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Lyu D, Duan Q, Duan R, Qin S, Zheng X, Lu X, Bukai A, Zhang P, Han H, He Z, Sha H, Wu D, Xiao M, Jing H, Wang X. Symbiosis of a lytic bacteriophage and Yersinia pestis and characteristics of plague in Marmota himalayana. Appl Environ Microbiol 2024:e0099524. [PMID: 39023266 DOI: 10.1128/aem.00995-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/27/2024] [Indexed: 07/20/2024] Open
Abstract
Surveillance for animal plague was conducted in the Marmota himalayana plague focus of the Qinghai-Tibet Plateau from 2020 to 2023. A 22.89% positive rate of serum F1 antibody was detected in live-caught marmots, alongside a 43.40% incidence of Yersinia pestis isolation from marmot carcasses. Marmot carcasses infected with plague exhibited a significantly higher spleen-somatic index (P < 0.05). Twenty-one Y. pestis-specific phages were isolated, among which one Y. pestis lytic phage (AKS2022HT87GU_phi) was isolated from the bone marrow of a marmot carcass (no. AKS2022HT87) and was found to be symbiotic with Y. pestis. Microscopy revealed the coexistence of lysed and non-lysed colonies of Y. pestis AKS2022HT87. Genome-wide analysis showed that certain strains of the Y. pestis AKS2022HT87 carried phage DNA fragments consistent with phage AKS2022HT87GU_phi. The rare symbiotic relationship between a lytic phage and Y. pestis observed in vitro was highlighted in this study, laying the basis for further exploring the relationship between Y. pestis and its bacteriophages.IMPORTANCEBacteriophages and host bacteria commonly coexist in vivo or in soil environments through complex and interdependent microbial interactions. However, recapitulating this symbiotic state remains challenging in vitro due to limited medium nutrients. In this work, the natural symbiosis between Yersinia pestis and specific phages has been discovered in a Marmota himalayana specimen. Epidemiological analysis presented the characteristics of the Y. pestis and specific phages in the area with a strong plague epidemic. Crucially, comparative genomics has been conducted to analyze the genetic changes in both the Y. pestis and phages over different periods, revealing the dynamic and evolving nature of their symbiosis. These are the critical steps to study the mechanism of the symbiosis.
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Affiliation(s)
- Dongyue Lyu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qun Duan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ran Duan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuai Qin
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaojin Zheng
- Akesai Kazakh Autonomous County Center for Disease Control and Prevention, Jiuquan, Gansu, China
| | - Xinmin Lu
- Akesai Kazakh Autonomous County Center for Disease Control and Prevention, Jiuquan, Gansu, China
| | - Asaiti Bukai
- Akesai Kazakh Autonomous County Center for Disease Control and Prevention, Jiuquan, Gansu, China
| | - Peng Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haonan Han
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhaokai He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hanyu Sha
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Di Wu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Meng Xiao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huaiqi Jing
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Narancic J, Gavric D, Kostanjsek R, Knezevic P. First Characterization of Acinetobacter baumannii-Specific Filamentous Phages. Viruses 2024; 16:857. [PMID: 38932150 PMCID: PMC11209303 DOI: 10.3390/v16060857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Filamentous bacteriophages belonging to the order Tubulavirales, family Inoviridae, significantly affect the properties of Gram-negative bacteria, but filamentous phages of many important pathogens have not been described so far. The aim of this study was to examine A. baumannii filamentous phages for the first time and to determine their effect on bacterial virulence. The filamentous phages were detected in 15.3% of A. baumannii strains as individual prophages in the genome or as tandem repeats, and a slightly higher percentage was detected in the culture collection (23.8%). The phylogenetic analyses revealed 12 new genera within the Inoviridae family. Bacteriophages that were selected and isolated showed structural and genomic characteristics of the family and were unable to form plaques. Upon host infection, these phages did not significantly affect bacterial twitching motility and capsule production but significantly affected growth kinetics, reduced biofilm formation, and increased antibiotic sensitivity. One of the possible mechanisms of reduced resistance to antibiotics is the observed decreased expression of efflux pumps after infection with filamentous phages.
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Affiliation(s)
- Jelena Narancic
- PK Lab., Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, 21000 Novi Sad, Serbia; (J.N.); (D.G.)
| | - Damir Gavric
- PK Lab., Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, 21000 Novi Sad, Serbia; (J.N.); (D.G.)
| | - Rok Kostanjsek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jaminkarjeva 101, SI-1000 Ljubljana, Slovenia;
| | - Petar Knezevic
- PK Lab., Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, 21000 Novi Sad, Serbia; (J.N.); (D.G.)
