hideaki Hanaki
- Research Center for Infections and Antimicrobials, Kitasato Institute for Life Sciences, Kitasato UniversityTokyo, Japan
| | - Masanori Daibata
- Department of Microbiology and Infection, Faculty of Medicine, Kochi UniversityNankoku City, Kochi, Japan
- Center for Innovative and Translational Medicine, Faculty of Medicine, Kochi UniversityNankoku City, Kochi, Japan
| | - Shigenobu Matsuzaki
- Department of Microbiology and Infection, Faculty of Medicine, Kochi UniversityNankoku City, Kochi, Japan
- Center for Innovative and Translational Medicine, Faculty of Medicine, Kochi UniversityNankoku City, Kochi, Japan
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26
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Experimental phage therapy against lethal lung-derived septicemia caused by Staphylococcus aureus in mice. Microbes Infect 2014; 16:512-7. [PMID: 24631574 DOI: 10.1016/j.micinf.2014.02.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 02/06/2014] [Accepted: 02/28/2014] [Indexed: 02/02/2023]
Abstract
Nosocomial respiratory infections caused by methicillin-resistant Staphylococcus aureus (MRSA) can progress to lethal systemic infections. Bacteriophage (phage) therapy is expected to be effective against these critical infections. Previously, phage S13' was proposed as a potential therapeutic phage. We here examined phage treatment in a mouse model of lung-derived septicemia using phage S13'. Intraperitoneal phage administration at 6 h postinfection reduced the severity of infection and rescued the infected mice. Phage S13' can efficiently lyse hospital-acquired MRSA strains causing pneumonia-associated bacteremia in vitro. Thus, phage therapy may be a possible therapeutic intervention in staphylococcal lung-derived septicemia.
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27
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Kraushaar B, Thanh MD, Hammerl JA, Reetz J, Fetsch A, Hertwig S. Isolation and characterization of phages with lytic activity against methicillin-resistant Staphylococcus aureus strains belonging to clonal complex 398. Arch Virol 2013; 158:2341-50. [PMID: 23760627 DOI: 10.1007/s00705-013-1707-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/25/2013] [Indexed: 10/26/2022]
Abstract
Some years ago, MRSA clonal complex (CC) 398 emerged, which spread extensively in livestock animals. People in contact with food production animals are at high risk of colonization. A reduction of MRSA CC398 in livestock might be achieved by application of virulent phages. However, there have not yet been any reports published on phages lysing MRSA CC398 strains. In this study, three virulent phages (PSa1, PSa2 and PSa3) with lytic activity against MRSA CC398 strains were isolated from German pig farms. Morphologically, the phages are members of the family Podoviridae, and they exhibited an identical host range. They lysed 52 (60 %) out of 86 tested MRSA CC398 strains representing 18 different spa types. While the PSa1 and PSa3 genomes have a similar size of approximately 17.5 kb, the PSa2 genome is somewhat larger (ca. 18.5 kb). Southern hybridization revealed strong DNA homologies between the phages, which was confirmed by sequence analysis of cloned restriction fragments and PCR products. Moreover, the whole PSa3 genomic sequence (17,602 bp) showed a close relationship to 44AHJD-like phages, which are not known to contain virulence-associated genes. To assess whether these phages might be candidates for applications, in vitro experiments were carried out in which the number of MRSA CC398 cells could be reduced by up to four log10 units. The phages were stable at a wide range of temperatures and pH values.
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Affiliation(s)
- Britta Kraushaar
- Department for Biological Safety, Federal Institute for Risk Assessment, Max-Dohrn Str. 8-10, 10589, Berlin, Germany
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28
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Abstract
Due to their crucial role in pathogenesis and virulence, phages of Staphylococcus aureus have been extensively studied. Most of them encode and disseminate potent staphylococcal virulence factors. In addition, their movements contribute to the extraordinary versatility and adaptability of this prominent pathogen by improving genome plasticity. In addition to S. aureus, phages from coagulase-negative Staphylococci (CoNS) are gaining increasing interest. Some of these species, such as S. epidermidis, cause nosocomial infections and are therefore problematic for public health. This review provides an overview of the staphylococcal phages family extended to CoNS phages. At the morphological level, all these phages characterized so far belong to the Caudovirales order and are mainly temperate Siphoviridae. At the molecular level, comparative genomics revealed an extensive mosaicism, with genes organized into functional modules that are frequently exchanged between phages. Evolutionary relationships within this family, as well as with other families, have been highlighted. All these aspects are of crucial importance for our understanding of evolution and emergence of pathogens among bacterial species such as Staphylococci.
