scholarly journals VCGIDB: A Database and Web Resource for the Genomic Islands from Vibrio cholerae

Pathogens ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 261
Author(s):  
YoungJae Hur ◽  
Mauricio Chalita ◽  
Sung-min Ha ◽  
Inwoo Baek ◽  
Jongsik Chun
Keyword(s):  
Vibrio Cholerae ◽  
Genomic Island ◽  
Diarrheal Disease ◽  
Prediction Method ◽  
Genomic Islands ◽  
Large Genome ◽  
Web Resource ◽  
Comprehensive Information ◽  
The World ◽  
Life Threatening

Vibrio cholerae is the causative agent of cholera, which is a severe, life-threatening diarrheal disease. The current seventh pandemic has not been eradicated and the outbreak is still ongoing around the world. The evolution of the pandemic-causing strain has been greatly influenced by lateral gene transfer, and the mechanisms of acquisition of pathogenicity in V. cholerae are mainly involved with genomic islands (GIs). Thus, detecting GIs and their comprehensive information is necessary to understand the continuing resurgence and newly emerging pathogenic V. cholerae strains. In this study, 798 V. cholerae strains were tested using the GI-Scanner algorithm, which was developed to detect candidate GIs and identify them in a comparative genomics approach. The algorithm predicted 435 highly possible genomic islands, and we built a database, called Vibrio cholerae Genomic Island Database (VCGIDB). This database shows advanced results that were acquired from a large genome set using phylogeny-based predictions. Moreover, VCGIDB is a highly expendable database that does not require intensive computation, which enables us to update it with a greater number of genomes using a novel genomic island prediction method. The VCGIDB website allows the user to browse the data and presents the results in a visual manner.

scholarly journals The Sodium-Driven Flagellar Motor Controls Exopolysaccharide Expression in Vibrio cholerae

2004 ◽  
Vol 186 (15) ◽  
pp. 4864-4874 ◽  
Author(s):  
Crystal M. Lauriano ◽  
Chandradipa Ghosh ◽  
Nidia E. Correa ◽  
Karl E. Klose
Keyword(s):  
Vibrio Cholerae ◽  
Gene Transcription ◽  
Biofilm Formation ◽  
Diarrheal Disease ◽  
Response Regulator ◽  
Gene Clusters ◽  
Signaling Cascade ◽  
Genes Encoding ◽  
Life Threatening

ABSTRACT Vibrio cholerae causes the life-threatening diarrheal disease cholera. This organism persists in aquatic environments in areas of endemicity, and it is believed that the ability of the bacteria to form biofilms in the environment contributes to their persistence. Expression of an exopolysaccharide (EPS), encoded by two vps gene clusters, is essential for biofilm formation and causes a rugose colonial phenotype. We previously reported that the lack of a flagellum induces V. cholerae EPS expression. To uncover the signaling pathway that links the lack of a flagellum to EPS expression, we introduced into a rugose flaA strain second-site mutations that would cause reversion back to the smooth phenotype. Interestingly, mutation of the genes encoding the sodium-driven motor (mot) in a nonflagellated strain reduces EPS expression, biofilm formation, and vps gene transcription, as does the addition of phenamil, which specifically inhibits the sodium-driven motor. Mutation of vpsR, which encodes a response regulator, also reduces EPS expression, biofilm formation, and vps gene transcription in nonflagellated cells. Complementation of a vpsR strain with a constitutive vpsR allele likely to mimic the phosphorylated state (D59E) restores EPS expression and biofilm formation, while complementation with an allele predicted to remain unphosphorylated (D59A) does not. Our results demonstrate the involvement of the sodium-driven motor and suggest the involvement of phospho-VpsR in the signaling cascade that induces EPS expression. A nonflagellated strain expressing EPS is defective for intestinal colonization in the suckling mouse model of cholera and expresses reduced amounts of cholera toxin and toxin-coregulated pili in vitro. Wild-type levels of virulence factor expression and colonization could be restored by a second mutation within the vps gene cluster that eliminated EPS biosynthesis. These results demonstrate a complex relationship between the flagellum-dependent EPS signaling cascade and virulence.

