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Jiang L, Zheng R, Sun Q, Li C. Isolation, characterization, and application of Salmonella paratyphi phage KM16 against Salmonella paratyphi biofilm. BIOFOULING 2021; 37:276-288. [PMID: 33947280 DOI: 10.1080/08927014.2021.1900130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 02/20/2021] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Salmonella biofilm prevention and control is of great importance. This study, investigated the use of the isolated phage KM16 belonging to the family Myoviridae in the order Caudovirales. The phage genome size was 170,126 bp. Almost all phages were adsorbed to the host within 20 min. KM16 had a latent period of 70 min followed by a rise period of 40 min. Phage KM16 had the ability to lytically infect 10 out of the 12 clinical strains of S. paratyphi tested. Phylogenetic analysis indicated that the S. paratyphi 16S rRNA, crispr 1 and fimA genes correlated with the lytic spectrum of phage KM16. The lytic spectrum of phage KM16 correlated with Salmonella pili (fimA), and Salmonella pili were the recognition site for phage adsorption to the host. Phage KM16 (MOI = 0.1) had a better anti-biofilm effect than kanamycin sulfate (10 ug ml-1) in high-concentration Salmonella cultures.
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Affiliation(s)
- Liming Jiang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, PR China
| | - Rui Zheng
- Department of Clinical laboratory, The First People's Hospital of Yunnan Province, Kunming, PR China
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
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Korf IHE, Kittler S, Bierbrodt A, Mengden R, Rohde C, Rohde M, Kroj A, Lehnherr T, Fruth A, Flieger A, Lehnherr H, Wittmann J. In Vitro Evaluation of a Phage Cocktail Controlling Infections with Escherichia coli. Viruses 2020; 12:v12121470. [PMID: 33352791 PMCID: PMC7768485 DOI: 10.3390/v12121470] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Worldwide, poultry industry suffers from infections caused by avian pathogenic Escherichia coli. Therapeutic failure due to resistant bacteria is of increasing concern and poses a threat to human and animal health. This causes a high demand to find alternatives to fight bacterial infections in animal farming. Bacteriophages are being especially considered for the control of multi-drug resistant bacteria due to their high specificity and lack of serious side effects. Therefore, the study aimed on characterizing phages and composing a phage cocktail suitable for the prevention of infections with E. coli. Six phages were isolated or selected from our collections and characterized individually and in combination with regard to host range, stability, reproduction, and efficacy in vitro. The cocktail consisting of six phages was able to inhibit formation of biofilms by some E. coli strains but not by all. Phage-resistant variants arose when bacterial cells were challenged with a single phage but not when challenged by a combination of four or six phages. Resistant variants arising showed changes in carbon metabolism and/or motility. Genomic comparison of wild type and phage-resistant mutant E28.G28R3 revealed a deletion of several genes putatively involved in phage adsorption and infection.
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Affiliation(s)
- Imke H. E. Korf
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (C.R.); (J.W.)
- Correspondence:
| | - Sophie Kittler
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany;
| | | | - Ruth Mengden
- Food Inspection, Animal Welfare and Veterinary Service of the Land of Bremen, Border Control Post Bremerhaven, Senator-Borttscheller-Straße 8, 27568 Bremerhaven, Germany;
| | - Christine Rohde
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (C.R.); (J.W.)
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany;
| | - Andrea Kroj
- PTC Phage Technology Center GmbH, Siemensstraße 42, 59199 Bönen, Germany; (A.K.); (T.L.); (H.L.)
| | - Tatiana Lehnherr
- PTC Phage Technology Center GmbH, Siemensstraße 42, 59199 Bönen, Germany; (A.K.); (T.L.); (H.L.)
| | - Angelika Fruth
- Robert Koch Institute, Burgstraße 37, 38855 Wernigerode, Germany; (A.F.); (A.F.)
| | - Antje Flieger
- Robert Koch Institute, Burgstraße 37, 38855 Wernigerode, Germany; (A.F.); (A.F.)
| | - Hansjörg Lehnherr
- PTC Phage Technology Center GmbH, Siemensstraße 42, 59199 Bönen, Germany; (A.K.); (T.L.); (H.L.)
| | - Johannes Wittmann
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (C.R.); (J.W.)
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Khalatbari-Limaki S, Hosseinzadeh S, Shekarforoush SS, Berizi E. The morphological and biological characteristics of a virulent PI phage isolated from slaughterhouse sewage in Shiraz, Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2020; 12:616-624. [PMID: 33613917 PMCID: PMC7884271 DOI: 10.18502/ijm.v12i6.5037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND OBJECTIVES Foodborne pathogens are among the serious problems all around the world and thus a novel and natural strategy to control and to inhibit such pathogens is highly demanded nowadays. The aim of this study was to isolate a specific bacteriophage of Escherichia coli O157:H7 from sewage in Fars province, Iran to determine its morphological and antimicrobial activities. MATERIALS AND METHODS In order to isolate the bacteriophage of E. coli O157:H7, 10 samples of slaughterhouse wastewaters were used. Double-Layer Agar method was employed to isolate the bacteriophage. To identify the fine structure of the bacteriophage, electron microscope was employed. Host range and antibacterial activity of the phage was also investigated, in vitro. RESULTS The morphological and biological characteristics of a virulent Siphoviridae phage, PI, are reported. It was found that infection of E. coli O157:H7 strains with this specific bacteriophage produce clear plaques. In the one-step growth analysis, it was confirmed that the phage has been characterized with a very short rise period (around 15 min), an average burst size of 193 PFU/cell, high infectivity and potent lytic action. The bacteriolytic activity of PI was also investigated, in vitro. It was also clarified that at the MOI of 100, 10 and 1, the phage rapidly lysed the bacterial cells within 0.5 or 2 h. CONCLUSION These results indicate that the phage PI is a newly discovered phage against E. coli O157:H7 in Iran which may be recommended to use as bio-control purposes.
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Affiliation(s)
- Sepideh Khalatbari-Limaki
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Saeid Hosseinzadeh
- 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, Nutrition Research Center, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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Fan C, Tie D, Sun Y, Jiang J, Huang H, Gong Y, Zhao C. Characterization and Genomic Analysis of Escherichia coli O157:H7 Bacteriophage FEC14, a New Member of Genus Kuttervirus. Curr Microbiol 2020; 78:159-166. [PMID: 33185717 DOI: 10.1007/s00284-020-02283-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 11/02/2020] [Indexed: 12/20/2022]
Abstract
Escherichia coli O157:H7 is an important foodborne pathogen that has become a major worldwide factor affecting the public safety of food. Bacteriophage has gradually attracted attention because of its ability to kill specific pathogens. In this study, a lytic phage of E. coli O157:H7, named FEC14, was isolated from hospital sewage. Transmission electron microscopy analysis showed that phage FEC14 had an isometric head 80 ± 5 nm in diameter and a contractile tail whose terminal spikes present an umbrella-like structure. Phage FEC14 revealed 158,639 bp double-stranded DNA, with the G+C content of 44.6%, 209 ORFs and four tRNAs. Genome DNA of FEC14 could not be digested by some endonucleases. Many of the features of phage FEC14 are very similar to those of the newly classified genus "Kuttervirus", including morphology, genome size and organization, etc. Phage FEC14 is proposed to be a new isolate of genus "Kuttervirus" within the family Ackermannviridae, moreover, the endonuclease resistance of phage FEC14, has priority over other genera of bacteriophages for its use in biocontrol of foodborne pathogens.
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Affiliation(s)
- Congcong Fan
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Dandan Tie
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Yanbo Sun
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Jie Jiang
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Honglan Huang
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, People's Republic of China
| | - Yunwei Gong
- Changchun Center for Disease Control and Prevention Department of Microbiology, Changchun, Jilin, People's Republic of China
| | - Chunyan Zhao
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, People's Republic of China.
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55
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Easwaran M, De Zoysa M, Shin HJ. Application of phage therapy: Synergistic effect of phage EcSw (ΦEcSw) and antibiotic combination towards antibiotic-resistant Escherichia coli. Transbound Emerg Dis 2020; 67:2809-2817. [PMID: 32453904 DOI: 10.1111/tbed.13646] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 04/20/2020] [Accepted: 05/15/2020] [Indexed: 11/30/2022]
Abstract
Bacteriophage therapy is acknowledged as a potential tool to prevent or treat multidrug-resistant bacterial infections. In this study, our major focus was on the bacteriolytic activity of phage EcSw (ΦEcSw) against the emergence of the clinically important Escherichia coli Sw1 and E. coli O157:H7. The amount of the antibiotics was changed in a concentration-dependent manner, and the ΦEcSw susceptibility to antibiotics was determined. The kanamycin and chloramphenicol inhibited the titre of phage, but ampicillin did not show phage inhibition. Though the kanamycin and chloramphenicol controlled the growth of Sw1 in a concentration-dependent manner, the ampicillin did not due to the resistance. The combined activity of the ΦEcSw with antibiotics (kanamycin and chloramphenicol) compared with the antibiotics alone showed significant lytic activity p < .001). In addition, phage-based therapy was evaluated for controlling the multidrug-resistant E. coli Sw1 and E. coli O157:H7 in zebrafish and BALB/c mice, respectively. Our results provide novel advantages of phage therapy and phage-antibiotic therapy to control antibiotic-resistant bacteria.
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Affiliation(s)
- Maheswaran Easwaran
- College of Veterinary Medicine, Chungnam National University, Daejeon, Korea
| | - Mahanama De Zoysa
- College of Veterinary Medicine, Chungnam National University, Daejeon, Korea
- Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, Korea
| | - Hyun-Jin Shin
- College of Veterinary Medicine, Chungnam National University, Daejeon, Korea
- Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, Korea
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56
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Yamaki S, Yamazaki K. Development of a Novel Food Antimicrobial Technology: Application of Bacteriophages. J JPN SOC FOOD SCI 2020. [DOI: 10.3136/nskkk.67.352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Shogo Yamaki
- Faculty of Fisheries Sciences, Hokkaido University
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57
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Nguyen MM, Gil J, Brown M, Cesar Tondo E, Soraya Martins de Aquino N, Eisenberg M, Erickson S. Accurate and sensitive detection of Salmonella in foods by engineered bacteriophages. Sci Rep 2020; 10:17463. [PMID: 33060781 PMCID: PMC7567081 DOI: 10.1038/s41598-020-74587-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022] Open
Abstract
Salmonella is a major causative agent of foodborne illness and rapid identification of this pathogen is essential to prevent disease. Currently most assays require high bacterial burdens or prolonged enrichment to achieve acceptable performance. A reduction in testing time without loss of sensitivity is critical to allow food processors to safely decrease product holding time. To meet this need, a method was developed to detect Salmonella using luciferase reporter bacteriophages. Bacteriophages were engineered to express NanoLuc, a novel optimized luciferase originating from the deep-sea shrimp Oplophorus gracilirostris. NanoLuc-expressing bacteriophages had a limit of detection of 10-100 CFU per mL in culture without enrichment. Luciferase reporters demonstrated a broad host range covering all Salmonella species with one reporter detecting 99.3% of 269 inclusivity strains. Cross-reactivity was limited and only observed with other members of the Enterobacteriaceae family. In food matrix studies, a cocktail of engineered bacteriophages accurately detected 1 CFU in either 25 g of ground turkey with a 7 h enrichment or 100 g of powdered infant formula with a 16 h enrichment. Use of the NanoLuc reporter assay described herein resulted in a considerable reduction in enrichment time without a loss of sensitivity.
