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Kim SG, Wang SX, Foley SL. Complete genome sequence of two chromosomes of Vibrio metoecus strain ZF102 isolated from the abdominal cavity of moribund laboratory zebrafish ( Danio rerio). Microbiol Resour Announc 2024; 13:e0021624. [PMID: 38712933 PMCID: PMC11237558 DOI: 10.1128/mra.00216-24] [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: 03/04/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024] Open
Abstract
Vibrio metoecus was isolated from the abdominal cavity of moribund laboratory zebrafish. We report complete genomic sequences of V. metoecus strain ZF102 that has two circular chromosomes of 2,872,299 and 1,170,691 bp and two plasmids of 5,265 and 2,361 bp.
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Affiliation(s)
- Sung Guk Kim
- Surveillance/Diagnostic Laboratory, Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Sharon X Wang
- Surveillance/Diagnostic Laboratory, Office of Scientific Coordination, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Steven L Foley
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
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2
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Molina-Quiroz RC, Camilli A, Silva-Valenzuela CA. Role of Bacteriophages in the Evolution of Pathogenic Vibrios and Lessons for Phage Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:149-173. [PMID: 36792875 PMCID: PMC10587905 DOI: 10.1007/978-3-031-22997-8_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Viruses of bacteria, i.e., bacteriophages (or phages for short), were discovered over a century ago and have played a major role as a model system for the establishment of the fields of microbial genetics and molecular biology. Despite the relative simplicity of phages, microbiologists are continually discovering new aspects of their biology including mechanisms for battling host defenses. In turn, novel mechanisms of host defense against phages are being discovered at a rapid clip. A deeper understanding of the arms race between bacteria and phages will continue to reveal novel molecular mechanisms and will be important for the rational design of phage-based prophylaxis and therapies to prevent and treat bacterial infections, respectively. Here we delve into the molecular interactions of Vibrio species and phages.
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Affiliation(s)
- Roberto C Molina-Quiroz
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts Medical Center and Tufts University, Boston, MA, USA
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University, School of Medicine, Boston, MA, USA
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3
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Orata FD, Hussain NAS, Liang KYH, Hu D, Boucher YF. Genomes of Vibrio metoecus co-isolated with Vibrio cholerae extend our understanding of differences between these closely related species. Gut Pathog 2022; 14:42. [PMID: 36404338 PMCID: PMC9677704 DOI: 10.1186/s13099-022-00516-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/04/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Vibrio cholerae, the causative agent of cholera, is a well-studied species, whereas Vibrio metoecus is a recently described close relative that is also associated with human infections. The availability of V. metoecus genomes provides further insight into its genetic differences from V. cholerae. Additionally, both species have been co-isolated from a cholera-free brackish coastal pond and have been suggested to interact with each other by horizontal gene transfer (HGT). RESULTS The genomes of 17 strains from each species were sequenced. All strains share a large core genome (2675 gene families) and very few genes are unique to each species (< 3% of the pan-genome of both species). This led to the identification of potential molecular markers-for nitrite reduction, as well as peptidase and rhodanese activities-to further distinguish V. metoecus from V. cholerae. Interspecies HGT events were inferred in 21% of the core genes and 45% of the accessory genes. A directional bias in gene transfer events was found in the core genome, where V. metoecus was a recipient of three times (75%) more genes from V. cholerae than it was a donor (25%). CONCLUSION V. metoecus was misclassified as an atypical variant of V. cholerae due to their resemblance in a majority of biochemical characteristics. More distinguishing phenotypic assays can be developed based on the discovery of potential gene markers to avoid any future misclassifications. Furthermore, differences in relative abundance or seasonality were observed between the species and could contribute to the bias in directionality of HGT.
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Affiliation(s)
- Fabini D. Orata
- grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Alberta Canada ,grid.17089.370000 0001 2190 316XDepartment of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta Canada
| | - Nora A. S. Hussain
- grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Alberta Canada
| | - Kevin Y. H. Liang
- grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Alberta Canada ,grid.14709.3b0000 0004 1936 8649Department of Quantitative Life Sciences, McGill University, Montréal, Québec Canada ,grid.14709.3b0000 0004 1936 8649Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec Canada
| | - Dalong Hu
- grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Yann F. Boucher
- grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Alberta Canada ,grid.4280.e0000 0001 2180 6431Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore and National University Hospital System, Singapore, Singapore
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Adade NE, Aniweh Y, Mosi L, Valvano MA, Duodu S, Ahator SD. Comparative analysis of Vibrio cholerae isolates from Ghana reveals variations in genome architecture and adaptation of outbreak and environmental strains. Front Microbiol 2022; 13:998182. [PMID: 36312941 PMCID: PMC9608740 DOI: 10.3389/fmicb.2022.998182] [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] [Received: 07/19/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022] Open
Abstract
Recurrent epidemics of cholera denote robust adaptive mechanisms of Vibrio cholerae for ecological shifting and persistence despite variable stress conditions. Tracking the evolution of pathobiological traits requires comparative genomic studies of isolates from endemic areas. Here, we investigated the genetic differentiation among V. cholerae clinical and environmental isolates by highlighting the genomic divergence associated with gene decay, genome plasticity, and the acquisition of virulence and adaptive traits. The clinical isolates showed high phylogenetic relatedness due to a higher frequency of shared orthologs and fewer gene variants in contrast to the evolutionarily divergent environmental strains. Divergence of the environmental isolates is linked to extensive genomic rearrangements in regions containing mobile genetic elements resulting in numerous breakpoints, relocations, and insertions coupled with the loss of virulence determinants acf, zot, tcp, and ctx in the genomic islands. Also, four isolates possessed the CRISPR-Cas systems with spacers specific for Vibrio phages and plasmids. Genome synteny and homology analysis of the CRISPR-Cas systems suggest horizontal acquisition. The marked differences in the distribution of other phage and plasmid defense systems such as Zorya, DdmABC, DdmDE, and type-I Restriction Modification systems among the isolates indicated a higher propensity for plasmid or phage disseminated traits in the environmental isolates. Our results reveal that V. cholerae strains undergo extensive genomic rearrangements coupled with gene acquisition, reflecting their adaptation during ecological shifts and pathogenicity.
