scholarly journals Hybrid Vibrio cholerae El Tor Lacking SXT Identified as the Cause of a Cholera Outbreak in the Philippines

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
David C. Klinzing ◽  
Seon Young Choi ◽  
Nur A. Hasan ◽  
Ronald R. Matias ◽  
Enrique Tayag ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Variable Number Tandem Repeat ◽  
The Philippines ◽  
Type I ◽  
Cholera Outbreak ◽  
Modification System ◽  
Content Type ◽  
Global Epidemiology ◽  
Geographical Regions ◽  
El Tor

ABSTRACTCholera continues to be a global threat, with high rates of morbidity and mortality. In 2011, a cholera outbreak occurred in Palawan, Philippines, affecting more than 500 people, and 20 individuals died.Vibrio choleraeO1 was confirmed as the etiological agent. Source attribution is critical in cholera outbreaks for proper management of the disease, as well as to control spread. In this study, threeV. choleraeO1 isolates from a Philippines cholera outbreak were sequenced and their genomes analyzed to determine phylogenetic relatedness toV. choleraeO1 isolates from recent outbreaks of cholera elsewhere. The PhilippinesV. choleraeO1 isolates were determined to beV. choleraeO1 hybrid El Tor belonging to the seventh-pandemic clade. They clustered tightly, forming a monophyletic clade closely related toV. choleraeO1 hybrid El Tor from Asia and Africa. The isolates possess a unique multilocus variable-number tandem repeat analysis (MLVA) genotype (12-7-9-18-25 and 12-7-10-14-21) and lack SXT. In addition, they possess a novel 15-kb genomic island (GI-119) containing a predicted type I restriction-modification system. The CTXΦ-RS1 array of the Philippines isolates was similar to that ofV. choleraeO1 MG116926, a hybrid El Tor strain isolated in Bangladesh in 1991. Overall, the data indicate that the PhilippinesV. choleraeO1 isolates are unique, differing from recentV. choleraeO1 isolates from Asia, Africa, and Haiti. Furthermore, the results of this study support the hypothesis that the Philippines isolates ofV. choleraeO1 are indigenous and exist locally in the aquatic ecosystem of the Philippines.IMPORTANCEGenetic characterization and phylogenomics analysis of outbreak strains have proven to be critical for probing clonal relatedness to strains isolated in different geographical regions and over time. Recently, extensive genetic analyses ofV. choleraeO1 strains isolated in different countries have been done. However, genome sequences ofV. choleraeO1 isolates from the Philippines have not been available for epidemiological investigation. In this study, molecular typing and phylogenetic analysis ofVibrio choleraeisolated from both clinical and environmental samples in 2011 confirmed unique genetic features of the Philippines isolates, which are helpful to understand the global epidemiology of cholera.

Molecular characterization of Vibrio cholerae O1 isolates obtained from outbreaks in the Philippines, 2015–2016

2021 ◽  
Vol 70 (11) ◽  
Author(s):  
Mark Philip Bugayong ◽  
Hidemasa Izumiya ◽  
Josie M. Bilar ◽  
Masatomo Morita ◽  
Eiji Arakawa ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Type Species ◽  
Variable Number Tandem Repeat ◽  
The Philippines ◽  
Large Chromosome ◽  
Content Type ◽  
Link Type ◽  
Mlva Type ◽  
El Tor

Introduction. The Philippines, comprising three island groups, namely, Luzon, Visayas and Mindanao, experienced an increase in cholera outbreaks in 2016. Previous studies have shown that Vibrio cholerae isolates obtained from the Philippines are novel hybrid El Tor strains that have evolved in the country and are clearly distinct from those found in Mozambique and Cameroon. Gap statement. The characterization of the strains isolated from outbreaks has been limited to phenotypic characteristics, such as biochemical and serological characteristics, in most previous studies. Aim. We performed multilocus variable-number tandem repeat (VNTR) analysis (MLVA) for V. cholerae isolates obtained from 2015 to 2016 to further characterize and understand the emergence and dissemination of the strains in the Philippines. Methodology. A total of 139 V . cholerae O1 Ogawa biotype El Tor isolates were obtained from the Philippines during diarrhoeal outbreaks in 18 provinces between 2015 and 2016. VNTR data were analysed to classify the MLVA profiles where the large-chromosome types (LCTs) were applied for grouping. Results. We identified 50 MLVA types among 139 isolates originating from 18 provinces, and 14 LCTs. The distribution of the LCTs was variable, and a few were located in specific areas or even in specific provinces. Based on eBURST analysis, 99 isolates with 7 LCTs and 32 MLVA types belonged to 1 group, suggesting that they were related to each other. LCT A was predominant (n=67) and was isolated from Luzon and Visayas. LCT A had 14 MLVA types; however, it mostly emerged during a single quarter of a year. Eight clusters were identified, each of which involved specific MLVA type(s). The largest cluster involved 23 isolates showing 3 MLVA types, 21 of which were MLVA type A-14 isolated from Negros Occidental during quarter 4 of 2016. Comparative analysis showed that almost all isolates from the Philippines were distinct from those in other countries. Conclusions. The genotypic relationship of the V. cholerae isolates obtained during outbreaks in the Philippines was studied, and their emergence and dissemination were elucidated. MLVA revealed the short-term dynamics of V. cholerae genotypes in the Philippines.