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Affiliation(s)
- Minh M Nguyen
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
| | - Jose Gil
- Laboratory Corporation of America Holdings, Los Angeles, CA, 90062, USA
| | - Matthew Brown
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Eduardo Cesar Tondo
- Laboratório de Microbiologia e Controle de Alimentos, Instituto de Ciência e Tecnologia de Alimentos, Universidade Federal do Rio Grande do Sul (ICTA/UFRGS), Porto Alegre, RS, 91501-970, Brazil
| | - Nathanyelle Soraya Martins de Aquino
- Laboratório de Microbiologia e Controle de Alimentos, Instituto de Ciência e Tecnologia de Alimentos, Universidade Federal do Rio Grande do Sul (ICTA/UFRGS), Porto Alegre, RS, 91501-970, Brazil
| | - Marcia Eisenberg
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Stephen Erickson
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA.
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58
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Challenges & opportunities for phage-based in situ microbiome engineering in the gut. J Control Release 2020; 326:106-119. [DOI: 10.1016/j.jconrel.2020.06.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 06/14/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022]
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59
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Choi IY, Park DH, Chin BA, Lee C, Lee J, Park MK. Exploring the feasibility of Salmonella Typhimurium-specific phage as a novel bio-receptor. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:668-681. [PMID: 33089232 PMCID: PMC7553841 DOI: 10.5187/jast.2020.62.5.668] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 11/23/2022]
Abstract
The purpose of this study was aimed to isolate a Salmonella
Typhimurium-specific phage (KFS-ST) from washing water in a poultry processing
facility and to investigate the feasibility of the KFS-ST as a novel
bio-receptor for the magnetoelastic (ME) biosensor method. KFS-ST against
S. Typhimurium was isolated, propagated, and purified using
a CsCl-gradient ultracentrifugation. Morphological characteristics of KFS-ST
were analyzed using transmission electron microscopy (TEM). Its specificity and
efficiency of plating analysis were conducted against 39 foodborne pathogens.
The temperature and pH stabilities of KFS-ST were investigated by the exposure
of the phage to various temperatures (−70°C–70°C)
and pHs (1–12) for 1 h. A one-step growth curve analysis was performed to
determine the eclipse time, latent time and burst size of phage. The storage
stability of KFS-ST was studied by exposing KFS-ST to various storage
temperatures (−70°C, −20°C, 4°C, and
22°C) for 12 weeks. KFS-ST was isolated and purified with a high
concentration of (11.47 ± 0.25) Log PFU/mL. It had an icosahedral head
(56.91 ± 2.90 nm) and a non-contractile tail (225.49 ± 2.67 nm),
which was classified into the family of Siphoviridae in the
order of Caudovirales. KFS-ST exhibited an excellent
specificity against only S. Typhimurium and S.
Enteritidis, which are considered two of the most problematic
Salmonella strains in the meat and poultry. However, KFS-ST
did not exhibit any specificity against six other Salmonella
and 27 non-Salmonella strains. KFS-ST was stable at temperature
of 4°C to 50°C and at pH of 4 to 12. The eclipse time, latent
time, and burst size of KFS-ST were determined to be 10 min, 25 min and 26 PFU/
infected cell, respectively. KFS-ST was relatively stable during the 12-week
storage period at all tested temperatures. Therefore, this study demonstrated
the feasibility of KFS-ST as a novel bio-receptor for the detection of
S. Typhimurium and S. Enteritidis in meat
and poultry products using the ME biosensor method.
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Affiliation(s)
- In Young Choi
- School of Food Science and Biotechnology, and Food and Bio-Industry Research Institute, Kyungpook National University, Daegu 41566, Korea
| | - Do Hyeon Park
- School of Food Science and Biotechnology, and Food and Bio-Industry Research Institute, Kyungpook National University, Daegu 41566, Korea
| | - Brayan A Chin
- Materials Research and Education Center, Auburn University, Auburn, AL 36849, USA
| | - Cheonghoon Lee
- Graduate School of Public Health, and Institute of Health and Environment, Seoul National University, Seoul 08826, Korea
| | - Jinyoung Lee
- Gyedong General Education Institute, Sangmyung University, Cheonan 31066, Korea
| | - Mi-Kyung Park
- School of Food Science and Biotechnology, and Food and Bio-Industry Research Institute, Kyungpook National University, Daegu 41566, Korea
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Structure and function of bacteriophage CBA120 ORF211 (TSP2), the determinant of phage specificity towards E. coli O157:H7. Sci Rep 2020; 10:15402. [PMID: 32958885 PMCID: PMC7506556 DOI: 10.1038/s41598-020-72373-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/27/2020] [Indexed: 11/17/2022] Open
Abstract
The genome of Escherichia coli O157:H7 bacteriophage vB_EcoM_CBA120 encodes four distinct tailspike proteins (TSPs). The four TSPs, TSP1-4, attach to the phage baseplate forming a branched structure. We report the 1.9 Å resolution crystal structure of TSP2 (ORF211), the TSP that confers phage specificity towards E. coli O157:H7. The structure shows that the N-terminal 168 residues involved in TSPs complex assembly are disordered in the absence of partner proteins. The ensuing head domain contains only the first of two fold modules seen in other phage vB_EcoM_CBA120 TSPs. The catalytic site resides in a cleft at the interface between adjacent trimer subunits, where Asp506, Glu568, and Asp571 are located in close proximity. Replacement of Asp506 and Asp571 for alanine residues abolishes enzyme activity, thus identifying the acid/base catalytic machinery. However, activity remains intact when Asp506 and Asp571 are mutated into asparagine residues. Analysis of additional site-directed mutants in the background of the D506N:D571N mutant suggests engagement of an alternative catalytic apparatus comprising Glu568 and Tyr623. Finally, we demonstrate the catalytic role of two interacting glutamate residues of TSP1, located in a cleft between two trimer subunits, Glu456 and Glu483, underscoring the diversity of the catalytic apparatus employed by phage vB_EcoM_CBA120 TSPs.
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Bujak K, Decewicz P, Kaminski J, Radlinska M. Identification, Characterization, and Genomic Analysis of Novel Serratia Temperate Phages from a Gold Mine. Int J Mol Sci 2020; 21:ijms21186709. [PMID: 32933193 PMCID: PMC7556043 DOI: 10.3390/ijms21186709] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 12/14/2022] Open
Abstract
Bacteria of the genus Serratia inhabit a variety of ecological niches like water, soil, and the bodies of animals, and have a wide range of lifestyles. Currently, the complete genome sequences of 25 Serratia phages are available in the NCBI database. All of them were isolated from nutrient-rich environments like sewage, with the use of clinical Serratia strains as hosts. In this study, we identified a novel Serratia myovirus named vB_SspM_BZS1. Both the phage and its host Serratia sp. OS31 were isolated from the same oligotrophic environment, namely, an abandoned gold mine (Zloty Stok, Poland). The BZS1 phage was thoroughly characterized here in terms of its genomics, morphology, and infection kinetics. We also demonstrated that Serratia sp. OS31 was lysogenized by mitomycin-inducible siphovirus vB_SspS_OS31. Comparative analyses revealed that vB_SspM_BZS1 and vB_SspS_OS31 were remote from the known Serratia phages. Moreover, vB_SspM_BZS1 was only distantly related to other viruses. However, we discovered similar prophage sequences in genomes of various bacteria here. Additionally, a protein-based similarity network showed a high diversity of Serratia phages in general, as they were scattered across nineteen different clusters. In summary, this work broadened our knowledge on the diverse relationships of Serratia phages.
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Kim HJ, Kim YT, Kim HB, Choi SH, Lee JH. Characterization of bacteriophage VVP001 and its application for the inhibition of Vibrio vulnificus causing seafood-borne diseases. Food Microbiol 2020; 94:103630. [PMID: 33279062 DOI: 10.1016/j.fm.2020.103630] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/08/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022]
Abstract
Vibrio vulnificus is a major food-borne pathogen that causes septicemia and cellulitis with a mortality rate of >50%. However, there are no efficient natural food preservatives or biocontrol agents to control V. vulnificus in seafood. In this study, we isolated and characterized a novel bacteriophage VVP001. Host range and transmission electron microscopy morphology observations revealed that VVP001 belongs to the family Siphoviridae and specifically infects V. vulnificus. Phage stability tests showed that VVP001 is stable at a broad temperature range of -20 °C to 65 °C and a pH range from 3 to 11, which are conditions for food applications (processing, distribution, and storage). In vitro challenge assays revealed that VVP001 inhibited V. vulnificus MO6-24/O (a clinical isolate) growth up to a 3.87 log reduction. In addition, complete genome analysis revealed that the 76 kb VVP001 contains 102 open reading frames with 49.64% G + C content and no gene encoding toxins or other virulence factors, which is essential for food applications. Application of VVP001 to fresh abalone samples contaminated with V. vulnificus demonstrated its ability to inhibit V. vulnificus growth, and an in vivo mouse survival test showed that VVP001 protects mice against high mortality (survival rate >70% at a multiplicity of infection of 1000 for up to 7 days). Therefore, the bacteriophage VVP001 can be used as a good natural food preservative and biocontrol agent for food applications.
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Affiliation(s)
- Hye-Jin Kim
- Department of Food Science and Biotechnology, Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - You-Tae Kim
- Department of Food Science and Biotechnology, Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea; Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, And Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyeun Bum Kim
- Department of Animal Resources Science, Dankook University, Cheonan 31116, Republic of Korea
| | - Sang Ho Choi
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, And Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Ju-Hoon Lee
- Department of Food Science and Biotechnology, Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea; Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, And Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea.
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63
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Lu Z, Pérez-Díaz IM, Hayes JS, Breidt F. Bacteriophages Infecting Gram-Negative Bacteria in a Commercial Cucumber Fermentation. Front Microbiol 2020; 11:1306. [PMID: 32670232 PMCID: PMC7332585 DOI: 10.3389/fmicb.2020.01306] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/22/2020] [Indexed: 11/30/2022] Open
Abstract
Cucumber fermentations are one of the most important vegetable fermentations in the United States. The fermentation is usually driven by lactic acid bacteria (LAB) indigenous to fresh cucumbers. But LAB are greatly outnumbered by many Gram-negative bacteria on fresh cucumbers, which may influence the growth of LAB and the incidence of bloater defect (hollow cavities formed inside fermented cucumbers) leading to serious economic loss to the pickle industry. Rapid elimination of Gram-negative bacteria is crucial to the dominance of LAB and the reduction of bloater defect in the fermentation. Various factors can affect the viability of Gram-negative bacteria in cucumber fermentation. Bacteriophages (phages) may be one of such factors. This study explored the abundance, diversity, and functional role of phages infecting Gram-negative bacteria in a commercial cucumber fermentation. Cover brine samples were taken from a commercial fermentation tank over a 30-day period. On day 1 and day 3 of the fermentation, 39 Gram-negative bacteria and 26 independent phages were isolated. Nearly 67% of Gram-negative bacterial isolates were susceptible to phage infection. Phage hosts include Enterobacter, Citrobacter, Escherichia, Pantoea, Serratia, Leclercia, Providencia, and Pseudomonas species. About 88% of the isolated phages infected the members in the family Enterobacteriaceae and 58% of phages infected Enterobacter species. Eight phages with unique host ranges were characterized. These phages belong to the Myoviridae, Siphoviridae, or Podoviridae family and showed distinct protein profiles and DNA fingerprints. The infectivity of a phage against Enterobacter cancerogenus was evaluated in cucumber juice as a model system. The phage infection at the multiplicity of infection 1 or 100 resulted in a 5-log reduction in cell concentration within 3 h and rapidly eliminated its host. This study revealed the abundance and variety of phages infecting Gram-negative bacteria, particularly Enterobacteriaceae, in the commercial cucumber fermentation, suggesting that phages may play an important role in the elimination of Gram-negative bacteria, thereby facilitating the dominance of LAB and minimizing bloater defect. To our knowledge, this is the first report on the ecology of phages infecting Gram-negative bacteria in commercial cucumber fermentations.