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Affiliation(s)
- Marie Deghorain
- Author to whom correspondence should be addressed; (L.V.M.); (M.D.); Tel.: +32-2-650-97-76 (M.D.); +32-2-650-97-78 (L.V.M.); Fax: +32-2-650-97-70
| | - Laurence Van Melderen
- Author to whom correspondence should be addressed; (L.V.M.); (M.D.); Tel.: +32-2-650-97-76 (M.D.); +32-2-650-97-78 (L.V.M.); Fax: +32-2-650-97-70
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29
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Vandersteegen K, Kropinski AM, Nash JHE, Noben JP, Hermans K, Lavigne R. Romulus and Remus, two phage isolates representing a distinct clade within the Twortlikevirus genus, display suitable properties for phage therapy applications. J Virol 2013; 87:3237-47. [PMID: 23302893 PMCID: PMC3592175 DOI: 10.1128/jvi.02763-12] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/07/2012] [Indexed: 11/20/2022] Open
Abstract
The renewed interest in controlling Staphylococcus aureus infections using their natural enemies, bacteriophages, has led to the isolation of a limited number of virulent phages so far. These phages are all members of the Twortlikevirus, displaying little variance. We present two novel closely related (95.9% DNA homology) lytic myoviruses, Romulus and Remus, with double-stranded DNA (dsDNA) genomes of 131,333 bp and 134,643 bp, respectively. Despite their relatedness to Staphylococcus phages K, G1, ISP, and Twort and Listeria phages A511 and P100, Romulus and Remus can be proposed as isolates of a new species within the Twortlikevirus genus. A distinguishing feature for these phage genomes is the unique distribution of group I introns compared to that in other staphylococcal myoviruses. In addition, a hedgehog/intein domain was found within their DNA polymerase genes, and an insertion sequence-encoded transposase exhibits splicing behavior and produces a functional portal protein. From a phage therapy application perspective, Romulus and Remus infected approximately 70% of the tested S. aureus isolates and displayed promising lytic activity against these isolates. Furthermore, both phages showed a rapid initial adsorption and demonstrated biofilm-degrading capacity in a proof-of-concept experiment.
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Affiliation(s)
- Katrien Vandersteegen
- Laboratory of Gene Technology, Division of Gene Technology, University of Leuven, Heverlee, Belgium
| | - Andrew M. Kropinski
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, Ontario, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - John H. E. Nash
- Public Health Agency of Canada, Laboratory for Foodborne Zoonoses, Guelph, Ontario, Canada
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Katleen Hermans
- Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Division of Gene Technology, University of Leuven, Heverlee, Belgium
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H. Narasimhaiah M, Y. Asrani J, M. Palaniswamy S, Bhat J, E. George S, Srinivasan R, Vipra A, N. Desai S, Patil Junjappa R, Roy P, Sriram B, Padmanabhan S. Therapeutic Potential of Staphylococcal Bacteriophages for Nasal Decolonization of <i>Staphylococcus aureus</i> in Mice. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/aim.2013.31008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Łobocka M, Hejnowicz MS, Dąbrowski K, Gozdek A, Kosakowski J, Witkowska M, Ulatowska MI, Weber-Dąbrowska B, Kwiatek M, Parasion S, Gawor J, Kosowska H, Głowacka A. Genomics of staphylococcal Twort-like phages--potential therapeutics of the post-antibiotic era. Adv Virus Res 2012; 83:143-216. [PMID: 22748811 DOI: 10.1016/b978-0-12-394438-2.00005-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Polyvalent bacteriophages of the genus Twort-like that infect clinically relevant Staphylococcus strains may be among the most promising phages with potential therapeutic applications. They are obligatorily lytic, infect the majority of Staphylococcus strains in clinical strain collections, propagate efficiently and do not transfer foreign DNA by transduction. Comparative genomic analysis of 11 S. aureus/S. epidermidis Twort-like phages, as presented in this chapter, emphasizes their strikingly high similarity and clear divergence from phage Twort of the same genus, which might have evolved in hosts of a different species group. Genetically, these phages form a relatively isolated group, which minimizes the risk of acquiring potentially harmful genes. The order of genes in core parts of their 127 to 140-kb genomes is conserved and resembles that found in related representatives of the Spounavirinae subfamily of myoviruses. Functions of certain conserved genes can be predicted based on their homology to prototypical genes of model spounavirus SPO1. Deletions in the genomes of certain phages mark genes that are dispensable for phage development. Nearly half of the genes of these phages have no known homologues. Unique genes are mostly located near termini of the virion DNA molecule and are expressed early in phage development as implied by analysis of their potential transcriptional signals. Thus, many of them are likely to play a role in host takeover. Single genes encode homologues of bacterial virulence-associated proteins. They were apparently acquired by a common ancestor of these phages by horizontal gene transfer but presumably evolved towards gaining functions that increase phage infectivity for bacteria or facilitate mature phage release. Major differences between the genomes of S. aureus/S. epidermidis Twort-like phages consist of single nucleotide polymorphisms and insertions/deletions of short stretches of nucleotides, single genes, or introns of group I. Although the number and location of introns may vary between particular phages, intron shuffling is unlikely to be a major factor responsible for specificity differences.