scholarly journals Functional Analysis of Bacteriophage Immunity through a Type I-E CRISPR-Cas System in Vibrio cholerae and Its Application in Bacteriophage Genome Engineering

2015 ◽  
Vol 198 (3) ◽  
pp. 578-590 ◽  
Author(s):  
Allison M. Box ◽  
Matthew J. McGuffie ◽  
Brendan J. O'Hara ◽  
Kimberley D. Seed
Keyword(s):  
Vibrio Cholerae ◽  
Genome Engineering ◽  
Region Of Interest ◽  
Lytic Phage ◽  
Genomic Feature ◽  
Type I ◽  
Content Type ◽  
Protospacer Adjacent Motif ◽  
Associated Proteins ◽  
El Tor

ABSTRACTThe classical and El Tor biotypes ofVibrio choleraeserogroup O1, the etiological agent of cholera, are responsible for the sixth and seventh (current) pandemics, respectively. A genomic island (GI), GI-24, previously identified in a classical biotype strain ofV. cholerae, is predicted to encode clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins); however, experimental evidence in support of CRISPR activity inV. choleraehas not been documented. Here, we show that CRISPR-Cas is ubiquitous in strains of the classical biotype but excluded from strains of the El Tor biotype. We also providein silicoevidence to suggest that CRISPR-Cas actively contributes to phage resistance in classical strains. We demonstrate that transfer of GI-24 toV. choleraeEl Tor via natural transformation enables CRISPR-Cas-mediated resistance to bacteriophage CP-T1 under laboratory conditions. To elucidate the sequence requirements of this type I-E CRISPR-Cas system, we engineered a plasmid-based system allowing the directed targeting of a region of interest. Through screening for phage mutants that escape CRISPR-Cas-mediated resistance, we show that CRISPR targets must be accompanied by a 3′ TT protospacer-adjacent motif (PAM) for efficient interference. Finally, we demonstrate that efficient editing ofV. choleraelytic phage genomes can be performed by simultaneously introducing an editing template that allows homologous recombination and escape from CRISPR-Cas targeting.IMPORTANCECholera, caused by the facultative pathogenVibrio cholerae, remains a serious public health threat. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) provide prokaryotes with sequence-specific protection from invading nucleic acids, including bacteriophages. In this work, we show that one genomic feature differentiating sixth pandemic (classical biotype) strains from seventh pandemic (El Tor biotype) strains is the presence of a CRISPR-Cas system in the classical biotype. We demonstrate that the CRISPR-Cas system from a classical biotype strain can be transferred to aV. choleraeEl Tor biotype strain and that it is functional in providing resistance to phage infection. Finally, we show that this CRISPR-Cas system can be used as an efficient tool for the editing ofV. choleraelytic phage genomes.

scholarly journals Characterization of Vibrio cholerae Strains Isolated from the Nigerian Cholera Outbreak in 2010

2016 ◽  
Vol 54 (10) ◽  
pp. 2618-2621 ◽  
Author(s):  
Susann Dupke ◽  
Kehinde A. Akinsinde ◽  
Roland Grunow ◽  
Bamidele A. Iwalokun ◽  
Daniel K. Olukoya ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Accurate Diagnosis ◽  
Watery Diarrhea ◽  
Clinical Samples ◽  
Cholera Outbreak ◽  
Content Type ◽  
Life Saving ◽  
Acute Watery Diarrhea ◽  
El Tor

We examined clinical samples from Nigerian patients with acute watery diarrhea forVibrio choleraeduring the 2010 cholera outbreak. A total of 109 suspected isolates were characterized, but only 57V. choleraestrains could be confirmed using multiplex real-time PCR as well asrpoBsequencing and typed asV. choleraeO:1 Ogawa biotype El Tor. This finding highlighted the need for accurate diagnosis of cholera in epidemic countries to implement life-saving interventions.

