1
|
Liu T, Kang L, Xu J, Wang J, Gao S, Li Y, Li J, Yuan Y, Yuan B, Wang J, Zhao B, Xin W. PVBase: A MALDI-TOF MS Database for Fast Identification and Characterization of Potentially Pathogenic Vibrio Species From Multiple Regions of China. Front Microbiol 2022; 13:872825. [PMID: 35656002 PMCID: PMC9152771 DOI: 10.3389/fmicb.2022.872825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
The potentially pathogenic species of the genus Vibrio pose a threat to both humans and animals, creating medical burdens and economic losses to the mariculture industry. Improvements in surveillance and diagnosis are needed to successfully manage vibriosis outbreaks. Matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) can provide rapid diagnosis and has been widely used in the identification of Vibrio spp. The main weakness of this technology is the limited number of strains and species of Vibrio in the existing commercial database. Here, we develop a new in-house database named PVBase containing 790 main spectra projections (MSP) of ten Vibrio species that come from various regions of China and include abundant clinical and environmental strains. PVBase was validated through a blind test of 65 Vibrio strains. The identification accuracy and scoring of Vibrio strains was greatly improved through the addition of PVBase. Identification accuracy increased from 73.4 to 100%. The number of strains with identification scores above 2.2 increased from 53.1% to 96.9% and 53.1% of strains had an identification score above 2.59. Moreover, perfect discrimination was obtained when using all of the MSPs created for the Vibrio species, even for very closely related species such as V. cholerae, V. albensis, and V. mimicus or V. alginolyticus, V. parahaemolyticus, and V. harveyi. In addition, we used phyloproteomic analysis to study whether there are differences in protein fingerprints of different regions or pathogenic strains. We found that MSP characteristics of Vibrio species were not related to their region or source. With the construction of PVBase, the identification efficiency of potentially pathogenic Vibrio species has been greatly improved, which is an important advance for epidemic prevention and control, and aquaculture disease detection.
Collapse
Affiliation(s)
- Tingting Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Lin Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jinglin Xu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jing Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Shan Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Yanwei Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jiaxin Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Yuan Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Bing Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Baohua Zhao
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Wenwen Xin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| |
Collapse
|
2
|
Characterization of Potential Virulence Factors of Vibrio mimicus Isolated from Fishery Products and Water. Int J Microbiol 2021; 2021:8397930. [PMID: 33628259 PMCID: PMC7889394 DOI: 10.1155/2021/8397930] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 12/14/2020] [Accepted: 01/29/2021] [Indexed: 11/17/2022] Open
Abstract
Vibrio mimicus is a Gram-negative bacterium that is closely related to V. cholerae and causes gastroenteritis in humans due to contaminated fish consumption and seafood. This bacterium was isolated and identified from 238 analyzed samples of sea water, oysters, and fish. Twenty strains were identified as V. mimicus according to amplification of the vmhA gene, which is useful as a marker of identification of the species. The production of lipases, proteases, and nucleases was detected; 45% of the strains were able to produce thermonucleases and 40% were capable of producing hydroxamate-type siderophores, and the fragment of the iuT gene was amplified in all of the V. mimicus strains. Seventy-five percent of V. mimicus strains showed cytopathic effect on Chinese hamster ovary (CHO) cells and destruction of the monolayer, and 100% of the strains were adherent on the HEp-2 cell line with an aggregative adherence pattern. The presence of virulence factors in V. mimicus strains obtained from fishery products suggests that another member of the Vibrio genus could represent a risk to the consumer due to production of different metabolites that allows it to subsist in the host.
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Guan H, Xue P, Zhou H, Sha D, Wang D, Gao H, Li J, Diao B, Zhao H, Kan B, Zhang J. A multiplex PCR assay for the detection of five human pathogenic Vibrio species and Plesiomonas. Mol Cell Probes 2020; 55:101689. [PMID: 33338586 DOI: 10.1016/j.mcp.2020.101689] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 01/07/2023]
Abstract
A multiplex PCR (mPCR) assay was established to detect five pathogenic Vibrio species and Plesiomonas shigelloides. Twelve genes were included: ompW, ctxA, rfbN, and wbfR from V. cholerae; tl, tdh, and trh from V. parahaemolyticus; toxR and vmhA from V. mimicus; toxR from V. fluvialis; vvhA from V. vulnificus; and the 23S rRNA gene from P. shigelloides. The specificity of the mPCR assay was 100% for the detection of 136 strains and the limits of detection (LoD) were 12.5-50 pg/reaction. The assay exhibited higher sensitivity than cultivation methods in the detection of APW cultures of 113 diarrhea samples. In the analysis of 369 suspected Vibrio populations from estuarine water samples, the specificity of the mPCR for V. cholerae and V. parahaemolyticus was 100% for both, while the sensitivities were 100% and 96.1%, respectively. The assay can be applied to screen enrichment cultures and suspected colonies from environmental and clinical samples.