scholarly journals Characterization of the Immune Response to Vibrio cholerae Infection in a Natural Host Model

2021 ◽  
Vol 11 ◽  
Author(s):  
Dustin A. Farr ◽  
Dhrubajyoti Nag ◽  
Jeffrey H. Withey
Keyword(s):  
Immune Response ◽  
Vibrio Cholerae ◽  
Diarrheal Disease ◽  
Natural Host ◽  
Zebrafish Model ◽  
Mucin Production ◽  
Immunological Markers ◽  
Contaminated Food ◽  
Life Threatening ◽  
El Tor

The gram-negative bacterium Vibrio cholerae causes the life-threatening diarrheal disease cholera, which is spread through the ingestion of contaminated food or water. Cholera epidemics occur largely in developing countries that lack proper infrastructure to treat sewage and provide clean water. Numerous vertebrate fish species have been found to be natural V. cholerae hosts. Based on these findings, zebrafish (Danio rerio) have been developed as a natural host model for V. cholerae. Diarrheal symptoms similar to those seen in humans are seen in zebrafish as early as 6 hours after exposure. Our understanding of basic zebrafish immunology is currently rudimentary, and no research has been done to date exploring the immune response of zebrafish to V. cholerae infection. In the present study, zebrafish were infected with either pandemic El Tor or non-pandemic, environmental V. cholerae strains and select immunological markers were assessed to determine cellular immunity and humoral immunity. Significant increases in the gene expression of two transcription factors, T-bet and GATA3, were observed in response to infection with both V. cholerae strains, as were levels of mucosal related antibodies. Additionally, the cytokine IL-13 was shown to be significantly elevated and paralleled the mucin output in zebrafish excretions, strengthening our knowledge of IL-13 induced mucin production in cholera. The data presented here further solidify the relevancy of the zebrafish model in studying V. cholerae, as well as expanding its utility in the field of cholera immunology.

scholarly journals Mr.Vc: a database of microarray and RNA-seq of Vibrio cholerae

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Zhiyuan Zhang ◽  
Guozhong Chen ◽  
Jun Hu ◽  
Wajid Hussain ◽  
Fenxia Fan ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Diarrheal Disease ◽  
Gene Annotation ◽  
Relevant Information ◽  
Differentially Expressed ◽  
Data Repository ◽  
Rna Seq ◽  
Experimental Conditions ◽  
Life Threatening ◽  
Infectious Cycle

AbstractGram-negative bacterium Vibrio cholerae is the causative agent of cholera, a life-threatening diarrheal disease. During its infectious cycle, V. cholerae routinely switches niches between aquatic environment and host gastrointestinal tract, in which V. cholerae modulates its transcriptome pattern accordingly for better survival and proliferation. A comprehensive resource for V. cholerae transcriptome will be helpful for cholera research, including prevention, diagnosis and intervention strategies. In this study, we constructed a microarray and RNA-seq database of V. cholerae (Mr.Vc), containing gene transcriptional expression data of 145 experimental conditions of V. cholerae from various sources, covering 25 937 entries of differentially expressed genes. In addition, we collected relevant information including gene annotation, operons they may belong to and possible interaction partners of their protein products. With Mr.Vc, users can easily find transcriptome data they are interested in, such as the experimental conditions in which a gene of interest was differentially expressed in, or all genes that were differentially expressed in an experimental condition. We believe that Mr.Vc database is a comprehensive data repository dedicated to V. cholerae and could be a useful resource for all researchers in related fields. Mr.Vc is available for free at http://bioinfo.life.hust.edu.cn/mrvc.

scholarly journals Genomic characterization of the non-O1/non-O139 Vibrio cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018