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Affiliation(s)
- Nana Eghele Adade
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
- Department of Microbiology, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Yaw Aniweh
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Lydia Mosi
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Miguel A. Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, United Kingdom
| | - Samuel Duodu
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Stephen Dela Ahator
- Centre for New Antibacterial Strategies (CANS) and Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
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5
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Islam MT, Liang K, Orata FD, Im MS, Alam M, Lee CC, Boucher YF. Vibrio tarriae sp. nov., a novel member of the Cholerae clade. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A number of bacteria with close resemblance to
Vibrio cholerae
have been isolated over the years by the Centres for Disease Control and Prevention (CDC), which could not be assigned a proper taxonomic designation on the basis of the results from preliminary identification methods. Nine such isolates have been found to share 16S rRNA gene identity exceeding 99 % with V. cholerae, yet DNA–DNA hybridization (60.4–62.1 %) and average nucleotide identity values (94.4–95.1 %) were below the species cut-off, indicating a potentially novel species. Phylogenetic analysis of core genomes places this group of isolates in a monophyletic clade, within the ‘Cholerae clade’, but distinct from any other species. Extensive phenotypic characterization reveals unique biochemical properties that distinguish this novel species from
V. cholerae
. Comparative genomic analysis reveals a unique set of siderophore genes, indicating that iron acquisition strategies could be vital for the divergence of the novel species from a common ancestor with
V. cholerae
. On the basis of the genetic, phylogenetic and phenotypic differences observed, we propose that these isolates represent a novel species of the genus
Vibrio
, for which the name Vibrio tarriae sp. nov. is proposed. Strain 2521-89 T (= DSM 112461=CCUG 75318), isolated from lake water, is the type strain.
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Affiliation(s)
- Mohammad Tarequl Islam
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Kevin Liang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Fabini D. Orata
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Monica S. Im
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Munirul Alam
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Christine C. Lee
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yann F. Boucher
- Saw Swee Hock School of Public Health and National University Hospital System, National University of Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore
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Nasreen T, Hussain NA, Ho JY, Aw VZJ, Alam M, Yanow SK, Boucher YF. Assay for Evaluating the Abundance of Vibrio cholerae and Its O1 Serogroup Subpopulation from Water without DNA Extraction. Pathogens 2022; 11:pathogens11030363. [PMID: 35335687 PMCID: PMC8953119 DOI: 10.3390/pathogens11030363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Cholera is a severe diarrheal disease caused by Vibrio cholerae, a natural inhabitant of brackish water. Effective control of cholera outbreaks depends on prompt detection of the pathogen from clinical specimens and tracking its source in the environment. Although the epidemiology of cholera is well studied, rapid detection of V. cholerae remains a challenge, and data on its abundance in environmental sources are limited. Here, we describe a sensitive molecular quantification assay by qPCR, which can be used on-site in low-resource settings on water without the need for DNA extraction. This newly optimized method exhibited 100% specificity for total V. cholerae as well as V. cholerae O1 and allowed detection of as few as three target CFU per reaction. The limit of detection is as low as 5 × 103 CFU/L of water after concentrating biomass from the sample. The ability to perform qPCR on water samples without DNA extraction, portable features of the equipment, stability of the reagents at 4 °C and user-friendly online software facilitate fast quantitative analysis of V. cholerae. These characteristics make this assay extremely useful for field research in resource-poor settings and could support continuous monitoring in cholera-endemic areas.
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Affiliation(s)
- Tania Nasreen
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (T.N.); (N.A.S.H.)
| | - Nora A.S. Hussain
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (T.N.); (N.A.S.H.)
| | - Jia Yee Ho
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), National University of Singapore, Singapore 637551, Singapore; (J.Y.H.); (V.Z.J.A.)
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore 117549, Singapore
| | - Vanessa Zhi Jie Aw
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), National University of Singapore, Singapore 637551, Singapore; (J.Y.H.); (V.Z.J.A.)
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore 117549, Singapore
| | - Munirul Alam
- Centre for Communicable Diseases, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka 1212, Bangladesh;
| | - Stephanie K. Yanow
- School of Public Health, University of Alberta, Edmonton, AB T6G 2E9, Canada;
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Yann F. Boucher
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), National University of Singapore, Singapore 637551, Singapore; (J.Y.H.); (V.Z.J.A.)
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, Singapore 117549, Singapore
- Correspondence:
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7
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Islam MT, Nasreen T, Kirchberger PC, Liang KYH, Orata FD, Johura FT, Hussain NAS, Im MS, Tarr CL, Alam M, Boucher YF. Population Analysis of Vibrio cholerae in Aquatic Reservoirs Reveals a Novel Sister Species ( Vibrio paracholerae sp. nov.) with a History of Association with Humans. Appl Environ Microbiol 2021; 87:e0042221. [PMID: 34132593 PMCID: PMC8357300 DOI: 10.1128/aem.00422-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Most efforts to understand the biology of Vibrio cholerae have focused on a single group, the pandemic-generating lineage harboring the strains responsible for all known cholera pandemics. Consequently, little is known about the diversity of this species in its native aquatic environment. To understand the differences in the V. cholerae populations inhabiting regions with a history of cholera cases and those lacking such a history, a comparative analysis of population composition was performed. Little overlap was found in lineage compositions between those in Dhaka, Bangladesh (where cholera is endemic), located in the Ganges Delta, and those in Falmouth, MA (no known history of cholera), a small coastal town on the United States east coast. The most striking difference was the presence of a group of related lineages at high abundance in Dhaka, which was completely absent from Falmouth. Phylogenomic analysis revealed that these lineages form a cluster at the base of the phylogeny for the V. cholerae species and were sufficiently differentiated genetically and phenotypically to form a novel species. A retrospective search revealed that strains from this species have been anecdotally found from around the world and were isolated as early as 1916 from a British soldier in Egypt suffering from choleraic diarrhea. In 1935, Gardner and Venkatraman unofficially referred to a member of this group as Vibrio paracholerae. In recognition of this earlier designation, we propose the name Vibrio paracholerae sp. nov. for this bacterium. Genomic analysis suggests a link with human populations for this novel species and substantial interaction with its better-known sister species. IMPORTANCE Cholera continues to remain a major public health threat around the globe. Understanding the ecology, evolution, and environmental adaptation of the causative agent (Vibrio cholerae) and tracking the emergence of novel lineages with pathogenic potential are essential to combat the problem. In this study, we investigated the population dynamics of Vibrio cholerae in an inland locality, which is known as endemic for cholera, and compared them with those of a cholera-free coastal location. We found the consistent presence of the pandemic-generating lineage of V. cholerae in Dhaka, where cholera is endemic, and an exclusive presence of a lineage phylogenetically distinct from other V. cholerae lineages. Our study suggests that this lineage represents a novel species that has pathogenic potential and a human link to its environmental abundance. The possible association with human populations and coexistence and interaction with toxigenic V. cholerae in the natural environment make this potential human pathogen an important subject for future studies.