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Affiliation(s)
- Zhongjing Lu
- Department of Molecular & Cellular Biology, Kennesaw State University, Kennesaw, GA, United States
| | - Ilenys M Pérez-Díaz
- United States Department of Agriculture, Agricultural Research Service, Washington, DC, United States.,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Janet S Hayes
- United States Department of Agriculture, Agricultural Research Service, Washington, DC, United States.,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Fred Breidt
- United States Department of Agriculture, Agricultural Research Service, Washington, DC, United States.,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
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64
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Buttimer C, Lynch C, Hendrix H, Neve H, Noben JP, Lavigne R, Coffey A. Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus. Antibiotics (Basel) 2020; 9:E352. [PMID: 32575906 PMCID: PMC7344957 DOI: 10.3390/antibiotics9060352] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
To date, Certrevirus is one of two genera of bacteriophage (phage), with phages infecting Pectobacterium atrosepticum, an economically important phytopathogen that causes potato blackleg and soft rot disease. This study provides a detailed description of Pectobacterium phage CB7 (vB_PatM_CB7), which specifically infects P. atrosepticum. Host range, morphology, latent period, burst size and stability at different conditions of temperature and pH were examined. Analysis of its genome (142.8 kbp) shows that the phage forms a new species of Certrevirus, sharing sequence similarity with other members, highlighting conservation within the genus. Conserved elements include a putative early promoter like that of the Escherichia coli sigma70 promoter, which was found to be shared with other genus members. A number of dissimilarities were observed, relating to DNA methylation and nucleotide metabolism. Some members do not have homologues of a cytosine methylase and anaerobic nucleotide reductase subunits NrdD and NrdG, respectively. Furthermore, the genome of CB7 contains one of the largest numbers of homing endonucleases described in a single phage genome in the literature to date, with a total of 23 belonging to the HNH and LAGLIDADG families. Analysis by RT-PCR of the HNH homing endonuclease residing within introns of genes for the large terminase, DNA polymerase, ribonucleotide reductase subunits NrdA and NrdB show that they are splicing competent. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was also performed on the virion of CB7, allowing the identification of 26 structural proteins-20 of which were found to be shared with the type phages of the genera of Vequintavirus and Seunavirus. The results of this study provide greater insights into the phages of the Certrevirus genus as well as the subfamily Vequintavirinae.
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Affiliation(s)
- Colin Buttimer
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland; (C.B.); (C.L.)
- APC Microbiome Institute, University College, T12 YT20 Cork, Ireland
| | - Caoimhe Lynch
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland; (C.B.); (C.L.)
| | - Hanne Hendrix
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; (H.H.); (R.L.)
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany;
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, 3590 Hasselt, Belgium;
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; (H.H.); (R.L.)
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland; (C.B.); (C.L.)
- APC Microbiome Institute, University College, T12 YT20 Cork, Ireland
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65
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Yıldirim Z, Sakin T, Akçelik M, Akçelik N. Identification and characterization of lytic bacteriophages specific to foodborne pathogenic Escherichia coli O157:H7. FOOD SCI TECHNOL INT 2020; 27:56-72. [PMID: 32536218 DOI: 10.1177/1082013220929836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The objective of this study was to identify and characterize five different lytic bacteriophages specific to Escherichia coli O157:H7. vB_EcoM-P12, vB_EcoM-P13, vB_EcoM-P23, and vB_EcoM-P34 phages belonged to the Myoviridae family and vB_EcoS-P24 phage was in the Siphoviridae family. Their plaque sizes changed between 0.48 ± 0.03 and 0.90 ± 0.03 mm in diameter. stx1 and stx2 virulent gene regions were absent in the genome of five Eco-phages and their genome size was 33 kbp. The protein band profiles of the five phages were found to be different from each other. Their latent period, burst size, and burst time changed between 10-15 min, 72-144 PFU/cell and 20-35 min, respectively. Multiplicity of infection values and mutant frequency of the phages were among 0.1-0.001 and 1.14 × 10-7-3.69 × 10-8, respectively. The phages had strong lytic activity against their host bacteria (E. coli NCTC 12900, ATCC 43888, and ATCC 35150) at 5-37 ℃ and adsorbed to their host cells by 92.7-97.5% in the first five minutes of incubation. These phages are thought to be good candidates as therapeutic and biocontrol agents against E. coli O157:H7 in the veterinary science and food industry due to short latent period, high burst size, rapid development in host cells, high lytic activity, high adsorption rate, stability over a wide pH range and high temperature, and absence of stx1 and stx2 genes.
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Affiliation(s)
- Zeliha Yıldirim
- Department of Food Engineering, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Tuba Sakin
- Department of Food Engineering, Niğde Ömer Halisdemir University, Niğde, Turkey
| | | | - Nefise Akçelik
- Institute of Biotechnology, Ankara University, Ankara, Turkey
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66
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Lee C, Choi IY, Park DH, Park MK. Isolation and characterization of a novel Escherichia coli O157:H7-specific phage as a biocontrol agent. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2020; 18:189-199. [PMID: 32399231 PMCID: PMC7203308 DOI: 10.1007/s40201-020-00452-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 01/20/2020] [Indexed: 05/05/2023]
Abstract
PURPOSE Escherichia coli O157:H7 is one of the major foodborne pathogens of global public concern. Bacteriophages (phages) have emerged as a promising alternative to antibiotics for controlling pathogenic bacteria. Here, a lytic E. coli O157:H7-specific phage (KFS-EC) was isolated, identified, and characterized to evaluate its potential as a biocontrol agent for E. coli O157:H7. METHODS KFS-EC was isolated from slaughterhouse in Korea. Morphological analysis, genomic analysis and several physiological tests were performed to identify and characterize the KFS-EC. RESULTS A specificity test indicated KFS-EC was strictly specific to E. coli O157:H7 strains among 60 bacterial strains tested. Morphological and phylogenetic analyses confirmed that KFS-EC belongs to the Rb49virus genus, Tevenvirinae subfamily, and the Myoviridae family of phages. KFS-EC genome consists of 164,725 bp and a total of 270 coding sequence features, of which 114 open reading frames (ORFs) were identified as phage functional genes. KFS-EC does not contain genes encoding lysogenic property and pathogenicity, which ensure its safe application. KFS-EC was relatively stable (~1 log decrease) under stressed conditions such as temperatures (20 °C-50 °C), pHs (3-11), organic solvents (ethanol and chloroform), and biocides (0.1% citric acid, 1% citric acid, and 0.1% peracetic acid). KFS-EC was able to inhibit E. coli O157:H7 efficiently at a multiplicity of infection (MOI) of 0.01 for 8 h with greater inhibitory effect and durability and was stable at 4 °C and 22 °C over a 12-week storage period. CONCLUSIONS Our results suggest that KFS-EC could be used as a biocontrol agent to E. coli O157:H7.
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Affiliation(s)
- Cheonghoon Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul, Republic of Korea
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
| | - In Young Choi
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Do Hyeon Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Mi-Kyung Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
- Food and Bio-industry Research Institute, Kyungpook National University, Daegu, Republic of Korea
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67
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Brenner T, Fong K, Lee S, Wang S. A Dynamic Method for Broad-Spectrum Bacteriophage Cocktail Formulation Against Poultry-Associated Salmonella enterica. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:109-117. [PMID: 36147893 PMCID: PMC9041457 DOI: 10.1089/phage.2020.0002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background: Poultry products are the largest food category linked to salmonellosis in Canada. Bacteriophages (phages) have been proposed as a novel antimicrobial in the poultry industry due to their documented ubiquity, efficacy, and safety benefits. Materials and Methods: A library of 78 lytic phages was rapidly screened against 50 prominent poultry-associated Salmonella enterica isolates procured from British Columbia, Canada. Results: A phage cocktail was successfully formulated using only three sewage-isolated phages (SE4, SE13, and SE20) to achieve broad-spectrum antimicrobial efficacy across all S. enterica serovars. Highly promising phages were also characterized using one-step growth curves and transmission electron microscopy. Conclusion: Relative host efficiency is a new agar-based semiquantitative metric developed here for the rapid comparison of different phages against a panel of known bacterial targets.
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Affiliation(s)
- Thomas Brenner
- Division of Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Karen Fong
- Division of Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Spencer Lee
- Division of Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Siyun Wang
- Division of Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
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68
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Jiang L, Zheng R. Isolation and Characterization of a Lytic Salmonella paratyphi Phage and Its Antibiofilm Activity Individually or Collaborative with Kanamycin Sulfate. Viral Immunol 2020; 33:521-529. [PMID: 32397917 DOI: 10.1089/vim.2020.0030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Salmonella is among the most serious of foodborne pathogens worldwide and distributed widely in the natural environment; in addition, it has caused severe medical problems and foodborne diseases. Bacterial biofilm was the multicellular community of microorganisms that attached to nonbiological and biological surfaces. Phages and their derivatives are ideal candidates for replacing and compensating antibiotic resistance problems in the future. In this study, a virulent phage of KM15 was isolated from pig slaughterhouse sump samples in Kunming, China. It belonged to the Siphoviridae family, and optimal growth temperature was 42°C, the pH of optimal preservation buffer was 6-7, optimal multiplicity of infection was 0.0001, and the genome size was 41,869 bp. The Salmonella paratyphi A and Salmonella paratyphi B have a broad spectrum of antibiotic resistance and were isolated from clinical patients in the First People's Hospital of Yunnan Province; fortunately, most of them can be lysed by phage KM15. Collaboration of phage KM15 and kanamycin sulfate has a better antibiofilm effect than KM15 and kanamycin sulfate alone, in low-concentration bacterial culture; KM15 has better antibiofilm effect than kanamycin sulfate in high-concentration bacterial culture. The data of this study provided a strong evidence of application of phage to reduce the growth of Salmonella biofilm, which was important for public health.