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Bonczarowska JH, Susat J, Krause-Kyora B, Dangvard Pedersen D, Boldsen J, Larsen LA, Seeberg L, Nebel A, Unterweger D. Ancient Yersinia pestis genomes lack the virulence-associated Ypf Φ prophage present in modern pandemic strains. Proc Biol Sci 2023; 290:20230622. [PMID: 37464758 DOI: 10.1098/rspb.2023.0622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/19/2023] [Indexed: 07/20/2023] Open
Abstract
Yersinia pestis is the causative agent of at least three major plague pandemics (Justinianic, Medieval and Modern). Previous studies on ancient Y. pestis genomes revealed that several genomic alterations had occurred approximately 5000-3000 years ago and contributed to the remarkable virulence of this pathogen. How a subset of strains evolved to cause the Modern pandemic is less well-understood. Here, we examined the virulence-associated prophage (YpfΦ), which had been postulated to be exclusively present in the genomes of strains associated with the Modern pandemic. The analysis of two new Y. pestis genomes from medieval/early modern Denmark confirmed that the phage is absent from the genome of strains dating to this time period. An extended comparative genome analysis of over 300 strains spanning more than 5000 years showed that the prophage is found in the genomes of modern strains only and suggests an integration into the genome during recent Y. pestis evolution. The phage-encoded Zot protein showed structural homology to a virulence factor of Vibrio cholerae. Similar to modern Y. pestis, we observed phages with a common origin to YpfΦ in individual strains of other bacterial species. Our findings present an updated view on the prevalence of YpfΦ, which might contribute to our understanding of the host spectrum, geographical spread and virulence of Y. pestis responsible for the Modern pandemic.
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Affiliation(s)
- Joanna H Bonczarowska
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, Kiel 24105, Germany
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, Kiel 24105, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, Kiel 24105, Germany
| | - Dorthe Dangvard Pedersen
- Unit of Anthropology, Department of Forensic Medicine, University of Southern Denmark, Odense M, 5230, Denmark
| | - Jesper Boldsen
- Unit of Anthropology, Department of Forensic Medicine, University of Southern Denmark, Odense M, 5230, Denmark
| | | | - Lone Seeberg
- Museum Horsens Arkæologisk Afdeling, Fussingsvej 8, Horsens 8700, Denmark
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, Kiel 24105, Germany
| | - Daniel Unterweger
- Institute for Experimental Medicine, Kiel University, Michaelisstraße 5, Kiel 24105, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, Plön 24306, Germany
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Two Novel Yersinia pestis Bacteriophages with a Broad Host Range: Potential as Biocontrol Agents in Plague Natural Foci. Viruses 2022; 14:v14122740. [PMID: 36560744 PMCID: PMC9785759 DOI: 10.3390/v14122740] [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: 11/11/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Bacteriophages (phages) have been successfully used as disinfectors to kill bacteria in food and the environment and have been used medically for curing human diseases. The objective of this research was to elucidate the morphological and genomic characteristics of two novel Yersinia pestis phages, vB_YpeM_ MHS112 (MHS112) and vB_YpeM_GMS130 (GMS130), belonging to the genus Gaprivervirus, subfamily Tevenvirinae, family Myoviridae. Genome sequencing showed that the sizes of MHS112 and GMS130 were 170507 and 168552 bp, respectively. A total of 303 and 292 open reading frames with 2 tRNA and 3 tRNA were predicted in MHS112 and GMS130, respectively. The phylogenetic relationships were analysed among the two novel Y. pestis phages, phages in the genus Gaprivervirus, and several T4-like phages infecting the Yersinia genus. The bacteriophage MHS112 and GMS130 exhibited a wider lytic host spectrum and exhibited comparative temperature and pH stability. Such features signify that these phages do not need to rely on Y. pestis as their host bacteria in the ecological environment, while they could be based on more massive Enterobacteriales species to propagate and form ecological barriers against Y. pestis pathogens colonised in plague foci. Such characteristics indicated that the two phages have potential as biocontrol agents for eliminating the endemics of animal plague in natural plague foci.