The evolution of the pathogen and the clinical and epidemiological features of the recent cholera (el tor)

2012 ◽  
Vol 17 (5) ◽  
pp. 31-35
Author(s):  
V. N. Savelyev ◽  
I. V. Savelyeva ◽  
B. V. Babenyshev ◽  
A. N. Kulichenko
Keyword(s):  
Genetic Structure ◽  
Vibrio Cholerae ◽  
Causative Agent ◽  
Genetically Modified ◽  
Causative Factor ◽  
Prevention Measures ◽  
Cholera Outbreak ◽  
The Caucasus ◽  
Epidemiological Features ◽  
El Tor

In a comparative perspective studied cholera outbreak in the Caucasus due to typical toxigenic and genetically modified (hybrid) El Tor variant strains have been studied. Revealed features of the genetic structure of the genome, factors and ways of transmission of the causative agent of modern cholera El tor should be considered when improving the program of epidemiological supervision in terms of enhancing antiepidemic and prevention measures in cholera, the causative factor of which are of hybrid variants of Vibrio cholerae El tor.

scholarly journals Evaluation of Whole-Genome Sequencing for Identification and Typing of Vibrio cholerae

2018 ◽  
Vol 56 (11) ◽  
Author(s):  
David R. Greig ◽  
Ulf Schaefer ◽  
Sophie Octavia ◽  
Ebony Hunter ◽  
Marie A. Chattaway ◽  
...  
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Vibrio Cholerae ◽  
Species Identification ◽  
Genome Sequencing ◽  
National Level ◽  
Whole Genome ◽  
Content Type ◽  
El Tor ◽  
The Impact

ABSTRACT Epidemiological and microbiological data on Vibrio cholerae strains isolated between April 2004 and March 2018 (n = 836) and held at the Public Health England culture archive were reviewed. The traditional biochemical species identification and serological typing results were compared with the genome-derived species identification and serotype for a subset of isolates (n = 152). Of the 836 isolates, 750 (89.7%) were from a fecal specimen, 206 (24.6%) belonged to serogroup O1, and 7 (0.8%) were serogroup O139; 792 (94.7%) isolates were from patients reporting recent travel abroad, most commonly to India (n = 209) and Pakistan (n = 104). Of the 152 V. cholerae isolates identified by use of kmer, 149 (98.1%) were concordant with those identified using the traditional biochemical approach. Traditional serotyping results were 100% concordant with those of the whole-genome sequencing (WGS) analysis for the identification of serogroups O1 and O139 and classical and El Tor biotypes. ctxA was detected in all isolates of V. cholerae O1 El Tor and O139 belonging to sequence type 69 (ST69) and in V. cholerae O1 classical variants belonging to ST73. A phylogeny of isolates belonging to ST69 from U.K. travelers clustered geographically, with isolates from India and Pakistan located on separate branches. Moving forward, WGS data from U.K. travelers will contribute to global surveillance programs and the monitoring of emerging threats to public health and the global dissemination of pathogenic lineages. At the national level, these WGS data will inform the timely reinforcement of direct public health messaging to travelers and mitigate the impact of imported infections and the associated risks to public health.

scholarly journals The Cpx System Regulates Virulence Gene Expression in Vibrio cholerae

2015 ◽  
Vol 83 (6) ◽  
pp. 2396-2408 ◽  
Author(s):  
Nicole Acosta ◽  
Stefan Pukatzki ◽  
Tracy L. Raivio
Keyword(s):  
Vibrio Cholerae ◽  
Response Regulator ◽  
Bacterial Species ◽  
Virulence Gene ◽  
Receptor Protein ◽  
Virulence Determinants ◽  
Content Type ◽  
Virulence Gene Expression ◽  
Envelope Stress ◽  
El Tor

Bacteria possess signal transduction pathways capable of sensing and responding to a wide variety of signals. The Cpx envelope stress response, composed of the sensor histidine kinase CpxA and the response regulator CpxR, senses and mediates adaptation to insults to the bacterial envelope. The Cpx response has been implicated in the regulation of a number of envelope-localized virulence determinants across bacterial species. Here, we show that activation of the Cpx pathway inVibrio choleraeEl Tor strain C6706 leads to a decrease in expression of the major virulence factors in this organism, cholera toxin (CT) and the toxin-coregulated pilus (TCP). Our results indicate that this occurs through the repression of production of the ToxT regulator and an additional upstream transcription factor, TcpP. The effect of the Cpx response on CT and TCP expression is mostly abrogated in a cyclic AMP receptor protein (CRP) mutant, although expression of thecrpgene is unaltered. Since TcpP production is controlled by CRP, our data suggest a model whereby the Cpx response affects CRP function, which leads to diminished TcpP, ToxT, CT, and TCP production.