2019 ◽  
Author(s):  
Mónica Arteaga ◽  
Juliana Velasco ◽  
Shelly Rodriguez ◽  
Maricel Vidal ◽  
Carolina Arellano ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Diarrheal Disease ◽  
Sequence Data ◽  
Genomic Islands ◽  
Cholerae Strain ◽  
Supplementary Data ◽  
Gastroenteritis Outbreak ◽  
Secretion Systems ◽  
Pathogenic Potential ◽  
Data Files

AbstractVibrio cholerae is a human pathogen, which is transmitted by the consumption of contaminated food or water. V. cholerae strains belonging to the serogroups O1 and O139 can cause cholera outbreaks and epidemics, a severe life-threatening diarrheal disease. In contrast, serogroups other than O1 and O139, denominated as non-O1/non-O139, have been mainly associated with sporadic cases of moderate or mild diarrhea, bacteremia and wound infections. Here we investigated the virulence determinants and phylogenetic origin of a non-O1/non-O139 V. cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018. We found that this outbreak strain lacks the classical virulence genes harboured by O1 and O139 strains, including the cholera toxin (CT) and the toxin-coregulated pilus (TCP). However, this strain carries genomic islands (GIs) encoding Type III and Type VI secretion systems (T3SS/T6SS) and antibiotic resistance genes. Moreover, we found these GIs are wide distributed among several lineages of non-O1/non-O139 strains. Our results suggest that the acquisition of these GIs may enhance the virulence of non-O1/non-O139 strains that lack the CT and TCP-encoding genes. Our results highlight the pathogenic potential of these V. cholerae strains.DATA SUMMARYSequence data were submitted to GenBank under the accession number SRLP00000000. The authors confirm that all supporting data and protocols have been provided within the article or through supplementary data files.Data statementAll supporting data, code and protocols have been provided within the article or through supplementary data files. Four supplementary tables are available with the online version of this article.

scholarly journals A Combination of Metagenomic and Cultivation Approaches Reveals Hypermutator Phenotypes within Vibrio cholerae-Infected Patients

mSystems ◽  
2021 ◽  
Author(s):  
Inès Levade ◽  
Ashraful I. Khan ◽  
Fahima Chowdhury ◽  
Stephen B. Calderwood ◽  
Edward T. Ryan ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Whole Genome Sequencing ◽  
Vibrio Cholerae ◽  
Genome Sequencing ◽  
Diarrheal Disease ◽  
Asymptomatic Infection ◽  
Whole Genome ◽  
Metagenomic Sequencing ◽  
Content Type ◽  
Life Threatening

Pathogen evolution within patients can impact phenotypes such as drug resistance and virulence, potentially affecting clinical outcomes. V. cholerae infection can result in life-threatening diarrheal disease or asymptomatic infection. Here, we describe whole-genome sequencing of V. cholerae isolates and culture-free metagenomic sequencing from stool of symptomatic cholera patients and asymptomatic carriers.

scholarly journals IncA/C Conjugative Plasmids Mobilize a New Family of Multidrug Resistance Islands in Clinical Vibrio cholerae Non-O1/Non-O139 Isolates from Haiti

mBio ◽  
2016 ◽  
Vol 7 (4) ◽  
Author(s):  
Nicolas Carraro ◽  
Nicolas Rivard ◽  
Daniela Ceccarelli ◽  
Rita R. Colwell ◽  
Vincent Burrus
Keyword(s):  
Multidrug Resistance ◽  
Vibrio Cholerae ◽  
Resistance Genes ◽  
Genomic Island ◽  
Genomic Islands ◽  
Dependent Manner ◽  
Pathogenic Species ◽  
Conjugative Plasmids ◽  
New Family ◽  
Multidrug Resistance Genes