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Affiliation(s)
| | - Tania Nasreen
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Paul C. Kirchberger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Kevin Y. H. Liang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Fabini D. Orata
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Fatema-Tuz Johura
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Nora A. S. Hussain
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Monica S. Im
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Cheryl L. Tarr
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Munirul Alam
- Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Yann F. Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
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8
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Luo Y, Wang H, Liang J, Qian H, Ye J, Chen L, Yang X, Chen Z, Wang F, Octavia S, Payne M, Song X, Jiang J, Jin D, Lan R. Population Structure and Multidrug Resistance of Non-O1/Non-O139 Vibrio cholerae in Freshwater Rivers in Zhejiang, China. MICROBIAL ECOLOGY 2021; 82:319-333. [PMID: 33410933 DOI: 10.1007/s00248-020-01645-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
To understand the environmental reservoirs of Vibrio cholerae and their public health significance, we surveyed freshwater samples from rivers in two cities (Jiaxing [JX] and Jiande [JD]) in Zhejiang, China. A total of 26 sampling locations were selected, and river water was sampled 456 times from 2015 to 2016 yielding 200 V. cholerae isolates, all of which were non-O1/non-O139. The average isolation rate was 47.3% and 39.1% in JX and JD, respectively. Antibiotic resistance profiles of the V. cholerae isolates were examined with nonsusceptibility to cefazolin (68.70%, 79/115) being most common, followed by ampicillin (47.83%, 55/115) and imipenem (27.83%, 32/115). Forty-two isolates (36.52%, 42/115) were defined as multidrug resistant (MDR). The presence of virulence genes was also determined, and the majority of the isolates were positive for toxR (198/200, 99%) and hlyA (196/200, 98%) with few other virulence genes observed. The population structure of the V. cholerae non-O1/non-O139 sampled was examined using multilocus sequence typing (MLST) with 200 isolates assigned to 128 STs and 6 subpopulations. The non-O1/non-O139 V. cholerae population in JX was more varied than in JD. By clonal complexes (CCs), 31 CCs that contained isolates from this study were shared with other parts of China and/or other countries, suggesting widespread presence of some non-O1/non-O139 clones. Drug resistance profiles differed between subpopulations. The findings suggest that non-O1/non-O139 V. cholerae in the freshwater environment is a potential source of human infections. Routine surveillance of non-O1/non-O139 V. cholerae in freshwater rivers will be of importance to public health.
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Affiliation(s)
- Yun Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310052, Zhejiang, China
| | - Henghui Wang
- Jiaxing Center for Disease Control and Prevention, Jiaxing, 314050, Zhejiang, China
| | - Jie Liang
- Jiande Center for Disease Control and Prevention, Hangzhou, 311600, Zhejiang, China
| | - Huiqin Qian
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310052, Zhejiang, China
| | - Julian Ye
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310052, Zhejiang, China
| | - Lixia Chen
- Jiaxing Center for Disease Control and Prevention, Jiaxing, 314050, Zhejiang, China
| | - Xianqing Yang
- Jiande Center for Disease Control and Prevention, Hangzhou, 311600, Zhejiang, China
| | - Zhongwen Chen
- Jiaxing Center for Disease Control and Prevention, Jiaxing, 314050, Zhejiang, China
| | - Fei Wang
- Jiande Center for Disease Control and Prevention, Hangzhou, 311600, Zhejiang, China
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Xiaojun Song
- Centre of Laboratory Medicine, Zhejiang Provincial People Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Jianmin Jiang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310052, Zhejiang, China
| | - Dazhi Jin
- Centre of Laboratory Medicine, Zhejiang Provincial People Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, 310058, Zhejiang, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
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9
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Guardiola-Avila I, Sánchez-Busó L, Acedo-Félix E, Gomez-Gil B, Zúñiga-Cabrera M, González-Candelas F, Noriega-Orozco L. Core and Accessory Genome Analysis of Vibrio mimicus. Microorganisms 2021; 9:microorganisms9010191. [PMID: 33477474 PMCID: PMC7831076 DOI: 10.3390/microorganisms9010191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 01/21/2023] Open
Abstract
Vibrio mimicus is an emerging pathogen, mainly associated with contaminated seafood consumption. However, little is known about its evolution, biodiversity, and pathogenic potential. This study analyzes the pan-, core, and accessory genomes of nine V. mimicus strains. The core genome yielded 2424 genes in chromosome I (ChI) and 822 genes in chromosome II (ChII), with an accessory genome comprising an average of 10.9% of the whole genome for ChI and 29% for ChII. Core genome phylogenetic trees were obtained, and V. mimicus ATCC-33654 strain was the closest to the outgroup in both chromosomes. Additionally, a phylogenetic study of eight conserved genes (ftsZ, gapA, gyrB, topA, rpoA, recA, mreB, and pyrH), including Vibrio cholerae, Vibrio parilis, Vibrio metoecus, and Vibrio caribbenthicus, clearly showed clade differentiation. The main virulence genes found in ChI corresponded with type I secretion proteins, extracellular components, flagellar proteins, and potential regulators, while, in ChII, the main categories were type-I secretion proteins, chemotaxis proteins, and antibiotic resistance proteins. The accessory genome was characterized by the presence of mobile elements and toxin encoding genes in both chromosomes. Based on the genome atlas, it was possible to characterize differential regions between strains. The pan-genome of V. mimicus encompassed 3539 genes for ChI and 2355 genes for ChII. These results give us an insight into the virulence and gene content of V. mimicus, as well as constitute the first approach to its diversity.
