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Hammerl JA, Pham MA, El-Ahmad S, Manta D, Jäckel C, Hertwig S. Biological and genomic characterization of three psychrophilic Y. enterocolitica phages. Front Microbiol 2024; 15:1423610. [PMID: 39056006 PMCID: PMC11269248 DOI: 10.3389/fmicb.2024.1423610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
Yersinia (Y.) enterocolitica is an important foodborne pathogenic species that is mainly transmitted by the consumption of contaminated meat, particularly pork. To combat the bacteria along the food chain, the application of strictly lytic phages may be a promising tool. As the temperatures in the gut of animals and during food processing can differ significantly, a phage cocktail intended to be used for applications should comprise phages that are active at various temperatures. In this study, we isolated and characterized three phages with a myoviridal morphology (vB_YenM_P8, vB_YenM_P744 and vB_YenM_P778), which lysed the most important Y. enterocolitica serotypes O:3, O:9 and O:5,27 at a low multiplicity of infection (MOI) and at low temperatures down to 6°C. While vB_YenM_P8 is a member of the T4 family, vB_YenM_P744 and vB_YenM_P778 are novel phages that do not show relationship to known phages. The three phages were mixed in a cocktail with the already described phages vB_YenM_P281 and vB_YenP_Rambo. The cocktail revealed a strong lytic activity and lysed a mixture of Y. enterocolitica serotypes at room temperature (RT) within few hours with a reduction of up to 4.8 log10 units. Moreover, at even lower temperatures the mixture was significantly reduced after incubation overnight. The strongest reductions were determined at 6°C (4.0 log10 units) suggesting that the cocktail can lyse the psychrophilic Y. enterocolitica also during food processing. To determine possible phage resistance, 100 colonies that survived the infection by the phages were isolated and analysed regarding their serotype and phage susceptibility. Most isolates belonged to serotype O:9, but all of them were still sensitive to at least one phage of the cocktail.
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Affiliation(s)
| | | | | | | | | | - Stefan Hertwig
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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Huang S, Li Y, Hong C, Jin Y, Li S, Xu X, Xia Y, Zhang L, Lou Y, Guan W. Whole-genome sequencing-based analysis of antimicrobial resistance, virulence factors, and genetic diversity in Yersinia isolated in Wenzhou, China 2020. Mol Phylogenet Evol 2023; 188:107903. [PMID: 37574177 DOI: 10.1016/j.ympev.2023.107903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/20/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Yersinia spp. vary significantly in their ability to cause diseases that threaten public health. Their pathogenicity is frequently associated with increasing antimicrobial resistance (AMR) and various virulence factors. The aim of the study was to investigate the AMR genes, virulence factors, and genetic diversity of Yersinia strains isolated from meats and fish in Wenzhou in 2020 by using whole-genome sequencing (WGS). A total of 50 isolates were collected. The phylogenetic relationships among the Yersinia species were also analyzed using multilocus sequence typing (MLST), core genome multi-locus sequence typing (cgMLST), and single nucleotide polymorphism (SNP) analysis. According to the results, all the strains could be classified into five species, with most isolated from beef, followed by poultry, pork, and fish. AMR genes were identified in 23 strains. And the qnrD1 genes were all located in the Col3M plasmid. Virulence genes, such as yaxA, ystB, pla, and yplA, were also found in the 15 Y. enterocolitica strains. And this study also found the presence of icm/dot type IVB-related genes in one Yersinia massiliensis isolate. MLST analysis identified 43 sequence types (STs), 19 of which were newly detected in Yersinia. Moreover, cgMLST analysis revealed that no dense genotype clusters were formed (cgMLST 5341, 5344, 5346-5350, 5353-5390). Instead, the strains appeared to be dispersed over large distances, except when multiple isolates shared the same ST. Isolates Y4 and Y26 were closely related to strains originating from South Korea and Denmark. This study showed considerable diversity in Yersinia spp. isolated from local areas (Wenzhou City). The data generated in our study may enrich the molecular traceability database of Yersinia and provide a basis for the development of more effective antipathogen control strategies.
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Affiliation(s)
- Shaojie Huang
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Yi Li
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China.
| | - Chengji Hong
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China.
| | - Yafang Jin
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Shengkai Li
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Xuelian Xu
- Yuhang Center for Disease Control and Prevention, Yuhang, China.
| | - Yanmei Xia
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Leyi Zhang
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China.