ABSTRACT Mobile genetic elements play a pivotal role in the adaptation of bacterial populations, allowing them to rapidly cope with hostile conditions, including the presence of antimicrobial compounds. IncA/C conjugative plasmids (ACPs) are efficient vehicles for dissemination of multidrug resistance genes in a broad range of pathogenic species of Enterobacteriaceae . ACPs have sporadically been reported in Vibrio cholerae , the infectious agent of the diarrheal disease cholera. The regulatory network that controls ACP mobility ultimately depends on the transcriptional activation of multiple ACP-borne operons by the master activator AcaCD. Beyond ACP conjugation, AcaCD has also recently been shown to activate the expression of genes located in the Salmonella genomic island 1 (SGI1). Here, we describe MGI Vch Hai6, a novel and unrelated mobilizable genomic island (MGI) integrated into the 3′ end of trmE in chromosome I of V. cholerae HC-36A1, a non-O1/non-O139 multidrug-resistant clinical isolate recovered from Haiti in 2010. MGI Vch Hai6 contains a mercury resistance transposon and an integron In104-like multidrug resistance element similar to the one of SGI1. We show that MGI Vch Hai6 excises from the chromosome in an AcaCD-dependent manner and is mobilized by ACPs. Acquisition of MGI Vch Hai6 confers resistance to β-lactams, sulfamethoxazole, tetracycline, chloramphenicol, trimethoprim, and streptomycin/spectinomycin. In silico analyses revealed that MGI Vch Hai6-like elements are carried by several environmental and clinical V. cholerae strains recovered from the Indian subcontinent, as well as from North and South America, including all non-O1/non-O139 clinical isolates from Haiti. IMPORTANCE Vibrio cholerae , the causative agent of cholera, remains a global public health threat. Seventh-pandemic V. cholerae acquired multidrug resistance genes primarily through circulation of SXT/R391 integrative and conjugative elements. IncA/C conjugative plasmids have sporadically been reported to mediate antimicrobial resistance in environmental and clinical V. cholerae isolates. Our results showed that while IncA/C plasmids are rare in V. cholerae populations, they play an important yet insidious role by specifically propagating a new family of genomic islands conferring resistance to multiple antibiotics. These results suggest that nonepidemic V. cholerae non-O1/non-O139 strains bearing these genomic islands constitute a reservoir of transmissible resistance genes that can be propagated by IncA/C plasmids to V. cholerae populations in epidemic geographical areas as well to pathogenic species of Enterobacteriaceae . We recommend future epidemiological surveys take into account the circulation of these genomic islands.

scholarly journals Role of Zooplankton Diversity in Vibrio cholerae Population Dynamics and in the Incidence of Cholera in the Bangladesh Sundarbans

2011 ◽  
Vol 77 (17) ◽  
pp. 6125-6132 ◽  
Author(s):  
Guillaume Constantin de Magny ◽  
Pronob K. Mozumder ◽  
Christopher J. Grim ◽  
Nur A. Hasan ◽  
M. Niamul Naser ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Vibrio Cholerae ◽  
Diarrheal Disease ◽  
Ecological Factors ◽  
Crustacean Zooplankton ◽  
Content Type ◽  
Life Threatening ◽  
Bodies Of Water ◽  
Zooplankton Communities

ABSTRACTVibrio cholerae, a bacterium autochthonous to the aquatic environment, is the causative agent of cholera, a severe watery, life-threatening diarrheal disease occurring predominantly in developing countries.V. cholerae, including both serogroups O1 and O139, is found in association with crustacean zooplankton, mainly copepods, and notably in ponds, rivers, and estuarine systems globally. The incidence of cholera and occurrence of pathogenicV. choleraestrains with zooplankton were studied in two areas of Bangladesh: Bakerganj and Mathbaria. Chitinous zooplankton communities of several bodies of water were analyzed in order to understand the interaction of the zooplankton population composition with the population dynamics of pathogenicV. choleraeand incidence of cholera. Two dominant zooplankton groups were found to be consistently associated with detection ofV. choleraeand/or occurrence of cholera cases, namely, rotifers and cladocerans, in addition to copepods. Local differences indicate there are subtle ecological factors that can influence interactions betweenV. cholerae, its plankton hosts, and the incidence of cholera.