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Wendling CC, Lange J, Liesegang H, Sieber M, Pöhlein A, Bunk B, Rajkov J, Goehlich H, Roth O, Brockhurst MA. Higher phage virulence accelerates the evolution of host resistance. Proc Biol Sci 2022; 289:20221070. [PMID: 36196537 PMCID: PMC9532999 DOI: 10.1098/rspb.2022.1070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Pathogens vary strikingly in their virulence and the selection they impose on their hosts. While the evolution of different virulence levels is well studied, the evolution of host resistance in response to different virulence levels is less understood and, at present, mainly based on observations and theoretical predictions with few experimental tests. Increased virulence can increase selection for host resistance evolution if the benefits of avoiding infection outweigh resistance costs. To test this, we experimentally evolved the bacterium Vibrio alginolyticus in the presence of two variants of a filamentous phage that differ in their virulence. The bacterial host exhibited two alternative defence strategies: (1) super infection exclusion (SIE), whereby phage-infected cells were immune to subsequent infection at the cost of reduced growth, and (2) surface receptor mutations (SRM), providing resistance to infection by preventing phage attachment. While SIE emerged rapidly against both phages, SRM evolved faster against the high- than the low-virulence phage. Using a mathematical model of our system, we show that increasing virulence strengthens selection for SRM owing to the higher costs of infection suffered by SIE immune hosts. Thus, by accelerating the evolution of host resistance, more virulent phages caused shorter epidemics.
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Affiliation(s)
- Carolin C Wendling
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Düsternbrooker Weg 20, 24105 Kiel, Germany.,ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, CHN D 33, 8092 Zürich, Switzerland
| | - Janina Lange
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Heiko Liesegang
- Department of genomic and applied microbiology, Georg-August-University Göttingen, Grisebachstr 8, 37077 Göttingen, Germany
| | - Michael Sieber
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Anja Pöhlein
- Department of genomic and applied microbiology, Georg-August-University Göttingen, Grisebachstr 8, 37077 Göttingen, Germany
| | - Boyke Bunk
- Department Bioinformatics and Databases, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38114 Braunschweig, Germany
| | - Jelena Rajkov
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Düsternbrooker Weg 20, 24105 Kiel, Germany.,Marine Evolutionary Biology, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Henry Goehlich
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Olivia Roth
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Evolutionary Ecology, Düsternbrooker Weg 20, 24105 Kiel, Germany.,Marine Evolutionary Biology, Kiel University, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Michael A Brockhurst
- Division of Evolution and Genomic Sciences, University of Manchester, Dover Street, Manchester M13 9PT, UK
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Host Range, Morphology and Sequence Analysis of Ten Temperate Phages Isolated from Pathogenic Yersinia enterocolitica Strains. Int J Mol Sci 2022; 23:ijms23126779. [PMID: 35743219 PMCID: PMC9224151 DOI: 10.3390/ijms23126779] [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: 05/20/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 02/01/2023] Open
Abstract
Yersinia enterocolitica is a heterogeneous species comprising highly pathogenic, weakly pathogenic and non-pathogenic strains. Previous data suggest that gene exchange may occur in Yersinia. Only scarce information exists about temperate phages of Y. enterocolitica, even though many prophage sequences are present in this species. We have examined 102 pathogenic Y. enterocolitica strains for the presence of inducible prophages by mitomycin C treatment. Ten phages were isolated from nine strains belonging to the bio (B)/serotypes (O) B2/O:5,27, B2/O:9 and 1B/O:8. All phages are myoviruses showing lytic activity only at room temperature. Whole-genome sequencing of the phage genomes revealed that they belong to three groups, which, however, are not closely related to known phages. Group 1 is composed of five phages (type phage: vB_YenM_06.16.1) with genome sizes of 43.8 to 44.9 kb, whereas the four group 2 phages (type phage: vB_YenM_06.16.2) possess smaller genomes of 29.5 to 33.2 kb. Group 3 contains only one phage (vB_YenM_42.18) whose genome has a size of 36.5 kb, which is moderately similar to group 2. The host range of the phages differed significantly. While group 1 phages almost exclusively lysed strains of B2/O:5,27, phages of group 2 and 3 were additionally able to lyse B4/O:3, and some of them even B2/O:9 and 1B/O:8 strains.