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Wanchun Guan
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
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Lin Y, Liu Y, Zhang Y, Yuan W, Wang D, Zhu W. Biological and genomic characterization of a polyvalent bacteriophage (S19cd) strongly inhibiting Salmonella enterica serovar Choleraesuis. Vet Microbiol 2023; 284:109822. [PMID: 37437367 DOI: 10.1016/j.vetmic.2023.109822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 06/08/2023] [Accepted: 06/26/2023] [Indexed: 07/14/2023]
Abstract
Bacteriophages are a promising alternative for the control of pathogenic bacteria. In this study, we isolated a virulent bacteriophage, S19cd, from pig gut that could infect both a non-pathogenic bacteria Escherichia coli 44 (EC44) and two pathogenic bacterial strains (ATCC 13312 (SC13312) and CICC 21493 (SC21493)) of Salmonella enterica serovar Choleraesuis (SC). S19cd exhibited strong lytic ability in both SC13312 and SC21493 with an optimal multiplicity of infection (MOI) of 10-6 and 10-5, respectively, and inhibited their growth at an MOI of 10-7 within 24 h. Mice pre-treated with S19cd exhibited protection against the SC13312 challenge. Moreover, S19cd has good heat resistance (80 ℃) and pH tolerance (pH 3-12). Genome analysis revealed that S19cd belongs to the Felixounavirus genus and does not contain any virulence or drug-resistance-related genes. Additionally, S19cd encodes an adenine-specific methyltransferase that has no similarity to methyltransferases from other Felixounavirus phages and shares limited similarity with other methyltransferases in the NCBI protein database. Metagenomic analysis of S19cd genomes from 500 pigs revealed that S19cd-like phages may be widespread in Chinese pig gut. In conclusion, S19cd can be a potential phage therapy targeting SC infections.
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Affiliation(s)
- Yan Lin
- National Center for International Research on Animal Gut Nutrition, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yankun Liu
- National Center for International Research on Animal Gut Nutrition, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuyu Zhang
- National Center for International Research on Animal Gut Nutrition, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenyuan Yuan
- National Center for International Research on Animal Gut Nutrition, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongyang Wang
- National Center for International Research on Animal Gut Nutrition, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiyun Zhu
- National Center for International Research on Animal Gut Nutrition, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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Kong X, Wang H, Guo G, Li P, Tong P, Liu M, Ma X, Dong C, Li Y, Zhang H, Zhang W. Duck sewage source coliphage P762 can lyse STEC and APEC. Virus Genes 2022; 58:436-447. [PMID: 35705841 DOI: 10.1007/s11262-022-01915-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 05/10/2022] [Indexed: 11/27/2022]
Abstract
Multiple pathogenic types or serotypes restrict treatment for colibacillosis. In addition, rising antibiotic resistance has heightened public awareness to prevent and control pathogenic Escherichia coli. The bacteriophage is a viable technique to treat colibacillosis as an alternative to antibiotics. P762, a coliphage isolated from duck farm sewage, was demonstrated to cloud lyse Shiga toxin-producing Escherichia Coli serotypes O157 and non-O157 (17/39), Avian pathogenic E. coli covered serotype O78, O83, and O9 (5/19), and other pathogenic Escherichia coli (5/17). Additional fundamental biological characteristics analysis revealed that P762 is stable at pH 3 ~ 11 and temperature between 4 °C and 60 °C, and its optimum multiplicity of infection (MOI) is 0.1. The one-step curve of P762 exhibited three bursts of growth stage: two rapid and one slow stage. Furthermore, the first rapid burst size is 80 CFU/PFU, the burst size of the slow stage is 10 CFU/PFU, and the second rapid burst size is about 990 CFU/PFU. In addition, P762 can form a "halo" on a double agar plate, implying that the phage secretes depolymerase. With 95.14% identity and 90% query coverage, genome sequence analysis revealed that P762 is most closely related to Escherichia phage DY1, which belongs to the genus Kayfunavirus. After screening using RAST and VFDB, no virulence factors were discovered in P762. In vitro antibacterial tests revealed that P762 has high bactericidal activity in lettuce leaves contaminated with STEC. In conclusion, phage P762 might be employed in the future to prevent and control pathogenic Escherichia coli.
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Affiliation(s)
- Xuewei Kong
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Hui Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Genglin Guo
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Pei Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Panpan Tong
- College of Veterinary Medicine, Shihezi Agricultural University, Xinjiang, China
| | - Maojun Liu
- Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xun Ma
- College of Animal Science and Technology, Xinjiang Agricultural University, Xinjiang, China
| | - Chen Dong
- Jiangsu Province CDC: Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yubao Li
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | - Haiyan Zhang
- Department of Food and Biology Engineering, Wuhu Institute of Technology, Wuhu, China.