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Affiliation(s)
- Liming Jiang
- School of Marine Sciences, Ningbo University, Ningbo, P.R. China.,State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, P.R. China.,Jiangsu Key Laboratory of Advanced Food Manufacturing Equipment and Technology, Jiangnan University, Wuxi, P.R. China
| | - Rui Zheng
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, Kunming, P.R. China.,Department of Clinical Laboratory, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, P.R. China
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69
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Li M, Lin H, Jing Y, Wang J. Broad-host-range Salmonella bacteriophage STP4-a and its potential application evaluation in poultry industry. Poult Sci 2020; 99:3643-3654. [PMID: 32616261 PMCID: PMC7597861 DOI: 10.1016/j.psj.2020.03.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/23/2020] [Accepted: 03/23/2020] [Indexed: 12/28/2022] Open
Abstract
Salmonella is regarded as the predominant cause of foodborne illnesses worldwide, and the increase of these antimicrobial-resistant strains makes it more difficult to prevent. On this occasion, bacteriophages (phages) stand out as an alternative biocontrol agent with high efficiency and low mutation rates. Salmonella phages have confronted challenges to counteract with more than 2,500 serovars of Salmonella spp. and overcome the universality of antibiotics to different species, and thus, broad-host-range phages infecting Salmonella spp. are urgently required to realize precise poultry treatment or clinical therapy. First, phage STP4-a was screened to have a broad host range through bioinformatics analysis, and then the host range assay proved that phage STP4-a could inhibit 88 out of 91 Salmonella strains. Then, in silico analysis excluded the possibility of phage STP4-a possessing any known lysogeny factors, toxins, pathogen-related genes, or foodborne allergens, and oral toxicity studies further ensured the safety of unknown factors or suspected risks. In addition, strong inhibition effects of phage STP4-a were seen on both single Salmonella strain and multiple Salmonella strains in vitro, reducing 3-5 log in 30 min. Phage STP4-a could survive and keep more than 50% activity in simulated stomach or intestine environments in vitro. In terms of antimicrobial activities in chickens, pretreatment with phage STP4-a was the most efficient approach to Salmonella biocontrol, non-detectable in feces during the 14-day experimental period. Therefore, phage STP4-a was an extremely broad-host-range and safe biocontrol agent, performing its potential as a food additive or therapeutic drug in poultry industry.
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Affiliation(s)
- Mengzhe Li
- Department of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Hong Lin
- Department of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Yujie Jing
- Department of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Jingxue Wang
- Department of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China.
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70
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Application of a Novel Phage LPSEYT for Biological Control of Salmonella in Foods. Microorganisms 2020; 8:microorganisms8030400. [PMID: 32178465 PMCID: PMC7142823 DOI: 10.3390/microorganisms8030400] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/08/2020] [Accepted: 03/10/2020] [Indexed: 01/21/2023] Open
Abstract
Salmonella is a leading cause of foodborne diseases, and in recent years, many isolates have exhibited a high level of antibiotic resistance, which has led to huge pressures on public health. Phages are a promising strategy to control food-borne pathogens. In this study, one of our environmental phage isolates, LPSEYT, was to be able to restrict the growth of zoonotic Salmonellaenterica in vitro over a range of multiplicity of infections. Phage LPSEYT exhibited wide-ranging pH and thermal stability and rapid reproductive activity with a short latent period and a large burst size. Phage LPSEYT demonstrated potential efficiency as a biological control agent against Salmonella in a variety of food matrices, including milk and lettuce. Morphological observation, comparative genomic, and phylogenetic analysis revealed that LPSEYT does not belong to any of the currently identified genera within the Myoviridae family, and we suggest that LPSEYT represents a new genus, the LPSEYTvirus. This study contributes a phage database, develops beneficial phage resources, and sheds light on the potential application value of phages LPSEYT on food safety.
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71
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Bacteriophage-Insensitive Mutants of Antimicrobial-Resistant Salmonella Enterica are Altered in their Tetracycline Resistance and Virulence in Caco-2 Intestinal Cells. Int J Mol Sci 2020; 21:ijms21051883. [PMID: 32164202 PMCID: PMC7084636 DOI: 10.3390/ijms21051883] [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: 02/18/2020] [Revised: 02/26/2020] [Accepted: 03/06/2020] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages have shown promise as therapeutic alternatives to antibiotics for the control of infectious bacteria, including the human pathogen Salmonella. However, the development of effective phage-based applications requires the elucidation of key interactions between phages and target hosts, particularly since host resistance to phage is inevitable. Little is known about the alteration of host phenotypes following the development of resistance to phage. The aim of this study is to evaluate the antibiotic susceptibility and virulence of a Salmonella isolate following the development of resistance to bacteriophage SI1. We observed enhanced susceptibility to tetracycline and decreased invasion capacity in a differentiated Caco-2 intestinal cell line. Whole genome sequence analysis revealed an array of mutations, most notably, truncations in vgrG1_2, a core gene involved in Type VI secretion and mutations in the lipopolysaccharide, thereby indicating the plausible attachment site of phage SI1. These findings shed light on understanding the underlying mechanism for phage immunity within the host. Importantly, we reveal an associated genetic cost to the bacterial host with developing resistance to phages. Taken together, these results will aid in advancing strategies to delay or eliminate the development of host resistance when designing informed phage-based antimicrobials.
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72
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Characteristics and complete genome sequence of the virulent Vibrio alginolyticus phage VAP7, isolated in Hainan, China. Arch Virol 2020; 165:947-953. [PMID: 32130520 DOI: 10.1007/s00705-020-04535-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/27/2019] [Indexed: 02/08/2023]
Abstract
A novel Vibrio alginolyticus phage, VAP7, was isolated from seawater collected from Sanya, Hainan province, China. Whole-genome sequencing analysis revealed that phage VAP7 has a linear, double-stranded DNA genome of 144,685 bp with an average G+C content of 41.9% and a high degree of sequence similarity to Vibrio phage VP-1. Annotation results identified 193 open reading frames and one transfer RNA-encoding gene in the phage genome. The morphology and the results of phylogenetic analysis suggest that VAP7 should be classified as a new member of the family Ackermannviridae. Moreover, phage VAP7 grew over a wide pH (5.0-10.0) and temperature (4-40 °C) range. Host-range experiments revealed that VAP7 could infect 31 Vibrio alginolyticus strains. Thus, VAP7 infecting Vibrio alginolyticus strains represents a potential new candidate for use in phage therapy.
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73
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Cepko LCS, Garling EE, Dinsdale MJ, Scott WP, Bandy L, Nice T, Faber-Hammond J, Mellies JL. Myoviridae phage PDX kills enteroaggregative Escherichia coli without human microbiome dysbiosis. J Med Microbiol 2020; 69:309-323. [PMID: 32011231 PMCID: PMC7431101 DOI: 10.1099/jmm.0.001162] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Introduction. Bacteriophage therapy can be developed to target emerging diarrhoeal pathogens, but doing so in the absence of microbiome disruption, which occurs with antibiotic treatment, has not been established.Aim. Identify a therapeutic bacteriophage that kills diarrhoeagenic enteroaggregative Escherichia coli (EAEC) while leaving the human microbiome intact.Methodology. Phages from wastewater in Portland, OR, USA were screened for bacteriolytic activity by overlay assay. One isolated phage, PDX, was classified by electron microscopy and genome sequencing. A mouse model of infection determined whether the phage was therapeutic against EAEC. 16S metagenomic analysis of anaerobic cultures determined whether a normal human microbiome was altered by treatment.Results. Escherichia virus PDX, a member of the strictly lytic family Myoviridae, killed a case-associated EAEC isolate from a child in rural Tennessee in a dose-dependent manner, and killed EAEC isolates from Columbian children. A single dose of PDX (multiplicity of infection: 100) 1 day post-infection reduced EAEC recovered from mouse faeces. PDX also killed EAEC when cultured anaerobically in the presence of human faecal bacteria. While the addition of EAEC reduced the β-diversity of the human microbiota, that of the cultures with either faeces alone, faeces with EAEC and PDX, or with just PDX phage was not different statistically.Conclusion. PDX killed EAEC isolate EN1E-0007 in vivo and in vitro, while not altering the diversity of normal human microbiota in anaerobic culture, and thus could be part of an effective therapy for children in developing countries and those suffering from EAEC-mediated traveller's diarrhoea without causing dysbiosis.
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Affiliation(s)
- Leah C S Cepko
- 320 Longwood Avenue, Enders Building, Department of Infectious Disease, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eliotte E Garling
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Madeline J Dinsdale
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - William P Scott
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Loralee Bandy
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Tim Nice
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Joshua Faber-Hammond
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
| | - Jay L Mellies
- Biology Department, Reed College, 3203 SE Woodstock Blvd, Portland, OR, 97202, USA
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74
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Duc HM, Son HM, Yi HPS, Sato J, Ngan PH, Masuda Y, Honjoh KI, Miyamoto T. Isolation, characterization and application of a polyvalent phage capable of controlling Salmonella and Escherichia coli O157:H7 in different food matrices. Food Res Int 2020; 131:108977. [PMID: 32247506 DOI: 10.1016/j.foodres.2020.108977] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/01/2020] [Accepted: 01/01/2020] [Indexed: 12/17/2022]
Abstract
Salmonella Enteritidis, Salmonella Typhimurium, and Escherichia coli O157:H7 are the most important foodborne pathogens, causing serious food poisoning outbreaks worldwide. Bacteriophages are increasingly considered as novel antibacterial agents to control foodborne pathogens. In this study, 8 Salmonella phages and 10 E. coli O157:H7 phages were isolated from chicken products. A polyvalent phage PS5 capable of infecting S. Enteritidis, S. Typhimurium, and E. coli O157:H7 was further characterized and its efficacy in reducing these foodborne pathogens was evaluated in in vitro and in foods. Morphology, one-step growth, and stability assay showed that phage PS5 was a myovirus, with relatively short latent periods, large burst sizes, and high stability. Genome sequencing analysis revealed that the genome of PS5 does not contain any genes associated to antibiotic resistance, toxins, lysogeny, and virulence factors. In broth, phage PS5 significantly decreased the viable counts of all the three bacterial hosts by more than 1.3 log CFU/mL compared to controls after 2 h of incubation at 4 °C and 24 °C. In foods, treatment with PS5 also resulted in significant reductions of viable counts of all the three bacterial hosts compared to controls at temperatures tested. This is the first report on single phage capable of simultaneously controlling S. Enteritidis, S. Typhimurium and E. coli O157:H7 in both in vitro and in foods.
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Affiliation(s)
- Hoang Minh Duc
- Laboratory of Food Hygienic Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University. 6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
| | - Hoang Minh Son
- Laboratory of Food Hygienic Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University. 6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Hazel Pang Shu Yi
- Laboratory of Food Hygienic Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University. 6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Jun Sato
- Safety Science Research, R&D, Kao Corporation, 2606 Akabane, Ichikai-Machi, Haga-Gun, Tochigi 321-3497, Japan.
| | - Pham Hong Ngan
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Viet Nam
| | - Yoshimitsu Masuda
- Laboratory of Food Hygienic Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University. 6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
| | - Ken-Ichi Honjoh
- Laboratory of Food Hygienic Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University. 6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
| | - Takahisa Miyamoto
- Laboratory of Food Hygienic Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University. 6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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75
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Characterization of the Three New Kayviruses and Their Lytic Activity Against Multidrug-Resistant Staphylococcus aureus. Microorganisms 2019; 7:microorganisms7100471. [PMID: 31635437 PMCID: PMC6843549 DOI: 10.3390/microorganisms7100471] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 11/17/2022] Open
Abstract
The development of antimicrobial resistance has become a global concern. One approach to overcome the problem of drug resistance is the application of bacteriophages. This study aimed at characterizing three phages isolated from sewage, which show lytic activity against clinical isolates of multidrug-resistant Staphylococcus aureus. Morphology, genetics and biological properties, including host range, adsorption rate, latent time, phage burst size and lysis profiles, were studied in all three phages. As analyzed by transmission electron microscopy (TEM), phages vB_SauM-A, vB_SauM-C, vB_SauM-D have a myovirion morphology. One of the tested phages, vB_SauM-A, has relatively rapid adsorption (86% in 17.5 min), short latent period (25 min) and extremely large burst size (~500 plaque-forming units (PFU) per infected cell). The genomic analysis revealed that vB_SauM-A, vB_SauM-C, vB_SauM-D possess large genomes (vB_SauM-A 139,031 bp, vB_SauM-C 140,086 bp, vB_SauM-D 139,088 bp) with low G+C content (~30.4%) and are very closely related to the phage K (95-97% similarity). The isolated bacteriophages demonstrate broad host range against MDR S. aureus strains, high lytic activity corresponding to strictly virulent life cycle, suggesting their potential to treat S. aureus infections.