scholarly journals A Quinazoline-2,4-Diamino Analog Suppresses Vibrio cholerae Flagellar Motility by Interacting with Motor Protein PomB and Induces Envelope Stress

2013 ◽  
Vol 57 (8) ◽  
pp. 3950-3959 ◽  
Author(s):  
Hongxia Wang ◽  
Li Zhang ◽  
Anisia J. Silva ◽  
Jorge A. Benitez
Keyword(s):  
Cholera Toxin ◽  
Vibrio Cholerae ◽  
Motor Protein ◽  
Polar Flagellum ◽  
Flagellar Motility ◽  
Extracellular Rna ◽  
Content Type ◽  
Envelope Stress ◽  
Causative Agents ◽  
El Tor

ABSTRACTVibrio choleraestrains of serogroups O1 and O139, the causative agents of the diarrheal illness cholera, express a single polar flagellum powered by sodium motive force and require motility to colonize and spread along the small intestine. In a previous study, we described a high-throughput assay for screening for small molecules that selectively inhibit bacterial motility and identified a family of quinazoline-2,4-diamino analogs (Q24DAs) that (i) paralyzed the sodium-driven polar flagellum ofVibriosand (ii) diminished cholera toxin secreted by El Tor biotypeV. cholerae. In this study, we provide evidence that a Q24DA paralyzes the polar flagellum by interacting with the motor protein PomB. Inhibition of motility with the Q24DA enhanced the transcription of the cholera toxin genes in both biotypes. We also show that the Q24DA interacts with outer membrane protein OmpU and other porins to induce envelope stress and expression of the extracellular RNA polymerase sigma factor σE. We suggest that Q24DA-induced envelope stress could affect the correct folding, assembly, and secretion of pentameric cholera toxin in El Tor biotypeV. choleraeindependently of its effect on motility.

scholarly journals The EcoKI Type I Restriction-Modification System in Escherichia coli Affects but Is Not an Absolute Barrier for Conjugation

2014 ◽  
Vol 197 (2) ◽  
pp. 337-342 ◽  
Author(s):  
Louise Roer ◽  
Frank M. Aarestrup ◽  
Henrik Hasman
Keyword(s):  
Escherichia Coli ◽  
Rapid Evolution ◽  
Type I ◽  
Modification System ◽  
Major Barrier ◽  
Exogenous Dna ◽  
Content Type ◽  
Restriction Modification System ◽  
K 12 ◽  
Restriction Modification

The rapid evolution of bacteria is crucial to their survival and is caused by exchange, transfer, and uptake of DNA, among other things. Conjugation is one of the main mechanisms by which bacteria share their DNA, and it is thought to be controlled by varied bacterial immune systems. Contradictory results about restriction-modification systems based on phenotypic studies have been presented as reasons for a barrier to conjugation with and other means of uptake of exogenous DNA. In this study, we show that inactivation of the R.EcoKI restriction enzyme in strainEscherichia coliK-12 strain MG1655 increases the conjugational transfer of plasmid pOLA52, which carriers two EcoKI recognition sites. Interestingly, the results were not absolute, and uptake of unmethylated pOLA52 was still observed in the wild-type strain (with an intacthsdRgene) but at a reduction of 85% compared to the uptake of the mutant recipient with a disruptedhsdRgene. This leads to the conclusion that EcoKI restriction-modification affects the uptake of DNA by conjugation but is not a major barrier to plasmid transfer.

scholarly journals Genomic Epidemiology of the Haitian Cholera Outbreak: a Single Introduction Followed by Rapid, Extensive, and Continued Spread Characterized the Onset of the Epidemic

mBio ◽  
2014 ◽  
Vol 5 (6) ◽  
Author(s):  
Mark Eppinger ◽  
Talima Pearson ◽  
Sara S. K. Koenig ◽  
Ofori Pearson ◽  
Nathan Hicks ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Molecular Evidence ◽  
Whole Genome ◽  
Cholera Outbreak ◽  
Content Type ◽  
Genomic Epidemiology ◽  
Southern Asia ◽  
Strain Collection