scholarly journals A Review on Diagnostic Methods for the Identification of Vibrio cholerae

2020 ◽  
pp. 136-164
Author(s):  
Tarh, Jacqueline Ebob
Keyword(s):  
Vibrio Cholerae ◽  
Diarrheal Disease ◽  
Variable Number Tandem Repeat ◽  
Simultaneous Detection ◽  
Diagnostic Methods ◽  
Cholerae Strain ◽  
Low Resource Settings ◽  
Remote Areas ◽  
Low Resource ◽  
Life Threatening

The severe diarrheal disease Cholera, has gained public health importance because of its life-threatening effect. The detection of the causative agent of this disease (Vibrio cholerae (V.  Cholerae) O1 or O139) from a specimen (stool, vomitus of food sample) remains a major concern in the world today. Phenotypic finger printing (the conventional methods) of the toxigenic V. cholerae strain, remains the gold standard for the laboratory diagnosis of cholera; especially during cholera epidemic outbreaks. Detection around the remote areas which are usually rampaged by these outbreaks is usually difficult due to lack of required diagnostic facilities in small laboratories. However, the use of phenotypic approaches have some major setbacks as they are usually labor-intensive and time consuming. This delays treatment commencement especially in life threatening cases.To alleviate these setbacks, rapid molecular typing techniques involving the Polymerase chain reaction (PCR) amplification, hybridization methods, Pulsed Field Gel Electrophoresis (PFGE), Multilocus Sequence Typing (MLST), Multiple-Locus Variable Number Tandem Repeat Analysis (MVLA), Fluorescent Amplified Fragment Length Polymorphism (FAFLP),  Whole Genome Sequencing (WGS) etc. represent promising tools for early detection of the pathogen V. cholerae O1/O139 even in remote areas where laboratory resources are poor. Immunoassay-based techniques like enzyme-linked immune-sorbent assay (ELISA), coagglutination, immunofluorescence, and quartz crystal microbalance (QCM), are capital/labour intensive and expensive for low resource settings. Rapid diagnostic tests based on immune-chromatography principle have also been developed for simultaneous detection of V. choleraesero groups O1 and O139. These test kits are easy to use, transport, and fast. All these methods enable the subtyping of unrelated bacterial strains and they all operate with different accuracies, discriminatory ability, and reproducibility. This review sought to address some of the methods used in diagnosing the disease cholera, with the objective of identifying the best and easiest of the methods that can help to curb the cholera problem (deaths) often encountered, especially in low resource settings in the developing countries (Nigeria inclusive).

scholarly journals Dominant Vibrio cholerae phage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite

2019 ◽  
Author(s):  
Stephanie G. Hays ◽  
Kimberley D. Seed
Keyword(s):  
Vibrio Cholerae ◽  
Diarrheal Disease ◽  
Single Cells ◽  
Bacterial Genome ◽  
Genomic Islands ◽  
Phage Infection ◽  
Etiological Agent ◽  
Clinical Samples ◽  
Host Bacterium ◽  
Lysis Inhibition