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7
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Nankam WLN, Kwetche PRF, Tazemda-Kuitsouc GB, Chouna GJD, Tekam JM. Hospitalization and colonization by methicillin-resistant Staphylococcus aureus in the surgical department of 03 health facilities in the Ndé division, West-Cameroon. Ann Clin Microbiol Antimicrob 2021; 20:48. [PMID: 34281527 PMCID: PMC8290526 DOI: 10.1186/s12941-021-00451-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/07/2021] [Indexed: 11/30/2022] Open
Abstract
Background Commensal flora colonization during hospitalization by bacteria is the first step for nosocomial infections while antibiotic resistance reduces therapeutic options. In aim to control this phenomenon, we initiated this study to describe the impact of hospitalization on colonization by methicillin-resistant Staphylococcus aureus in the surgical department of 03 health facilities in the Ndé division, West-Cameroon. Methods This study was carried out on patients admitted for surgery in 03 health facilities of the Ndé division, West-Cameroon (District Hospital of Bangangté, Protestant Hospital of Bangwa and Cliniques Universitaires des Montagnes). After obtaining ethical clearance and authorizations, nasal swabs were performed at admission and discharge, with the aim of isolating bacteria and performing their antibiotic susceptibility tests. Informations on each participant's antibiotic therapy were recorded. Laboratory investigations were carried out according to standard protocols (CASFM, 2019). Results The most commonly used antibiotics were β-lactams. A total of 104 nasal swabs were performed on 52 patients who agreed to participate to the study. From the analysis, 110 (57 at admission versus 53 at discharge) Staphylococcus isolates were obtained. Overall, susceptibility testing showed that antibiotic resistance rates were higher at discharge than at admission; with significant differences between the susceptibility profiles obtained at admission and discharge for β-lactams and not significant for fluoroquinolones and aminoglycosides. Globally, frequency of nasal carriage of methicillin-resistant Staphylococcus aureus at discharge 16 (30.77%) was significantly higher than at admission 07 (13.46%) with Chi-2 = 4.52 and p = 0.0335. Conclusion The high rates of antibiotic resistance of bacteria isolated at discharge compared to those isolated at admission obtained in the present investigation, highlights the important role that hospitalization plays in the selection and dissemination of methicillin-resistant Staphylococcus aureus and colonization by these bacteria in health structures of Ndé division. As a result, further investigations to find the factors that promote this phenomenon should be carried out.
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Affiliation(s)
- William Lelorel Nguekap Nankam
- School of Medical Biology, Higher Institute of Health Sciences, Université Des Montagnes, Bangangté, Cameroon. .,Laboratory of Microbiology, Université Des Montagnes Teaching Hospital, Bangangté, Cameroon.
| | - Pierre René Fotsing Kwetche
- School of Medical Biology, Higher Institute of Health Sciences, Université Des Montagnes, Bangangté, Cameroon.,Laboratory of Microbiology, Université Des Montagnes Teaching Hospital, Bangangté, Cameroon.,School of Pharmacy, Higher Institute of Health Sciences, Université Des Montagnes, Bangangté, Cameroon.,School of Human Medicine, Higher Institute of Health Sciences, Université Des Montagnes, Bangangté, Cameroon
| | - Gildas Boris Tazemda-Kuitsouc
- School of Medical Biology, Higher Institute of Health Sciences, Université Des Montagnes, Bangangté, Cameroon.,School of Human Medicine, Higher Institute of Health Sciences, Université Des Montagnes, Bangangté, Cameroon.,Réseau Des Hygiénistes du Cameroun, Bangangté, Cameroon
| | - Golda Joyce Djeutsa Chouna
- School of Medical Biology, Higher Institute of Health Sciences, Université Des Montagnes, Bangangté, Cameroon.,Laboratory of Microbiology, Université Des Montagnes Teaching Hospital, Bangangté, Cameroon
| | - Jean Michel Tekam
- School of Pharmacy, Higher Institute of Health Sciences, Université Des Montagnes, Bangangté, Cameroon
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Piekarowicz A, Kłyż A, Adamczyk-Popławska M, Stein DC. Association of host proteins with the broad host range filamentous phage NgoΦ6 of Neisseria gonorrhoeae. PLoS One 2020; 15:e0240579. [PMID: 33057372 PMCID: PMC7561177 DOI: 10.1371/journal.pone.0240579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
All Neisseria gonorrhoeae strains contain multiple copies of integrated filamentous phage genomes with undefined structures. In this study, we sought to characterize the capsid proteins of filamentous N. gonorrhoeae bacteriophage NgoΦ6 and phagemids propagated in different bacteria. The data demonstrate that purified phage contain phage-encoded structural proteins and bacterial host proteins; host proteins consistently copurified with the phage particles. The bacterial host proteins associated with the phage filament (as identified by mass spectrometry) tended to be one of the predominant outer membrane components of the host strain, plus minor additional host proteins. We were able to copurify a functional ß-lactamase, a phagemid-encoded protein, with phage filaments. We used protein modeling and immunological analysis to identify the major phage encoded structural proteins. The antigenic properties of these proteins depended on the bacterium where the phages were propagated. Polyclonal antibodies against N. gonorrhoeae phage NgoΦ6 recognized phage-encoded proteins if the phage was propagated in N. gonorrhoeae or H. influenzae cells but not if it was propagated in Salmonella or E. coli. We show that the phage filaments isolated from gonococci and Haemophilus are glycosylated, and this may explain the antigenic diversity seen. Taken en toto, the data demonstrate that while the neisserial filamentous phage are similar to other Inovirus with respect to overall genomic organization, their ability to closely associate with host proteins suggests that they have unique surface properties and are secreted by a here-to-fore unknown secretory pathway.