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76
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Isolation, Characterisation and Complete Genome Sequence of a Tequatrovirus Phage, Escherichia phage KIT03, Which Simultaneously Infects Escherichia coli O157:H7 and Salmonella enterica. Curr Microbiol 2019; 76:1130-1137. [DOI: 10.1007/s00284-019-01738-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/03/2019] [Indexed: 12/24/2022]
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77
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Rivera D, Hudson LK, Denes TG, Hamilton-West C, Pezoa D, Moreno-Switt AI. Two Phages of the Genera Felixounavirus Subjected to 12 Hour Challenge on Salmonella Infantis Showed Distinct Genotypic and Phenotypic Changes. Viruses 2019; 11:E586. [PMID: 31252667 PMCID: PMC6669636 DOI: 10.3390/v11070586] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/23/2019] [Accepted: 06/25/2019] [Indexed: 12/15/2022] Open
Abstract
Salmonella Infantis is considered in recent years an emerging Salmonella serovar, as it has been associated with several outbreaks and multidrug resistance phenotypes. Phages appear as a possible alternative strategy to control Salmonella Infantis (SI). The aims of this work were to characterize two phages of the Felixounavirus genus, isolated using the same strain of SI, and to expose them to interact in challenge assays to identify genetic and phenotypic changes generated from these interactions. These two phages have a shared nucleotide identity of 97% and are differentiated by their host range: one phage has a wide host range (lysing 14 serovars), and the other has a narrow host range (lysing 6 serovars). During the 12 h challenge we compared: (1) optical density of SI, (2) proportion of SI survivors from phage-infected cultures, and (3) phage titer. Isolates obtained through the assays were evaluated by efficiency of plating (EOP) and by host-range characterization. Genomic modifications were characterized by evaluation of single nucleotide polymorphisms (SNPs). The optical density (600 nm) of phage-infected SI decreased, as compared to the uninfected control, by an average of 0.7 for SI infected with the wide-host-range (WHR) phage and by 0.3 for SI infected with the narrow-host-range (NHR) phage. WHR phage reached higher phage titer (7 × 1011 PFU/mL), and a lower proportion of SI survivor was obtained from the challenge assay. In SI that interacted with phages, we identified SNPs in two genes (rfaK and rfaB), which are both involved in lipopolysaccharide (LPS) polymerization. Therefore, mutations that could impact potential phage receptors on the host surface were selected by lytic phage exposure. This work demonstrates that the interaction of Salmonella phages (WHR and NHR) with SI for 12 h in vitro leads to emergence of new phenotypic and genotypic traits in both phage and host. This information is crucial for the rational design of phage-based control strategies.
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Affiliation(s)
- Dácil Rivera
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8320000, Chile.
- Departamento de Ciencia de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380492, Chile.
| | - Lauren K Hudson
- Department of Food Science, University of Tennessee, Knoxville, TN 37996, USA.
| | - Thomas G Denes
- Department of Food Science, University of Tennessee, Knoxville, TN 37996, USA.
| | - Christopher Hamilton-West
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias, Universidad de Chile, Santiago 8330015, Chile.
| | - David Pezoa
- Escuela de Medicina Veterinaria, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.
| | - Andrea I Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8320000, Chile.
- Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago 7550000, Chile.
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78
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Structure and tailspike glycosidase machinery of ORF212 from E. coli O157:H7 phage CBA120 (TSP3). Sci Rep 2019; 9:7349. [PMID: 31089181 PMCID: PMC6517402 DOI: 10.1038/s41598-019-43748-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/30/2019] [Indexed: 12/19/2022] Open
Abstract
Bacteriophage tailspike proteins mediate virion absorption through reversible primary receptor binding, followed by lipopolysaccharide or exopolysaccharide degradation. The Escherichia coli O157:H7 bacteriophage CBA120 genome encodes four distinct tailspike proteins, annotated as ORFs 210 through 213. Previously, we reported the crystal structure of ORF210 (TSP1). Here we describe the crystal structure of ORF212 (TSP3) determined at 1.85 Å resolution. As observed with other tailspike proteins, TSP3 assembles into a trimer. Each subunit of TSP3 has an N-terminal head domain that is structurally similar to that of TSP1, consistent with their high amino acid sequence identity. In contrast, despite sharing a β-helix fold, the overall structure of the C-terminal catalytic domain of TSP3 is quite different when compared to TSP1. The TSP3 structure suggests that the glycosidase active site resides in a cleft at the interface between two adjacent subunits where three acidic residues, Glu362 and Asp383 on one subunit, and Asp426 on a second subunit, are located in close proximity. Comparing the glycosidase activity of wild-type TSP3 to various point mutants revealed that catalysis requires the carboxyl groups of Glu362 and Asp426, and not of Asp383, confirming the enzyme employs two carboxyl groups to degrade lippopolysaccharide using an acid/base mechanism.
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79
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Gencay YE, Gambino M, Prüssing TF, Brøndsted L. The genera of bacteriophages and their receptors are the major determinants of host range. Environ Microbiol 2019; 21:2095-2111. [PMID: 30888719 DOI: 10.1111/1462-2920.14597] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 01/21/2023]
Abstract
The host range of phages is a key to understand their impact on bacterial ecology and evolution. Because of the complexity of phage-host interactions, the variables that determine the breadth of a phage host range remain poorly understood. Here, we propose a novel holistic approach to identify the host range determinants of a new collection of phages infecting Salmonella, isolated from animal, environmental and wastewater samples that were able to infect 58 of the 71 Salmonella strains in our collection. By using a set of statistic approaches (non-metric dimensional scaling, Bray-Curtis distance, PERMANOVA), we analysed phenotypic (host range on wild-type and receptor mutants) and genetic data (taxonomic assignment and receptor binding proteins) to evaluate the impact of isolation strain and niche, phage receptor and genus on the host range. Statistical analysis revealed that two phage characteristics influence the host range by explaining the most variance: the receptor by 45% and the genus by 51%. Interestingly, phage genus and receptor in combination explained 79% of the variance, establishing these characteristics as the major determinants of the host range. This study demonstrates the power and the novelty of applying statistical approaches to phenotypic and genetic data to investigate the ecology of phage-host interactions.
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Affiliation(s)
- Yilmaz Emre Gencay
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Michela Gambino
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Tessa From Prüssing
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
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80
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Chang Y, Bai J, Lee JH, Ryu S. Mutation of a Staphylococcus aureus temperate bacteriophage to a virulent one and evaluation of its application. Food Microbiol 2019; 82:523-532. [PMID: 31027814 DOI: 10.1016/j.fm.2019.03.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 01/21/2023]
Abstract
Bacteriophages have been suggested as alternative antimicrobial agents based on their host specificity and lytic activity. Therefore, it is necessary to obtain a virulent phage from a temperate one using molecular techniques to control Staphylococcus aureus efficiently. SA13, a novel temperate phage infecting S. aureus, was isolated and characterized. From this phage, mutant phages were generated by random deletion mutations, and a virulent mutant phage SA13m was selected. Comparative genome analysis revealed that the SA13m genome contains various nucleotide deletions in six genes encoding three hypothetical proteins and three lysogeny-associated proteins, including putative integrase, putative CI, and putative anti-repressor proteins. Mitomycin C induction of SA13m-resistant strains revealed that this mutant phage does not form lysogen, suggesting that SA13m is a virulent phage. In addition, SA13m showed rapid and long-lasting host cell growth inhibition activity. Furthermore, application of SA13m in sterilized milk showed that S. aureus was reduced to non-detectable levels both at refrigerator temperature (4 °C) and room temperature (25 °C), suggesting that SA13m can efficiently control the growth of S. aureus in foods. The virulent mutant phage SA13m could be used as a promising biocontrol agent against S. aureus without lysogen formation.
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Affiliation(s)
- Yoonjee Chang
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jaewoo Bai
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ju-Hoon Lee
- Department of Food Science and Biotechnology, Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea.
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea.
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81
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Guo Y, Chen P, Lin Z, Wang T. Characterization of Two Pseudomonas aeruginosa Viruses vB_PaeM_SCUT-S1 and vB_PaeM_SCUT-S2. Viruses 2019; 11:v11040318. [PMID: 30939832 PMCID: PMC6521218 DOI: 10.3390/v11040318] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/17/2019] [Accepted: 03/28/2019] [Indexed: 12/13/2022] Open
Abstract
The sophisticated antibiotic resistance mechanism of Pseudomonas aeruginosa has urged the development of alternative antibacterial strategies. Phage therapy has been proven successful for the treatment of multidrug-resistant infections. In this study, we reported two virulent P. aeruginosa phages, vB_PaeM_SCUT-S1 (S1) and vB_PaeM_SCUT-S2 (S2), which were characterized at morphological, genomic, and proteomic levels. Phages S1 and S2 were assigned to the Myoviridae family. The genome sequencing showed that the genome size of Phage S1 was 66,046 bp and that of Phage S2 was 94,434 bp. The phylogenetic tree indicated that the two phages were distantly related to each other and were classified in the genera Pbunavirus and Pakpunavirus respectively. Thirty-one proteins were identified for each phage by mass spectrometry and were used to substantiate the function of the predicted coding genes. The two phages inhibited the growth of P. aeruginosa strain PAO1 at low multiplicity of infection levels and had good performance both on preventing biofilm formation and eradicating preformed biofilms. They were also stable over a wide range of temperature and pH values, supporting their potential use in the treatment of P. aeruginosa infections.
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Affiliation(s)
- Yangyijun Guo
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, Higher Education Mega Centre, Guangzhou, Guangdong 510006, China.
| | - Ping Chen
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, Higher Education Mega Centre, Guangzhou, Guangdong 510006, China.
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, Higher Education Mega Centre, Guangzhou, Guangdong 510006, China.
| | - Tingting Wang
- School of Biology and Biological Engineering, South China University of Technology, 382 East Outer Loop Road, Higher Education Mega Centre, Guangzhou, Guangdong 510006, China.