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Affiliation(s)
- Małgorzata Łobocka
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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32
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Structural investigations of a Podoviridae streptococcus phage C1, implications for the mechanism of viral entry. Proc Natl Acad Sci U S A 2012; 109:14001-6. [PMID: 22891295 DOI: 10.1073/pnas.1207730109] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Podoviridae phage C1 was one of the earliest isolated bacteriophages and the first virus documented to be active against streptococci. The icosahedral and asymmetric reconstructions of the virus were calculated using cryo-electron microscopy. The capsid protein has an HK97 fold arranged into a T = 4 icosahedral lattice. The C1 tail is terminated with a ϕ29-like knob, surrounded by a skirt of twelve long appendages with novel morphology. Several C1 structural proteins have been identified, including a candidate for an appendage. The crystal structure of the knob has an N-terminal domain with a fold observed previously in tube forming proteins of Siphoviridae and Myoviridae phages. The structure of C1 suggests the mechanisms by which the virus digests the cell wall and ejects its genome. Although there is little sequence similarity to other phages, conservation of the structural proteins demonstrates a common origin of the head and tail, but more recent evolution of the appendages.
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33
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Nirmal Kumar GP, Sundarrajan S, Paul VD, Nandini S, Saravanan RS, Hariharan S, Sriram B, Padmanabhan S. Use of prophage free host for achieving homogenous population of bacteriophages: new findings. Virus Res 2012; 169:182-7. [PMID: 22917718 DOI: 10.1016/j.virusres.2012.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Revised: 07/18/2012] [Accepted: 07/24/2012] [Indexed: 01/21/2023]
Abstract
We demonstrate that the prophage status of bacteria plays a critical role in achieving homogenous population of a phage preparation. When a lytic Staphylococcus bacteriophage 44AHJD was propagated in a Staphylococcus clinical isolate, the enriched phage showed 44AHJD phage virions along with the released prophages from the baiting host. The released prophage was identified as a siphophage by transmission electron microscopy. To obtain a phage preparation free of prophages, when we carried out multiplication of the 44AHJD phage in a prophage free Staphyloccoccus aureus host namely RN4220, we were surprised not to see any phage plaques in spite of the phage exhibiting >99.9% adsorption to such cells. Since RN4220 host is devoid of restriction modification system and prophages, we hypothesized that in spite of successful infection and multiplication, the phage virions might have failed to show plaques due to its insignificant release from the cell possibly due to insufficient endolysin expressed from phage virions during phage development and assembly. Our hypothesis was confirmed when we observed plaques of 44AHJD phage in RN4220 cells where additional phage endolysin protein was supplemented via a plasmid. Endolysin protein from various types of Staphylococcus phages showed plaques of 44AHJD in RN4220 cells confirming our hypothesis. Also, we demonstrate for the first time that propagation of 44AHJD phage with endolysin supplementation in prophage free RN4220 host yields pure phage preparation.
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Affiliation(s)
- G P Nirmal Kumar
- Gangagen Biotechnologies Pvt Ltd, No 12, 5th Cross, Raghavendra Layout, Opp MEI Ltd, Tumkur Road, Yeshwantpur, Bangalore 560022, India
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34
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Borysowski J, Lobocka M, Międzybrodzki R, Weber-Dabrowska B, Górski A. Potential of bacteriophages and their lysins in the treatment of MRSA: current status and future perspectives. BioDrugs 2012; 25:347-55. [PMID: 22050337 DOI: 10.2165/11595610-000000000-00000] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacteriophages (phages) are viruses that specifically infect and kill bacteria. Lysins are enzymes of bacteriophage origin that cleave covalent bonds in peptidoglycan, thereby inducing rapid lysis of a bacterial cell. As potential antibacterial agents, phages and lysins have some important features in common, especially the capacity to kill antibiotic-resistant bacteria, a narrow antibacterial range, and lack of toxic effects on mammalian cells. In this article we present the staphylococcal phages and their lysins that can be used to combat methicillin-resistant Staphylococcus aureus (MRSA), one of today's most dangerous pathogens. We also discuss the use of phages as vectors specifically delivering different antibacterial agents to bacterial cells. Experimental data show that both phages and lysins could be effective in the treatment of MRSA.
