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Alam MT, Stern SR, Frison D, Taylor K, Tagliamonte MS, Nazmus SS, Paisie T, Hilliard NB, Jones RG, Iovine NM, Cherabuddi K, Mavian C, Myers P, Salemi M, Ali A, Morris JG. Seafood-Associated Outbreak of ctx-Negative Vibrio mimicus Causing Cholera-Like Illness, Florida, USA. Emerg Infect Dis 2023; 29:2141-2144. [PMID: 37735754 PMCID: PMC10521627 DOI: 10.3201/eid2910.230486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
Vibrio mimicus caused a seafood-associated outbreak in Florida, USA, in which 4 of 6 case-patients were hospitalized; 1 required intensive care for severe diarrhea. Strains were ctx-negative but carried genes for other virulence determinants (hemolysin, proteases, and types I-IV and VI secretion systems). Cholera toxin-negative bacterial strains can cause cholera-like disease.
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Affiliation(s)
| | | | - Devin Frison
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Katie Taylor
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Massimiliano S. Tagliamonte
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - S. Sakib Nazmus
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Taylor Paisie
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Nicole B. Hilliard
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Riley G. Jones
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Nicole M. Iovine
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Kartik Cherabuddi
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Carla Mavian
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Paul Myers
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
| | - Marco Salemi
- University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (M.T. Alam, M.S. Tagliamonte, S.N. Sakib, T. Paisie, C. Mavian, M. Salemi, A. Ali, J.G Morris, Jr.)
- University of Florida College of Public Health and Health Professions, Gainesville (M.T. Alam, S.S. Nazmus, A. Ali)
- University of Florida College of Medicine, Gainesville (S.R. Stern, K. Taylor, M.S. Tagliamonte, T. Paisie, R.G. Jones, N.M. Iovine, K. Cherabuddi, C. Mavian, M. Salemi, J.G. Morris, Jr.)
- Florida Department of Health in Alachua County, Gainesville (D. Frison, P. Myers)
- University of Florida Health and Shands Hospital, Gainesville (N.B. Hilliard, N.M. Iovine, K. Cherabuddi)
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2
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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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3
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Halder M, Saha S, Mookerjee S, Palit A. Exploring the dynamics of toxigenic environmental Vibrio mimicus and its comparative analysis with Vibrio cholerae of the southern Gangetic delta. Arch Microbiol 2022; 204:420. [PMID: 35748957 DOI: 10.1007/s00203-022-03028-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022]
Abstract
Vibrio mimicus and Vibrio cholerae are closely related species. Environmental V.mimicus were comparatively analyzed with V.cholerae, for the presence of virulence genes, antibiotic susceptibility, resistance genes, in-vitro hemolysis, and biofilm formation. Phylogenetic analysis was performed depending on toxin-gene disposition and isolation area. One V.mimicus isolate harbored ctxA, tcp El-Tor, toxT and toxS, whereas several strains contained incomplete copies of virulence cassettes and associated toxin genes. V.cholerae isolates harbored ctx, tcp and toxT genes, with a higher preponderance of hlyA, rtxA and toxR genes. V.mimicus were highly sensitive to amino/carboxy-penicillins, furazolidone & gentamycin, with quinolone & tetracycline resistance genes. V.cholerae isolates were sensitive to penicillins and cephalosporins, with 29% of the strains bearing the sxt gene. Phylogenetically, the apomorphic strains of both species were unique to the inland sites. V.cholerae has embodied an enormous public health burden globally but our findings emphasize the role of V.mimicus as an emerging etiological agent with similar epidemic potential.
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Affiliation(s)
- Madhumanti Halder
- Division of Bacteriology, Indian Council of Medical Research- National Institute of Cholera & Enteric Diseases, P- 33, Scheme-XM, CIT Road, Beliaghata, Kolkata, 700 010, India
| | - Suvajit Saha
- Division of Bacteriology, Indian Council of Medical Research- National Institute of Cholera & Enteric Diseases, P- 33, Scheme-XM, CIT Road, Beliaghata, Kolkata, 700 010, India
| | - Subham Mookerjee
- Division of Bacteriology, Indian Council of Medical Research- National Institute of Cholera & Enteric Diseases, P- 33, Scheme-XM, CIT Road, Beliaghata, Kolkata, 700 010, India
| | - Anup Palit
- Division of Bacteriology, Indian Council of Medical Research- National Institute of Cholera & Enteric Diseases, P- 33, Scheme-XM, CIT Road, Beliaghata, Kolkata, 700 010, India.
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4
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Abdalla T, Al-Rumaithi H, Osaili TM, Hasan F, Obaid RS, Abushelaibi A, Ayyash MM. Prevalence, Antibiotic-Resistance, and Growth Profile of Vibrio spp. Isolated From Fish and Shellfish in Subtropical-Arid Area. Front Microbiol 2022; 13:861547. [PMID: 35464960 PMCID: PMC9019552 DOI: 10.3389/fmicb.2022.861547] [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: 01/24/2022] [Accepted: 03/18/2022] [Indexed: 12/03/2022] Open
Abstract
The study aimed to determine the prevalence of different species of Vibrio spp. in fish and shellfish sold in subtropical-arid countries (United Arab Emirates). It also examined the antimicrobial resistance of the isolated species and their growth behavior upon in vitro environmental changes concerning temperature, pH, and salinity. The prevalence of Vibrio spp. in fish and shellfish samples, was 64.5 and 92%, respectively. However, Vibrio parahemolyticus were detected in a mere 7.5 and 13.0% of the samples, respectively. On the other hand, Vibrio mimicus was detected in 1.5 and 8.5% of the samples, respectively. None of the six antibiotics studied except for Sulfamethoxazole-trimethoprim were effective against fish Vibrio spp. isolates. On a similar note, three antibiotics, namely Penicillin, Daptomycin, and Vancomycin, were ineffective against the shellfish isolates. The growth of the microorganisms did not show any significant trend with changes in pH and salinity. The optimum temperature for Vibrio spp. growth was observed to be 37°C.
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Affiliation(s)
- Tarfa Abdalla
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Hind Al-Rumaithi
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
| | - Tareq M Osaili
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
| | - Fayeza Hasan
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Reyad S Obaid
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Aisha Abushelaibi
- Campus Director at Higher Colleges of Technology, Dubai, United Arab Emirates
| | - Mutamed M Ayyash
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University (UAEU), Al Ain, United Arab Emirates
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Cordone A, Coppola A, Severino A, Correggia M, Selci M, Cascone A, Vetriani C, Giovannelli D. From Sequences to Enzymes: Comparative Genomics to Study Evolutionarily Conserved Protein Functions in Marine Microbes. Methods Mol Biol 2022; 2498:77-88. [PMID: 35727541 DOI: 10.1007/978-1-0716-2313-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Comparative genomics is a research field that allows comparison between genomes of different life forms providing information on the organization of the compared genomes, both in terms of structure and encoded functions. Moreover, this approach provides a powerful tool to study and understand the evolutionary changes and adaptation among organisms. Comparative genomics can be used to compare phylogenetically close marine organisms showing different vital strategies and lifestyles and obtain information regarding specific adaptations and/or their evolutionary history. Here we report a basic comparative genomics protocol to extrapolate evolutionary information about a protein of interest conserved across diverse marine microbes. The outlined approach can be used in a number of different settings and might help to gain new insights into the evolution and adaptation of marine microorganisms.
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Affiliation(s)
- Angelina Cordone
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | - Angelica Severino
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Monica Correggia
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Matteo Selci
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Antonio Cascone
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
| | - Donato Giovannelli
- Department of Biology, University of Naples Federico II, Naples, Italy.
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA.