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82
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Born Y, Knecht LE, Eigenmann M, Bolliger M, Klumpp J, Fieseler L. A major-capsid-protein-based multiplex PCR assay for rapid identification of selected virulent bacteriophage types. Arch Virol 2019; 164:819-830. [PMID: 30673846 PMCID: PMC6394723 DOI: 10.1007/s00705-019-04148-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/14/2018] [Indexed: 12/17/2022]
Abstract
Bacteriophages represent a promising alternative for controlling pathogenic bacteria. They are ubiquitous in the environment, and their isolation is usually simple and fast. However, not every phage is suitable for biocontrol applications. It must be virulent (i.e., strictly lytic), non-transducing, and safe. We have developed a method for identifying selected types of virulent phages at an early stage of the isolation process to simplify the search for suitable candidates. Using the major capsid protein (MCP) as a phylogenetic marker, we designed degenerate primers for the identification of Felix O1-, GJ1-, N4-, SP6-, T4-, T7-, and Vi1-like phages in multiplex PCR setups with single phage plaques as templates. Performance of the MCP PCR assay was evaluated with a set of 26 well-characterized phages. Neither false-positive nor false-negative results were obtained. In addition, 154 phages from enrichment cultures from various environmental samples were subjected to MCP PCR analysis. Eight of them, specific for Salmonella enterica, Escherichia coli, or Erwinia amylovora, belonged to one of the selected phage types. Their PCR-based identification was successfully confirmed by pulsed-field gel electrophoresis of the phage genomes, electron microscopy, and sequencing of the amplified mcp gene fragment. The MCP PCR assay was shown to be a simple method for preliminary assignment of new phages to a certain group and thus to identify candidates for biocontrol immediately after their isolation. Given that sufficient sequence data are available, this method can be extended to any phage group of interest.
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Affiliation(s)
- Yannick Born
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, 8820, Wädenswil, Switzerland
| | - Leandra E Knecht
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, 8820, Wädenswil, Switzerland
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Mirjam Eigenmann
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, 8820, Wädenswil, Switzerland
| | - Michel Bolliger
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, 8820, Wädenswil, Switzerland
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Lars Fieseler
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, 8820, Wädenswil, Switzerland.
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83
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Tian C, Zhao J, Zhang Z, Chen X, Wei X, Li H, Lin W, Ke Y, Hu L, Jiang A, Feng R, Yang W, Jing Y, Yuan J, Luo Y, Zhao X. Identification and molecular characterization of Serratia marcescens phages vB_SmaA_2050H1 and vB_SmaM_2050HW. Arch Virol 2019; 164:1085-1094. [DOI: 10.1007/s00705-019-04169-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/11/2019] [Indexed: 10/27/2022]
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84
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Bai J, Jeon B, Ryu S. Effective inhibition of Salmonella Typhimurium in fresh produce by a phage cocktail targeting multiple host receptors. Food Microbiol 2019; 77:52-60. [PMID: 30297056 DOI: 10.1016/j.fm.2018.08.011] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 04/13/2018] [Accepted: 08/21/2018] [Indexed: 01/12/2023]
Abstract
Salmonella contamination of fresh produce is the primary bacterial cause of a significant number of foodborne outbreaks and infections. Bacteriophages can be used as natural antibacterial agents to control foodborne pathogens. However, the rapid development of bacterial resistance to phage infection is a significant barrier to practical phage application. To overcome this problem, we developed a novel phage cocktail consisting of the three phages (BSPM4, BSP101 and BSP22A) that target different host receptors, including flagella, O-antigen and BtuB, respectively. Whole genome sequence analysis of the phages revealed that three phages do not harbor genes involved in lysogen formation or toxin production, suggesting they are safe for use as biocontrol agents in foods. In vitro treatment of the phage cocktail resulted in a significant reduction in the development of bacterial resistance. Phage cocktail treatments achieved 4.7-5.5 log CFU/cm2 reduction of viable cell number in iceberg lettuce and 4.8-5.8 log CFU/cm2 reduction in cucumber after 12 h at room temperature (25 °C). The phage cocktail exhibited good antimicrobial efficiency, suggesting that it could reduce S. Typhimurium contamination of fresh produce. The strategy of developing cocktails of phages that target multiple host receptors can be used to develop novel biocontrol agents of S. Typhimurium.
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Affiliation(s)
- Jaewoo Bai
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Byeonghwa Jeon
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea; Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea.
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85
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Lytic KFS-SE2 phage as a novel bio-receptor for Salmonella Enteritidis detection. J Microbiol 2019; 57:170-179. [PMID: 30706346 DOI: 10.1007/s12275-019-8610-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/26/2018] [Accepted: 12/03/2018] [Indexed: 10/27/2022]
Abstract
Since Salmonella Enteritidis is one of the major foodborne pathogens, on-site applicable rapid detection methods have been required for its control. The purpose of this study was to isolate and purify S. Enteritidis-specific phage (KFS-SE2 phage) from an eel farm and to investigate its feasibility as a novel, efficient, and reliable bio-receptor for its employment. KFS-SE2 phage was successfully isolated at a high concentration of (2.31 ± 0.43) × 1011 PFU/ml, and consisted of an icosahedral head of 65.44 ± 10.08 nm with a non-contractile tail of 135.21 ± 12.41 nm. The morphological and phylogenetic analysis confirmed that it belongs to the Pis4avirus genus in the family of Siphoviridae. KFS-SE2 genome consisted of 48,608 bp with 45.7% of GC content. Genome analysis represented KFS-SE2 to have distinctive characteristics as a novel phage. Comparative analysis of KFS-SE2 phage with closely related strains confirmed its novelty by the presence of unique proteins. KFS-SE2 phage exhibited excellent specificity to S. Enteritidis and was stable under the temperature range of 4 to 50°C and pH of 3 to 11 (P < 0.05). The latent time was determined to be 20 min. Overall, a new lytic KFS-SE2 phage was successfully isolated from the environment at a high concentration and the excellent feasibility of KFS-SE2 phage was demonstrated as a new bio-receptor for S. Enteritidis detection.
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86
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Cha Y, Chun J, Son B, Ryu S. Characterization and Genome Analysis of Staphylococcus aureus Podovirus CSA13 and Its Anti-Biofilm Capacity. Viruses 2019; 11:v11010054. [PMID: 30642091 PMCID: PMC6356323 DOI: 10.3390/v11010054] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/04/2019] [Accepted: 01/10/2019] [Indexed: 12/16/2022] Open
Abstract
Staphylococcus aureus is one of the notable human pathogens that can be easily encountered in both dietary and clinical surroundings. Among various countermeasures, bacteriophage therapy is recognized as an alternative method for resolving the issue of antibiotic resistance. In the current study, bacteriophage CSA13 was isolated from a chicken, and subsequently, its morphology, physiology, and genomics were characterized. This Podoviridae phage displayed an extended host inhibition effect of up to 23 h of persistence. Its broad host spectrum included methicillin susceptible S. aureus (MSSA), methicillin resistant S. aureus (MRSA), local S. aureus isolates, as well as non-aureus staphylococci strains. Moreover, phage CSA13 could successfully remove over 78% and 93% of MSSA and MRSA biofilms in an experimental setting, respectively. Genomic analysis revealed a 17,034 bp chromosome containing 18 predicted open reading frames (ORFs) without tRNAs, representing a typical chromosomal structure of the staphylococcal Podoviridae family. The results presented here suggest that phage CSA13 can be applicable as an effective biocontrol agent against S. aureus.
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Affiliation(s)
- Yoyeon Cha
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.
| | - Jihwan Chun
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
| | - Bokyung Son
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.
- Center for Food and Bioconvergence4, Seoul National University, Seoul 08826, Korea.
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
- Center for Food and Bioconvergence4, Seoul National University, Seoul 08826, Korea.
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87
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Newase S, Kapadnis BP, Shashidhar R. Isolation and Genome Sequence Characterization of Bacteriophage vB_SalM_PM10, a Cba120virus, Concurrently Infecting Salmonella enterica Serovars Typhimurium, Typhi, and Enteritidis. Curr Microbiol 2018; 76:86-94. [PMID: 30361843 DOI: 10.1007/s00284-018-1588-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/19/2018] [Indexed: 01/21/2023]
Abstract
The prevalence of multidrug-resistant Salmonella is ever increasing and calls for alternatives to antibiotics. The use of phages has been anticipated to reduce the multidrug-resistant human pathogens in food environment. Salmonella phage vB_SalM_PM10 (PM10) was isolated from sewage-polluted river in India. It shows an icosahedral head (94 ± 4 nm) along with a long contractile tail (106 ± 7 × 18 ± 2 nm), a morphotype of family Ackermannviridae. Additionally, the phage displayed the features resembling to existing Cba120viruses. Phage PM10 could infect S. enterica serovars Typhimurium, Typhi, and Enteritidis. The genome sequencing analysis of phage PM10 revealed circular 158.08 kb double-stranded DNA, with the GC content of 44.6%. Two hundred and nine ORFs, 171 putative promoters, 122 rho-independent terminators, and 5 transfer RNA encoding genes were found in the genome. The genome-wide comparisons and phylogenetic analyses showed that phage PM10 is closely related to Salmonella phage PhiSH19. Comparison of the tail-spike protein sequences encoded in PM10 and PhiSH19 genome showed the variation, which might have facilitated PM10's simultaneous infectivity to aforementioned S. enterica serovars. This is a varied host range than that of PhiSH19 or any other Cba120viruses.
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Affiliation(s)
- Sandeep Newase
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India.,Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Balu P Kapadnis
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India.
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88
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Son HM, Duc HM, Masuda Y, Honjoh KI, Miyamoto T. Application of bacteriophages in simultaneously controlling Escherichia coli O157:H7 and extended-spectrum beta-lactamase producing Escherichia coli. Appl Microbiol Biotechnol 2018; 102:10259-10271. [DOI: 10.1007/s00253-018-9399-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 11/29/2022]
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89
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Buttimer C, Lucid A, Neve H, Franz CMAP, O'Mahony J, Turner D, Lavigne R, Coffey A. Pectobacterium atrosepticum Phage vB_PatP_CB5: A Member of the Proposed Genus ' Phimunavirus'. Viruses 2018; 10:E394. [PMID: 30050020 PMCID: PMC6115819 DOI: 10.3390/v10080394] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 11/23/2022] Open
Abstract
Pectobacterium atrosepticum is a phytopathogen of economic importance as it is the causative agent of potato blackleg and soft rot. Here we describe the Pectobacterium phage vB_PatP_CB5 (abbreviated as CB5), which specifically infects the bacterium. The bacteriophage is characterized in detail and TEM micrographs indicate that it belongs to the Podoviridae family. CB5 shares significant pairwise nucleotide identity (≥80%) with P. atrosepticum phages φM1, Peat1, and PP90 and also shares common genome organization. Phylograms constructed using conserved proteins and whole-genome comparison-based amino acid sequences show that these phages form a distinct clade within the Autographivirinae. They also possess conserved RNA polymerase recognition and specificity loop sequences. Their lysis cassette resembles that of KP34virus, containing in sequential order a U-spanin, a holin, and a signal⁻arrest⁻release (SAR) endolysin. However, they share low pairwise nucleotide identity with the type phage of the KP34virus genus, Klebsiella phage KP34. In addition, phage KP34 does not possess several conserved proteins associated with these P. atrosepticum phages. As such, we propose the allocation of phages CB5, Peat1, φM1, and PP90 to a separate new genus designated Phimunavirus.
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Affiliation(s)
- Colin Buttimer
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland.
| | - Alan Lucid
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland.
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany.
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany.
| | - Jim O'Mahony
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland.
| | - Dann Turner
- Department of Applied Sciences, University of the West of England, Bristol, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK.
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium.
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland.
- APC Microbiome Institute, University College, T12 YT20 Cork, Ireland.