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Affiliation(s)
- Jan Borysowski
- Department of Clinical Immunology, Transplantation Institute, Warsaw Medical University, Poland.
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35
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Volozhantsev NV, Oakley BB, Morales CA, Verevkin VV, Bannov VA, Krasilnikova VM, Popova AV, Zhilenkov EL, Garrish JK, Schegg KM, Woolsey R, Quilici DR, Line JE, Hiett KL, Siragusa GR, Svetoch EA, Seal BS. Molecular characterization of podoviral bacteriophages virulent for Clostridium perfringens and their comparison with members of the Picovirinae. PLoS One 2012; 7:e38283. [PMID: 22666499 PMCID: PMC3362512 DOI: 10.1371/journal.pone.0038283] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 05/02/2012] [Indexed: 01/21/2023] Open
Abstract
Clostridium perfringens is a Gram-positive, spore-forming anaerobic bacterium responsible for human food-borne disease as well as non-food-borne human, animal and poultry diseases. Because bacteriophages or their gene products could be applied to control bacterial diseases in a species-specific manner, they are potential important alternatives to antibiotics. Consequently, poultry intestinal material, soil, sewage and poultry processing drainage water were screened for virulent bacteriophages that lysed C. perfringens. Two bacteriophages, designated ΦCPV4 and ΦZP2, were isolated in the Moscow Region of the Russian Federation while another closely related virus, named ΦCP7R, was isolated in the southeastern USA. The viruses were identified as members of the order Caudovirales in the family Podoviridae with short, non-contractile tails of the C1 morphotype. The genomes of the three bacteriophages were 17.972, 18.078 and 18.397 kbp respectively; encoding twenty-six to twenty-eight ORF's with inverted terminal repeats and an average GC content of 34.6%. Structural proteins identified by mass spectrometry in the purified ΦCP7R virion included a pre-neck/appendage with putative lyase activity, major head, tail, connector/upper collar, lower collar and a structural protein with putative lysozyme-peptidase activity. All three podoviral bacteriophage genomes encoded a predicted N-acetylmuramoyl-L-alanine amidase and a putative stage V sporulation protein. Each putative amidase contained a predicted bacterial SH3 domain at the C-terminal end of the protein, presumably involved with binding the C. perfringens cell wall. The predicted DNA polymerase type B protein sequences were closely related to other members of the Podoviridae including Bacillus phage Φ29. Whole-genome comparisons supported this relationship, but also indicated that the Russian and USA viruses may be unique members of the sub-family Picovirinae.
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Affiliation(s)
- Nikolay V. Volozhantsev
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
- * E-mail: (NV); (BS)
| | - Brian B. Oakley
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, Athens, Georgia, United States of America
| | - Cesar A. Morales
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, Athens, Georgia, United States of America
| | - Vladimir V. Verevkin
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
| | - Vasily A. Bannov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
| | - Valentina M. Krasilnikova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
| | - Anastasia V. Popova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
| | - Eugeni L. Zhilenkov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
| | - Johnna K. Garrish
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, Athens, Georgia, United States of America
| | - Kathleen M. Schegg
- Nevada Proteomics Center, University of Nevada, Reno, Nevada, United States of America
| | - Rebekah Woolsey
- Nevada Proteomics Center, University of Nevada, Reno, Nevada, United States of America
| | - David R. Quilici
- Nevada Proteomics Center, University of Nevada, Reno, Nevada, United States of America
| | - J. Eric Line
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, Athens, Georgia, United States of America
| | - Kelli L. Hiett
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, Athens, Georgia, United States of America
| | | | - Edward A. Svetoch
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation
| | - Bruce S. Seal
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, Athens, Georgia, United States of America
- * E-mail: (NV); (BS)
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36
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The genome sequence and proteome of bacteriophage ΦCPV1 virulent for Clostridium perfringens. Virus Res 2011; 155:433-9. [DOI: 10.1016/j.virusres.2010.11.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2010] [Revised: 11/22/2010] [Accepted: 11/28/2010] [Indexed: 11/19/2022]
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37
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Deschavanne P, DuBow MS, Regeard C. The use of genomic signature distance between bacteriophages and their hosts displays evolutionary relationships and phage growth cycle determination. Virol J 2010; 7:163. [PMID: 20637121 PMCID: PMC2917420 DOI: 10.1186/1743-422x-7-163] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 07/17/2010] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Bacteriophage classification is mainly based on morphological traits and genome characteristics combined with host information and in some cases on phage growth lifestyle. A lack of molecular tools can impede more precise studies on phylogenetic relationships or even a taxonomic classification. The use of methods to analyze genome sequences without the requirement for homology has allowed advances in classification. RESULTS Here, we proposed to use genome sequence signature to characterize bacteriophages and to compare them to their host genome signature in order to obtain host-phage relationships and information on their lifestyle. We analyze the host-phage relationships in the four most representative groups of Caudoviridae, the dsDNA group of phages. We demonstrate that the use of phage genomic signature and its comparison with that of the host allows a grouping of phages and is also able to predict the host-phage relationships (lytic vs. temperate). CONCLUSIONS We can thus condense, in relatively simple figures, this phage information dispersed over many publications.