- National Research Council-Institute of Marine Biological Resources and Biotechnologies CNR-IRBIM, Ancona, Italy.
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.
- Marine Chemistry & Geochemistry Department, Woods Hole Oceanographic Institution, Falmouth, MA, USA.
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6
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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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7
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Nilavan E, Vaiyapuri M, Sadanandan Sheela G, Nadella RK, Thandapani M, Kumar A, Mothadaka MP. Prevalence of Vibrio mimicus in Fish, Fishery Products, and Environment of South West Coast of Kerala, India. J AOAC Int 2021; 104:790-794. [PMID: 33484252 DOI: 10.1093/jaoacint/qsab001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 11/12/2022]
Abstract
BACKGROUND Vibrio mimicus is a seafood-borne bacterium involved in incidences of human infections following consumption of raw or undercooked seafood. Regular monitoring of seafood for V.mimicus is necessary for risk assessment and to establish mitigation measures. METHOD During the period 2017-2020, a total of 250 samples comprising finfish, shellfish, water, ice, and sediment samples were collected from fish markets, fish landing centers, and fish farms in the Ernakulum district on the Southwest coast of Kerala, India. V. mimicus was isolated using enrichment in alkaline peptone water for 18 h followed by plating on thiosulfate citrate bile salts sucrose agar and then incubated at 37°C for 18-24 h. The presumptive V. mimicus isolates were confirmed by biochemical characterization and molecularly with vmh gene-specific for V. mimicus. RESULTS The study revealed that the prevalence of V. mimicus is 5.6% in the total of samples screened. The highest occurrence was observed in brackish water fish (19%) followed by freshwater fish (18%) and marine fish (2%) samples. The study points out the risk of brackish water fishes as potential carriers of this pathogen. This requires preventive measures to mitigate health hazards associated with V. mimicus entering into the seafood production chain.
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Affiliation(s)
- Ezhil Nilavan
- ICAR-Central Institute of Fisheries Technology, Matsyapuri Post, Willingdon Island, Cochin, Kerala, India
| | - Murugadas Vaiyapuri
- ICAR-Central Institute of Fisheries Technology, Matsyapuri Post, Willingdon Island, Cochin, Kerala, India
| | - Greeshma Sadanandan Sheela
- ICAR-Central Institute of Fisheries Technology, Matsyapuri Post, Willingdon Island, Cochin, Kerala, India
| | - Ranjit Kumar Nadella
- ICAR-Central Institute of Fisheries Technology, Matsyapuri Post, Willingdon Island, Cochin, Kerala, India
| | - Muthulakshmi Thandapani
- ICAR-Central Institute of Fisheries Technology, Matsyapuri Post, Willingdon Island, Cochin, Kerala, India
| | - Abhay Kumar
- Mumbai Research Centre of ICAR-Central Institute of Fisheries Technology, Navi Mumbai, Maharashtra, India
| | - Mukteswar Prasad Mothadaka
- ICAR-Central Institute of Fisheries Technology, Matsyapuri Post, Willingdon Island, Cochin, Kerala, India
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8
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Bhandari M, Jennison AV, Rathnayake IU, Huygens F. Evolution, distribution and genetics of atypical Vibrio cholerae - A review. INFECTION GENETICS AND EVOLUTION 2021; 89:104726. [PMID: 33482361 DOI: 10.1016/j.meegid.2021.104726] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 12/21/2022]
Abstract
Vibrio cholerae is the etiological agent of cholera, a severe diarrheal disease, which can occur as either an epidemic or sporadic disease. Cholera pandemic-causing V. cholerae O1 and O139 serogroups originated from the Indian subcontinent and spread globally and millions of lives are lost each year, mainly in developing and underdeveloped countries due to this disease. V. cholerae O1 is further classified as classical and El Tor biotype which can produce biotype specific cholera toxin (CT). Since 1961, the current seventh pandemic El Tor strains replaced the sixth pandemic strains resulting in the classical biotype strain that produces classical CT. The ongoing evolution of Atypical El Tor V. cholerae srains encoding classical CT is of global concern. The severity in the pathophysiology of these Atypical El Tor strains is significantly higher than El Tor or classical strains. Pathogenesis of V. cholerae is a complex process that involves coordinated expression of different sets of virulence-associated genes to cause disease. We are yet to understand the complete virulence profile of V. cholerae, including direct and indirect expression of genes involved in its survival and stress adaptation in the host. In recent years, whole genome sequencing has paved the way for better understanding of the evolution and strain distribution, outbreak identification and pathogen surveillance for the implementation of direct infection control measures in the clinic against many infectious pathogens including V. cholerae. This review provides a synopsis of recent studies that have contributed to the understanding of the evolution, distribution and genetics of the seventh pandemic Atypical El Tor V. cholerae strains.
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Affiliation(s)
- Murari Bhandari
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia; Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Amy V Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Irani U Rathnayake
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Flavia Huygens
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, 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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Fu Y, Zhang YA, Shen J, Tu J. Immunogenicity study of OmpU subunit vaccine against Vibrio mimicus in yellow catfish, Pelteobagrus fulvidraco. FISH & SHELLFISH IMMUNOLOGY 2021; 108:80-85. [PMID: 33285164 DOI: 10.1016/j.fsi.2020.11.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/17/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
The outer membrane protein U (OmpU) is a conserved outer membrane protein in a variety of pathogenic Vibrio species and has been considered as a vital protective antigen for vaccine development. Vibrio mimicus (V. mimicus) is the pathogen causing ascites disease in aquatic animals. In this study, the prokaryotically expressed and purified His-tagged OmpU of V. mimicus (His-OmpU) was used as a subunit vaccine. The formalin inactivated V. mimicus, purified His tag (His-tag), and PBS were used as controls. The vaccinated yellow catfish were challenged with V. mimicus at 28 days post-vaccination, and the results showed that the His-OmpU and inactivated V. mimicus groups exhibited much higher survival rates than the His-tag and PBS groups. To fully understand the underlying mechanism, we detected the expression levels of several immune-related genes in the spleen of fish at 28 days post-vaccination and 24 h post-challenge. The results showed that most of the detected immune-related genes were significantly upregulated in His-OmpU and inactivated V. mimicus groups. In addition, we performed the serum bactericidal activity assay, and the results showed that the serum from His-OmpU and inactivated V. mimicus groups exhibited much stronger bactericidal activity against V. mimicus than those of His-tag and PBS groups. Finally, the serum agglutination antibody was detected, and the antibody could be detected in His-OmpU and inactivated V. mimicus groups with the antibody titers increasing along with the time post-vaccination, but not in His-tag or PBS group. Our data reveal that the recombinant OmpU elicits potent protective immune response and is an effective vaccine candidate against V. mimicus in yellow catfish.
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Affiliation(s)
- Yu Fu
- State Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, Hubei, China
| | - Yong-An Zhang
- State Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, Hubei, China
| | - Jinyu Shen
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China.
| | - Jiagang Tu
- State Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, Hubei, China.
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11
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Ashrafudoulla M, Mizan MFR, Park SH, Ha SD. Current and future perspectives for controlling Vibrio biofilms in the seafood industry: a comprehensive review. Crit Rev Food Sci Nutr 2020; 61:1827-1851. [PMID: 32436440 DOI: 10.1080/10408398.2020.1767031] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The contamination of seafood with Vibrio species can have severe repercussions in the seafood industry. Vibrio species can form mature biofilms and persist on the surface of several seafoods such as crabs, oysters, mussels, and shrimp, for extended duration. Several conventional approaches have been employed to inhibit the growth of planktonic cells and prevent the formation of Vibrio biofilms. Since Vibrio biofilms are mostly resistant to these control measures, novel alternative methods need to be urgently developed. In this review, we propose environmentally friendly approaches to suppress Vibrio biofilm formation using a hypothesized mechanism of action.