| | - Wei Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
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Hammerl JA, Barac A, Bienert A, Demir A, Drüke N, Jäckel C, Matthies N, Jun JW, Skurnik M, Ulrich J, Hertwig S. Birds Kept in the German Zoo "Tierpark Berlin" Are a Common Source for Polyvalent Yersinia pseudotuberculosis Phages. Front Microbiol 2022; 12:634289. [PMID: 35046908 PMCID: PMC8762354 DOI: 10.3389/fmicb.2021.634289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 11/30/2021] [Indexed: 11/15/2022] Open
Abstract
Yersinia pseudotuberculosis is an important animal pathogen, particularly for birds, rodents, and monkeys, which is also able to infect humans. Indeed, an increasing number of reports have been published on zoo animals that were killed by this species. One option to treat diseased animals is the application of strictly lytic (virulent) phages. However, thus far relatively few phages infecting Y. pseudotuberculosis have been isolated and characterized. To determine the prevalence of Y. pseudotuberculosis phages in zoo animals, fecal samples of birds and some primates, maras, and peccaries kept in the Tierpark Berlin were analyzed. Seventeen out of 74 samples taken in 2013 and 2017 contained virulent phages. The isolated phages were analyzed in detail and could be allocated to three groups. The first group is composed of 10 T4-like phages (PYps2T taxon group: Myoviridae; Tevenvirinae; Tequatrovirus), the second group (PYps23T taxon group: Chaseviridae; Carltongylesvirus; Escherichia virus ST32) consists of five phages encoding a podovirus-like RNA polymerase that is related to an uncommon genus of myoviruses (e.g., Escherichia coli phage phiEcoM-GJ1), while the third group is comprised of two podoviruses (PYps50T taxon group: Autographiviridae; Studiervirinae; Berlinvirus) which are closely related to T7. The host range of the isolated phages differed significantly. Between 5.5 and 86.7% of 128 Y. pseudotuberculosis strains belonging to 20 serotypes were lysed by each phage. All phages were additionally able to lyse Y. enterocolitica B4/O:3 strains, when incubated at 37°C. Some phages also infected Y. pestis strains and even strains belonging to other genera of Enterobacteriaceae. A cocktail containing two of these phages would be able to lyse almost 93% of the tested Y. pseudotuberculosis strains. The study indicates that Y. pseudotuberculosis phages exhibiting a broad-host range can be isolated quite easily from zoo animals, particularly birds.
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Affiliation(s)
- Jens Andre Hammerl
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Andrea Barac
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Anja Bienert
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Aslihan Demir
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Niklas Drüke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Claudia Jäckel
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Nina Matthies
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jin Woo Jun
- Department of Aquaculture, Korea National College of Agriculture and Fisheries, Jeonju, South Korea
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Juliane Ulrich
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Stefan Hertwig
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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BtuB-Dependent Infection of the T5-like Yersinia Phage ϕR2-01. Viruses 2021; 13:v13112171. [PMID: 34834977 PMCID: PMC8624392 DOI: 10.3390/v13112171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
Yersinia enterocolitica is a food-borne Gram-negative pathogen responsible for several gastrointestinal disorders. Host-specific lytic bacteriophages have been increasingly used recently as an alternative or complementary treatment to combat bacterial infections, especially when antibiotics fail. Here, we describe the proteogenomic characterization and host receptor identification of the siphovirus vB_YenS_ϕR2-01 (in short, ϕR2-01) that infects strains of several Yersinia enterocolitica serotypes. The ϕR2-01 genome contains 154 predicted genes, 117 of which encode products that are homologous to those of Escherichia bacteriophage T5. The ϕR2-01 and T5 genomes are largely syntenic, with the major differences residing in areas encoding hypothetical ϕR2-01 proteins. Label-free mass-spectrometry-based proteomics confirmed the expression of 90 of the ϕR2-01 genes, with 88 of these being either phage particle structural or phage-particle-associated proteins. In vitro transposon-based host mutagenesis and ϕR2-01 adsorption experiments identified the outer membrane vitamin B12 receptor BtuB as the host receptor. This study provides a proteogenomic characterization of a T5-type bacteriophage and identifies specific Y. enterocolitica strains sensitive to infection with possible future applications of ϕR2-01 as a food biocontrol or phage therapy agent.