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Affiliation(s)
- Patrick Deschavanne
- Molécules Thérapeutiques in Silico MTI, INSERM UMR-M 973, Université Paris Diderot - Paris 7, Bât Lamarck, 75205, Paris Cedex 13, France.
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38
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Hoshiba H, Uchiyama J, Kato SI, Ujihara T, Muraoka A, Daibata M, Wakiguchi H, Matsuzaki S. Isolation and characterization of a novel Staphylococcus aureus bacteriophage, ϕMR25, and its therapeutic potential. Arch Virol 2010; 155:545-52. [DOI: 10.1007/s00705-010-0623-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Accepted: 12/28/2009] [Indexed: 11/25/2022]
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39
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Antibacterial and biofilm removal activity of a podoviridae Staphylococcus aureus bacteriophage SAP-2 and a derived recombinant cell-wall-degrading enzyme. Appl Microbiol Biotechnol 2009; 86:1439-49. [PMID: 20013118 DOI: 10.1007/s00253-009-2386-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 11/24/2009] [Accepted: 11/24/2009] [Indexed: 10/20/2022]
Abstract
Antibacterial and biofilm removal activity of a new podoviridae Staphylococcus aureus bacteriophage (SAP-2), which belongs to the phi29-like phage genus of the Podoviridae family, and a cell-wall-degrading enzyme (SAL-2), which is derived from bacteriophage SAP-2, have been characterized. The cell-wall-degrading enzyme SAL-2 was expressed in Escherichia coli in a soluble form using a low-temperature culture. The cell-wall-degrading enzyme SAL-2 had specific lytic activity against S. aureus, including methicillin-resistant strains, and showed a minimum inhibitory concentration of about 1 microg/ml. In addition, this enzyme showed a broader spectrum of activity within the Staphylococcus genus compared with bacteriophage SAP-2 in its ability to remove the S. aureus biofilms. Thus, the cell-wall-degrading enzyme SAL-2 can be used to prevent and treat biofilm-associated S. aureus infections either on its own or in combination with other cell-wall-degrading enzymes with anti-S. aureus activity.
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40
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Son JS, Jun SY, Kim EB, Park JE, Paik HR, Yoon SJ, Kang SH, Choi YJ. Complete genome sequence of a newly isolated lytic bacteriophage, EFAP-1 of Enterococcus faecalis, and antibacterial activity of its endolysin EFAL-1. J Appl Microbiol 2009; 108:1769-79. [PMID: 19863688 DOI: 10.1111/j.1365-2672.2009.04576.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
AIMS In this work, we aimed to identify an effective treatment of infections caused by Enterococcus spp. strains resistant to conventional antibiotics. METHODS AND RESULTS We report the isolation and characterization of a new lytic bacteriophage, designated bacteriophage EFAP-1, that is capable of lysing Enterococcus faecalis bacteria that exhibit resistance to multiple antibiotics. EFAP-1 has low sequence similarity to all known bacteriophages. Transmission electron microscopy confirmed that EFAP-1 belongs to the Siphoviridae family. A putative lytic protein of EFAP-1, endolysin EFAL-1, is encoded in ORF 2 and was expressed in Escherichia coli. Recombinant EFAL-1 had broad-spectrum lytic activity against several Gram-positive pathogens, including Ent. faecalis and Enterococcus faecium. CONCLUSIONS The complete genome sequence of the newly isolated enterococcal lytic phage was analysed, and it was demonstrated that its recombinant endolysin had broad lytic activity against various Gram-positive pathogens. SIGNIFICANCE AND IMPACT OF THE STUDY Bacteriophage EFAP-1 and its lytic protein, EFAL-1, can be utilized as potent antimicrobial agents against Enterococcus spp. strains resistant to conventional antibiotics in hospital infections and also as environmental disinfectants to control disease-causing Enterococcus spp. in dairy farms.