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Affiliation(s)
- A. Piekarowicz
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - A. Kłyż
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - M. Adamczyk-Popławska
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - D. C. Stein
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States of America
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9
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Yeh TY. XerD-dependent integration of a novel filamentous phage Cf2 into the Xanthomonas citri genome. Virology 2020; 548:160-167. [PMID: 32838937 DOI: 10.1016/j.virol.2020.06.010] [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] [Received: 02/15/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 11/27/2022]
Abstract
Filamentous Inoviridae phages integrate into the chromosome of plant pathogens Xanthomonas as prophages, but their diversity and integrative mechanism are not completely understood. A proviral Cf2 sequence of 6454 bases from Xanthomonas citri genome was revived as infectious virions able to lysogenize its host. Unlike other Xanthomonas phages (Cf1c, φLf, Xf109, XacF1), Cf2 phage has RstA/RstB replication protein, and its attP has XerD binding arm and dif central region but lacks XerC binding arm. XerC+/Xf109 and XerD+/Cf2 attPs are in the opposite direction in phage genomes. Moreover, XerCD binding and XerD catalysis for strand exchange are necessary for site-specific integration of XerD+/Cf2 and XerC+/Xf109 attPs. Taken together, these results provide a new insight into the mechanism of XerCD-mediated recombination at XerD + attP.
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Affiliation(s)
- Ting-Yu Yeh
- Agricultural Biotechnology Laboratory, Auxergen Inc., Columbus Center, Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, 21202, USA.
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10
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Shapiro JW, Putonti C. UPΦ phages, a new group of filamentous phages found in several members of Enterobacteriales. Virus Evol 2020; 6:veaa030. [PMID: 32607251 PMCID: PMC7307601 DOI: 10.1093/ve/veaa030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Filamentous phages establish chronic infections in their bacterial hosts, and new phages are secreted by infected bacteria for multiple generations, typically without causing host death. Often, these viruses integrate in their host's genome by co-opting the host's XerCD recombinase system. In several cases, these viruses also encode genes that increase bacterial virulence in plants and animals. Here, we describe a new filamentous phage, UPϕ901, which we originally found integrated in a clinical isolate of Escherichia coli from urine. UPϕ901 and closely related phages can be found in published genomes of over 200 other bacteria, including strains of Citrobacter koseri, Salmonella enterica, Yersinia enterocolitica, and Klebsiella pneumoniae. Its closest relatives are consistently found in urine or in the blood and feces of patients with urinary tract infections. More distant relatives can be found in isolates from other environments, including sewage, water, soil, and contaminated food. Each of these phages, which we collectively call 'UPϕ viruses', also harbors two or more novel genes of unknown function.
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Affiliation(s)
- Jason W Shapiro
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, 1032 W Sheridan Rd, Chicago, IL 60660, USA.,Department of Computer Science, Loyola University Chicago, 1052 W Loyola Ave, Chicago, IL, 60626, USA.,Bioinformatics Program, Loyola University Chicago, 1052 W Loyola Ave, Chicago, IL 60626, USA.,Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, 2160 S First Ave, Maywood, IL 60153, USA
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11
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Hay ID, Lithgow T. Filamentous phages: masters of a microbial sharing economy. EMBO Rep 2019; 20:e47427. [PMID: 30952693 PMCID: PMC6549030 DOI: 10.15252/embr.201847427] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/30/2019] [Accepted: 03/19/2019] [Indexed: 12/11/2022] Open
Abstract
Bacteriophage ("bacteria eaters") or phage is the collective term for viruses that infect bacteria. While most phages are pathogens that kill their bacterial hosts, the filamentous phages of the sub-class Inoviridae live in cooperative relationships with their bacterial hosts, akin to the principal behaviours found in the modern-day sharing economy: peer-to-peer support, to offset any burden. Filamentous phages impose very little burden on bacteria and offset this by providing service to help build better biofilms, or provision of toxins and other factors that increase virulence, or modified behaviours that provide novel motile activity to their bacterial hosts. Past, present and future biotechnology applications have been built on this phage-host cooperativity, including DNA sequencing technology, tools for genetic engineering and molecular analysis of gene expression and protein production, and phage-display technologies for screening protein-ligand and protein-protein interactions. With the explosion of genome and metagenome sequencing surveys around the world, we are coming to realize that our knowledge of filamentous phage diversity remains at a tip-of-the-iceberg stage, promising that new biology and biotechnology are soon to come.