Collapse
Affiliation(s)
- Hongxia Guan
- Wuxi Center for Disease Control and Prevention, Jiangsu, 214023, China
| | - Panpan Xue
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Haijian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Dan Sha
- Wuxi Center for Disease Control and Prevention, Jiangsu, 214023, China
| | - Duochun Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - He Gao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jie Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Baowei Diao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Hongqun Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Jingyun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| |
Collapse
|
5
|
Diverse Horizontally-Acquired Gene Clusters Confer Sucrose Utilization to Different Lineages of the Marine Pathogen Photobacterium damselae subsp. damselae. Genes (Basel) 2020; 11:genes11111244. [PMID: 33105683 PMCID: PMC7690375 DOI: 10.3390/genes11111244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022] Open
Abstract
The ability to metabolize sucrose is a variable trait within the family Vibrionaceae. The marine bacterium Photobacterium damselae subsp. damselae (Pdd), pathogenic for marine animals and humans, is generally described as negative for sucrose utilization (Scr−). Previous studies have reported sucrose-utilizing isolates (Scr+), but the genetic basis of this variable phenotype remains uncharacterized. Here, we carried out the genome sequencing of five Scr+ and two Scr−Pdd isolates and conducted a comparative genomics analysis with sixteen additional Pdd genomes sequenced in previous studies. We identified two different versions of a four-gene cluster (scr cluster) exclusive of Scr+ isolates encoding a PTS system sucrose-specific IIBC component (scrA), a fructokinase (scrK), a sucrose-6-phosphate hydrolase (scrB), and a sucrose operon repressor (scrR). A scrA deletion mutant did not ferment sucrose and was impaired for growth with sucrose as carbon source. Comparative genomics analyses suggested that scr clusters were acquired by horizontal transfer by different lineages of Pdd and were inserted into a recombination hot-spot in the Pdd genome. The incongruence of phylogenies based on housekeeping genes and on scr genes revealed that phylogenetically diverse gene clusters for sucrose utilization have undergone extensive horizontal transfer among species of Vibrio and Photobacterium.
Collapse
|
6
|
|
7
|
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.
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Diversity of Vibrio spp in Karstic Coastal Marshes in the Yucatan Peninsula. PLoS One 2015; 10:e0134953. [PMID: 26252792 PMCID: PMC4529161 DOI: 10.1371/journal.pone.0134953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 07/15/2015] [Indexed: 11/19/2022] Open
Abstract
Coastal bodies of water formed by the combination of seawater, underground rivers and rainwater comprise the systems with the greatest solar energy flow and biomass production on the planet. These characteristics make them reservoirs for a large number species, mainly microorganisms. Bacteria of the genus Vibrio are natural inhabitants of these environments and their presence is determined by variations in the nutrient, temperature and salinity cycles generated by the seasonal hydrologic behavior of these lagoon systems. This study determined the diversity of the genus Vibrio in 4 coastal bodies of water on the Yucatan Peninsula (Celestun Lagoon, Chelem Lagoon, Rosada Lagoon and Sabancuy Estuary). Using the molecular technique of 454 pyrosequencing, DNA extracted from water samples was analyzed and 32,807 reads were obtained belonging to over 20 culturable species of the genus Vibrio and related genera. OTU (operational taxonomic unit) richness and Chao2 and Shannon Weaver diversity indices were obtained with the database from this technique. Physicochemical and environmental parameters were determined and correlated with Vibrio diversity measured in OTUs.