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Affiliation(s)
- Iliana Guardiola-Avila
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora 83304, Mexico; (I.G.-A.); (E.A.-F.)
| | - Leonor Sánchez-Busó
- Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), 46020 Valencia, Spain;
| | - Evelia Acedo-Félix
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Hermosillo, Sonora 83304, Mexico; (I.G.-A.); (E.A.-F.)
| | - Bruno Gomez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD) Mazatlán, Unit for Aquaculture and Environmental Management, Mazatlan, Sinaloa 82112, Mexico;
| | - Manuel Zúñiga-Cabrera
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSSIC), 46980 Paterna, Spain;
| | - Fernando González-Candelas
- Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de Valencia, I2SysBio, CIBERESP, 46980 Valencia, Spain;
| | - Lorena Noriega-Orozco
- Guaymas Unit, Centro de Investigación en Alimentación y Desarrollo (CIAD), Guaymas, Sonora 85480, Mexico
- Correspondence: ; Tel.: +52-662-289-2400
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10
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Nasreen T, Hussain NAS, Islam MT, Orata FD, Kirchberger PC, Case RJ, Alam M, Yanow SK, Boucher YF. Simultaneous Quantification of Vibrio metoecus and Vibrio cholerae with Its O1 Serogroup and Toxigenic Subpopulations in Environmental Reservoirs. Pathogens 2020; 9:pathogens9121053. [PMID: 33339261 PMCID: PMC7766680 DOI: 10.3390/pathogens9121053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 12/14/2022] Open
Abstract
Vibrio metoecus is a recently described aquatic bacterium and opportunistic pathogen, closely related to and often coexisting with Vibrio cholerae. To study the relative abundance and population dynamics of both species in aquatic environments of cholera-endemic and cholera-free regions, we developed a multiplex qPCR assay allowing simultaneous quantification of total V. metoecus and V. cholerae (including toxigenic and O1 serogroup) cells. The presence of V. metoecus was restricted to samples from regions that are not endemic for cholera, where it was found at 20% of the abundance of V. cholerae. In this environment, non-toxigenic O1 serogroup V. cholerae represents almost one-fifth of the total V. cholerae population. In contrast, toxigenic O1 serogroup V. cholerae was also present in low abundance on the coast of cholera-endemic regions, but sustained in relatively high proportions throughout the year in inland waters. The majority of cells from both Vibrio species were recovered from particles rather than free-living, indicating a potential preference for attached versus planktonic lifestyles. This research further elucidates the population dynamics underpinning V. cholerae and its closest relative in cholera-endemic and non-endemic regions through culture-independent quantification from environmental samples.
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Affiliation(s)
- Tania Nasreen
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (T.N.); (N.A.S.H.); (M.T.I.); (F.D.O.); (R.J.C.)
| | - Nora A. S. Hussain
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (T.N.); (N.A.S.H.); (M.T.I.); (F.D.O.); (R.J.C.)
| | - Mohammad Tarequl Islam
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (T.N.); (N.A.S.H.); (M.T.I.); (F.D.O.); (R.J.C.)
| | - Fabini D. Orata
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (T.N.); (N.A.S.H.); (M.T.I.); (F.D.O.); (R.J.C.)
| | - Paul C. Kirchberger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA;
| | - Rebecca J. Case
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (T.N.); (N.A.S.H.); (M.T.I.); (F.D.O.); (R.J.C.)
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Munirul Alam
- Centre for Communicable Diseases, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka 1000, Bangladesh;
| | - Stephanie K. Yanow
- School of Public Health, University of Alberta, Edmonton, AB T6G 1C9, Canada;
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Yann F. Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; (T.N.); (N.A.S.H.); (M.T.I.); (F.D.O.); (R.J.C.)
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), National University of Singapore, Singapore 637551, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
- Correspondence:
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Liang KYH, Orata FD, Islam MT, Nasreen T, Alam M, Tarr CL, Boucher YF. A Vibrio cholerae Core Genome Multilocus Sequence Typing Scheme To Facilitate the Epidemiological Study of Cholera. J Bacteriol 2020; 202:e00086-20. [PMID: 32540931 PMCID: PMC7685551 DOI: 10.1128/jb.00086-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/07/2020] [Indexed: 12/11/2022] Open
Abstract
Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies-level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for Vibrio cholerae, a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in V. cholerae were used to analyze a comprehensive data set of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates that could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single-nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease of use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for V. cholerae research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST (https://pubmlst.org/vcholerae/).IMPORTANCE Toxigenic Vibrio cholerae isolates of the O1 and O139 serogroups are the causative agents of cholera, an acute diarrheal disease that plagued the world for centuries, if not millennia. Here, we introduce a core genome multilocus sequence typing scheme for V. cholerae Using this scheme, we have standardized the definition for subspecies-level classification, facilitating global collaboration in the surveillance of V. cholerae In addition, this typing scheme allows for quick identification of outbreak-related isolates that can guide subsequent analyses, serving as an important first step in epidemiological research. This scheme is also easily scalable to analyze thousands of isolates at various levels of resolution, making it an invaluable tool for large-scale ecological and evolutionary analyses.
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Affiliation(s)
- Kevin Y H Liang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Tania Nasreen
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Munirul Alam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Cheryl L Tarr
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yann F Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Singapore Center for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
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Huang Z, Yu K, Fang Y, Dai H, Cai H, Li Z, Kan B, Wei Q, Wang D. Comparative Genomics and Transcriptomics Analyses Reveal a Unique Environmental Adaptability of Vibrio fujianensis. Microorganisms 2020; 8:microorganisms8040555. [PMID: 32294952 PMCID: PMC7232310 DOI: 10.3390/microorganisms8040555] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
The genus Vibrio is ubiquitous in marine environments and uses numerous evolutionary characteristics and survival strategies in order to occupy its niche. Here, a newly identified species, Vibrio fujianensis, was deeply explored to reveal a unique environmental adaptability. V. fujianensis type strain FJ201301T shared 817 core genes with the Vibrio species in the population genomic analysis, but possessed unique genes of its own. In addition, V. fujianensis FJ201301T was predicated to carry 106 virulence-related factors, several of which were mostly found in other pathogenic Vibrio species. Moreover, a comparative transcriptome analysis between the low-salt (1% NaCl) and high-salt (8% NaCl) condition was conducted to identify the genes involved in salt tolerance. A total of 913 unigenes were found to be differentially expressed. In a high-salt condition, 577 genes were significantly upregulated, whereas 336 unigenes were significantly downregulated. Notably, differentially expressed genes have a significant association with ribosome structural component and ribosome metabolism, which may play a role in salt tolerance. Transcriptional changes in ribosome genes indicate that V. fujianensis may have gained a predominant advantage in order to adapt to the changing environment. In conclusion, to survive in adversity, V. fujianensis has enhanced its environmental adaptability and developed various strategies to fill its niche.
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Affiliation(s)
- Zhenzhou Huang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China; (Z.H.); (K.Y.); (H.D.); (H.C.); (Z.L.); (B.K.)
- Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, China
| | - Keyi Yu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China; (Z.H.); (K.Y.); (H.D.); (H.C.); (Z.L.); (B.K.)
- Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, China
| | - Yujie Fang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China;
| | - Hang Dai
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China; (Z.H.); (K.Y.); (H.D.); (H.C.); (Z.L.); (B.K.)
- Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, China
| | - Hongyan Cai
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China; (Z.H.); (K.Y.); (H.D.); (H.C.); (Z.L.); (B.K.)
- Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, China
| | - Zhenpeng Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China; (Z.H.); (K.Y.); (H.D.); (H.C.); (Z.L.); (B.K.)
| | - Biao Kan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China; (Z.H.); (K.Y.); (H.D.); (H.C.); (Z.L.); (B.K.)
| | - Qiang Wei
- Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, China
- Office of Laboratory Management, China CDC, Beijing 102206, China
- Correspondence: (Q.W.); (D.W.)
| | - Duochun Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China; (Z.H.); (K.Y.); (H.D.); (H.C.); (Z.L.); (B.K.)
- Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, China
- Correspondence: (Q.W.); (D.W.)
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Kirchberger PC, Orata FD, Nasreen T, Kauffman KM, Tarr CL, Case RJ, Polz MF, Boucher YF. Culture-independent tracking of Vibrio cholerae lineages reveals complex spatiotemporal dynamics in a natural population. Environ Microbiol 2020; 22:4244-4256. [PMID: 31970854 DOI: 10.1111/1462-2920.14921] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 01/26/2023]
Abstract
Populations of the bacterium Vibrio cholerae consist of dozens of distinct lineages, with primarily (but not exclusively) members of the pandemic generating lineage capable of causing the diarrhoeal disease cholera. Assessing the composition and temporal dynamics of such populations requires extensive isolation efforts and thus only rarely covers large geographic areas or timeframes exhaustively. We developed a culture-independent amplicon sequencing strategy based on the protein-coding gene viuB (vibriobactin utilization) to study the structure of a V. cholerae population over the course of a summer. We show that the 26 co-occurring V. cholerae lineages continuously compete for limited space on nutrient-rich particles where only a few of them can grow to large numbers. Differential abundance of lineages between locations and size-fractions associated with a particle-attached or free-swimming lifestyle could reflect adaptation to various environmental niches. In particular, a major V. cholerae lineage occasionally grows to large numbers on particles but remain undetectable using isolation-based methods, indicating selective culturability for some members of the species. We thus demonstrate that isolation-based studies may not accurately reflect the structure and complex dynamics of V. cholerae populations and provide a scalable high-throughput method for both epidemiological and ecological approaches to studying this species.
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Affiliation(s)
- Paul C Kirchberger
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Tania Nasreen
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Kathryn M Kauffman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Cheryl L Tarr
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Rebecca J Case
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yann F Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
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Ryan MP, Slattery S, Pembroke JT. A Novel Arsenate-Resistant Determinant Associated with ICEpMERPH, a Member of the SXT/R391 Group of Mobile Genetic Elements. Genes (Basel) 2019; 10:genes10121048. [PMID: 31888308 PMCID: PMC6947025 DOI: 10.3390/genes10121048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022] Open
Abstract
ICEpMERPH, the first integrative conjugative element (ICE) of the SXT/R391 family isolated in the United Kingdom and Europe, was analyzed to determine the nature of its adaptive functions, its genetic structure, and its homology to related elements normally found in pathogenic Vibrio or Proteus species. Whole genome sequencing of Escherichia coli (E. coli) isolate K802 (which contains the ICEpMERPH) was carried out using Illumina sequencing technology. ICEpMERPH has a size of 110 Kb and 112 putative open reading frames (ORFs). The “hotspot regions” of the element were found to contain putative restriction digestion systems, insertion sequences, and heavy metal resistance genes that encoded resistance to mercury, as previously reported, but also surprisingly to arsenate. A novel arsenate resistance system was identified in hotspot 4 of the element, unrelated to other SXT/R391 elements. This arsenate resistance system was potentially linked to two genes: orf69, encoding an organoarsenical efflux major facilitator superfamily (MFS) transporter-like protein related to ArsJ, and orf70, encoding nicotinamide adenine dinucleotide (NAD)-dependent glyceraldehyde-3-phosphate dehydrogenase. Phenotypic analysis using isogenic strains of Escherichia coli strain AB1157 with and without the ICEpMERPH revealed resistance to low levels of arsenate in the range of 1–5 mM. This novel, low-level resistance may have an important adaptive function in polluted environments, which often contain low levels of arsenate contamination. A bioinformatic analysis on the novel determinant and the phylogeny of ICEpMERPH was presented.
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Ina-Salwany MY, Al-Saari N, Mohamad A, Mursidi FA, Mohd-Aris A, Amal MNA, Kasai H, Mino S, Sawabe T, Zamri-Saad M. Vibriosis in Fish: A Review on Disease Development and Prevention. JOURNAL OF AQUATIC ANIMAL HEALTH 2019; 31:3-22. [PMID: 30246889 DOI: 10.1002/aah.10045] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/16/2018] [Indexed: 05/19/2023]
Abstract
Current growth in aquaculture production is parallel with the increasing number of disease outbreaks, which negatively affect the production, profitability, and sustainability of the global aquaculture industry. Vibriosis is among the most common diseases leading to massive mortality of cultured shrimp, fish, and shellfish in Asia. High incidence of vibriosis can occur in hatchery and grow-out facilities, but juveniles are more susceptible to the disease. Various factors, particularly the source of fish, environmental factors (including water quality and farm management), and the virulence factors of Vibrio, influence the occurrence of the disease. Affected fish show weariness, with necrosis of skin and appendages, leading to body malformation, slow growth, internal organ liquefaction, blindness, muscle opacity, and mortality. A combination of control measures, particularly a disease-free source of fish, biosecurity of the farm, improved water quality, and other preventive measures (e.g., vaccination) might be able to control the infection. Although some control measures are expensive and less practical, vaccination is effective, relatively cheap, and easily implemented. In this review, the latest knowledge on the pathogenesis and control of vibriosis, including vaccination, is discussed.