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Affiliation(s)
- Md Ashrafudoulla
- Department of Food Science and Technology, Advanced Food Safety Research Group, Chung-Ang University, Anseong, Gyunggi-do, Republic of Korea
| | - Md Furkanur Rahaman Mizan
- Department of Food Science and Technology, Advanced Food Safety Research Group, Chung-Ang University, Anseong, Gyunggi-do, Republic of Korea
| | - Si Hong Park
- Food Science and Technology, Oregon State University, Corvallis, Oregon, USA
| | - Sang-Do Ha
- Department of Food Science and Technology, Advanced Food Safety Research Group, Chung-Ang University, Anseong, Gyunggi-do, Republic of Korea
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12
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Novel Cholera Toxin Variant and ToxT Regulon in Environmental Vibrio mimicus Isolates: Potential Resources for the Evolution of Vibrio cholerae Hybrid Strains. Appl Environ Microbiol 2019; 85:AEM.01977-18. [PMID: 30446560 DOI: 10.1128/aem.01977-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/29/2018] [Indexed: 11/20/2022] Open
Abstract
Atypical El Tor strains of Vibrio cholerae O1 harboring variant ctxB genes of cholera toxin (CT) have gradually become a major cause of recent cholera epidemics. Vibrio mimicus occasionally produces CT, encoded by ctxAB on CTXФ genome; toxin-coregulated pilus (TCP), a major intestinal colonization factor; and also the CTXФ-specific receptor. This study carried out extensive molecular characterization of CTXФ and ToxT regulon in V. mimicus ctx-positive (ctx +) strains (i.e., V. mimicus strains containing ctx) isolated from the Bengal coast. Southern hybridization, PCR, and DNA sequencing of virulence-related genes revealed the presence of an El Tor type CTX prophage (CTXET) carrying a novel ctxAB, tandem copies of environmental type pre-CTX prophage (pre-CTXEnv), and RS1 elements, which were organized as an RS1-CTXET-RS1-pre-CTXEnv-pre-CTXEnv array. Additionally, novel variants of tcpA and toxT, respectively, showing phylogenetic lineage to a clade of V. cholerae non-O1 and to a clade of V. cholerae non-O139, were identified. The V. mimicus strains lacked the RTX (repeat in toxin) and TLC (toxin-linked cryptic) elements and lacked Vibrio seventh-pandemic islands of the El Tor strains but contained five heptamer (TTTTGAT) repeats in ctxAB promoter region similar to those seen with some classical strains of V. cholerae O1. Pulsed-field gel electrophoresis (PFGE) analysis showed that all the ctx + V. mimicus strains were clonally related. However, their in vitro CT production and in vivo toxigenicity characteristics were variable, which could be explainable by differential transcription of virulence genes along with the ToxR regulon. Taken together, our findings strongly suggest that environmental V. mimicus strains act as a potential reservoir of atypical virulence factors, including variant CT and ToxT regulons, and may contribute to the evolution of V. cholerae hybrid strains.IMPORTANCE Natural diversification of CTXФ and ctxAB genes certainly influences disease severity and shifting patterns in major etiological agents of cholera, e.g., the overwhelming emergence of hybrid El Tor variants, replacing the prototype El Tor strains of V. cholerae This report, showing the occurrence of CTXET comprising a novel variant of ctxAB in V. mimicus, points out a previously unnoticed evolutionary event that is independent of the evolutionary event associated with the El Tor strains of V. cholerae Identification and cluster analysis of the newly discovered alleles of tcpA and toxT suggest their horizontal transfer from an uncommon clone of V. cholerae The genomic contents of ToxT regulon and of tandemly arranged multiple pre-CTXФEnv and of a CTXФET in V. mimicus probably act as salient raw materials that induce natural recombination among the hallmark virulence genes of hybrid V. cholerae strains. This report provides valuable information to enrich our knowledge on the evolution of new variant CT and ToxT regulons.
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13
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Klein S, Pipes S, Lovell CR. Occurrence and significance of pathogenicity and fitness islands in environmental vibrios. AMB Express 2018; 8:177. [PMID: 30377851 PMCID: PMC6207609 DOI: 10.1186/s13568-018-0704-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/19/2018] [Indexed: 12/29/2022] Open
Abstract
Pathogenicity islands (PAIs) are large genomic regions that contain virulence genes, which aid pathogens in establishing infections. While PAIs in clinical strains (strains isolated from a human infection) are well-studied, less is known about the occurrence of PAIs in strains isolated from the environment. In this study we describe three PAIs found in environmental Vibrio vulnificus and Vibrio parahaemolyticus strains, as well as a genomic fitness island found in a Vibrio diabolicus strain. All four islands had markedly different GC profiles than the rest of the genome, indicating that all of these islands were acquired via lateral gene transfer. Genes on the PAIs and fitness island were characterized. The PAI found in V. parahaemolyticus contained the tdh gene, a collagenase gene, and genes involved in the type 3 secretion system II (T3SS2). A V. vulnificus environmental strain contained two PAIs, a small 25 kbp PAI and a larger 143 kbp PAI. Both PAIs contained virulence genes. Toxin-antitoxin (TA) genes were found in all three species: on the V. diabolicus fitness island, and on the V. parahaemolyticus and V. vulnificus PAIs.
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Affiliation(s)
- Savannah Klein
- Department of Biological Sciences, University of South Carolina, 715 Sumter St, Room 401, Columbia, SC 29208 USA
| | - Shannon Pipes
- Department of Biological Sciences, University of South Carolina, 715 Sumter St, Room 401, Columbia, SC 29208 USA
| | - Charles R. Lovell
- Department of Biological Sciences, University of South Carolina, 715 Sumter St, Room 401, Columbia, SC 29208 USA
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14
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Misra HS, Maurya GK, Kota S, Charaka VK. Maintenance of multipartite genome system and its functional significance in bacteria. J Genet 2018; 97:1013-1038. [PMID: 30262715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bacteria are unicellular organisms that do not show compartmentalization of the genetic material and other cellular organelles as seen in higher organisms. Earlier, bacterial genomes were defined as single circular chromosome and extrachromosomal plasmids. Recently, many bacteria were found harbouringmultipartite genome system and the numbers of copies of genome elements including chromosomes vary from one to several per cell. Interestingly, it is noticed that majority of multipartite genome-harbouring bacteria are either stress tolerant or pathogens. Further, it is observed that the secondary genomes in these bacteria encode proteins that are involved in bacterial genome maintenance and also contribute to higher stress tolerance, and pathogenicity in pathogenic bacteria. Surprisingly, in some bacteria the genes encoding the proteins of classical homologous recombination pathways are present only on the secondary chromosomes, and some do not have either of the classical homologous recombination pathways. This review highlights the presence of ploidy and multipartite genomes in bacterial system, the underlying mechanisms of genome maintenance and the possibilities of these features contributing to higher abiotic and biotic stress tolerance in these bacteria.