Collapse
|
10
|
gbpA as a Novel qPCR Target for the Species-Specific Detection of Vibrio cholerae O1, O139, Non-O1/Non-O139 in Environmental, Stool, and Historical Continuous Plankton Recorder Samples. PLoS One 2015; 10:e0123983. [PMID: 25915771 PMCID: PMC4411143 DOI: 10.1371/journal.pone.0123983] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/24/2015] [Indexed: 02/07/2023] Open
Abstract
The Vibrio cholerae N-acetyl glucosamine-binding protein A (GbpA) is a chitin-binding protein involved in V. cholerae attachment to environmental chitin surfaces and human intestinal cells. We previously investigated the distribution and genetic variations of gbpA in a large collection of V. cholerae strains and found that the gene is consistently present and highly conserved in this species. Primers and probe were designed from the gbpA sequence of V. cholerae and a new Taq-based qPCR protocol was developed for diagnostic detection and quantification of the bacterium in environmental and stool samples. In addition, the positions of primers targeting the gbpA gene region were selected to obtain a short amplified fragment of 206 bp and the protocol was optimized for the analysis of formalin-fixed samples, such as historical Continuous Plankton Recorder (CPR) samples. Overall, the method is sensitive (50 gene copies), highly specific for V. cholerae and failed to amplify strains of the closely-related species Vibrio mimicus. The sensitivity of the assay applied to environmental and stool samples spiked with V. cholerae ATCC 39315 was comparable to that of pure cultures and was of 102 genomic units/l for drinking and seawater samples, 101 genomic units/g for sediment and 102 genomic units/g for bivalve and stool samples. The method also performs well when tested on artificially formalin-fixed and degraded genomic samples and was able to amplify V. cholerae DNA in historical CPR samples, the earliest of which date back to August 1966. The detection of V. cholerae in CPR samples collected in cholera endemic areas such as the Benguela Current Large Marine Ecosystem (BCLME) is of particular significance and represents a proof of concept for the possible use of the CPR technology and the developed qPCR assay in cholera studies.
Collapse
|
11
|
Chapman C, Henry M, Bishop-Lilly KA, Awosika J, Briska A, Ptashkin RN, Wagner T, Rajanna C, Tsang H, Johnson SL, Mokashi VP, Chain PSG, Sozhamannan S. Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity. PLoS One 2015; 10:e0120311. [PMID: 25794000 PMCID: PMC4368569 DOI: 10.1371/journal.pone.0120311] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/20/2015] [Indexed: 01/08/2023] Open
Abstract
Historically, cholera outbreaks have been linked to V. cholerae O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 V. cholerae in causing cholera and the lack of genomic sequences of such strains from around the world. Here we address these gaps by scanning a global collection of V. cholerae strains as a first step towards understanding the population genetic diversity and epidemic potential of non O1/non-O139 strains. Whole Genome Mapping (Optical Mapping) based bar coding produces a high resolution, ordered restriction map, depicting a complete view of the unique chromosomal architecture of an organism. To assess the genomic diversity of non-O1/non-O139 V. cholerae, we applied a Whole Genome Mapping strategy on a well-defined and geographically and temporally diverse strain collection, the Sakazaki serogroup type strains. Whole Genome Map data on 91 of the 206 serogroup type strains support the hypothesis that V. cholerae has an unprecedented genetic and genomic structural diversity. Interestingly, we discovered chromosomal fusions in two unusual strains that possess a single chromosome instead of the two chromosomes usually found in V. cholerae. We also found pervasive chromosomal rearrangements such as duplications and indels in many strains. The majority of Vibrio genome sequences currently in public databases are unfinished draft sequences. The Whole Genome Mapping approach presented here enables rapid screening of large strain collections to capture genomic complexities that would not have been otherwise revealed by unfinished draft genome sequencing and thus aids in assembling and finishing draft sequences of complex genomes. Furthermore, Whole Genome Mapping allows for prediction of novel V. cholerae non-O1/non-O139 strains that may have the potential to cause future cholera outbreaks.