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Affiliation(s)
- M Y Ina-Salwany
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nurhidayu Al-Saari
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- International Institute for Halal Research and Training, International Islamic University Malaysia, KICT Building, Level 3, 53100, Gombak, Selangor, Malaysia
| | - Aslah Mohamad
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Fathin-Amirah Mursidi
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Aslizah Mohd-Aris
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Biology, School of Biology, Universiti Teknologi MARA, Kampus Kuala Pilah, 72000, Kuala Pilah, Negeri Sembilan, Malaysia
| | - M N A Amal
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Hisae Kasai
- Laboratory of Fish Pathology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - M Zamri-Saad
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Veterinary Laboratory Diagnosis, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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Dias GM, Bidault A, Le Chevalier P, Choquet G, Der Sarkissian C, Orlando L, Medigue C, Barbe V, Mangenot S, Thompson CC, Thompson FL, Jacq A, Pichereau V, Paillard C. Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs. Front Microbiol 2018; 9:227. [PMID: 29515533 PMCID: PMC5825899 DOI: 10.3389/fmicb.2018.00227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The Brown Ring Disease (BRD) caused high mortality rates since 1986 in the Manila clam Venerupis philippinarum introduced and cultured in Western Europe from the 1970s. The causative agent of BRD is a Gram-Negative bacterium, Vibrio tapetis, which is also pathogenic to fish. Here we report the first assembly of the complete genome of V. tapetis CECT4600T, together with the genome sequences of 16 additional strains isolated across a broad host and geographic range. Our extensive genome dataset allowed us to describe the pathogen pan- and core genomes and to identify putative virulence factors. The V. tapetis core genome consists of 3,352 genes, including multiple potential virulence factors represented by haemolysins, transcriptional regulators, Type I restriction modification system, GGDEF domain proteins, several conjugative plasmids, and a Type IV secretion system. Future research on the coevolutionary arms race between V. tapetis virulence factors and host resistance mechanisms will improve our understanding of how pathogenicity develops in this emerging pathogen.
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Affiliation(s)
- Graciela M. Dias
- Laboratoire des Sciences de l'Environnement Marin, Université de Bretagne Occidentale, UMR 6539 UBO/Centre National de la Recherche Scientifique/IRD/Ifremer, Institut Universitaire Européen de la Mer, Plouzané, France
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adeline Bidault
- Laboratoire des Sciences de l'Environnement Marin, Université de Bretagne Occidentale, UMR 6539 UBO/Centre National de la Recherche Scientifique/IRD/Ifremer, Institut Universitaire Européen de la Mer, Plouzané, France
| | - Patrick Le Chevalier
- Laboratoire de Biotechnologie et Chimie Marine, Université de Bretagne Occidentale, Quimper, France
| | - Gwenaëlle Choquet
- Laboratoire des Sciences de l'Environnement Marin, Université de Bretagne Occidentale, UMR 6539 UBO/Centre National de la Recherche Scientifique/IRD/Ifremer, Institut Universitaire Européen de la Mer, Plouzané, France
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Centre National de la Recherche Scientifique UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Claudine Medigue
- CEA, Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université d'Evry, Centre National de la Recherche Scientifique-UMR 8030, Evry, France
| | - Valerie Barbe
- CEA, Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université d'Evry, Centre National de la Recherche Scientifique-UMR 8030, Evry, France
| | - Sophie Mangenot
- CEA, Institut de biologie François-Jacob, Genoscope, Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, Evry, France
| | - Cristiane C. Thompson
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabiano L. Thompson
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Annick Jacq
- Institute for Integrative Biology of the Cell, CEA, Centre National de la Recherche Scientifique, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Vianney Pichereau
- Laboratoire des Sciences de l'Environnement Marin, Université de Bretagne Occidentale, UMR 6539 UBO/Centre National de la Recherche Scientifique/IRD/Ifremer, Institut Universitaire Européen de la Mer, Plouzané, France
| | - Christine Paillard
- Laboratoire des Sciences de l'Environnement Marin, Université de Bretagne Occidentale, UMR 6539 UBO/Centre National de la Recherche Scientifique/IRD/Ifremer, Institut Universitaire Européen de la Mer, Plouzané, France
- *Correspondence: Christine Paillard
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Carda-Diéguez M, Ghai R, Rodríguez-Valera F, Amaro C. Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution. MICROBIOME 2017; 5:162. [PMID: 29268781 PMCID: PMC5740887 DOI: 10.1186/s40168-017-0376-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 11/21/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in natural environments. We aimed to test this hypothesis by searching for metagenomic and genomic evidences in the SMS-microbiome of a model fish species (Anguilla Anguilla or eel), from different ecosystems (four natural environments of different water salinity and one eel farm) as well as the water microbiome (W-microbiome) surrounding the host. RESULTS Remarkably, potentially pathogenic Vibrio monopolized wild eel SMS-microbiome from natural ecosystems, Vibrio anguillarum/Vibrio vulnificus and Vibrio cholerae/Vibrio metoecus being the most abundant ones in SMS from estuary and lake, respectively. Functions encoded in the SMS-microbiome differed significantly from those in the W-microbiome and allowed us to predict that successful mucus colonizers should have specific genes for (i) attachment (mainly by forming biofilms), (ii) bacterial competence and communication, and (iii) resistance to mucosal innate immunity, predators (amoeba), and heavy metals/drugs. In addition, we found several mobile genetic elements (mainly integrative conjugative elements) as well as a series of evidences suggesting that bacteria exchange DNA in SMS. Further, we isolated and sequenced a V. metoecus strain from SMS. This isolate shares pathogenicity islands with V. cholerae O1 from intestinal infections that are absent in the rest of sequenced V. metoecus strains, all of them from water and extra-intestinal infections. CONCLUSIONS We have obtained metagenomic and genomic evidence in favor of the hypothesis on the role of fish mucosal surfaces as a specialized habitat selecting microbes capable of colonizing and persisting on other comparable mucosal surfaces, e.g., the human intestine.
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Affiliation(s)
- Miguel Carda-Diéguez
- Department of Microbiology and Ecology abd Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), University of Valencia, Valencia, Spain
| | - Rohit Ghai
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Center of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Francisco Rodríguez-Valera
- Evolutionary Genomics Group, Department de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | - Carmen Amaro
- Department of Microbiology and Ecology abd Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), University of Valencia, Valencia, Spain.
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Domman D, Quilici ML, Dorman MJ, Njamkepo E, Mutreja A, Mather AE, Delgado G, Morales-Espinosa R, Grimont PAD, Lizárraga-Partida ML, Bouchier C, Aanensen DM, Kuri-Morales P, Tarr CL, Dougan G, Parkhill J, Campos J, Cravioto A, Weill FX, Thomson NR. Integrated view of Vibrio cholerae in the Americas. Science 2017; 358:789-793. [DOI: 10.1126/science.aao2136] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/10/2017] [Indexed: 01/24/2023]
Abstract
Latin America has experienced two of the largest cholera epidemics in modern history; one in 1991 and the other in 2010. However, confusion still surrounds the relationships between globally circulating pandemic Vibrio cholerae clones and local bacterial populations. We used whole-genome sequencing to characterize cholera across the Americas over a 40-year time span. We found that both epidemics were the result of intercontinental introductions of seventh pandemic El Tor V. cholerae and that at least seven lineages local to the Americas are associated with disease that differs epidemiologically from epidemic cholera. Our results consolidate historical accounts of pandemic cholera with data to show the importance of local lineages, presenting an integrated view of cholera that is important to the design of future disease control strategies.