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Affiliation(s)
- Hari Sharan Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
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15
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Misra HS, Maurya GK, Kota S, Charaka VK. Maintenance of multipartite genome system and its functional significance in bacteria. J Genet 2018. [DOI: 10.1007/s12041-018-0969-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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Guardiola-Avila I, Martínez-Vázquez V, Requena-Castro R, Juárez-Rendón K, Aguilera-Arreola M, Rivera G, Bocanegra-García V. Isolation and identification ofVibriospecies in the Rio Bravo/Grande and water bodies from Reynosa, Tamaulipas. Lett Appl Microbiol 2018; 67:190-196. [DOI: 10.1111/lam.13009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/11/2018] [Accepted: 05/12/2018] [Indexed: 02/02/2023]
Affiliation(s)
- I. Guardiola-Avila
- CONACyT Research Fellow; Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - V. Martínez-Vázquez
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - R. Requena-Castro
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - K. Juárez-Rendón
- CONACyT Research Fellow; Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - M.G. Aguilera-Arreola
- Escuela Nacional de Ciencias Biológicas; Instituto Politécnico Nacional; Ciudad de México; Mexico City México
| | - G. Rivera
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
| | - V. Bocanegra-García
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Reynosa Tamaulipas México
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17
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Okeyo AN, Nontongana N, Fadare TO, Okoh AI. Vibrio Species in Wastewater Final Effluents and Receiving Watershed in South Africa: Implications for Public Health. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15061266. [PMID: 29914048 PMCID: PMC6025350 DOI: 10.3390/ijerph15061266] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/21/2018] [Accepted: 06/07/2018] [Indexed: 11/17/2022]
Abstract
Wastewater treatment facilities in South Africa are obliged to make provision for wastewater effluent quality management, with the aim of securing the integrity of the surrounding watersheds and environments. The Department of Water Affairs has documented regulatory parameters that have, over the years, served as a guideline for quality monitoring/management purposes. However, these guidelines have not been regularly updated and this may have contributed to some of the water quality anomalies. Studies have shown that promoting the monitoring of the current routinely monitored parameters (both microbial and physicochemical) may not be sufficient. Organisms causing illnesses or even outbreaks, such as Vibrio pathogens with their characteristic environmental resilience, are not included in the guidelines. In South Africa, studies that have been conducted on the occurrence of Vibrio pathogens in domestic and wastewater effluent have made it apparent that these pathogens should also be monitored. The importance of effective wastewater management as one of the key aspects towards protecting surrounding environments and receiving watersheds, as well as protecting public health, is highlighted in this review. Emphasis on the significance of the Vibrio pathogen in wastewater is a particular focus.
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Affiliation(s)
- Allisen N Okeyo
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa.
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa.
- Department of Biochemistry and Microbiology, University of Fort Hare, P/Bag X1314, Eastern Cape, Alice 5700, South Africa.
| | - Nolonwabo Nontongana
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa.
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa.
- Department of Biochemistry and Microbiology, University of Fort Hare, P/Bag X1314, Eastern Cape, Alice 5700, South Africa.
| | - Taiwo O Fadare
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa.
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa.
- Department of Biochemistry and Microbiology, University of Fort Hare, P/Bag X1314, Eastern Cape, Alice 5700, South Africa.
| | - Anthony I Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa.
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa.
- Department of Biochemistry and Microbiology, University of Fort Hare, P/Bag X1314, Eastern Cape, Alice 5700, South Africa.
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18
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Diaz MH, Desai HP, Morrison SS, Benitez AJ, Wolff BJ, Caravas J, Read TD, Dean D, Winchell JM. Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. PLoS One 2017; 12:e0174701. [PMID: 28410368 PMCID: PMC5391922 DOI: 10.1371/journal.pone.0174701] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/13/2017] [Indexed: 11/28/2022] Open
Abstract
Mycoplasma pneumoniae is a significant cause of respiratory illness worldwide. Despite a minimal and highly conserved genome, genetic diversity within the species may impact disease. We performed whole genome sequencing (WGS) analysis of 107 M. pneumoniae isolates, including 67 newly sequenced using the Pacific BioSciences RS II and/or Illumina MiSeq sequencing platforms. Comparative genomic analysis of 107 genomes revealed >3,000 single nucleotide polymorphisms (SNPs) in total, including 520 type-specific SNPs. Population structure analysis supported the existence of six distinct subgroups, three within each type. We developed a predictive model to classify an isolate based on whole genome SNPs called against the reference genome into the identified subtypes, obviating the need for genome assembly. This study is the most comprehensive WGS analysis for M. pneumoniae to date, underscoring the power of combining complementary sequencing technologies to overcome difficult-to-sequence regions and highlighting potential differential genomic signatures in M. pneumoniae.
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Affiliation(s)
- Maureen H. Diaz
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Heta P. Desai
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Shatavia S. Morrison
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alvaro J. Benitez
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Bernard J. Wolff
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jason Caravas
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Deborah Dean
- Center for Immunobiology and Vaccine Research, University of California San Francisco Benioff Children’s Hospital Oakland Research Institute, Oakland, California, United States of America
- Joint Graduate Program in Bioengineering, University of California San Francisco and University of California Berkeley, Oakland, California, United States of America
| | - Jonas M. Winchell
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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19
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Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits. mSystems 2017; 2:mSystems00001-17. [PMID: 28293680 PMCID: PMC5347184 DOI: 10.1128/msystems.00001-17] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/30/2017] [Indexed: 01/30/2023] Open
Abstract
Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes. Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity. However, the pan-genome revealed that six out of nine high-virulence strains possessed a unique accessory genome that was attributed to pathogenic genomic islands, prophage-like elements, virulence factors, and a new set of gene clusters involved in biosynthesis, modification, and transport of polysaccharides. In contrast, V. anguillarum strains that were medium to nonvirulent had a high degree of genomic homogeneity. Finally, we found that a phylogeny based on the core genomes clustered the strains with moderate to no virulence, while six out of nine high-virulence strains represented phylogenetically separate clusters. Hence, we suggest a link between genotype and virulence characteristics of Vibrio anguillarum, which can be used to unravel the molecular evolution of V. anguillarum and can also be important from survey and diagnostic perspectives. IMPORTANCE Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes.
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Characterization of Vibrio cholerae Strains Isolated from the Nigerian Cholera Outbreak in 2010. J Clin Microbiol 2016; 54:2618-21. [PMID: 27487957 DOI: 10.1128/jcm.01467-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 07/29/2016] [Indexed: 01/21/2023] Open
Abstract
We examined clinical samples from Nigerian patients with acute watery diarrhea for Vibrio cholerae during the 2010 cholera outbreak. A total of 109 suspected isolates were characterized, but only 57 V. cholerae strains could be confirmed using multiplex real-time PCR as well as rpoB sequencing and typed as V. cholerae O:1 Ogawa biotype El Tor. This finding highlighted the need for accurate diagnosis of cholera in epidemic countries to implement life-saving interventions.
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Li J, Xue F, Yang Z, Zhang X, Zeng D, Chao G, Jiang Y, Li B. Vibrio parahaemolyticus Strains of Pandemic Serotypes Identified from Clinical and Environmental Samples from Jiangsu, China. Front Microbiol 2016; 7:787. [PMID: 27303379 PMCID: PMC4885827 DOI: 10.3389/fmicb.2016.00787] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/09/2016] [Indexed: 01/22/2023] Open
Abstract
Vibrio parahaemolyticus has emerged as a major foodborne pathogen in China, Japan, Thailand, and other Asian countries. In this study, 72 strains of V. parahaemolyticus were isolated from clinical and environmental samples between 2006 and 2014 in Jiangsu, China. The serotypes and six virulence genes including thermostable direct hemolysin (TDR) and TDR-related hemolysin (TRH) genes were assessed among the isolates. Twenty five serotypes were identified and O3:K6 was one of the dominant serotypes. The genetic diversity was assessed by multilocus sequence typing (MLST) analysis, and 48 sequence types (STs) were found, suggesting this V. parahaemolyticus group is widely dispersed and undergoing rapid evolution. A total of 25 strains of pandemic serotypes such as O3:K6, O5:K17, and O1:KUT were identified. It is worth noting that the pandemic serotypes were not exclusively identified from clinical samples, rather, nine strains were also isolated from environmental samples; and some of these strains harbored several virulence genes, which may render those strains pathogenicity potential. Therefore, the emergence of these "environmental" pandemic V. parahaemolyticus strains may poses a new threat to the public health in China. Furthermore, six novel serotypes and 34 novel STs were identified among the 72 isolates, indicating that V. parahaemolyticus were widely distributed and fast evolving in the environment in Jiangsu, China. The findings of this study provide new insight into the phylogenic relationship between V. parahaemolyticus strains of pandemic serotypes from clinical and environmental sources and enhance the MLST database; and our proposed possible O- and K- antigen evolving paths of V. parahaemolyticus may help understand how the serotypes of this dispersed bacterial population evolve.