Collapse
Affiliation(s)
- Carol Chapman
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
| | - Matthew Henry
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
| | - Kimberly A. Bishop-Lilly
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
| | - Joy Awosika
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
| | - Adam Briska
- OpGen, Inc., Gaithersburg, Maryland, United States of America
| | | | - Trevor Wagner
- OpGen, Inc., Gaithersburg, Maryland, United States of America
| | - Chythanya Rajanna
- University of Florida, Gainesville, Florida, United States of America
| | - Hsinyi Tsang
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
| | - Shannon L. Johnson
- Genome Science, Biosciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Vishwesh P. Mokashi
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
| | - Patrick S. G. Chain
- Genome Science, Biosciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Shanmuga Sozhamannan
- Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Naval Medical Research Center—Frederick, Fort Detrick, Maryland, United States of America
- * E-mail:
| |
Collapse
|
12
|
Liu X, Gao H, Xiao N, Liu Y, Li J, Li L. Outer membrane protein U (OmpU) mediates adhesion of Vibrio mimicus to host cells via two novel N-terminal motifs. PLoS One 2015; 10:e0119026. [PMID: 25742659 PMCID: PMC4351038 DOI: 10.1371/journal.pone.0119026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/08/2015] [Indexed: 11/19/2022] Open
Abstract
Vibrio mimicus (V.mimicus) is a causative agent of ascites disease in aquatic animals. Our previous studies have demonstrated that the outer membrane protein U (OmpU) from V.mimicus is an immunoprotective antigen with six immunodominant linear B-cell epitopes. Although the N-terminus of OmpU contains potential binding motifs, it remained unclear whether OmpU possesses adhesion function. Here, the adhesive capacity of recombinant OmpU and V.mimicus to epithelioma papulosum cyprinid (EPC) cells was determined by immunofluorescence and adherence assay. The results showed that after co-incubated with rOmpU, an obvious visible green fluorescence could be observed on the EPC cell surface and the nuclei exhibited blue fluorescence; while the control cell surface did not show any signal, only nuclei exhibited blue fluorescence. The average number of wild-type strain adhered to each cell was 32.3 ± 4.5. The average adhesion number of OmpU gene deletion mutant was significantly reduced to 10.8 ± 0.5 (P < 0.01) and restored to 31.3 ± 2.8 by complement strain (P >0.05). Pretreatment of cells with rOmpU reduced the average adhesion number of wild-type strain to 9.7 ± 2.9 (P < 0.01). Likewise, binding was significantly decreased to 8.8 ± 3.2 (P < 0.01) due to blocking role of OmpU antibodies. To determine binding motifs of OmpU, six immunodominant B-cell epitope peptides labeled with FITC were employed in flow cytometry-based binding assay. Two FITC-labeled epitope peptides (aa90-101 and aa173-192) showed strong binding to EPC cells (the fluorescence positive cell rate was 99 ± 0.6% and 98 ± 0.3%, respectively), which could be specifically competed by excess corresponding unlabeled peptides, whereas the remaining four showed a low level of background binding. This is the first demonstration that OmpU possesses adhesion function and its N terminal 90-101 and 173-192 amino acid regions are critical sites for cell surface binding.
Collapse
Affiliation(s)
- Xueqin Liu
- Key Laboratory of Zoonoses, College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Huihui Gao
- Key Laboratory of Zoonoses, College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Nin Xiao
- Key Laboratory of Zoonoses, College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Yan Liu
- Key Laboratory of Zoonoses, College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Jinnian Li
- Key Laboratory of Zoonoses, College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| | - Lin Li
- Key Laboratory of Zoonoses, College of Animal Science and Technology, Anhui Agricultural University, Hefei, P. R. China
| |
Collapse
|
13
|
Design and evaluation of a tandemly arranged outer membrane protein U (OmpU) multi-epitope as a potential vaccine antigen against Vibrio mimicus in grass carps (Ctenopharyngodon idella). Vet Immunol Immunopathol 2014; 160:61-9. [PMID: 24751414 DOI: 10.1016/j.vetimm.2014.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 03/18/2014] [Accepted: 03/27/2014] [Indexed: 01/07/2023]
Abstract
Vibrio mimicus (V. mimicus) is an extracellular pathogen that causes ascites disease in aquatic animals. In our previous studies, the outer membrane protein U (OmpU) of V. mimicus has been proven to be a protective antigen, and several mimotopes of the protein were identified. Here, a tandemly arranged multi-epitope peptide (named 6EPIS) was designed with six mimotopes and heterologously expressed. Then, the immunoprotection efficacy of recombinant 6EPIS (r6EPIS) was evaluated in grass carps (Ctenopharyngodon idella) by determining relative percentage survival (RPS), specific immunoglobulin M (IgM) antibody titer, and transcriptional levels of immune-related genes of inoculated grass carps. Fish vaccinated with r6EPIS via intraperitoneal injection exhibited 85.71% RPS over the control, when challenged with V. mimicus. The enzyme-linked immunosorbent assay titer of specific IgM antibodies against r6EPIS reached 1:12,800 on Day 28 post the primary immunization. After 28 days post immunization, the transcriptional level of total IgM mRNA was significantly higher in the r6EPIS-vaccinated fish than in those vaccinated with recombinant OmpU, inactivated bacterin and rHis tag peptide (p<0.05). In addition, the transcription levels of interleukin-1β and tumor necrosis factor-α genes in the spleen and head kidney of r6EPIS-vaccinated fish were significantly increased during the period of immunization and early phase of infection, while the transcription level of interleukin-10 gene was significantly increased from Day 3 to 7 post challenge, compared to the control level. These results show that r6EPIS was highly immunogenic and could elicit strong protective immune responses. It may be an attractive vaccine candidate against V. mimicus infection.