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Hammerl JA, Barac A, Erben P, Fuhrmann J, Gadicherla A, Kumsteller F, Lauckner A, Müller F, Hertwig S. Properties of Two Broad Host Range Phages of Yersinia enterocolitica Isolated from Wild Animals. Int J Mol Sci 2021; 22:11381. [PMID: 34768812 PMCID: PMC8583763 DOI: 10.3390/ijms222111381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/11/2021] [Accepted: 10/19/2021] [Indexed: 12/18/2022] Open
Abstract
Yersinia (Y.) enterocolitica and Y. pseudotuberculosis are important zoonotic agents which can infect both humans and animals. To combat these pathogens, the application of strictly lytic phages may be a promising tool. Since only few Yersinia phages have been described yet, some of which demonstrated a high specificity for certain serotypes, we isolated two phages from game animals and characterized them in terms of their morphology, host specificity, lytic activity on two bio-/serotypes and genome composition. The T7-related podovirus vB_YenP_Rambo and the myovirus vB_YenM_P281, which is very similar to a previously described phage PY100, showed a broad host range. Together, they lysed all the 62 tested pathogenic Y. enterocolitica strains belonging to the most important bio-/serotypes in Europe. A cocktail containing these two phages strongly reduced cultures of a bio-/serotype B4/O:3 and a B2/O:9 strain, even at very low MOIs (multiplicity of infection) and different temperatures, though, lysis of bio-/serotype B2/O:9 by vB_YenM_P281 and also by the related phage PY100 only occurred at 37 °C. Both phages were additionally able to lyse various Y. pseudotuberculosis strains at 28 °C and 37 °C, but only when the growth medium was supplemented with calcium and magnesium cations.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Stefan Hertwig
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn Str. 8-10, D-10589 Berlin, Germany; (J.A.H.); (A.B.); (P.E.); (J.F.); (A.G.); (F.K.); (A.L.); (F.M.)
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León Y, Faherty CS. Bacteriophages against enteropathogens: rediscovery and refinement of novel antimicrobial therapeutics. Curr Opin Infect Dis 2021; 34:491-499. [PMID: 34524200 PMCID: PMC8447223 DOI: 10.1097/qco.0000000000000772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW Alarming rates of antibiotic resistance in bacteria and gastrointestinal dysbiosis associated with traditional antimicrobial therapy have led to renewed interests in developing bacteriophages as novel therapeutics. In this review, we highlight some of the recent advances in bacteriophage therapeutic development targeting important enteropathogens of the gastrointestinal tract. RECENT FINDINGS Bacteriophages are viruses that infect bacteria, either to utilize the bacterial machinery to produce new progeny or stably integrate into the bacterial chromosome to ensure maintenance of the viral genome. With recent advances in synthetic biology and the discovery of CRISPR-Cas systems used by bacteria to protect against bacteriophages, novel molecular applications are taking us beyond the discovery of bacteriophages and toward innovative applications, including the targeting of bacterial virulence factors, the use of temperate bacteriophages, and the production of bacteriophage proteins as antimicrobial agents. These technologies offer promise to target enteropathogens without disrupting the healthy microbiota of the gastrointestinal tract. Moreover, the use of nanoparticle technology and other modifications are helping researchers circumvent the harsh gastrointestinal conditions that could limit the efficacy of bacteriophages against enteric pathogens. SUMMARY This era of discovery and development offers significant potential to modify bacteriophages and overcome the global impact of enteropathogens.
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Affiliation(s)
- Yrvin León
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Christina S. Faherty
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
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Dudina LG, Novikova OD, Portnyagina OY, Khomenko VA, Konyshev IV, Byvalov AA. Role of Lipopolysaccharide and Nonspecific Porins of Yersinia pseudotuberculosis in the Reception of Pseudotuberculous Diagnostic Bacteriophage. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821040049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Salem M, Pajunen MI, Jun JW, Skurnik M. T4-like Bacteriophages Isolated from Pig Stools Infect Yersinia pseudotuberculosis and Yersinia pestis Using LPS and OmpF as Receptors. Viruses 2021; 13:v13020296. [PMID: 33668618 PMCID: PMC7917993 DOI: 10.3390/v13020296] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 12/22/2022] Open
Abstract
The Yersinia bacteriophages fPS-2, fPS-65, and fPS-90, isolated from pig stools, have long contractile tails and elongated heads, and they belong to genus Tequatroviruses in the order Caudovirales. The phages exhibited relatively wide host ranges among Yersinia pseudotuberculosis and related species. One-step growth curve experiments revealed that the phages have latent periods of 50-80 min with burst sizes of 44-65 virions per infected cell. The phage genomes consist of circularly permuted dsDNA of 169,060, 167,058, and 167,132 bp in size, respectively, with a G + C content 35.3%. The number of predicted genes range from 267 to 271. The phage genomes are 84-92% identical to each other and ca 85% identical to phage T4. The phage receptors were identified by whole genome sequencing of spontaneous phage-resistant mutants. The phage-resistant strains had mutations in the ompF, galU, hldD, or hldE genes. OmpF is a porin, and the other genes encode lipopolysaccharide (LPS) biosynthetic enzymes. The ompF, galU, and hldE mutants were successfully complemented in trans with respective wild-type genes. The host recognition was assigned to long tail fiber tip protein Gp38, analogous to that of T-even phages such as Salmonella phage S16, specifically to the distal β-helices connecting loops.
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Affiliation(s)
- Mabruka Salem
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (M.S.); (M.I.P.)