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Affiliation(s)
- Jingjiao Li
- Animal Quarantine Laboratory, Jiangsu Entry-Exit Inspection and Quarantine BureauNanjing, China; Key Laboratory of Veterinary Biotechnology, Department of Animal Science, School of Agriculture and Biology, Shanghai JiaoTong UniversityShanghai, China
| | - Feng Xue
- Animal Quarantine Laboratory, Jiangsu Entry-Exit Inspection and Quarantine Bureau Nanjing, China
| | - Zhenquan Yang
- Jiangsu Key Laboratory of Zoonosis, School of Food Science and Engineering, Yangzhou University Yanghzou, China
| | - Xiaoping Zhang
- Beijing Kemufeng Biopharmaceutical Company Beijing, China
| | - Dexin Zeng
- Animal Quarantine Laboratory, Jiangsu Entry-Exit Inspection and Quarantine Bureau Nanjing, China
| | - Guoxiang Chao
- Yangzhou Key Centre for Disease Control and Prevention Yanghzou, China
| | - Yuan Jiang
- Animal Quarantine Laboratory, Jiangsu Entry-Exit Inspection and Quarantine Bureau Nanjing, China
| | - Baoguang Li
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, US Food and Drug Administration Laurel, MD, USA
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Guardiola-Avila I, Acedo-Felix E, Sifuentes-Romero I, Yepiz-Plascencia G, Gomez-Gil B, Noriega-Orozco L. Molecular and Genomic Characterization of Vibrio mimicus Isolated from a Frozen Shrimp Processing Facility in Mexico. PLoS One 2016; 11:e0144885. [PMID: 26730584 PMCID: PMC4701432 DOI: 10.1371/journal.pone.0144885] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 11/24/2015] [Indexed: 11/21/2022] Open
Abstract
Vibrio mimicus is a gram-negative bacterium responsible for diseases in humans. Three strains of V. mimicus identified as V. mimicus 87, V. mimicus 92 and V. mimicus 93 were isolated from a shrimp processing facility in Guaymas, Sonora, Mexico. The strains were analyzed using several molecular techniques and according to the cluster analysis they were different, their similarities ranged between 51.3% and 71.6%. ERIC-PCR and RAPD (vmh390R) were the most discriminatory molecular techniques for the differentiation of these strains. The complete genomes of two strains (V. mimicus 87, renamed as CAIM 1882, and V. mimicus 92, renamed as CAIM 1883) were sequenced. The sizes of the genomes were 3.9 Mb in both strains, with 2.8 Mb in ChI and 1.1 Mb in ChII. A 12.7% difference was found in the proteome content (BLAST matrix). Several virulence genes were detected (e.g. capsular polysaccharide, an accessory colonization factor and genes involved in quorum-sensing) which were classified in 16 categories. Variations in the gene content between these genomes were observed, mainly in proteins and virulence genes (e.g., hemagglutinin, mobile elements and membrane proteins). According to these results, both strains were different, even when they came from the same source, giving an insight of the diversity of V. mimicus. The identification of various virulence genes, including a not previously reported V. mimicus gene (acfD) in ChI in all sequenced strains, supports the pathogenic potential of this species. Further analysis will help to fully understand their potential virulence, environmental impact and evolution.
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Affiliation(s)
| | - Evelia Acedo-Felix
- Centro de Investigación en Alimentación y Desarrollo, A.C Hermosillo, Sonora, México
| | - Itzel Sifuentes-Romero
- Mazatlán Unit for Aquaculture and Environmental Management. Centro de Investigación en Alimentación y Desarrollo, A.C. Mazatlán, Sinaloa, México
| | | | - Bruno Gomez-Gil
- Mazatlán Unit for Aquaculture and Environmental Management. Centro de Investigación en Alimentación y Desarrollo, A.C. Mazatlán, Sinaloa, México
| | - Lorena Noriega-Orozco
- Guaymas Unit: Quality Assurance and Management of Natural Resources. Centro de Investigación en Alimentación y Desarrollo, A.C. Guaymas, Sonora, México
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Kim HJ, Ryu JO, Lee SY, Kim ES, Kim HY. Multiplex PCR for detection of the Vibrio genus and five pathogenic Vibrio species with primer sets designed using comparative genomics. BMC Microbiol 2015; 15:239. [PMID: 26502878 PMCID: PMC4624192 DOI: 10.1186/s12866-015-0577-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 10/19/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The genus Vibrio is clinically significant and major pathogenic Vibrio species causing human Vibrio infections are V. cholerae, V. parahaemolyticus, V. vulnificus, V. alginolyticus and V. mimicus. In this study, we screened for novel genetic markers using comparative genomics and developed a Vibrio multiplex PCR for the reliable diagnosis of the Vibrio genus and the associated major pathogenic Vibrio species. METHODS A total of 30 Vibrio genome sequences were subjected to comparative genomics, and specific genes of the Vibrio genus and five major pathogenic Vibrio species were screened. The designed primer sets from the screened genes were evaluated by single PCR using DNAs from various Vibrio spp. and other non-Vibrio bacterial strains. A sextuplet multiplex PCR using six primer sets was developed to enable detection of the Vibrio genus and five pathogenic Vibrio species. RESULTS The designed primer sets from the screened genes yielded specific diagnostic results for target the Vibrio genus and Vibrio species. The specificity of the developed multiplex PCR was confirmed with various Vibrio and non-Vibrio strains. This Vibrio multiplex PCR was evaluated using 117 Vibrio strains isolated from the south seashore areas in Korea and Vibrio isolates were identified as Vibrio spp., V. parahaemolyticus, V. vulnificus and V. alginolyticus, demonstrating the specificity and discriminative ability of the assay towards Vibrio species. CONCLUSIONS This novel multiplex PCR method could provide reliable and informative identification of the Vibrio genus and major pathogenic Vibrio species in the food safety industry and in early clinical treatment, thereby protecting humans against Vibrio infection.
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Affiliation(s)
- Hyun-Joong Kim
- Institute of Life Sciences & Resources and Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Republic of Korea.
| | - Ji-Oh Ryu
- Institute of Life Sciences & Resources and Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Republic of Korea.
| | - Shin-Young Lee
- Institute of Life Sciences & Resources and Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Republic of Korea.
| | - Ei-Seul Kim
- Institute of Life Sciences & Resources and Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Republic of Korea.
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, Republic of Korea.