Collapse
|
14
|
Banerjee R, Das B, Balakrish Nair G, Basak S. Dynamics in genome evolution of Vibrio cholerae. INFECTION GENETICS AND EVOLUTION 2014; 23:32-41. [PMID: 24462909 DOI: 10.1016/j.meegid.2014.01.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 01/09/2014] [Accepted: 01/11/2014] [Indexed: 12/31/2022]
Abstract
Vibrio cholerae, the etiological agent of the acute secretary diarrheal disease cholera, is still a major public health concern in developing countries. In former centuries cholera was a permanent threat even to the highly developed populations of Europe, North America, and the northern part of Asia. Extensive studies on the cholera bug over more than a century have made significant advances in our understanding of the disease and ways of treating patients. V. cholerae has more than 200 serogroups, but only few serogroups have caused disease on a worldwide scale. Until the present, the evolutionary relationship of these pandemic causing serogroups was not clear. In the last decades, we have witnessed a shift involving genetically and phenotypically varied pandemic clones of V. cholerae in Asia and Africa. The exponential knowledge on the genome of several representatives V. cholerae strains has been used to identify and analyze the key determinants for rapid evolution of cholera pathogen. Recent comparative genomic studies have identified the presence of various integrative mobile genetic elements (IMGEs) in V. cholerae genome, which can be used as a marker of differentiation of all seventh pandemic clones with very similar core genome. This review attempts to bring together some of the important researches in recent times that have contributed towards understanding the genetics, epidemiology and evolution of toxigenic V. cholerae strains.
Collapse
Affiliation(s)
- Rachana Banerjee
- Department of Bio-Physics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Bhabatosh Das
- Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, 496, Phase III, Udyog Vihar, Gurgaon 122016, Haryana, India
| | - G Balakrish Nair
- Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, 496, Phase III, Udyog Vihar, Gurgaon 122016, Haryana, India
| | - Surajit Basak
- Department of Molecular Biology & Bioinformatics, Tripura University, Suryamaninagar 799 022, Tripura, India; Bioinformatics Centre, Tripura University, Suryamaninagar 799 022, Tripura, India.
| |
Collapse
|
15
|
Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E, Thompson FL. Microbial genomic taxonomy. BMC Genomics 2013; 14:913. [PMID: 24365132 PMCID: PMC3879651 DOI: 10.1186/1471-2164-14-913] [Citation(s) in RCA: 241] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/18/2013] [Indexed: 01/23/2023] Open
Abstract
A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, <10 in Karlin genomic signature, and > 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups.
Collapse
Affiliation(s)
- Cristiane C Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | | | | | | | | | | |
Collapse
|
16
|
Teng JLL, Ho TCC, Yeung RSY, Wong AYP, Wang H, Chen C, Fung KSC, Lau SKP, Woo PCY. Evaluation of 16SpathDB 2.0, an automated 16S rRNA gene sequence database, using 689 complete bacterial genomes. Diagn Microbiol Infect Dis 2013; 78:105-15. [PMID: 24295571 DOI: 10.1016/j.diagmicrobio.2013.10.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 10/21/2013] [Accepted: 10/27/2013] [Indexed: 02/04/2023]
Abstract
Interpretation of 16S rRNA sequences is a difficult problem faced by clinical microbiologists and technicians. In this study, we evaluated the updated 16SpathDB 2.0 database, using 689 16S rRNA sequences from 689 complete genomes of medically important bacteria. Among these 689 16S rRNA sequences, none was wrongly identified, with 35.8% reported as a single bacterial species having >98% identity with the query sequence (category 1), 63.9% reported as more than 1 bacterial species having >98% identity with the query sequence (category 2), 0.3% reported to the genus level (category 3), and none reported as no match (category 4). For the 16S rRNA sequences of non-duplicated bacterial species reported as category 1 or 2, the percentage of bacterial species reported as category 1 was significantly higher for anaerobic Gram-positive/Gram-negative bacteria than aerobic/facultative anaerobic Gram-positive/Gram-negative bacteria. 16SpathDB 2.0 is a user-friendly and accurate database for 16S rRNA sequence interpretation in clinical laboratories.