- Department of Microbiology, Faculty of Medicine, University of Benghazi, Benghazi 16063, Libya
| | - Maria I. Pajunen
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (M.S.); (M.I.P.)
| | - Jin Woo Jun
- Department of Aquaculture, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea;
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (M.S.); (M.I.P.)
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, 00290 Helsinki, Finland
- Correspondence: ; Tel.: +358-50-336-0981
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Premaratne A, Zhang H, Wang R, Chinivasagam N, Billington C. Phage Biotechnology to Mitigate Antimicrobial Resistance in Agriculture. SUSTAINABLE AGRICULTURE REVIEWS 2021. [DOI: 10.1007/978-3-030-58259-3_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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12
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Pedersen JS, Kot W, Plöger M, Lametsh R, Neve H, Franz CM, Hansen LH. A Rare, Virulent Clostridium perfringens Bacteriophage Susfortuna Is the First Isolated Bacteriophage in a New Viral Genus. PHAGE (NEW ROCHELLE, N.Y.) 2020; 1:230-236. [PMID: 36147286 PMCID: PMC9041476 DOI: 10.1089/phage.2020.0038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background: Clostridium perfringens is a well known swine pathogen. C. perfringens type A is considered the causative agent of enteric diseases in neonatal and weaned piglets. Phage therapy using C. perfringens phages in vivo has previously proved effective. Materials and Methods: Pig fecal samples were used to isolate phages, with Clostridium perfringens type A as host. Complete genome sequencing, comparative genomics, a proteome analysis and electron microscopy were used to characterize the phage. Results: Clostridium phage Susfortuna has a double-stranded DNA genome of 19,046 bp with a G+C% content of 29.2, inverted terminal repeats and 28 predicted coding sequences (CDSs). Putative functions could not be assigned to most of the CDSs (64.3%). Transmission electron microscopy of phage Susfortuna revealed an isometric head and a short protruding tail stub resembling the structure of the Podoviridae family. A proteome analysis of phage Susfortuna identified seven structural proteins, but only one could be assigned with a putative function. Conclusions: Based on the morphology, the inverted terminal repeats and the small genome size, phage Susfortuna belongs to subfamily Picovirinae within the Podoviridae family in the order Caudovirales. Together with C. perfringens bacteriophage CPD7, phage Susfortuna represent a new genus of bacteriophages with very limited DNA sequence similarity to other known C. perfringens phages. Despite the limited DNA sequence similarity, the gene synteny among putative structural genes of phage Susfortuna is conserved among several C. perfringens bacteriophages belonging to the Podoviridae family indicating a common ancestor.
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Affiliation(s)
- Julie Stenberg Pedersen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Maja Plöger
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Réne Lametsh
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Charles M.A.P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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13
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Filik K, Szermer-Olearnik B, Wernecki M, Happonen LJ, Pajunen MI, Nawaz A, Qasim MS, Jun JW, Mattinen L, Skurnik M, Brzozowska E. The Podovirus ϕ80-18 Targets the Pathogenic American Biotype 1B Strains of Yersinia enterocolitica. Front Microbiol 2020; 11:1356. [PMID: 32636826 PMCID: PMC7316996 DOI: 10.3389/fmicb.2020.01356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/27/2020] [Indexed: 01/31/2023] Open
Abstract
We report here the complete genome sequence and characterization of Yersinia bacteriophage vB_YenP_ϕ80-18. ϕ80-18 was isolated in 1991 using a Y. enterocolitica serotype O:8 strain 8081 as a host from a sewage sample in Turku, Finland, and based on its morphological and genomic features is classified as a podovirus. The genome is 42 kb in size and has 325 bp direct terminal repeats characteristic for podoviruses. The genome contains 57 predicted genes, all encoded in the forward strand, of which 29 showed no similarity to any known genes. Phage particle proteome analysis identified altogether 24 phage particle-associated proteins (PPAPs) including those identified as structural proteins such as major capsid, scaffolding and tail component proteins. In addition, also the DNA helicase, DNA ligase, DNA polymerase, 5'-exonuclease, and the lytic glycosylase proteins were identified as PPAPs, suggesting that they might be injected together with the phage genome into the host cell to facilitate the take-over of the host metabolism. The phage-encoded RNA-polymerase and DNA-primase were not among the PPAPs. Promoter search predicted the presence of four phage and eleven host RNA polymerase -specific promoters in the genome, suggesting that early transcription of the phage is host RNA-polymerase dependent and that the phage RNA polymerase takes over later. The phage tolerates pH values between 2 and 12, and is stable at 50°C but is inactivated at 60°C. It grows slowly with a 50 min latent period and has apparently a low burst size. Electron microscopy revealed that the phage has a head diameter of about 60 nm, and a short tail of 20 nm. Whole-genome phylogenetic analysis confirmed that ϕ80-18 belongs to the Autographivirinae subfamily of the Podoviridae family, that it is 93.2% identical to Yersinia phage fHe-Yen3-01. Host range analysis showed that ϕ80-18 can infect in addition to Y. enterocolitica serotype O:8 strains also strains of serotypes O:4, O:4,32, O:20 and O:21, the latter ones representing similar to Y. enterocolitica serotype O:8, the American pathogenic biotype 1B strains. In conclusion, the phage ϕ80-18 is a promising candidate for the biocontrol of the American biotype 1B Y. enterocolitica.