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Orata FD, Kirchberger PC, Méheust R, Barlow EJ, Tarr CL, Boucher Y. The Dynamics of Genetic Interactions between Vibrio metoecus and Vibrio cholerae, Two Close Relatives Co-Occurring in the Environment. Genome Biol Evol 2015; 7:2941-54. [PMID: 26454015 PMCID: PMC4684700 DOI: 10.1093/gbe/evv193] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Vibrio metoecus is the closest relative of Vibrio cholerae, the causative agent of the potent diarrheal disease cholera. Although the pathogenic potential of this new species is yet to be studied in depth, it has been co-isolated with V. cholerae in coastal waters and found in clinical specimens in the United States. We used these two organisms to investigate the genetic interaction between closely related species in their natural environment. The genomes of 20 V. cholerae and 4 V. metoecus strains isolated from a brackish coastal pond on the US east coast, as well as 4 clinical V. metoecus strains were sequenced and compared with reference strains. Whole genome comparison shows 86-87% average nucleotide identity (ANI) in their core genes between the two species. On the other hand, the chromosomal integron, which occupies approximately 3% of their genomes, shows higher conservation in ANI between species than any other region of their genomes. The ANI of 93-94% observed in this region is not significantly greater within than between species, meaning that it does not follow species boundaries. Vibrio metoecus does not encode toxigenic V. cholerae major virulence factors, the cholera toxin and toxin-coregulated pilus. However, some of the pathogenicity islands found in pandemic V. cholerae were either present in the common ancestor it shares with V. metoecus, or acquired by clinical and environmental V. metoecus in partial fragments. The virulence factors of V. cholerae are therefore both more ancient and more widespread than previously believed. There is high interspecies recombination in the core genome, which has been detected in 24% of the single-copy core genes, including genes involved in pathogenicity. Vibrio metoecus was six times more often the recipient of DNA from V. cholerae as it was the donor, indicating a strong bias in the direction of gene transfer in the environment.
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Affiliation(s)
- Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Paul C Kirchberger
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Raphaël Méheust
- Unité Mixte de Recherche 7138, Evolution Paris-Seine, Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, Paris, France
| | - E Jed Barlow
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - Cheryl L Tarr
- Enteric Diseases Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | - Yan Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Rahaman MH, Islam T, Colwell RR, Alam M. Molecular tools in understanding the evolution of Vibrio cholerae. Front Microbiol 2015; 6:1040. [PMID: 26500613 PMCID: PMC4594017 DOI: 10.3389/fmicb.2015.01040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/13/2015] [Indexed: 12/25/2022] Open
Abstract
Vibrio cholerae, the etiological agent of cholera, has been a scourge for centuries. Cholera remains a serious health threat for developing countries and has been responsible for millions of deaths globally over the past 200 years. Identification of V. cholerae has been accomplished using a variety of methods, ranging from phenotypic strategies to DNA based molecular typing and currently whole genomic approaches. This array of methods has been adopted in epidemiological investigations, either singly or in the aggregate, and more recently for evolutionary analyses of V. cholerae. Because the new technologies have been developed at an ever increasing pace, this review of the range of fingerprinting strategies, their relative advantages and limitations, and cholera case studies was undertaken. The task was challenging, considering the vast amount of the information available. To assist the study, key references representative of several areas of research are provided with the intent to provide readers with a comprehensive view of recent advances in the molecular epidemiology of V. cholerae. Suggestions for ways to obviate many of the current limitations of typing techniques are also provided. In summary, a comparative report has been prepared that includes the range from traditional typing to whole genomic strategies.
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Affiliation(s)
- Md Habibur Rahaman
- Department of Biology and Chemistry, North South University, Dhaka Bangladesh
| | - Tarequl Islam
- Enteric and Food Microbiology Lab, Center for Communicable Diseases, International Center for Diarrheal Disease Research, Dhaka Bangladesh
| | - Rita R Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD USA ; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD USA
| | - Munirul Alam
- Enteric and Food Microbiology Lab, Center for Communicable Diseases, International Center for Diarrheal Disease Research, Dhaka Bangladesh
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Abstract
Integrons are versatile gene acquisition systems commonly found in bacterial genomes. They are ancient elements that are a hot spot for genomic complexity, generating phenotypic diversity and shaping adaptive responses. In recent times, they have had a major role in the acquisition, expression, and dissemination of antibiotic resistance genes. Assessing the ongoing threats posed by integrons requires an understanding of their origins and evolutionary history. This review examines the functions and activities of integrons before the antibiotic era. It shows how antibiotic use selected particular integrons from among the environmental pool of these elements, such that integrons carrying resistance genes are now present in the majority of Gram-negative pathogens. Finally, it examines the potential consequences of widespread pollution with the novel integrons that have been assembled via the agency of human antibiotic use and speculates on the potential uses of integrons as platforms for biotechnology.
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Tercero-Alburo JJ, González-Márquez H, Bonilla-González E, Quiñones-Ramírez EI, Vázquez-Salinas C. Identification of capsule, biofilm, lateral flagellum, and type IV pili in Vibrio mimicus strains. Microb Pathog 2014; 76:77-83. [PMID: 25246027 DOI: 10.1016/j.micpath.2014.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 10/24/2022]
Abstract
Vibrio mimicus is a bacterium that causes gastroenteritis; it is closely related to Vibrio cholerae, and can cause acute diarrhea like cholera- or dysentery-type diarrhea. It is distributed worldwide. Factors associated with virulence (such as hemolysins, enterotoxins, proteases, phospholipases, aerobactin, and hemagglutinin) have been identified; however, its pathogenicity mechanism is still unknown. In pathogenic Vibrio species such as V. cholerae, Vibrio. parahaemolyticus and Vibrio vulnificus, capsule, biofilms, lateral flagellum, and type IV pili are structures described as essential for pathogenicity. These structures had not been described in V. mimicus until this work. We used 20 V. mimicus strains isolated from water (6), oyster (9), and fish (5) samples and we were able to identify the capsule, biofilm, lateral flagellum, and type IV pili through phenotypic tests, electron microscopy, PCR, and sequencing. In all tested strains, we observed and identified the presence of capsular exopolysaccharide, biofilm formation in an in vitro model, as well as swarming, multiple flagellation, and pili. In addition, we identified homologous genes to those described in other bacteria of the genus in which these structures have been found. Identification of these structures in V. mimicus is a contribution to the biology of this organism and can help to reveal its pathogenic behavior.
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Affiliation(s)
- J J Tercero-Alburo
- Posgrado de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, México; Departamento de Biotecnología, Universidad Autónoma Metropolitana Iztapalapa, San Rafael Atlixco No.186, Col. Vicentina C.P. 09340, México
| | - H González-Márquez
- Laboratorio de Expresión Génica División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana Iztapalapa, San Rafael Atlixco No.186, Col. Vicentina C.P. 09340, México
| | - E Bonilla-González
- Laboratorio de Expresión Génica División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana Iztapalapa, San Rafael Atlixco No.186, Col. Vicentina C.P. 09340, México
| | - E I Quiñones-Ramírez
- Laboratorio de Microbiología Sanitaria, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N Col, Santo Tomás C.P. 11340, Distrito Federal, México
| | - C Vázquez-Salinas
- Departamento de Biotecnología, Universidad Autónoma Metropolitana Iztapalapa, San Rafael Atlixco No.186, Col. Vicentina C.P. 09340, México.
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Identification of genetic bases of vibrio fluvialis species-specific biochemical pathways and potential virulence factors by comparative genomic analysis. Appl Environ Microbiol 2014; 80:2029-37. [PMID: 24441165 DOI: 10.1128/aem.03588-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Vibrio fluvialis is an important food-borne pathogen that causes diarrheal illness and sometimes extraintestinal infections in humans. In this study, we sequenced the genome of a clinical V. fluvialis strain and determined its phylogenetic relationships with other Vibrio species by comparative genomic analysis. We found that the closest relationship was between V. fluvialis and V. furnissii, followed by those with V. cholerae and V. mimicus. Moreover, based on genome comparisons and gene complementation experiments, we revealed genetic mechanisms of the biochemical tests that differentiate V. fluvialis from closely related species. Importantly, we identified a variety of genes encoding potential virulence factors, including multiple hemolysins, transcriptional regulators, and environmental survival and adaptation apparatuses, and the type VI secretion system, which is indicative of complex regulatory pathways modulating pathogenesis in this organism. The availability of V. fluvialis genome sequences may promote our understanding of pathogenic mechanisms for this emerging pathogen.