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Affiliation(s)
- Daryl Domman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Marie-Laure Quilici
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Matthew J. Dorman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Elisabeth Njamkepo
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Ankur Mutreja
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0SP, UK
| | - Alison E. Mather
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Gabriella Delgado
- Department of Microbiology and Parasitology, Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico, D.F., Mexico
| | - Rosario Morales-Espinosa
- Department of Microbiology and Parasitology, Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico, D.F., Mexico
| | - Patrick A. D. Grimont
- Institut Pasteur, Unité Biodiversité des Bactéries Pathogènes Emergentes, Paris, 75015, France
| | | | | | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Pablo Kuri-Morales
- Subsecretaría de Prevención y Promoción de la Salud, Secretaría de Salud, Ciudad de México, Mexico
| | - Cheryl L. Tarr
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0SP, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Josefina Campos
- Instituto Nacional de Enfermedades Infecciosas, ANLIS, Buenos Aires, Argentina
| | - Alejandro Cravioto
- Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico, D.F., Mexico
| | - François-Xavier Weill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, 75015, France
| | - Nicholas R. Thomson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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20
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Sequential displacement of Type VI Secretion System effector genes leads to evolution of diverse immunity gene arrays in Vibrio cholerae. Sci Rep 2017; 7:45133. [PMID: 28327641 PMCID: PMC5361080 DOI: 10.1038/srep45133] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/17/2017] [Indexed: 11/09/2022] Open
Abstract
Type VI secretion systems (T6SS) enable bacteria to engage neighboring cells in contact-dependent competition. In Vibrio cholerae, three chromosomal clusters each encode a pair of effector and immunity genes downstream of those encoding the T6SS structural machinery for effector delivery. Different combinations of effector-immunity proteins lead to competition between strains of V. cholerae, which are thought to be protected only from the toxicity of their own effectors. Screening of all publically available V. cholerae genomes showed that numerous strains possess long arrays of orphan immunity genes encoded in the 3' region of their T6SS clusters. Phylogenetic analysis reveals that these genes are highly similar to those found in the effector-immunity pairs of other strains, indicating acquisition by horizontal gene transfer. Extensive genomic comparisons also suggest that successive addition of effector-immunity gene pairs replaces ancestral effectors, yet retains the cognate immunity genes. The retention of old immunity genes perhaps provides protection against nearby kin bacteria in which the old effector was not replaced. This mechanism, combined with frequent homologous recombination, is likely responsible for the high diversity of T6SS effector-immunity gene profiles observed for V. cholerae and closely related species.
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21
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Pretzer C, Druzhinina IS, Amaro C, Benediktsdóttir E, Hedenström I, Hervio-Heath D, Huhulescu S, Schets FM, Farnleitner AH, Kirschner AKT. High genetic diversity of Vibrio cholerae in the European lake Neusiedler See is associated with intensive recombination in the reed habitat and the long-distance transfer of strains. Environ Microbiol 2017; 19:328-344. [PMID: 27871138 PMCID: PMC5718291 DOI: 10.1111/1462-2920.13612] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 10/27/2016] [Accepted: 11/10/2016] [Indexed: 11/29/2022]
Abstract
Coastal marine Vibrio cholerae populations usually exhibit high genetic diversity. To assess the genetic diversity of abundant V. cholerae non-O1/non-O139 populations in the Central European lake Neusiedler See, we performed a phylogenetic analysis based on recA, toxR, gyrB and pyrH loci sequenced for 472 strains. The strains were isolated from three ecologically different habitats in a lake that is a hot-spot of migrating birds and an important bathing water. We also analyzed 76 environmental and human V. cholerae non-O1/non-O139 isolates from Austria and other European countries and added sequences of seven genome-sequenced strains. Phylogenetic analysis showed that the lake supports a unique endemic diversity of V. cholerae that is particularly rich in the reed stand. Phylogenetic trees revealed that many V. cholerae isolates from European countries were genetically related to the strains present in the lake belonging to statistically supported monophyletic clades. We hypothesize that the observed phenomena can be explained by the high degree of genetic recombination that is particularly intensive in the reed stand, acting along with the long distance transfer of strains most probably via birds and/or humans. Thus, the Neusiedler See may serve as a bioreactor for the appearance of new strains with new (pathogenic) properties.
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Affiliation(s)
- Carina Pretzer
- Medical University Vienna, Institute for Hygiene and Applied Immunology, Vienna, Austria.,Vienna University of Technology, Institute of Chemical Engineering, Vienna, Austria
| | - Irina S Druzhinina
- Vienna University of Technology, Institute of Chemical Engineering, Vienna, Austria
| | - Carmen Amaro
- ERI BioTecMed University of Valencia, Valencia, Spain
| | - Eva Benediktsdóttir
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | | | | | | | - Franciska M Schets
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Andreas H Farnleitner
- Vienna University of Technology, Institute of Chemical Engineering, Vienna, Austria.,Interuniversity Cooperation Centre for Water & Health, (www.waterandhealth.at), Vienna, Austria
| | - Alexander K T Kirschner
- Medical University Vienna, Institute for Hygiene and Applied Immunology, Vienna, Austria.,Interuniversity Cooperation Centre for Water & Health, (www.waterandhealth.at), Vienna, Austria
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22
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Origins of pandemic Vibrio cholerae from environmental gene pools. Nat Microbiol 2016; 2:16240. [DOI: 10.1038/nmicrobiol.2016.240] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 10/27/2016] [Indexed: 11/08/2022]
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23
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A genomic island in Vibrio cholerae with VPI-1 site-specific recombination characteristics contains CRISPR-Cas and type VI secretion modules. Sci Rep 2016; 6:36891. [PMID: 27845364 PMCID: PMC5109276 DOI: 10.1038/srep36891] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 10/10/2016] [Indexed: 12/12/2022] Open
Abstract
Cholera is a devastating diarrhoeal disease caused by certain strains of serogroup O1/O139 Vibrio cholerae. Mobile genetic elements such as genomic islands (GIs) have been pivotal in the evolution of O1/O139 V. cholerae. Perhaps the most important GI involved in cholera disease is the V. cholerae pathogenicity island 1 (VPI-1). This GI contains the toxin-coregulated pilus (TCP) gene cluster that is necessary for colonization of the human intestine as well as being the receptor for infection by the cholera-toxin bearing CTX phage. In this study, we report a GI (designated GIVchS12) from a non-O1/O139 strain of V. cholerae that is present in the same chromosomal location as VPI-1, contains an integrase gene with 94% nucleotide and 100% protein identity to the VPI-1 integrase, and attachment (att) sites 100% identical to those found in VPI-1. However, instead of TCP and the other accessory genes present in VPI-1, GIVchS12 contains a CRISPR-Cas element and a type VI secretion system (T6SS). GIs similar to GIVchS12 were identified in other V. cholerae genomes, also containing CRISPR-Cas elements and/or T6SS's. This study highlights the diversity of GIs circulating in natural V. cholerae populations and identifies GIs with VPI-1 recombination characteristics as a propagator of CRISPR-Cas and T6SS modules.