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Affiliation(s)
- J S Son
- Laboratory of Animal Cell Biotechnology, Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
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41
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Differentially conserved staphylococcal SH3b_5 cell wall binding domains confer increased staphylolytic and streptolytic activity to a streptococcal prophage endolysin domain. Gene 2009; 443:32-41. [DOI: 10.1016/j.gene.2009.04.023] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 04/16/2009] [Accepted: 04/24/2009] [Indexed: 11/19/2022]
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42
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Manoharadas S, Witte A, Bläsi U. Antimicrobial activity of a chimeric enzybiotic towards Staphylococcus aureus. J Biotechnol 2008; 139:118-23. [PMID: 18940209 DOI: 10.1016/j.jbiotec.2008.09.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 09/09/2008] [Accepted: 09/15/2008] [Indexed: 10/21/2022]
Abstract
Phage lytic enzymes (enzybiotics) have gained attention as prospective tools to eradicate Gram-positive pathogens resistant to antibiotics. Attempts to purify the P16 endolysin of Staphylococcus aureus phage P68 were unsuccessful owing to the poor solubility of the protein. To overcome this limitation, we constructed a chimeric endolysin (P16-17) comprised of the inferred N-terminal d-alanyl-glycyl endopeptidase domain and the C-terminal cell wall targeting domain of the S. aureus phage P16 endolysin and the P17 minor coat protein, respectively. The domain swapping approach and the applied purification procedure resulted in soluble P16-17 protein, which exhibited antimicrobial activity towards S. aureus. In addition, P16-17 augmented the antimicrobial efficacy of the antibiotic gentamicin. This synergistic effect could be useful to reduce the effective dose of aminoglycoside antibiotics.
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Affiliation(s)
- Salim Manoharadas
- Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria
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43
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Mann NH. The potential of phages to prevent MRSA infections. Res Microbiol 2008; 159:400-5. [PMID: 18541414 DOI: 10.1016/j.resmic.2008.04.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 03/25/2008] [Accepted: 04/14/2008] [Indexed: 11/19/2022]
Abstract
This short review attempts to examine whether there is a potential for the use of phages capable of infecting Staphylococcus aureus to eradicate or reduce nasal colonisation, thereby reducing the overall infection burden in patient populations identified as being at risk from MRSA infections. There is clear evidence that nasal decolonisation may be of benefit to certain patient groups and also that phages can effectively combat experimentally induced S. aureus infections in animals. However, this is not in itself enough to validate the use of phages for decolonisation and, given the appearance of strains resistant to currently used topical antibiotics, there is a need for clinical trials of this prophylactic use of phages.
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Affiliation(s)
- Nicholas H Mann
- Novolytics Ltd., Unit 26, Barclays Venture Centre, Sir William Lyons Road, Coventry CV4 7EZ, UK.
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44
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Lavigne R, Seto D, Mahadevan P, Ackermann HW, Kropinski AM. Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res Microbiol 2008; 159:406-14. [PMID: 18555669 DOI: 10.1016/j.resmic.2008.03.005] [Citation(s) in RCA: 235] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 03/18/2008] [Accepted: 03/31/2008] [Indexed: 11/19/2022]
Abstract
We defined phage genera by measuring genome relationships by the numbers of shared homologous/orthologous proteins. We used BLAST-based tools (CoreExtractor.vbs and CoreGenes) to analyze 55 fully sequenced bacteriophage genomes from the NCBI and EBI databases. This approach was first applied to the T7-related phages. Using a cut-off score of 40% homologous proteins, we identified three genera within the T7-related phages, redefined the phi29-related phages, and introduced five novel genera. The T7- and phi29-related phages were given subfamily status and named "Autographivirinae" and "Picovirinae", respectively. Our results confirm and refine the ICTV phage classification, enable elimination of errors in public databases, and provide a straightforward tool for the molecular classification of new phage genomes.