Collapse
Affiliation(s)
- Jade L L Teng
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
| | - Tom C C Ho
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ronald S Y Yeung
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; Department of Pathology, United Christian Hospital, Hong Kong, China
| | - Annette Y P Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong, 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
| | - 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
| | - Kitty S C Fung
- Department of Pathology, United Christian Hospital, Hong Kong, China
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China.
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China.
| |
Collapse
|
17
|
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.
Collapse
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:
| |
Collapse
|
18
|
Johnson CN. Fitness factors in vibrios: a mini-review. MICROBIAL ECOLOGY 2013; 65:826-851. [PMID: 23306394 DOI: 10.1007/s00248-012-0168-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 12/13/2012] [Indexed: 06/01/2023]
Abstract
Vibrios are Gram-negative curved bacilli that occur naturally in marine, estuarine, and freshwater systems. Some species include human and animal pathogens, and some vibrios are necessary for natural systems, including the carbon cycle and osmoregulation. Countless in vivo and in vitro studies have examined the interactions between vibrios and their environment, including molecules, cells, whole animals, and abiotic substrates. Many studies have characterized virulence factors, attachment factors, regulatory factors, and antimicrobial resistance factors, and most of these factors impact the organism's fitness regardless of its external environment. This review aims to identify common attributes among factors that increase fitness in various environments, regardless of whether the environment is an oyster, a rabbit, a flask of immortalized mammalian cells, or a planktonic chitin particle. This review aims to summarize findings published thus far to encapsulate some of the basic similarities among the many vibrio fitness factors and how they frame our understanding of vibrio ecology. Factors representing these similarities include hemolysins, capsular polysaccharides, flagella, proteases, attachment factors, type III secretion systems, chitin binding proteins, iron acquisition systems, and colonization factors.
Collapse
Affiliation(s)
- Crystal N Johnson
- Department of Environmental Sciences, Louisiana State University, Baton Rouge, LA, USA.
| |
Collapse
|
19
|
Theethakaew C, Feil EJ, Castillo-Ramírez S, Aanensen DM, Suthienkul O, Neil DM, Davies RL. Genetic relationships of Vibrio parahaemolyticus isolates from clinical, human carrier, and environmental sources in Thailand, determined by multilocus sequence analysis. Appl Environ Microbiol 2013; 79:2358-70. [PMID: 23377932 PMCID: PMC3623249 DOI: 10.1128/aem.03067-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 01/21/2013] [Indexed: 11/20/2022] Open
Abstract
Vibrio parahaemolyticus is a seafood-borne pathogenic bacterium that is a major cause of gastroenteritis worldwide. We investigated the genetic and evolutionary relationships of 101 V. parahaemolyticus isolates originating from clinical, human carrier, and various environmental and seafood production sources in Thailand using multilocus sequence analysis. The isolates were recovered from clinical samples (n = 15), healthy human carriers (n = 18), various types of fresh seafood (n = 18), frozen shrimp (n = 16), fresh-farmed shrimp tissue (n = 18), and shrimp farm water (n = 16). Phylogenetic analysis revealed a high degree of genetic diversity within the V. parahaemolyticus population, although isolates recovered from clinical samples and from farmed shrimp and water samples represented distinct clusters. The tight clustering of the clinical isolates suggests that disease-causing isolates are not a random sample of the environmental reservoir, although the source of infection remains unclear. Extensive serotypic diversity occurred among isolates representing the same sequence types and recovered from the same source at the same time. These findings suggest that the O- and K-antigen-encoding loci are subject to exceptionally high rates of recombination. There was also strong evidence of interspecies horizontal gene transfer and intragenic recombination involving the recA locus in a large proportion of isolates. As the majority of the intragenic recombinational exchanges involving recA occurred among clinical and carrier isolates, it is possible that the human intestinal tract serves as a potential reservoir of donor and recipient strains that is promoting horizontal DNA transfer, driving evolutionary change, and leading to the emergence of new, potentially pathogenic strains.
Collapse
Affiliation(s)
| | - Edward J. Feil
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | | | - David M. Aanensen
- Department of Infectious Disease Epidemiology, Imperial College London, St. Mary's Hospital Campus, London, United Kingdom
| | - Orasa Suthienkul
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Douglas M. Neil
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, United Kingdom
| | | |
Collapse
|
20
|
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.