ABSTRACT For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more than a century. By using whole-genome sequence typing and mapping strategies of 116 serotype O1 strains from global sources, including 44 Haitian genomes, we present a detailed reconstructed evolutionary history of the seventh pandemic with a focus on the Haitian outbreak. We catalogued subtle genomic alterations at the nucleotide level in the genome core and architectural rearrangements from whole-genome map comparisons. Isolates closely related to the Haitian isolates caused several recent outbreaks in southern Asia. This study provides evidence for a single-source introduction of cholera from Nepal into Haiti followed by rapid, extensive, and continued clonal expansion. The phylogeographic patterns in both southern Asia and Haiti argue for the rapid dissemination of V. cholerae across the landscape necessitating real-time surveillance efforts to complement the whole-genome epidemiological analysis. As eradication efforts move forward, phylogeographic knowledge will be important for identifying persistent sources and monitoring success at regional levels. The results of molecular and epidemiological analyses of this outbreak suggest that an indigenous Haitian source of V. cholerae is unlikely and that an indigenous source has not contributed to the genomic evolution of this clade. IMPORTANCE In this genomic epidemiology study, we have applied high-resolution whole-genome-based sequence typing methodologies on a comprehensive set of genome sequences that have become available in the aftermath of the Haitian cholera epidemic. These sequence resources enabled us to reassess the degree of genomic heterogeneity within the Vibrio cholerae O1 serotype and to refine boundaries and evolutionary relationships. The established phylogenomic framework showed how outbreak isolates fit into the global phylogeographic patterns compared to a comprehensive globally and temporally diverse strain collection and provides strong molecular evidence that points to a nonindigenous source of the 2010 Haitian cholera outbreak and refines epidemiological standards used in outbreak investigations for outbreak inclusion/exclusion following the concept of genomic epidemiology. The generated phylogenomic data have major public health relevance in translating sequence-based information to assist in future diagnostic, epidemiological, surveillance, and forensic studies of cholera.

scholarly journals Haitian-like genetic traits with creeping MIC of Azithromycin in Vibrio cholerae O1 isolates from Puducherry, India

2020 ◽  
Vol 69 (3) ◽  
pp. 372-378
Author(s):  
Regina Sumitha Mohanraj ◽  
Prosenjit Samanta ◽  
Asish K. Mukhopadhyay ◽  
Jharna Mandal
Keyword(s):  
Vibrio Cholerae ◽  
Postgraduate Medical Education ◽  
Tetracycline Resistance ◽  
Progressive Increase ◽  
Test Method ◽  
Genetic Traits ◽  
Content Type ◽  
Antimicrobial Resistance Genes ◽  
Jawaharlal Institute ◽  
El Tor

Introduction. The emergence of novel strains of Vibrio cholerae O1 El Tor biotype has gained attention due to causing several epidemics around the world. Variant strains have evolved as a result of the acquisition of genes that confer extended virulence and pathogenicity. Aim. This study aimed to determine the presence of the most recently emerging Haitian-like genetic traits among the isolates from Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, Southern India. We also wanted to detect the prevalence of the sulfamethoxazole and trimethoprim (SXT) element, which is an integrating conjugative element (ICE) and the antimicrobial resistance genes present in our isolates. Methodology. Identification of Haitian-specific alleles was done by mismatched amplification mutation assay PCR (MAMA-PCR). The presence of SXT elements was carried out by PCR by detecting int, eex, att-prfC and setR genes. Detection of antibiotic resistance determinant, sul(1,2,3); dfr(A1,18,5) for trimethoprim resistance, tet(A,B,C,D,E,Y,G,M), tet34 for tetracycline resistance and erm(A,B,C), mph(A,B), ere(A,B), msr(A,D) for azithromycin resistance were targeted by PCR. The MIC of tetracycline, ciprofloxacin and azithromycin was determined by the E-test method. Results. Of the 95 isolates, 60 % of the isolates were found to carry Haitian-specific alleles of ctxB, tcpA and rtxA gene, 100 % of the isolates were found to carry SXT elements. All the isolates harboured the four conserved genes of the SXT element, except one which had only eex, att-prfC, setR genes. About 99 % harboured sul2 and dfrA1 genes. No tet and macrolide genes were detected. We observed a progressive increase in the MIC of azithromycin ranging from 0.75 µg ml−1 to 2 µg ml−1. Conclusion. None of the isolates were the prototype El Tor biotype. All the isolates were a Haitian variant. The presence of SXT elements across all our isolates and their creeping MIC of azithromycin is a matter of concern. Further testing for other genetic determinants of resistance will be carried out in our future studies.

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