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Affiliation(s)
- Karolina Filik
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Bożena Szermer-Olearnik
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Maciej Wernecki
- Department of Microbiology, Institute of Genetics and Microbiology, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Lotta J Happonen
- Department of Biosciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Maria I Pajunen
- Research Programme Unit Immunobiology, Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ayesha Nawaz
- Research Programme Unit Immunobiology, Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Muhammad Suleman Qasim
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jin Woo Jun
- Department of Aquaculture, The Korea National College of Agriculture and Fisheries, Jeonju, South Korea
| | - Laura Mattinen
- Research Programme Unit Immunobiology, Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikael Skurnik
- Research Programme Unit Immunobiology, Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Ewa Brzozowska
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
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14
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Spruit CM, Wicklund A, Wan X, Skurnik M, Pajunen MI. Discovery of Three Toxic Proteins of Klebsiella Phage fHe-Kpn01. Viruses 2020; 12:E544. [PMID: 32429141 PMCID: PMC7291057 DOI: 10.3390/v12050544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 01/09/2023] Open
Abstract
The lytic phage, fHe-Kpn01 was isolated from sewage water using an extended-spectrum beta-lactamase-producing strain of Klebsiella pneumoniae as a host. The genome is 43,329 bp in size and contains direct terminal repeats of 222 bp. The genome contains 56 predicted genes, of which proteomics analysis detected 29 different proteins in purified phage particles. Comparison of fHe-Kpn01 to other phages, both morphologically and genetically, indicated that the phage belongs to the family Podoviridae and genus Drulisvirus. Because fHe-Kpn01 is strictly lytic and does not carry any known resistance or virulence genes, it is suitable for phage therapy. It has, however, a narrow host range since it infected only three of the 72 tested K. pneumoniae strains, two of which were of capsule type KL62. After annotation of the predicted genes based on the similarity to genes of known function and proteomics results on the virion-associated proteins, 22 gene products remained annotated as hypothetical proteins of unknown function (HPUF). These fHe-Kpn01 HPUFs were screened for their toxicity in Escherichia coli. Three of the HPUFs, encoded by the genes g10, g22, and g38, were confirmed to be toxic.
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Affiliation(s)
- Cindy M. Spruit
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (C.M.S.); (A.W.); (X.W.); (M.S.)
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands
| | - Anu Wicklund
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (C.M.S.); (A.W.); (X.W.); (M.S.)
- Division of Clinical Microbiology, HUSLAB, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Xing Wan
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (C.M.S.); (A.W.); (X.W.); (M.S.)
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00790 Helsinki, Finland
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (C.M.S.); (A.W.); (X.W.); (M.S.)
- Division of Clinical Microbiology, HUSLAB, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Maria I. Pajunen
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (C.M.S.); (A.W.); (X.W.); (M.S.)
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15
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Leon-Velarde CG, Jun JW, Skurnik M. Yersinia Phages and Food Safety. Viruses 2019; 11:E1105. [PMID: 31795231 PMCID: PMC6950378 DOI: 10.3390/v11121105] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022] Open
Abstract
One of the human- and animal-pathogenic species in genus Yersinia is Yersinia enterocolitica, a food-borne zoonotic pathogen that causes enteric infections, mesenteric lymphadenitis, and sometimes sequelae such as reactive arthritis and erythema nodosum. Y. enterocolitica is able to proliferate at 4 C, making it dangerous if contaminated food products are stored under refrigeration. The most common source of Y. enterocolitica is raw pork meat. Microbiological detection of the bacteria from food products is hampered by its slow growth rate as other bacteria overgrow it. Bacteriophages can be exploited in several ways to increase food safety with regards to contamination by Y. enterocolitica. For example, Yersinia phages could be useful in keeping the contamination of food products under control, or, alternatively, the specificity of the phages could be exploited in developing rapid and sensitive diagnostic tools for the identification of the bacteria in food products. In this review, we will discuss the present state of the research on these topics.