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Affiliation(s)
- Rob Lavigne
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, Leuven, B-3001, Belgium
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45
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Ackermann HW, Kropinski AM. Curated list of prokaryote viruses with fully sequenced genomes. Res Microbiol 2007; 158:555-66. [PMID: 17889511 DOI: 10.1016/j.resmic.2007.07.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2007] [Revised: 07/18/2007] [Accepted: 07/18/2007] [Indexed: 11/19/2022]
Abstract
Genome sequencing is of enormous importance for classification of prokaryote viruses and for understanding the evolution of these viruses. This survey covers 284 sequenced viruses for which a full description has been published and for which the morphology is known. This corresponds to 219 (4%) of tailed and 75 (36%) of tailless viruses of prokaryotes. The number of sequenced tailless viruses almost doubles if viruses of unknown morphology are counted. The sequences are from representatives of 15 virus families and three groups without family status, including eight taxa of archaeal viruses. Tailed phages, especially those with large genomes and hosts other than enterobacteria or lactococci, mycobacteria and pseudomonads, are vastly under investigated.
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Affiliation(s)
- Hans-W Ackermann
- Felix d'Herelle Reference Center for Bacterial Viruses, Department of Medical Biology, Faculty of Medicine, Laval University, Québec, QC G1K 7P4, Canada.
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46
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Takáč M, Witte A, Bläsi U. Functional analysis of the lysis genes of Staphylococcus aureus phage P68 in Escherichia coli. MICROBIOLOGY-SGM 2005; 151:2331-2342. [PMID: 16000723 DOI: 10.1099/mic.0.27937-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Double-stranded DNA phages of both Gram-positive and Gram-negative bacteria typically use a holin-endolysin system to achieve lysis of their host. In this study, the lysis genes of Staphylococcus aureus phage P68 were characterized. P68 gene lys16 was shown to encode a cell-wall-degrading enzyme, which causes cell lysis when externally added to clinical isolates of S. aureus. Another gene, hol15, was identified embedded in the -1 reading frame at the 3' end of lys16. The deduced Hol15 protein has three putative transmembrane domains, and thus resembles class I holins. An additional candidate holin gene, hol12, was found downstream of the endolysin gene lys16 based on two predicted transmembrane domains of the encoded protein, which is a typical trait of class II holins. The synthesis of either Hol12 or Hol15 resulted in growth retardation of Escherichia coli, and both hol15 and hol12 were able to complement a phage lambda Sam mutation. The hol15 gene has a dual start motif beginning with the codons Met1-Lys2-Met3.... Evidence is presented that the hol15 gene encodes a lysis inhibitor (anti-holin) and a lysis effector (actual holin). As depolarization of the membrane converted the anti-holin to a functional holin, these studies suggested that hol15 functions as a typical dual start motif class I holin. The unusual arrangement of the P68 lysis genes is discussed.
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Affiliation(s)
- Marian Takáč
- Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter, Dr Bohrgasse 9/4, 1030 Vienna, Austria
| | - Angela Witte
- Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter, Dr Bohrgasse 9/4, 1030 Vienna, Austria
| | - Udo Bläsi
- Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter, Dr Bohrgasse 9/4, 1030 Vienna, Austria
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47
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Sau K, Gupta SK, Sau S, Ghosh TC. Synonymous codon usage bias in 16 Staphylococcus aureus phages: implication in phage therapy. Virus Res 2005; 113:123-31. [PMID: 15970346 DOI: 10.1016/j.virusres.2005.05.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 05/06/2005] [Accepted: 05/10/2005] [Indexed: 11/22/2022]
Abstract
To reveal the factors influencing architecture of protein-coding genes in staphylococcal phages, relative synonymous codon usage variation has been investigated in 920 protein-coding genes of 16 staphylococcal phages. As expected for AT rich genomes, there are predominantly A and T ending codons in all 16 phages. Both Nc plot and correspondence analysis on relative synonymous codon usage indicates that mutation bias influences codon usage variation in the 16 phages. Correspondence analysis also suggests that translational selection and gene length also influence the codon usage variation in the phages to some extent and codon usage in staphylococcal phages is phage-specific but not S. aureus-specific. Further analysis indicates that among 16 staphylococcal phages, 44AHJD, P68 and K may be extremely virulent in nature as most of their genes have high translation efficiency. If this is true, then above three phages may be useful for curing staphylococcal infections.