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Val ME, Kennedy SP, Soler-Bistué AJ, Barbe V, Bouchier C, Ducos-Galand M, Skovgaard O, Mazel D. Fuse or die: how to survive the loss of Dam inVibrio cholerae. Mol Microbiol 2014; 91:665-78. [DOI: 10.1111/mmi.12483] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Marie-Eve Val
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
| | | | - Alfonso J. Soler-Bistué
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
| | | | | | - Magaly Ducos-Galand
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
| | - Ole Skovgaard
- Department of Science, Systems and Models; Roskilde University; DK-4000 Roskilde Denmark
| | - Didier Mazel
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
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Reichardt WT, Reyes JM, Pueblos MJ, Lluisma AO. Impact of milk fish farming in the tropics on potentially pathogenic vibrios. MARINE POLLUTION BULLETIN 2013; 77:325-332. [PMID: 24079922 DOI: 10.1016/j.marpolbul.2013.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 09/06/2013] [Accepted: 09/08/2013] [Indexed: 06/02/2023]
Abstract
Ratios of sucrose-negative to sucrose-positive vibrios on TCBS agar (suc-/suc+) indicate the abundance of potential human pathogenic non-cholera vibrios in coastal mariculture environments of the Lingayen Gulf (Philippines. In guts of adult maricultured milkfish (Chanos chanos) of suc- vibrios reached extreme peak values ranging between 2 and 545 million per g wet weight. Suc- vibrios outnumbered suc+ vibrios in anoxic sediments, too, and were rarely predominant in coastal waters or in oxidized sediments. Suc-/suc+ ratios in sediments increased toward the mariculture areas with distance from the open sea at decreasing redox potentials. There is circumstantial evidence that suc- vibrios can be dispersed from mariculture areas to adjacent environments including coral reefs. An immediate human health risk by pathogenic Vibrio species is discounted, since milkfish guts contained mainly members of the Enterovibrio group. A representative isolate of these contained proteolytic and other virulence factors, but no genes encoding toxins characteristic of clinical Vibrio species.
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Affiliation(s)
- W T Reichardt
- Marine Science Institute, University of the Philippines, Diliman, 1101 Quezon City, Philippines.
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Octavia S, Salim A, Kurniawan J, Lam C, Leung Q, Ahsan S, Reeves PR, Nair GB, Lan R. Population structure and evolution of non-O1/non-O139 Vibrio cholerae by multilocus sequence typing. PLoS One 2013; 8:e65342. [PMID: 23776471 PMCID: PMC3679125 DOI: 10.1371/journal.pone.0065342] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/24/2013] [Indexed: 01/09/2023] Open
Abstract
Pathogenic non-O1/non-O139 Vibrio cholerae strains can cause sporadic outbreaks of cholera worldwide. In this study, multilocus sequence typing (MLST) of seven housekeeping genes was applied to 55 non-O1/non-O139 isolates from clinical and environmental sources. Data from five published O1 isolates and 17 genomes were also included, giving a total of 77 isolates available for analysis. There were 66 sequence types (STs), with the majority being unique, and only three clonal complexes. The V. cholerae strains can be divided into four subpopulations with evidence of recombination among the subpopulations. Subpopulations I and III contained predominantly clinical strains. PCR screening for virulence factors including Vibrio pathogenicity island (VPI), cholera toxin prophage (CTXΦ), type III secretion system (T3SS), and enterotoxin genes (rtxA and sto/stn) showed that combinations of these factors were present in the clinical isolates with 85.7% having rtxA, 51.4% T3SS, 31.4% VPI, 31.4% sto/stn (NAG-ST) and 11.4% CTXΦ. These factors were also present in environmental isolates but at a lower frequency. Five strains previously mis-identified as V. cholerae serogroups O114 to O117 were also analysed and formed a separate population with V. mimicus. The MLST scheme developed in this study provides a framework to identify sporadic cholera isolates by genetic identity.
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Affiliation(s)
- Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Anna Salim
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Jacob Kurniawan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Connie Lam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Queenie Leung
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sunjukta Ahsan
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - Peter R. Reeves
- School of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
| | - G. Balakrish Nair
- Translational Health Science and Technology Institute, Gurgaon, Haryana, India
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail:
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Grim CJ, Kotewicz ML, Power KA, Gopinath G, Franco AA, Jarvis KG, Yan QQ, Jackson SA, Sathyamoorthy V, Hu L, Pagotto F, Iversen C, Lehner A, Stephan R, Fanning S, Tall BD. Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation. BMC Genomics 2013; 14:366. [PMID: 23724777 PMCID: PMC3680222 DOI: 10.1186/1471-2164-14-366] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 05/24/2013] [Indexed: 11/24/2022] Open
Abstract
Background Members of the genus Cronobacter are causes of rare but severe illness in neonates and preterm infants following the ingestion of contaminated infant formula. Seven species have been described and two of the species genomes were subsequently published. In this study, we performed comparative genomics on eight strains of Cronobacter, including six that we sequenced (representing six of the seven species) and two previously published, closed genomes. Results We identified and characterized the features associated with the core and pan genome of the genus Cronobacter in an attempt to understand the evolution of these bacteria and the genetic content of each species. We identified 84 genomic regions that are present in two or more Cronobacter genomes, along with 45 unique genomic regions. Many potentially horizontally transferred genes, such as lysogenic prophages, were also identified. Most notable among these were several type six secretion system gene clusters, transposons that carried tellurium, copper and/or silver resistance genes, and a novel integrative conjugative element. Conclusions Cronobacter have diverged into two clusters, one consisting of C. dublinensis and C. muytjensii (Cdub-Cmuy) and the other comprised of C. sakazakii, C. malonaticus, C. universalis, and C. turicensis, (Csak-Cmal-Cuni-Ctur) from the most recent common ancestral species. While several genetic determinants for plant-association and human virulence could be found in the core genome of Cronobacter, the four Cdub-Cmuy clade genomes contained several accessory genomic regions important for survival in a plant-associated environmental niche, while the Csak-Cmal-Cuni-Ctur clade genomes harbored numerous virulence-related genetic traits.
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Nair GB, Ramamurthy T, Sur D, Kurakawa T, Takahashi T, Nomoto K, Takeda Y. Vibrio cholerae/mimicus in fecal microbiota of healthy children in a cholera endemic urban slum setting in Kolkata, India. Microbiol Immunol 2013; 56:789-91. [PMID: 22882566 DOI: 10.1111/j.1348-0421.2012.00497.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
During a double-blind, randomized, placebo-controlled probiotic trial among 3758 children residing in an urban slum in Kolkata, India, Vibrio cholerae/mimicus was detected in fecal microbiota of healthy children. The importance of this finding in the local, regional and global transmission of cholera is discussed.
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Abstract
Vibrio mimicus is a Gram-negative bacterium associated with gastrointestinal diseases in humans around the world. We report the complete genome sequence of the Vibrio mimicus strain CAIM 602T (CDC1721-77, LMG 7896T, ATCC 33653T).