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Affiliation(s)
- Iain D Hay
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Vic., Australia
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12
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Sharma RS, Karmakar S, Kumar P, Mishra V. Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration. Ecol Evol 2019; 9:2263-2304. [PMID: 30847110 PMCID: PMC6392359 DOI: 10.1002/ece3.4743] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/25/2018] [Accepted: 10/30/2018] [Indexed: 02/06/2023] Open
Abstract
Theories in soil biology, such as plant-microbe interactions and microbial cooperation and antagonism, have guided the practice of ecological restoration (ecorestoration). Below-ground biodiversity (bacteria, fungi, invertebrates, etc.) influences the development of above-ground biodiversity (vegetation structure). The role of rhizosphere bacteria in plant growth has been largely investigated but the role of phages (bacterial viruses) has received a little attention. Below the ground, phages govern the ecology and evolution of microbial communities by affecting genetic diversity, host fitness, population dynamics, community composition, and nutrient cycling. However, few restoration efforts take into account the interactions between bacteria and phages. Unlike other phages, filamentous phages are highly specific, nonlethal, and influence host fitness in several ways, which make them useful as target bacterial inocula. Also, the ease with which filamentous phages can be genetically manipulated to express a desired peptide to track and control pathogens and contaminants makes them useful in biosensing. Based on ecology and biology of filamentous phages, we developed a hypothesis on the application of phages in environment to derive benefits at different levels of biological organization ranging from individual bacteria to ecosystem for ecorestoration. We examined the potential applications of filamentous phages in improving bacterial inocula to restore vegetation and to monitor changes in habitat during ecorestoration and, based on our results, recommend a reorientation of the existing framework of using microbial inocula for such restoration and monitoring. Because bacterial inocula and biomonitoring tools based on filamentous phages are likely to prove useful in developing cost-effective methods of restoring vegetation, we propose that filamentous phages be incorporated into nature-based restoration efforts and that the tripartite relationship between phages, bacteria, and plants be explored further. Possible impacts of filamentous phages on native microflora are discussed and future areas of research are suggested to preclude any potential risks associated with such an approach.
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Affiliation(s)
- Radhey Shyam Sharma
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental StudiesUniversity of DelhiDelhiIndia
| | - Swagata Karmakar
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental StudiesUniversity of DelhiDelhiIndia
| | - Pankaj Kumar
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental StudiesUniversity of DelhiDelhiIndia
| | - Vandana Mishra
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental StudiesUniversity of DelhiDelhiIndia
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Abstract
Bacteriophage play many varied roles in microbial ecology and evolution. This chapter collates a vast body of knowledge and expertise on Yersinia pestis phages, including the history of their isolation and classical methods for their isolation and identification. The genomic diversity of Y. pestis phage and bacteriophage islands in the Y. pestis genome are also discussed because all phage research represents a branch of genetics. In addition, our knowledge of the receptors that are recognized by Y. pestis phage, advances in phage therapy for Y. pestis infections, the application of phage in the detection of Y. pestis, and clustered regularly interspaced short palindromic repeats (CRISPRs) sequences of Y. pestis from prophage DNA are all reviewed here.
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Ilyina TS. Filamentous bacteriophages and their role in the virulence and evolution of pathogenic bacteria. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2015. [DOI: 10.3103/s0891416815010036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Mai-Prochnow A, Hui JGK, Kjelleberg S, Rakonjac J, McDougald D, Rice SA. 'Big things in small packages: the genetics of filamentous phage and effects on fitness of their host'. FEMS Microbiol Rev 2015; 39:465-87. [PMID: 25670735 DOI: 10.1093/femsre/fuu007] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 12/17/2014] [Indexed: 01/01/2023] Open
Abstract
This review synthesizes recent and past observations on filamentous phages and describes how these phages contribute to host phentoypes. For example, the CTXφ phage of Vibrio cholerae encodes the cholera toxin genes, responsible for causing the epidemic disease, cholera. The CTXφ phage can transduce non-toxigenic strains, converting them into toxigenic strains, contributing to the emergence of new pathogenic strains. Other effects of filamentous phage include horizontal gene transfer, biofilm development, motility, metal resistance and the formation of host morphotypic variants, important for the biofilm stress resistance. These phages infect a wide range of Gram-negative bacteria, including deep-sea, pressure-adapted bacteria. Many filamentous phages integrate into the host genome as prophage. In some cases, filamentous phages encode their own integrase genes to facilitate this process, while others rely on host-encoded genes. These differences are mediated by different sets of 'core' and 'accessory' genes, with the latter group accounting for some of the mechanisms that alter the host behaviours in unique ways. It is increasingly clear that despite their relatively small genomes, these phages exert signficant influence on their hosts and ultimately alter the fitness and other behaviours of their hosts.