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90
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Buttimer C, Hendrix H, Lucid A, Neve H, Noben JP, Franz C, O'Mahony J, Lavigne R, Coffey A. Novel N4-Like Bacteriophages of Pectobacterium atrosepticum. Pharmaceuticals (Basel) 2018; 11:E45. [PMID: 29757952 PMCID: PMC6027278 DOI: 10.3390/ph11020045] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/30/2018] [Accepted: 05/08/2018] [Indexed: 01/09/2023] Open
Abstract
Pectobacterium atrosepticum is an economically important phytopathogen that is responsible for potato blackleg and soft rot, and for which current control strategies are limited. In this study, stem samples of potato crops exhibiting blackleg were taken from three farms in Co. Cork, Ireland, and they were found to be infected with P. atrosepticum. Three closely related bacteriophages (phages) that are specific to this phytopathogen were isolated and characterized, namely vB_PatP_CB1, vB_PatP_CB3, and vB_PatP_CB4 (abbreviated as CB1, CB3, and CB4). Both CB1 and CB3 were determined to infect 12 strains and CB4 10 strains of the 19 strains of P. atrosepticum tested. Morphology, latent periods, burst sizes, and their stability at various temperatures and pHs were also examined. Genome sequencing of the three phages revealed that they shared a minimum nucleotide identity of 93% with each other. Their genomes exhibited an Enquartavirinae genome organization, possessing several conserved proteins that were associated with phages of this group, like the type species Escherichia virus N4. Tandem electrospray ionization-mass spectrometry (ESI-MS/MS) allowed for the identification of ten structural proteins that form the virion of CB1, six that are conserved in phage N4. Biocontrol experiments demonstrated that the phages suppress soft rot formation upon co-inoculation with P. atrosepticum on whole tubers. The results of this study indicate that CB1 related phages could be good candidates for phage-based control.
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Affiliation(s)
- Colin Buttimer
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland.
| | - Hanne Hendrix
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium.
| | - Alan Lucid
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland.
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany.
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, 3590 Hasselt, Belgium.
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany.
| | - Jim O'Mahony
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland.
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium.
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland.
- APC Microbiome Institute, University College, T12 YT20 Cork, Ireland.
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91
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Litt PK, Saha J, Jaroni D. Characterization of Bacteriophages Targeting Non-O157 Shiga Toxigenic Escherichia coli. J Food Prot 2018; 81:785-794. [PMID: 29624104 DOI: 10.4315/0362-028x.jfp-17-460] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Non-O157 Shiga toxigenic Escherichia coli (STEC) are an important group of foodborne pathogens, implicated in several outbreaks and recalls in the past 2 decades. It is therefore crucial to devise effective control strategies against these pathogens. Bacteriophages present an attractive alternative to conventional pathogen control methods in the food industry. Bacteriophages, targeting non-O157 STEC (O26, O45, O103, O111, O121, O145), were isolated from beef cattle operations in Oklahoma. Their host range and lytic ability were determined against several ( n = 21) non-O157 STEC isolates, by using the spot-on-lawn assay. Isolated phages were purified, and their morphology was determined under a transmission electron microscope. Infection kinetics of selected phages ( n = 19), particularly adsorption rate, rise period, latent period, and burst size, were determined. Phages were also evaluated for stability at a wide pH range (1 to 11) and temperature range (-80 to 90°C). In total, 45 phages were isolated and classified into Myoviridae, Siphoviridae, or Tectiviridae. The phages had a latent period between 8 and 37 min, a rise period between 19 and 40 min, and a large burst size (12 to 794 virions per infected cell), indicating high lytic activity. Tested phages were stable at pH 5 to 9 for 24 h, whereas a decrease in phage titer was observed at pHs 1, 2, and 11. Phages were stable at 40 and 60°C, except for O103-specific phages. At 70°C, all the phages lost viability after 20 min, except three phages targeting O26 and O121 and one phage targeting O45 and O111 STEC, which remained viable for 60 min. All the phages lost activity after 10 min at 90°C, except one each of O26 and O121 STEC-infecting phages that remained viable for 60 min. Phages remained stable for 90 days under refrigerated (4°C) and frozen (-20 and -80°C) storage. Characterization of phages, targeting diverse non-O157 STEC serotypes, could help in the development of effective biocontrol strategies for this group of pathogens in the food industry.
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Affiliation(s)
- Pushpinder Kaur Litt
- Food and Agricultural Products Center and Department of Animal Science, Oklahoma State University, Stillwater, Oklahoma 74075, USA (ORCID: http://orcid.org/0000-0002-2673-0728 [P.K.L.]; http://orcid.org/0000-0002-7994-0550 [D.J.])
| | - Joyjit Saha
- Food and Agricultural Products Center and Department of Animal Science, Oklahoma State University, Stillwater, Oklahoma 74075, USA (ORCID: http://orcid.org/0000-0002-2673-0728 [P.K.L.]; http://orcid.org/0000-0002-7994-0550 [D.J.])
| | - Divya Jaroni
- Food and Agricultural Products Center and Department of Animal Science, Oklahoma State University, Stillwater, Oklahoma 74075, USA (ORCID: http://orcid.org/0000-0002-2673-0728 [P.K.L.]; http://orcid.org/0000-0002-7994-0550 [D.J.])
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92
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Salem M, Skurnik M. Genomic Characterization of Sixteen Yersinia enterocolitica-Infecting Podoviruses of Pig Origin. Viruses 2018; 10:v10040174. [PMID: 29614052 PMCID: PMC5923468 DOI: 10.3390/v10040174] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/23/2018] [Accepted: 03/29/2018] [Indexed: 11/16/2022] Open
Abstract
Yersinia enterocolitica causes enteric infections in humans and animals. Human infections are often caused by contaminated pork meat. Y. enterocolitica colonizes pig tonsils and pigs secrete both the human pathogen and its specific bacteriophages into the stools. In this work, sixteen Y. enterocolitica—infecting lytic bacteriophages isolated from pig stools originating from several pig farms were characterized. All phages belong to the Podoviridae family and their genomes range between 38,391–40,451 bp in size. The overall genome organization of all the phages resembled that of T7-like phages, having 3–6 host RNA polymerase (RNAP)-specific promoters at the beginning of the genomes and 11–13 phage RNAP-specific promoters as well as 3–5 rho-independent terminators, scattered throughout the genomes. Using a ligation-based approach, the physical termini of the genomes containing direct terminal repeats of 190–224 bp were established. No genes associated with lysogeny nor any toxin, virulence factor or antibiotic resistance genes were present in the genomes. Even though the phages had been isolated from different pig farms the nucleotide sequences of their genomes were 90–97% identical suggesting that the phages were undergoing microevolution within and between the farms. Lipopolysaccharide was found to be the surface receptor of all but one of the phages. The phages are classified as new species within the T7virus genus of Autographivirinae subfamily.
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Affiliation(s)
- Mabruka Salem
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology, University of Helsinki, 00014 Helsinki, Finland.
- Department of Microbiology, Faculty of Medicine, University of Benghazi, Benghazi 16063, Libya.
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Research Programs Unit, Immunobiology, University of Helsinki, 00014 Helsinki, Finland.
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, 00029 Helsinki, Finland.
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93
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Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses. Proc Natl Acad Sci U S A 2018; 115:E3116-E3125. [PMID: 29555775 PMCID: PMC5889632 DOI: 10.1073/pnas.1714812115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Certain viruses of bacteria (bacteriophages) enzymatically hypermodify their DNA to protect their genetic material from host restriction endonuclease-mediated cleavage. Historically, it has been known that virion DNAs from the Delftia phage ΦW-14 and the Bacillus phage SP10 contain the hypermodified pyrimidines α-putrescinylthymidine and α-glutamylthymidine, respectively. These bases derive from the modification of 5-hydroxymethyl-2'-deoxyuridine (5-hmdU) in newly replicated phage DNA via a pyrophosphorylated intermediate. Like ΦW-14 and SP10, the Pseudomonas phage M6 and the Salmonella phage ViI encode kinase homologs predicted to phosphorylate 5-hmdU DNA but have uncharacterized nucleotide content [Iyer et al. (2013) Nucleic Acids Res 41:7635-7655]. We report here the discovery and characterization of two bases, 5-(2-aminoethoxy)methyluridine (5-NeOmdU) and 5-(2-aminoethyl)uridine (5-NedU), in the virion DNA of ViI and M6 phages, respectively. Furthermore, we show that recombinant expression of five gene products encoded by phage ViI is sufficient to reconstitute the formation of 5-NeOmdU in vitro. These findings point to an unexplored diversity of DNA modifications and the underlying biochemistry of their formation.
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94
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Safwat Mohamed D, Farouk Ahmed E, Mohamed Mahmoud A, Abd El-Baky RM, John J. Isolation and evaluation of cocktail phages for the control of multidrug-resistant Escherichia coli serotype O104: H4 and E. coli O157: H7 isolates causing diarrhea. FEMS Microbiol Lett 2018; 365. [DOI: 10.1093/femsle/fnx275] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
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95
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Fong K, LaBossiere B, Switt AIM, Delaquis P, Goodridge L, Levesque RC, Danyluk MD, Wang S. Characterization of Four Novel Bacteriophages Isolated from British Columbia for Control of Non-typhoidal Salmonella in Vitro and on Sprouting Alfalfa Seeds. Front Microbiol 2017; 8:2193. [PMID: 29187834 PMCID: PMC5694753 DOI: 10.3389/fmicb.2017.02193] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/25/2017] [Indexed: 01/12/2023] Open
Abstract
Alfalfa sprouts have been linked to numerous North American outbreaks of Salmonella in recent years. Conventionally, treatments involving chlorine, heat, and irradiation are used for alfalfa seed sanitation. However, such treatments may be highly variable in their efficacy for pathogen control and/or detrimental to sprout quality, therefore negatively perceived by consumers advocating for natural alternatives. The usage of bacteriophages for pathogen control in sprouts has been previously explored, although with conflicting and inconsistent results. Lytic phages, viral predators of bacteria, represent an attractive approach as they provide several advantages compared to conventional treatments, such as their high specificity for bacterial targets and their ubiquity in nature. In this study, four Salmonella phages were isolated from British Columbia, Canada and characterized with respect to host range, burst size, latent period, and environmental stability to assess their potential to control Salmonella. Phage isolate SI1 showed the greatest host range, highest burst size and shortest latent period, greatest stability across all pH and temperatures and was the most effective in control of S. Enteritidis in vitro. Therefore, SI1 was chosen for treatment of sprouting alfalfa seeds artificially contaminated with S. Enteritidis with a multiplicity of infection (MOI) of ∼110 PFU/CFU. A significant (p < 0.05) reduction of 38.3 ± 3.0% of viable Salmonella cells was observed following two h of phage treatment. On days two to six of the sprouting process, reductions of Salmonella were also observed, but were not significant compared to the control (p > 0.05). It was further demonstrated that the sprout yield was not significantly (p > 0.05) affected by phage treatment. These results highlight the potential of phages recovered from the British Columbia environment for use as biocontrol agents against Salmonella, although differing efficacies in vitro was observed. Moreover, the effectiveness of SI1 to significantly (p < 0.05) control Salmonella on sprouting alfalfa seeds on day 1 of treatment was demonstrated. Although promising, future work should aim to optimize this treatment to achieve more effective, and longer lasting, biocontrol of Salmonella in sprouting alfalfa seeds.