AbstractBacteriophages and their bacterial hosts are locked in a dynamic evolutionary arms race. Phage satellites, selfish genomic islands which exploit both host bacterium and target phage, further complicate the evolutionary fray. One such tripartite system involves the etiological agent of the diarrheal disease cholera – Vibrio cholerae, the predominant phage isolated from cholera patients – ICP1, and a phage satellite – PLE. When ICP1 infects V. cholerae harboring the integrated PLE genome, PLE accelerates host lysis, spreading the PLE while completely blocking phage production protecting V. cholerae at the population level. Here we identify a single PLE gene, lidI, sufficient to mediate accelerated lysis during ICP1 infection and demonstrate that LidI functions through disrupting lysis inhibition – an understudied outcome of phage infection when phages vastly outnumber their hosts. This work identifies ICP1-encoded holin and antiholin genes teaA and arrA respectively, that mediate this first example of lysis inhibition outside the T-even coliphages. Through lysis inhibition disruption, LidI is sufficient to limit the number of progeny phage produced from an infection. Consequently, this disruption bottlenecks ICP1 evolution as probed by recombination and CRISPR-Cas targeting assays. These studies link novel characterization of the classic phenomenon of lysis inhibition with a conserved protein in a dominant phage satellite, highlighting the importance of lysis timing during infection and parasitization, as well as providing insight into the populations, relationships, and evolution of bacteria, phages, and phage satellites in nature.ImportanceWith increasing awareness of microbiota impacting human health comes intensified examination of, not only bacteria and the bacteriophages that prey upon them, but also the mobile genetic elements (MGEs) that mediate interactions between them. Research is unveiling evolutionary strategies dependent on sensing the milieu: quorum sensing impacts phage infection, phage teamwork overcomes bacterial defenses, and abortive infections sacrifice single cells protecting populations. Yet, the first discovered environmental sensing by phages, known as lysis inhibition (LIN), has only been studied in the limited context of T-even coliphages. Here we characterize LIN in the etiological agent of the diarrheal disease cholera, Vibrio cholerae, infected by a phage ubiquitous in clinical samples. Further, we show that a specific MGE, the phage satellite PLE, collapses LIN with a conserved protein during its anti-phage program. The insights gleaned from this work add to our expanding understanding of microbial fitness in natural contexts beyond the canonical bacterial genome and into the realm of antagonistic evolution driven by phages and satellites.

Designing an Outer Membrane Protein (Omp-W) Based Vaccine for Immunization against Vibrio and Salmonella: An in silico Approach

2020 ◽  
Vol 14 (4) ◽  
pp. 312-324
Author(s):  
Sadra S. Tehrani ◽  
Abolfazl Jahangiri ◽  
Mortaza Taheri-Anganeh ◽  
Hossein Maghsoudi ◽  
Saeed Khalili ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Vibrio Cholerae ◽  
Gram Negative Bacteria ◽  
B Cell Epitopes ◽  
E Coli ◽  
Beta Barrel ◽  
The World ◽  
Cd4 Cell ◽  
Stimulating Factor ◽  
Topology Prediction

Background: Cholera triggered by Vibrio cholerae remains the main reason for morbidity and mortality all over the world. In addition, salmonellosis is regarded as an infectious disease that makes it essential for the identification and detection of Salmonella. With a beta-barrel structure consisting of eight non-parallel beta strands, OmpW family is widely distributed among gram-negative bacteria. Moreover, OmpW isolated from S. typhimurium and Vibrio cholerae can be used in vaccine design. Methods: Topology prediction was determined. T-cell and B-cell epitopes were selected from exposed areas, and sequence conservancy was evaluated. The remaining loops and inaccessible residues were removed to prepare OmpW-1. High antigenicity peptides were detected to replace inappropriate residues to obtain OmpW-2. Physicochemical properties were assessed, and antigenicity, hydrophobicity, flexibility, and accessibility were compared to the native Omp-W structure. Low score areas were removed from the designed structure for preparing the OmpW-3. To construct OmpW-4, TTFrC was used as T-CD4+ cell-stimulating factor and CTB as adjuvant to the end of the C-terminal of this sequence, which can increase the antigenicity and sequence density. The sequences were re-analyzed to delete the unfavorable residues. Besides, the solubility of the mature OmpW and the designed structure were predicted while overexpressed in E. coli. Results: The designed vaccine is a stable protein which has immune cells recognizing epitopes and is considered as an antigen. The construct can be overexpressed in a E. coli. Conclusion: The multi-epitope vaccine is a suitable stimulator for immune system and would be a candidate for experimental research. Recent patents describing numerous inventions related to the clinical facets of vaccine peptide against human infectious disease.

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