Collapse
|
21
|
Garza DR, Thompson CC, Loureiro ECB, Dutilh BE, Inada DT, Junior ECS, Cardoso JF, Nunes MRT, de Lima CPS, Silvestre RVD, Nunes KNB, Santos ECO, Edwards RA, Vicente ACP, de Sá Morais LLC. Genome-wide study of the defective sucrose fermenter strain of Vibrio cholerae from the Latin American cholera epidemic. PLoS One 2012; 7:e37283. [PMID: 22662140 PMCID: PMC3360680 DOI: 10.1371/journal.pone.0037283] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 04/17/2012] [Indexed: 12/31/2022] Open
Abstract
The 7th cholera pandemic reached Latin America in 1991, spreading from Peru to virtually all Latin American countries. During the late epidemic period, a strain that failed to ferment sucrose dominated cholera outbreaks in the Northern Brazilian Amazon region. In order to understand the genomic characteristics and the determinants of this altered sucrose fermenting phenotype, the genome of the strain IEC224 was sequenced. This paper reports a broad genomic study of this strain, showing its correlation with the major epidemic lineage. The potentially mobile genomic regions are shown to possess GC content deviation, and harbor the main V. cholera virulence genes. A novel bioinformatic approach was applied in order to identify the putative functions of hypothetical proteins, and was compared with the automatic annotation by RAST. The genome of a large bacteriophage was found to be integrated to the IEC224's alanine aminopeptidase gene. The presence of this phage is shown to be a common characteristic of the El Tor strains from the Latin American epidemic, as well as its putative ancestor from Angola. The defective sucrose fermenting phenotype is shown to be due to a single nucleotide insertion in the V. cholerae sucrose-specific transportation gene. This frame-shift mutation truncated a membrane protein, altering its structural pore-like conformation. Further, the identification of a common bacteriophage reinforces both the monophyletic and African-Origin hypotheses for the main causative agent of the 1991 Latin America cholera epidemics.
Collapse
Affiliation(s)
- Daniel Rios Garza
- Laboratory of Environmental Microbiology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| | - Cristiane C. Thompson
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | | - Bas E. Dutilh
- Centre for Molecular and Biomolecular Informatics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
- Centre for Molecular Life Sciences, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
- Department of Computer Science, San Diego State University, San Diego, California, United States of America
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Davi Toshio Inada
- Center for Technological Innovation, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| | | | | | | | | | | | | | | | - Robert A. Edwards
- Department of Computer Science, San Diego State University, San Diego, California, United States of America
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Ana Carolina P. Vicente
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | |
Collapse
|
22
|
Gardès J, Croce O, Christen R. In silico analyses of primers used to detect the pathogenicity genes of Vibrio cholerae. Microbes Environ 2012; 27:250-6. [PMID: 22673304 PMCID: PMC4036039 DOI: 10.1264/jsme2.me11317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In Vibrio cholerae, the etiological agent of cholera, most of the virulence genes are located in two pathogenicity islands, named TCP (Toxin-Co-regulated Pilus) and CTX (Cholera ToXins). For each V. cholerae pathogenicity gene, we retrieved every primer published since 1990 and every known allele in order to perform a complete in silico survey and assess the quality of the PCR primers used for amplification of these genes. Primers with a melting temperature in the range 55–60°C against any target sequence were considered valid. Our survey clearly revealed that two thirds of the published primers are not able to properly detect every genetic variant of the target genes. Moreover, the quality of primers did not improve with time. Their lifetime, i.e. the number of times they were cited in the literature, is also not a factor allowing the selection of valid primers. We were able to improve some primers or design new primers for the few cases where no valid primer was found. In conclusion, many published primers should be avoided or improved for use in molecular detection tests, in order to improve and perfect specificity and coverage. This study suggests that bioinformatic analyses are important to validate the choice of primers.
Collapse
Affiliation(s)
- Julien Gardès
- Centre de Biochimie, Université de Nice Sophia-Antipolis, Parc Valrose, F 06108 Nice, France.
| | | | | |
Collapse
|
23
|
Nelson OW, Garrity GM. Genome sequences of Bacteria and Archaea published outside of Standards in Genomic Sciences, June – September 2011. Stand Genomic Sci 2011. [DOI: 10.4056/sigs.2324675] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| |
Collapse
|