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Rapid and sensitive quantification of Vibrio cholerae and Vibrio mimicus cells in water samples by use of catalyzed reporter deposition fluorescence in situ hybridization combined with solid-phase cytometry. Appl Environ Microbiol 2012; 78:7369-75. [PMID: 22885749 DOI: 10.1128/aem.02190-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new protocol for rapid, specific, and sensitive cell-based quantification of Vibrio cholerae/Vibrio mimicus in water samples was developed. The protocol is based on catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) in combination with solid-phase cytometry. For pure cultures, we were able to quantify down to 6 V. cholerae cells on one membrane with a relative precision of 39% and down to 12 cells with a relative precision of 17% after hybridization with the horseradish peroxidase (HRP)-labeled probe Vchomim1276 (specific for V. cholerae and V. mimicus) and signal amplification. The corresponding position of the probe on the 16S rRNA is highly accessible even when labeled with HRP. For the first time, we were also able to successfully quantify V. cholerae/V. mimicus via solid-phase cytometry in extremely turbid environmental water samples collected in Austria. Cell numbers ranged from 4.5 × 10(1) cells ml(-1) in the large saline lake Neusiedler See to 5.6 × 10(4) cells ml(-1) in an extremely turbid shallow soda lake situated nearby. We therefore suggest CARD-FISH in combination with solid-phase cytometry as a powerful tool to quantify V. cholerae/V. mimicus in ecological studies as well as for risk assessment and monitoring programs.
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Abstract
The millions of deaths from cholera during the past 200 y, coupled with the morbidity and mortality of cholera in Haiti since October 2010, are grim reminders that Vibrio cholerae, the etiologic agent of cholera, remains a scourge. We report the isolation of both V. cholerae O1 and non-O1/O139 early in the Haiti cholera epidemic from samples collected from victims in 18 towns across eight Arrondissements of Haiti. The results showed two distinct populations of V. cholerae coexisted in Haiti early in the epidemic. As non-O1/O139 V. cholerae was the sole pathogen isolated from 21% of the clinical specimens, its role in this epidemic, either alone or in concert with V. cholerae O1, cannot be dismissed. A genomic approach was used to examine similarities and differences among the Haitian V. cholerae O1 and V. cholerae non-O1/O139 strains. A total of 47 V. cholerae O1 and 29 V. cholerae non-O1/O139 isolates from patients and the environment were sequenced. Comparative genome analyses of the 76 genomes and eight reference strains of V. cholerae isolated in concurrent epidemics outside Haiti and 27 V. cholerae genomes available in the public database demonstrated substantial diversity of V. cholerae and ongoing flux within its genome.
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Morrison SS, Williams T, Cain A, Froelich B, Taylor C, Baker-Austin C, Verner-Jeffreys D, Hartnell R, Oliver JD, Gibas CJ. Pyrosequencing-based comparative genome analysis of Vibrio vulnificus environmental isolates. PLoS One 2012; 7:e37553. [PMID: 22662170 PMCID: PMC3360785 DOI: 10.1371/journal.pone.0037553] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 04/25/2012] [Indexed: 01/22/2023] Open
Abstract
Between 1996 and 2006, the US Centers for Disease Control reported that the only category of food-borne infections increasing in frequency were those caused by members of the genus Vibrio. The Gram-negative bacterium Vibrio vulnificus is a ubiquitous inhabitant of estuarine waters, and is the number one cause of seafood-related deaths in the US. Many V. vulnificus isolates have been studied, and it has been shown that two genetically distinct subtypes, distinguished by 16S rDNA and other gene polymorphisms, are associated predominantly with either environmental or clinical isolation. While local genetic differences between the subtypes have been probed, only the genomes of clinical isolates have so far been completely sequenced. In order to better understand V. vulnificus as an agent of disease and to identify the molecular components of its virulence mechanisms, we have completed whole genome shotgun sequencing of three diverse environmental genotypes using a pyrosequencing approach. V. vulnificus strain JY1305 was sequenced to a depth of 33×, and strains E64MW and JY1701 were sequenced to lesser depth, covering approximately 99.9% of each genome. We have performed a comparative analysis of these sequences against the previously published sequences of three V. vulnificus clinical isolates. We find that the genome of V. vulnificus is dynamic, with 1.27% of genes in the C-genotype genomes not found in the E- genotype genomes. We identified key genes that differentiate between the genomes of the clinical and environmental genotypes. 167 genes were found to be specifically associated with environmental genotypes and 278 genes with clinical genotypes. Genes specific to the clinical strains include components of sialic acid catabolism, mannitol fermentation, and a component of a Type IV secretory pathway VirB4, as well as several other genes with potential significance for human virulence. Genes specific to environmental strains included several that may have implications for the balance between self-preservation under stress and nutritional competence.
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Affiliation(s)
- Shatavia S. Morrison
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Tiffany Williams
- Department of Biology, the University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Aurora Cain
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Brett Froelich
- Department of Biology, the University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Casey Taylor
- Department of Biology, the University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Craig Baker-Austin
- Centre for Environment, Fisheries, and Aquaculture Science, Weymouth, Dorset, United Kingdom
| | - David Verner-Jeffreys
- Centre for Environment, Fisheries, and Aquaculture Science, Weymouth, Dorset, United Kingdom
| | - Rachel Hartnell
- Centre for Environment, Fisheries, and Aquaculture Science, Weymouth, Dorset, United Kingdom
| | - James D. Oliver
- Department of Biology, the University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Cynthia J. Gibas
- Department of Bioinformatics and Genomics, the University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
- * E-mail:
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Wang D, Wang H, Zhou Y, Zhang Q, Zhang F, Du P, Wang S, Chen C, Kan B. Genome sequencing reveals unique mutations in characteristic metabolic pathways and the transfer of virulence genes between V. mimicus and V. cholerae. PLoS One 2011; 6:e21299. [PMID: 21731695 PMCID: PMC3120857 DOI: 10.1371/journal.pone.0021299] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 05/25/2011] [Indexed: 11/25/2022] Open
Abstract
Vibrio mimicus, the species most similar to V. cholerae, is a microbe present in the natural environmental and sometimes causes diarrhea and internal infections in humans. It shows similar phenotypes to V. cholerae but differs in some biochemical characteristics. The molecular mechanisms underlying the differences in biochemical metabolism between V. mimicus and V. cholerae are currently unclear. Several V. mimicus isolates have been found that carry cholera toxin genes (ctxAB) and cause cholera-like diarrhea in humans. Here, the genome of the V. mimicus isolate SX-4, which carries an intact CTX element, was sequenced and annotated. Analysis of its genome, together with those of other Vibrio species, revealed extensive differences within the Vibrionaceae. Common mutations in gene clusters involved in three biochemical metabolism pathways that are used for discrimination between V. mimicus and V. cholerae were found in V. mimicus strains. We also constructed detailed genomic structures and evolution maps for the general types of genomic drift associated with pathogenic characters in polysaccharides, CTX elements and toxin co-regulated pilus (TCP) gene clusters. Overall, the whole-genome sequencing of the V. mimicus strain carrying the cholera toxin gene provides detailed information for understanding genomic differences among Vibrio spp. V. mimicus has a large number of diverse gene and nucleotide differences from its nearest neighbor, V. cholerae. The observed mutations in the characteristic metabolism pathways may indicate different adaptations to different niches for these species and may be caused by ancient events in evolution before the divergence of V. cholerae and V. mimicus. Horizontal transfers of virulence-related genes from an uncommon clone of V. cholerae, rather than the seventh pandemic strains, have generated the pathogenic V. mimicus strain carrying cholera toxin genes.
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Affiliation(s)
- Duochun Wang
- National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention / State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Haiyin Wang
- National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention / State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Yanyan Zhou
- National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention / State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Qiuxiang Zhang
- Center for Diseases Control and Prevention of Shanxi Province, Taiyuan, China
| | - Fanfei Zhang
- Center for Diseases Control and Prevention of Shanxi Province, Taiyuan, China
| | - Pengcheng Du
- National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention / State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Shujing Wang
- National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention / State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
| | - Chen Chen
- National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention / State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
- * E-mail: (CC); (BK)
| | - Biao Kan
- National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention / State Key Laboratory for Infectious Disease Prevention and Control, Beijing, China
- * E-mail: (CC); (BK)
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