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A Small Number of Phylogenetically Distinct Clonal Complexes Dominate a Coastal Vibrio cholerae Population. Appl Environ Microbiol 2016; 82:5576-86. [PMID: 27371587 DOI: 10.1128/aem.01177-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/29/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Vibrio cholerae is a ubiquitous aquatic microbe in temperate and tropical coastal areas. It is a diverse species, with many isolates that are harmless to humans, while others are highly pathogenic. Most notable among them are strains belonging to the pandemic O1/O139 serogroup lineage, which contains the causative agents of cholera. The environmental selective regimes that led to this diversity are key to understanding how pathogens evolve in environmental reservoirs. A local population of V. cholerae and its close relative Vibrio metoecus from a coastal pond and lagoon system was extensively sampled during two consecutive months across four size fractions (480 isolates). In stark contrast to previous studies, the observed population was highly clonal, with 60% of V. cholerae isolates falling into one of five clonal complexes, which varied in abundance in the short temporal scale sampled. V. cholerae clonal complexes had significantly different distributions across size fractions and the two environments sampled, the pond and the lagoon. Sequencing the genomes of 20 isolates representing these five V. cholerae clonal complexes revealed different evolutionary trajectories, with considerable variations in gene content with potential ecological significance. Showing genotypic differentiation and differential spatial distribution, the dominant clonal complexes are likely ecologically divergent. Temporal variation in the relative abundance of these complexes suggests that transient blooms of specific clones could dominate local diversity. IMPORTANCE Vibrio cholerae is commonly found in coastal areas worldwide, with only a single group of this bacterium capable of causing severe cholera outbreaks. However, the potential to evolve the ability to cause disease exists in many strains of this species in its aquatic reservoir. Understanding how pathogenic bacteria evolve requires the study of their natural environments. By extensive sampling in a geographically restricted location in the United States, we found that most cells of a V. cholerae population belong to only a small number of strains. Analysis of their genome composition and spatial distribution indicates differential environmental adaptations between these strains. Other strains exist in smaller numbers, and the population was found to be temporally varied. This suggests frequent bloom and collapse cycles on a time scale of weeks. These population dynamics make it possible that more virulent strains could stochastically rise to large numbers, allowing for infection to occur.
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25
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Orata FD, Xu Y, Gladney LM, Rishishwar L, Case RJ, Boucher Y, Jordan IK, Tarr CL. Characterization of clinical and environmental isolates of Vibrio cidicii sp. nov., a close relative of Vibrio navarrensis. Int J Syst Evol Microbiol 2016; 66:4148-4155. [PMID: 27468862 DOI: 10.1099/ijsem.0.001327] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four Vibrio spp. isolates from the historical culture collection at the Centers for Disease Control and Prevention, obtained from human blood specimens (n=3) and river water (n=1), show characteristics distinct from those of isolates of the most closely related species, Vibrio navarrensis and Vibrio vulnificus, based on phenotypic and genotypic tests. They are specifically adapted to survival in both freshwater and seawater, being able to grow in rich media without added salts as well as salinities above that of seawater. Phenotypically, these isolates resemble V. navarrensis, their closest known relative with a validly published name, but the group of isolates is distinguished from V. navarrensis by the ability to utilize l-rhamnose. Average nucleotide identity and percent DNA-DNA hybridization values obtained from the pairwise comparisons of whole-genome sequences of these isolates to V. navarrensis range from 95.4-95.8 % and 61.9-64.3 %, respectively, suggesting that the group represents a different species. Phylogenetic analysis of the core genome, including four protein-coding housekeeping genes (pyrH, recA, rpoA and rpoB), places these four isolates into their own monophyletic clade, distinct from V. navarrensis and V. vulnificus. Based on these differences, we propose these isolates represent a novel species of the genus Vibrio, for which the name Vibrio cidicii sp. nov. is proposed; strain LMG 29267T (=CIP 111013T=2756-81T), isolated from river water, is the type strain.
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Affiliation(s)
- Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Yue Xu
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Lori M Gladney
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA.,IHRC, Incorporated, Atlanta, GA, USA
| | - Lavanya Rishishwar
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.,Applied Bioinformatics Laboratory, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Santiago de Cali, Valle del Cauca, Colombia
| | - Rebecca J Case
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Yan Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - I King Jordan
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.,PanAmerican Bioinformatics Institute, Santiago de Cali, Valle del Cauca, Colombia.,Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Cheryl L Tarr
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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26
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Shapiro BJ. How clonal are bacteria over time? Curr Opin Microbiol 2016; 31:116-123. [PMID: 27057964 DOI: 10.1016/j.mib.2016.03.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/20/2016] [Accepted: 03/22/2016] [Indexed: 11/15/2022]
Abstract
Bacteria and archaea reproduce clonally (vertical descent), but exchange genes by recombination (horizontal transfer). Recombination allows adaptive mutations or genes to spread rapidly within (or even between) species, and reduces the burden of deleterious mutations. Clonality-defined here as the balance between vertical and horizontal inheritance-is therefore a key microbial trait, determining how quickly a population can adapt and the size of its gene pool. Here, I discuss whether clonality varies over time and if it can be considered a stable trait of a given population. I show that, in some cases, clonality is clearly not static. For example, non-clonal (highly recombining) populations can give rise to clonal expansions, often of pathogens. However, an analysis of time-course metagenomic data from a lake suggests that a bacterial population's past clonality (as measured by its genetic diversity) is a good predictor of its future clonality. Clonality therefore appears to be relatively-but not completely-stable over evolutionary time.
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Affiliation(s)
- B Jesse Shapiro
- Département de sciences biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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