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Affiliation(s)
- Carlos G. Leon-Velarde
- Agriculture and Food Laboratory, Laboratory Services Division, University of Guelph, Guelph, ON N1H 8J7, Canada;
| | - Jin Woo Jun
- Department of Aquaculture, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea;
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 HY Helsinki, Finland
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, 00029 HUS Helsinki, Finland
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16
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Pacífico C, Hilbert M, Sofka D, Dinhopl N, Pap IJ, Aspöck C, Carriço JA, Hilbert F. Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples. Front Microbiol 2019; 10:2484. [PMID: 31736918 PMCID: PMC6834657 DOI: 10.3389/fmicb.2019.02484] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
The interaction between bacteriophages, bacteria and the human host as a tripartite system has recently captured attention. The taxonomic diversity of bacteriophages, as a natural parasite of bacteria, still remains obscure in human body biomes, representing a so-called “viral dark matter.” Here, we isolated and characterized coliphages from blood, urine and tracheal aspirates samples collected at a tertiary care hospital in Austria. Phages were more often isolated from blood, followed by urine and tracheal aspirates. Phylogenetic analysis and genome comparisons allowed the identification of phages belonging to the Tunavirinae subfamily, and to the Peduovirus and Tequintavirus genera. Tunavirinae phages cluster together and are found in samples from 14 patients, suggesting their prevalence across a variety of human samples. When compared with other phage genomes, the highest similarity level was at 87.69% average nucleotide identity (ANI), which suggests that these are in fact a newly isolated phage species. Tequintavirus phages share a 95.90% with phage 3_29, challenging the ANI threshold currently accepted to differentiate phage species. The isolated phages appear to be virulent, with the exception of the Peduovirus members, which are integrative and seem to reside as prophages in bacterial genomes.
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Affiliation(s)
- Cátia Pacífico
- Department of Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Miriam Hilbert
- Department of Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Dmitrij Sofka
- Department of Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Nora Dinhopl
- Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Ildiko-Julia Pap
- Institute of Hygiene and Microbiology, University Hospital St. Pölten, St. Pölten, Austria
| | - Christoph Aspöck
- Karl Landsteiner University of Health Sciences, Krems, Austria.,Institute of Hygiene and Microbiology, University Hospital St. Pölten, St. Pölten, Austria
| | - João André Carriço
- Faculty of Medicine, Instituto de Medicina Molecular, University of Lisbon, Lisbon, Portugal
| | - Friederike Hilbert
- Department of Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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17
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Pacífico C, Hilbert M, Sofka D, Dinhopl N, Pap IJ, Aspöck C, Hilbert F. Characterization of Bacteria and Inducible Phages in an Intensive Care Unit. J Clin Med 2019; 8:E1433. [PMID: 31510095 PMCID: PMC6780966 DOI: 10.3390/jcm8091433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/08/2019] [Indexed: 12/29/2022] Open
Abstract
Intensive care units (ICUs) are critical locations for the transmission of pathogenic and opportunistic microorganisms. Bacteria may develop a synergistic relationship with bacteriophages and more effectively resist various stresses, enabling them to persist despite disinfection and antimicrobial treatment. We collected 77 environmental samples from the surroundings of 12 patients with infection/colonizations by Escherichia coli, Staphylococcus aureus or Klebsiella spp in an ICU in Austria. Surface swabs were tested for lytic phages and bacterial isolates for mitomycin C-inducible prophages. No lytic bacteriophages were detected, but S. aureus was isolated from the surroundings of all patients. About 85% of the colonies isolated from surface samples were resistant to antimicrobials, with 94% of them multidrug resistant. Two inducible temperate bacteriophages-myovirus vB_EcoM_P5 and siphovirus vB_SauS_P9-were recovered from two clinical isolates. Staphylococci phage vB_SauS_P9 lysed S. aureus isolates from the surface swabs collected from the surroundings of three patients. No transductants were obtained on propagation in phage-sensitive antimicrobial-resistant isolates. The two phages were sensitive to 0.25% (v/v) of the disinfectant TPH Protect, which eliminated viable phages after 15 min. Coliphage vB_EcoM_P5 was inactivated at 70 °C and staphylococci phage vB_SauS_P9 at 60 °C after 60 min.
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Affiliation(s)
- Cátia Pacífico
- Department of Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
- Karl Landsteiner University of Health Sciences, 3500 Krems an der Donau, Austria
| | - Miriam Hilbert
- Department of Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
- Karl Landsteiner University of Health Sciences, 3500 Krems an der Donau, Austria
| | - Dmitrij Sofka
- Department of Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Nora Dinhopl
- Department of Pathobiology, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Ildiko-Julia Pap
- Institute of Hygiene and Microbiology, University Clinic St. Pölten, 3100 St. Pölten, Austria
| | - Christoph Aspöck
- Karl Landsteiner University of Health Sciences, 3500 Krems an der Donau, Austria
- Institute of Hygiene and Microbiology, University Clinic St. Pölten, 3100 St. Pölten, Austria
| | - Friederike Hilbert
- Department of Farm Animals and Veterinary Public Health, University of Veterinary Medicine, 1210 Vienna, Austria.