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Affiliation(s)
- Anne Mai-Prochnow
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia
| | - Janice Gee Kay Hui
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia
| | - Staffan Kjelleberg
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia The Singapore Centre on Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Jasna Rakonjac
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Diane McDougald
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia The Singapore Centre on Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Scott A Rice
- The Centre for Marine Bio-Innovation and the School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney NSW 2052, Australia The Singapore Centre on Environmental Life Sciences Engineering and the School of Biological Sciences, Nanyang Technological University, 637551, Singapore
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Derbise A, Carniel E. YpfΦ: a filamentous phage acquired by Yersinia pestis. Front Microbiol 2014; 5:701. [PMID: 25566217 PMCID: PMC4266046 DOI: 10.3389/fmicb.2014.00701] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 11/26/2014] [Indexed: 11/13/2022] Open
Abstract
Yersinia pestis, the plague bacillus, has an exceptional pathogenicity for humans. The plague bacillus emerged very recently (≈3,000 years ago) from the enteropathogen Y. pseudotuberculosis. Early after its emergence, Y. pestis became infected by a filamentous phage named YpfΦ. During the microevolution of the plague bacillus, the phage remained in the various lineages as an unstable extrachromosomal element. However, in the sub branch that caused the third plague pandemic, YpfΦ integrated itself into the bacterial chromosome to become a stable prophage. The genome of this phage has the same genetic organization as that of other filamentous phages such as the Vibrio cholerae CTXΦ phage, and shares high sequence identity with the CUS-1 filamentous phage of a high-virulence Escherichia coli K1 clone. In addition to genes involved in phage physiology, YpfΦ carries at each extremity of its genome two open reading frames with no predicted functions. This filamentous phage confers some selective properties to Y. pestis during the infectious process, which may explain why it was conserved duringY. pestis microevolution, despite its instability as an extrachromosomal element in most branches.
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Affiliation(s)
- Anne Derbise
- Yersinia Research Unit, Department of Microbiology, Institut Pasteur Paris, France
| | - Elisabeth Carniel
- Yersinia Research Unit, Department of Microbiology, Institut Pasteur Paris, France
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Marvin DA, Symmons MF, Straus SK. Structure and assembly of filamentous bacteriophages. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:80-122. [PMID: 24582831 DOI: 10.1016/j.pbiomolbio.2014.02.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/09/2014] [Indexed: 12/24/2022]
Abstract
Filamentous bacteriophages are interesting paradigms in structural molecular biology, in part because of the unusual mechanism of filamentous phage assembly. During assembly, several thousand copies of an intracellular DNA-binding protein bind to each copy of the replicating phage DNA, and are then displaced by membrane-spanning phage coat proteins as the nascent phage is extruded through the bacterial plasma membrane. This complicated process takes place without killing the host bacterium. The bacteriophage is a semi-flexible worm-like nucleoprotein filament. The virion comprises a tube of several thousand identical major coat protein subunits around a core of single-stranded circular DNA. Each protein subunit is a polymer of about 50 amino-acid residues, largely arranged in an α-helix. The subunits assemble into a helical sheath, with each subunit oriented at a small angle to the virion axis and interdigitated with neighbouring subunits. A few copies of "minor" phage proteins necessary for infection and/or extrusion of the virion are located at each end of the completed virion. Here we review both the structure of the virion and aspects of its function, such as the way the virion enters the host, multiplies, and exits to prey on further hosts. In particular we focus on our understanding of the way the components of the virion come together during assembly at the membrane. We try to follow a basic rule of empirical science, that one should chose the simplest theoretical explanation for experiments, but be prepared to modify or even abandon this explanation as new experiments add more detail.
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Affiliation(s)
- D A Marvin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - M F Symmons
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - S K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada.