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Affiliation(s)
- K Sau
- Bioinformatics Centre, Bose Institute, P1/12, CIT Scheme VII M, Calcutta 700 054, India.
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48
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Loessner MJ. Bacteriophage endolysins--current state of research and applications. Curr Opin Microbiol 2005; 8:480-7. [PMID: 15979390 DOI: 10.1016/j.mib.2005.06.002] [Citation(s) in RCA: 362] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Accepted: 06/09/2005] [Indexed: 11/27/2022]
Abstract
Endolysins are phage-encoded enzymes that break down bacterial peptidoglycan at the terminal stage of the phage reproduction cycle. Their action is tightly regulated by holins, by membrane arrest, and by conversion from their inactive to active state. Recent research has not only revealed the unexpected diversity of these highly specific hydrolases but has also yielded insights into their modular organization and their three-dimensional structures. Their N-terminal catalytic domains are able to target almost every possible bond in the peptidoglycan network, and their corresponding C-terminal cell wall binding domains target the enzymes to their substrate. Owing to their specificity and high activity, endolysins have been employed for various in vitro and in vivo aims, in food science, in microbial diagnostics, and for treatment of experimental infections. Clearly, phage endolysins represent great tools for use in molecular biology, biotechnology and in medicine, and we are just beginning to tap this potential.
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Affiliation(s)
- Martin J Loessner
- Institute of Food Science and Nutrition, Swiss Federal Institute of Technology (ETH), Schmelzbergstrasse 7, CH-8092 Zürich, Switzerland.
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49
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Takác M, Bläsi U. Phage P68 virion-associated protein 17 displays activity against clinical isolates of Staphylococcus aureus. Antimicrob Agents Chemother 2005; 49:2934-40. [PMID: 15980371 PMCID: PMC1168661 DOI: 10.1128/aac.49.7.2934-2940.2005] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Revised: 01/26/2005] [Accepted: 03/27/2005] [Indexed: 11/20/2022] Open
Abstract
Phage-encoded murein hydrolases are either part of the lysis cassette or found as structural components of the phage virion. Here, we show that Staphylococcus aureus bacteriophage P68 contains a virion-associated muralytic enzyme. Protein 17 has a composite structure. The N-terminal part comprises the muralytic activity, whereas the C-terminal part is required for binding to the cell surface. A high multiplicity of infection with phage P68 caused rapid lysis, and purified protein 17 triggered premature lysis when added to S. aureus cells prior to infection with P68, suggesting that it functions to weaken the murein at the site of phage DNA entry. Protein 17 displayed activity against clinical S. aureus isolates, which are resistant to infection by phage P68, demonstrating that the protein targets surface structures distinct from the phage receptor. This broad activity spectrum of protein 17 could qualify virion-associated muralytic enzymes as attractive antimicrobials.
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Affiliation(s)
- Marian Takác
- Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter, Dr. Bohrgasse 9/4, 1030 Vienna, Austria
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50
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Kwan T, Liu J, DuBow M, Gros P, Pelletier J. The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc Natl Acad Sci U S A 2005; 102:5174-9. [PMID: 15788529 PMCID: PMC556006 DOI: 10.1073/pnas.0501140102] [Citation(s) in RCA: 271] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages are the most abundant life forms in the biosphere. They play important roles in bacterial ecology, evolution, adaptation to new environments, and pathogenesis of human bacterial infections. Here, we report the complete genomic sequences, and predicted proteins of 27 bacteriophages of the Gram-positive bacterium Staphylococcus aureus. Comparative nucleotide and protein sequence analysis indicates that these phages are a remarkable source of untapped genetic diversity, encoding 2,170 predicted protein-encoding ORFs, of which 1,402 cannot be annotated for structure or function, and 522 are proteins with no similarity to other phage or bacterial sequences. Based on their genome size, organization of their gene map and comparative nucleotide and protein sequence analysis, the S. aureus phages can be organized into three groups. Comparison of their gene maps reveals extensive genome mosaicism, hinting to a large reservoir of unidentified S. aureus phage genes. Among the phages in the largest size class (178-214 kbp) that we characterized is phage Twort, the first discovered bacteriophage (responsible for the Twort-D'Herelle effect). These phage genomes offer an exciting opportunity to discern molecular mechanisms of phage evolution and diversity.
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Affiliation(s)
- Tony Kwan
- Targanta Therapeutics, 7170 Frederick Banting, Second Floor, Ville Saint Laurent, QC, Canada H4S 2A1
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