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Affiliation(s)
- Karen Fong
- Food, Nutrition, and Health, University of British Columbia, Vancouver, BC, Canada
| | - Brett LaBossiere
- Food, Nutrition, and Health, University of British Columbia, Vancouver, BC, Canada
| | - Andrea I. M. Switt
- Escuela de Medicina Veterinaria, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Santiago, Chile
| | | | - Lawrence Goodridge
- Department of Food Science and Agricultural Chemistry, McGill University, Montreal, QC, Canada
| | - Roger C. Levesque
- Institute for Integrative and Systems Biology, Université Laval, Québec City, QC, Canada
| | - Michelle D. Danyluk
- Department of Food Science and Human Nutrition, Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Siyun Wang
- Food, Nutrition, and Health, University of British Columbia, Vancouver, BC, Canada
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96
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Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014. Viruses 2017; 9:v9110328. [PMID: 29099783 PMCID: PMC5707535 DOI: 10.3390/v9110328] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 10/31/2017] [Accepted: 11/02/2017] [Indexed: 11/17/2022] Open
Abstract
Phage therapy has regained interest in recent years due to the alarming spread of antibiotic resistance. Whilst phage cocktails are commonly sold in pharmacies in countries such as Georgia and Russia, this is not the case in western countries due to western regulatory agencies requiring a thorough characterization of the drug. Here, DNA sequencing of constituent biological entities constitutes a first step. The pyophage (PYO) cocktail is one of the main commercial products of the Georgian Eliava Institute of Bacteriophage, Microbiology and Virology and is used to cure skin infections. Since its first production in the 1930s, the composition of the cocktail has been periodically modified to add phages effective against emerging pathogenic strains. In this paper, we compared the composition of three PYO cocktails from 1997 (PYO97), 2000 (PYO2000) and 2014 (PYO2014). Based on next generation sequencing, de novo assembly and binning of contigs into draft genomes based on tetranucleotide distance, thirty and twenty-nine phage draft genomes were predicted in PYO97 and PYO2014, respectively. Of these, thirteen and fifteen shared high similarity to known phages. Eleven draft genomes were found to be common in the two cocktails. One of these showed no similarity to publicly available phage genomes. Representatives of phages targeting E. faecalis, E. faecium, E. coli, Proteus, P. aeruginosa and S. aureus were found in both cocktails. Finally, we estimated larger overlap of the PYO2000 cocktail to PYO97 compared to PYO2014. Using next generation sequencing and metagenomics analysis, we were able to characterize and compare the content of PYO cocktails separated by 17 years in time. Even though the cocktail composition is upgraded every six months, we found it to remain relatively stable over the years.
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97
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Litt PK, Jaroni D. Isolation and Physiomorphological Characterization of Escherichia coli O157:H7-Infecting Bacteriophages Recovered from Beef Cattle Operations. Int J Microbiol 2017; 2017:7013236. [PMID: 29123549 PMCID: PMC5662819 DOI: 10.1155/2017/7013236] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/30/2017] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages, recovered from beef cattle environment and specifically targeting Escherichia coli O157:H7, were examined for their physiological and morphological characteristics. Degree of bacterial lysis and host range of isolated bacteriophages was determined against 55 isolates of E. coli O157:H7. Morphology of phages was examined under transmission electron microscope. Phage growth parameters, particularly rate of adsorption, rise period, latent period, and burst size were also determined. The stability of isolated phages was tested at acidic and alkaline pH, at high temperatures, and in cold storage. A total of 7 phages were isolated which showed lytic activity against 50 out of 55 isolates of E. coli O157:H7. Based on the morphology, phages were classified into Myoviridae or Siphoviridae family. Phages had a rise period between 19 and 40 min, a short latent period between 12 and 30 min, and a large burst size (89-631 virions per infected cell), indicating high lytic activity. Phages remained stable for 24 h at a wide pH (1-11) and temperature range (40-60°C) and for 90 d in cold storage. Characterization of bacteriophages, with a diverse host range of E. coli O157:H7, could aid in the development of effective biocontrol strategies for this pathogen in the food industry.
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Affiliation(s)
- Pushpinder Kaur Litt
- Department of Animal Science and Food and Agricultural Products Center, Oklahoma State University, 148 FAPC, Monroe St., Stillwater, OK 74078, USA
| | - Divya Jaroni
- Department of Animal Science and Food and Agricultural Products Center, Oklahoma State University, 148 FAPC, Monroe St., Stillwater, OK 74078, USA
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98
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Dreiseikelmann B, Bunk B, Spröer C, Rohde M, Nimtz M, Wittmann J. Characterization and genome comparisons of three Achromobacter phages of the family Siphoviridae. Arch Virol 2017; 162:2191-2201. [PMID: 28357512 DOI: 10.1007/s00705-017-3347-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 03/17/2017] [Indexed: 11/30/2022]
Abstract
In this study, we present the characterization and genomic data of three Achromobacter phages belonging to the family Siphoviridae. Phages 83-24, JWX and JWF were isolated from sewage samples in Paris and Braunschweig, respectively, and infect Achromobacter xylosoxidans, an emerging nosocomial pathogen in cystic fibrosis patients. Analysis of morphology and growth parameters revealed that phages 83-24 and JWX have similar properties, both have nearly the same head and tail measurements, and both have a burst size between 85 and 100 pfu/cell. In regard to morphological properties, JWF had a much longer and more flexible tail compared to other phages. The linear double-stranded DNAs of all three phages are terminally redundant and not circularly permutated. The complete nucleotide sequences consist of 81,541 bp for JWF, 49,714 bp for JWX and 48,216 bp for 83-24. Analysis of the genome sequences showed again that phages JWX and 83-24 are quite similar. Comparison to the GenBank database via BLASTN revealed partial similarities to Roseobacter phage RDJL phi1 and Burkholderia phage BcepGomr. In contrast, BLASTN analysis of the genome sequence of phage JWF revealed only few similarities to non-annotated prophage regions in different strains of Burkholderia and Mesorhizobium.
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Affiliation(s)
- Brigitte Dreiseikelmann
- Department of Microbiology/Genetechnology, University of Bielefeld, 33615, Bielefeld, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Brunswick, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Brunswick, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Manfred Nimtz
- Protein Analytics Platform, Helmholtz Centre for Infection Research, 38124, Brunswick, Germany
| | - Johannes Wittmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Brunswick, Germany.
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99
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Hamdi S, Rousseau GM, Labrie SJ, Tremblay DM, Kourda RS, Ben Slama K, Moineau S. Characterization of two polyvalent phages infecting Enterobacteriaceae. Sci Rep 2017; 7:40349. [PMID: 28091598 PMCID: PMC5238451 DOI: 10.1038/srep40349] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/05/2016] [Indexed: 01/30/2023] Open
Abstract
Bacteriophages display remarkable genetic diversity and host specificity. In this study, we explore phages infecting bacterial strains of the Enterobacteriaceae family because of their ability to infect related but distinct hosts. We isolated and characterized two novel virulent phages, SH6 and SH7, using a strain of Shigella flexneri as host bacterium. Morphological and genomic analyses revealed that phage SH6 belongs to the T1virus genus of the Siphoviridae family. Conversely, phage SH7 was classified in the T4virus genus of the Myoviridae family. Phage SH6 had a short latent period of 16 min and a burst size of 103 ± 16 PFU/infected cell while the phage SH7 latent period was 23 min with a much lower burst size of 26 ± 5 PFU/infected cell. Moreover, phage SH6 was sensitive to acidic conditions (pH < 5) while phage SH7 was stable from pH 3 to 11 for 1 hour. Of the 35 bacterial strains tested, SH6 infected its S. flexneri host strain and 8 strains of E. coli. Phage SH7 lysed additionally strains of E. coli O157:H7, Salmonella Paratyphi, and Shigella dysenteriae. The broader host ranges of these two phages as well as their microbiological properties suggest that they may be useful for controlling bacterial populations.
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Affiliation(s)
- Sana Hamdi
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Geneviève M. Rousseau
- Département de Biochimie, de Microbiologie, et de Bio-informatique and PROTEO, Faculté des Sciences et de Génie, Félix d’Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
| | - Simon J. Labrie
- Département de Biochimie, de Microbiologie, et de Bio-informatique and PROTEO, Faculté des Sciences et de Génie, Félix d’Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
| | - Denise M. Tremblay
- Département de Biochimie, de Microbiologie, et de Bio-informatique and PROTEO, Faculté des Sciences et de Génie, Félix d’Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
| | - Rim Saïed Kourda
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Karim Ben Slama
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie, et de Bio-informatique and PROTEO, Faculté des Sciences et de Génie, Félix d’Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval, Québec City, Québec, Canada
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100
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Lee H, Ku HJ, Lee DH, Kim YT, Shin H, Ryu S, Lee JH. Characterization and Genomic Study of the Novel Bacteriophage HY01 Infecting Both Escherichia coli O157:H7 and Shigella flexneri: Potential as a Biocontrol Agent in Food. PLoS One 2016; 11:e0168985. [PMID: 28036349 PMCID: PMC5201272 DOI: 10.1371/journal.pone.0168985] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 12/09/2016] [Indexed: 01/21/2023] Open
Abstract
Background Escherichia coli O157:H7 and Shigella flexneri are well-known food-borne pathogens causing severe food poisoning at low infectious doses. Bacteriophages have been approved for food applications by the US Food and Drug Administration (FDA) and have been suggested as natural food preservatives to control specific food-borne pathogens. To develop a novel natural food preservative against E. coli O157:H7 and S. flexneri, a new bacteriophage needs to be isolated and characterized. Methodology/Principal Findings Bacteriophage HY01 infecting both E. coli O157:H7 and S. flexneri was isolated from a swine fecal sample. HY01 belongs to the family Myoviridae and is stable under various temperature and pH conditions. One-step growth curve analysis showed relatively short eclipse and latent periods as well as large burst size. The 167-kb genome sequence of HY01 was sequenced, and a comparative genome analysis with T4 for non-O157:H7 E. coli suggests that the receptor recognition protein of HY01 plays an important role in determination of host recognition and specificity. In addition, food applications using edible cabbage were conducted with two E. coli O157:H7 strains (ATCC 43890 and ATCC 43895), showing that treatment with HY01 inhibits these clinical and food isolates with >2 log reductions in bacterial load during the first 2 h of incubation. Conclusions/Significance HY01 can inhibit both E. coli O157:H7 and S. flexneri with large burst size and stability under stress conditions. The ability of HY01 to infect both E. coli O157:H7 and S. flexneri may be derived from the presence of two different host specificity-associated tail genes in the genome. Food applications revealed the specific ability of HY01 to inhibit both pathogens in food, suggesting its potential as a novel biocontrol agent or novel natural food preservative against E. coli O157:H7 and potentially S. flexneri.
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Affiliation(s)
- Heyn Lee
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin, Republic of Korea
| | - Hye-Jin Ku
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin, Republic of Korea
| | - Dong-Hoon Lee
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin, Republic of Korea
| | - You-Tae Kim
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin, Republic of Korea
| | - Hakdong Shin
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Faculty of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Ju-Hoon Lee
- Department of Food Science and Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin, Republic of Korea
- * E-mail:
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