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Petrova M, Shcherbatova N, Kurakov A, Mindlin S. Genomic characterization and integrative properties of phiSMA6 and phiSMA7, two novel filamentous bacteriophages of Stenotrophomonas maltophilia. Arch Virol 2013; 159:1293-303. [DOI: 10.1007/s00705-013-1882-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/29/2013] [Indexed: 12/12/2022]
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Neisseria gonorrhoeae filamentous phage NgoΦ6 is capable of infecting a variety of Gram-negative bacteria. J Virol 2013; 88:1002-10. [PMID: 24198404 DOI: 10.1128/jvi.02707-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We constructed a phagemid consisting of the whole genome of the Neisseria gonorrhoeae bacteriophage NgoΦ6 cloned into a pBluescript plasmid derivative lacking the f1 origin of replication (named pBS::Φ6). Escherichia coli cells harboring pBS::Φ6 were able to produce a biologically active phagemid, NgoΦ6fm, capable of infecting, integrating its DNA into the chromosome of, and producing progeny phagemids in, a variety of taxonomically distant Gram-negative bacteria, including E. coli, Haemophilus influenzae, Neisseria sicca, Pseudomonas sp., and Paracoccus methylutens. A derivative of pBS::Φ6 lacking the phage orf7 gene, a positional homolog of filamentous phage proteins that mediate the interaction between the phage and the bacterial pilus, was capable of producing phagemid particles that were able to infect E. coli, Haemophilus influenzae, N. sicca, Pseudomonas sp., and Paracoccus methylutens, indicating that NgoΦ6 infects cells of these species using a mechanism that does not involve the Orf7 gene product and that NgoΦ6 initiates infection through a novel process in these species. We further demonstrate that the establishment of the lysogenic state does not require an active phage integrase. Since phagemid particles were capable of infecting diverse hosts, this indicates that NgoΦ6 is the first broad-host-range filamentous bacteriophage described.
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Gains and Losses in Yersinia enterocolitica subsp. palearctica Genomes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 954:23-9. [DOI: 10.1007/978-1-4614-3561-7_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Krupovic M, Prangishvili D, Hendrix RW, Bamford DH. Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol Mol Biol Rev 2011; 75:610-35. [PMID: 22126996 PMCID: PMC3232739 DOI: 10.1128/mmbr.00011-11] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, 25 rue du Dr. Roux, 75015 Paris, France.
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Batzilla J, Antonenka U, Höper D, Heesemann J, Rakin A. Yersinia enterocolitica palearctica serobiotype O:3/4--a successful group of emerging zoonotic pathogens. BMC Genomics 2011; 12:348. [PMID: 21733159 PMCID: PMC3161016 DOI: 10.1186/1471-2164-12-348] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 07/06/2011] [Indexed: 02/04/2023] Open
Abstract
Background High-pathogenic Y. enterocolitica ssp. enterocolitica caused several human outbreaks in Northern America. In contrast, low pathogenic Y. enterocolitica ssp. palearctica serobiotype O:3/4 is responsible for sporadic cases worldwide with asymptomatic pigs being the main source of infection. Genomes of three Y. enterocolitica ssp. palearctica serobiotype O:3/4 human isolates (including the completely sequenced Y11 German DSMZ type strain) were compared to the high-pathogenic Y. enterocolitica ssp. enterocolitica 8081 O:8/1B to address the peculiarities of the O:3/4 group. Results Most high-pathogenicity-associated determinants of Y. enterocolitica ssp. enterocolitica (like the High-Pathogenicity Island, yts1 type 2 and ysa type 3 secretion systems) are absent in Y. enterocolitica ssp. palearctica serobiotype O:3/4 genomes. On the other hand they possess alternative putative virulence and fitness factors, such as a different ysp type 3 secretion system, an RtxA-like and insecticidal toxins, and a N-acetyl-galactosamine (GalNAc) PTS system (aga-operon). Horizontal acquisition of two prophages and a tRNA-Asn-associated GIYep-01 genomic island might also influence the Y. enterocolitica ssp. palearctica serobiotype O:3/4 pathoadaptation. We demonstrated recombination activity of the PhiYep-3 prophage and the GIYep-01 island and the ability of the aga-operon to support the growth of the Y. enterocolitica ssp. enterocolitica O:8/1B on GalNAc. Conclusions Y. enterocolitica ssp. palearctica serobiotype O:3/4 experienced a shift to an alternative patchwork of virulence and fitness determinants that might play a significant role in its host pathoadaptation and successful worldwide dissemination.
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