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18
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Liang J, Kou Z, Qin S, Chen Y, Li Z, Li C, Duan R, Hao H, Zha T, Gu W, Huang Y, Xiao M, Jing H, Wang X. Novel Yersinia enterocolitica Prophages and a Comparative Analysis of Genomic Diversity. Front Microbiol 2019; 10:1184. [PMID: 31191498 PMCID: PMC6548840 DOI: 10.3389/fmicb.2019.01184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/09/2019] [Indexed: 12/18/2022] Open
Abstract
Yersinia enterocolitica is a major agent of foodborne diseases worldwide. Prophage plays an important role in the genetic evolution of the bacterial genome. Little is known about the genetic information about prophages in the genome of Y. enterocolitica, and no pathogenic Y. enterocolitica prophages have been described. In this study, we induced and described the genomes of six prophages from pathogenic Y. enterocolitica for the first time. Phylogenetic analysis based on whole genome sequencing revealed that these novel Yersinia phages are genetically distinct from the previously reported phages, showing considerable genetic diversity. Interestingly, the prophages induced from O:3 and O:9 Y. enterocolitica showed different genomic sequences and morphology but highly conserved among the same serotype strains, which classified into two diverse clusters. The three long-tailed Myoviridae prophages induced from serotype O:3 Y. enterocolitica were highly conserved, shared ≥99.99% identity and forming genotypic cluster A; the three Podoviridae prophages induced from the serotype O:9 strains formed cluster B, also shared more than 99.90% identity with one another. Cluster A was most closely related to O:5 non-pathogenic Y. enterocolitica prophage PY54 (61.72% identity). The genetic polymorphism of these two kinds of prophages and highly conserved among the same serotype strains, suggested a possible shared evolutionary past for these phages: originated from distinct ancestors, and entered pathogenic Y. enterocolitica as extrachromosomal genetic components during evolution when facing selective pressure. These results are critically important for further understanding of phage roles in host physiology and the pathology of disease.
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Affiliation(s)
- Junrong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases - Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Zengqiang Kou
- Shandong Provincial Centre for Disease Control and Prevention, Jinan, China
| | - Shuai Qin
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases - Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Yuhuang Chen
- Shenzhen Nanshan Maternity and Child Heath Care Hospital, Shenzhen, China
| | - Zhenpeng Li
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases - Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Chuchu Li
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases - Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.,Department of Pathogenic Biology, School of Medical Science, Jiangsu University, Zhenjiang, China
| | - Ran Duan
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases - Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Huijing Hao
- Chang Ping Women and Children Health Care Hospital, Beijing, China
| | - Tao Zha
- Wuhu Municipal Centre for Disease Control and Prevention, Wuhu, China
| | - Wenpeng Gu
- Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Yuanming Huang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases - Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Meng Xiao
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases - Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Huaiqi Jing
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases - Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Xin Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases - Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
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19
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Kajsík M, Bugala J, Kadličeková V, Szemes T, Turňa J, Drahovská H. Characterization of Dev-CD-23823 and Dev-CT57, new Autographivirinae bacteriophages infecting Cronobacter spp. Arch Virol 2019; 164:1383-1391. [DOI: 10.1007/s00705-019-04202-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/09/2019] [Indexed: 02/04/2023]
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20
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Analysis of 19 Highly Conserved Vibrio cholerae Bacteriophages Isolated from Environmental and Patient Sources Over a Twelve-Year Period. Viruses 2018; 10:v10060299. [PMID: 29857590 PMCID: PMC6024749 DOI: 10.3390/v10060299] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 12/28/2022] Open
Abstract
The Vibrio cholerae biotype “El Tor” is responsible for all of the current epidemic and endemic cholera outbreaks worldwide. These outbreaks are clonal, and it is hypothesized that they originate from the coastal areas near the Bay of Bengal, where the lytic bacteriophage ICP1 (International Centre for Diarrhoeal Disease Research, Bangladesh cholera phage 1) specifically preys upon these pathogenic outbreak strains. ICP1 has also been the dominant bacteriophage found in cholera patient stools since 2001. However, little is known about the genomic differences between the ICP1 strains that have been collected over time. Here, we elucidate the pan-genome and the phylogeny of the ICP1 strains by aligning, annotating, and analyzing the genomes of 19 distinct isolates that were collected between 2001 and 2012. Our results reveal that the ICP1 isolates are highly conserved and possess a large core-genome as well as a smaller, somewhat flexible accessory-genome. Despite its overall conservation, ICP1 strains have managed to acquire a number of unknown genes, as well as a CRISPR-Cas system which is known to be critical for its ongoing struggle for co-evolutionary dominance over its host. This study describes a foundation on which to construct future molecular and bioinformatic studies of these V. cholerae-associated bacteriophages.
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