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

ABSTRACTWe report the detection of PER-1 extended-spectrum β-lactamase (ESBL) in a clinical non-O1, non-O139Vibrio choleraestrain from China. ISCR1-mediatedblaPER-1was embedded in a complex In4family class 1 integron belonging to the lineage of Tn1696on a conjugative IncA/C plasmid. A free 8.98-kb circular molecule present with the ISCR1-blaPER-1–truncated 3′-conserved sequence (CS) structure was detected in this isolate. These findings may provide insight into the mobilization ofblaPER-1.

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Comparative Genomic Characterization of a Thailand–Myanmar Isolate, MS6, of Vibrio cholerae O1 El Tor, Which Is Phylogenetically Related to a “US Gulf Coast” Clone

PLoS ONE ◽

10.1371/journal.pone.0098120 ◽

2014 ◽

Vol 9 (6) ◽

pp. e98120 ◽

Cited By ~ 12

Author(s):

Kazuhisa Okada ◽

Mathukorn Na-Ubol ◽

Wirongrong Natakuathung ◽

Amonrattana Roobthaisong ◽

Fumito Maruyama ◽

...

Keyword(s):

Vibrio Cholerae ◽

Gulf Coast ◽

Comparative Genomic ◽

Genomic Characterization ◽

Vibrio Cholerae O1 ◽

El Tor

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Genomic characterization of antibiotic resistance‐encoding genes in clinical isolates of Vibrio cholerae non‐O1/non‐O139 strains from Kolkata, India: generation of novel types of genomic islands containing plural antibiotic resistance genes

Microbiology and Immunology ◽

10.1111/1348-0421.12790 ◽

2020 ◽

Vol 64 (6) ◽

pp. 435-444 ◽

Cited By ~ 2

Author(s):

Daichi Morita ◽

Eizo Takahashi ◽

Masatomo Morita ◽

Makoto Ohnishi ◽

Tamaki Mizuno ◽

...

Keyword(s):

Antibiotic Resistance ◽

Vibrio Cholerae ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Genomic Islands ◽

Clinical Isolates ◽

Genomic Characterization ◽

Encoding Genes

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Characterization of a novel protective antigen of cell-surface origin in a toxigenic non-O1 Vibrio cholerae strain

Vaccine ◽

10.1016/0264-410x(92)90254-h ◽

1992 ◽

Vol 10 (4) ◽

pp. 286

Author(s):

Tapas K. Sengupta ◽

Asoke C. Ghose

Keyword(s):

Cell Surface ◽

Vibrio Cholerae ◽

Protective Antigen ◽

Cholerae Strain

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Genome Dynamics of Vibrio cholerae Isolates Linked to Seasonal Outbreaks of Cholera in Dhaka, Bangladesh

mBio ◽

10.1128/mbio.03339-19 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 3

Author(s):

Ramani Baddam ◽

Nishat Sarker ◽

Dilruba Ahmed ◽

Razib Mazumder ◽

Ahmed Abdullah ◽

...

Keyword(s):

Vibrio Cholerae ◽

Clonal Expansion ◽

Multidrug Resistant ◽

Whole Genome ◽

Content Type ◽

Selective Forces ◽

Genomic Characterization ◽

Resistant Strains ◽

Genomic Data Analysis

ABSTRACT The temporal switching of serotypes from serotype Ogawa to Inaba and back to Ogawa was identified in Vibrio cholerae O1, which was responsible for seasonal outbreaks of cholera in Dhaka during the period 2015 to 2018. In order to delineate the factors responsible for this serotype transition, we performed whole-genome sequencing (WGS) of V. cholerae O1 multidrug-resistant strains belonging to both the serotypes that were isolated during this interval where the emergence and subsequent reduction of the Inaba serotype occurred. The whole-genome-based phylogenetic analysis revealed clonal expansion of the Inaba isolates mainly responsible for the peaks of infection during 2016 to 2017 and that they might have evolved from the prevailing Ogawa strains in 2015 which coclustered with them. Furthermore, the wbeT gene in these Inaba serotype isolates was inactivated due to insertion of a transposable element at the same position signifying the clonal expansion. Also, V. cholerae isolates in the Inaba serotype dominant clade mainly contained classical ctxB allele and revealed differences in the genetic composition of Vibrio seventh pandemic island II (VSP-II) and the SXT integrative and conjugative element (SXT-ICE) compared to those of Ogawa serotype strains which remerged in 2018. The variable presence of phage-inducible chromosomal island-like element 1 (PLE1) was also noted in the isolates of the Inaba serotype dominant clade. The detailed genomic characterization of the sequenced isolates has shed light on the forces which could be responsible for the periodic changes in serotypes of V. cholerae and has also highlighted the need to analyze the mobilome in greater detail to obtain insights into the mechanisms behind serotype switching. IMPORTANCE The switching of serotype from Ogawa to Inaba and back to Ogawa has been observed temporally in Vibrio cholerae O1, which is responsible for endemic cholera in Bangladesh. The serospecificity is key for effective intervention and for preventing cholera, a deadly disease that continues to cause significant morbidity and mortality worldwide. In the present study, WGS of V. cholerae allowed us to better understand the factors associated with the serotype switching events observed during 2015 to 2018. Genomic data analysis of strains isolated during this interval highlighted variations in the genes ctxB, tcpA, and rtxA and also identified significant differences in the genetic content of the mobilome, which included key elements such as SXT ICE, VSP-II, and PLE. Our results indicate that selective forces such as antibiotic resistance and phage resistance might contribute to the clonal expansion and predominance of a particular V. cholerae serotype responsible for an outbreak.

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

10.1101/835090 ◽

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.

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Genomic characterization of non-O1, non-O139 Vibrio cholerae reveals genes for a type III secretion system

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0409918102 ◽

2005 ◽

Vol 102 (9) ◽

pp. 3465-3470 ◽

Cited By ~ 144

Author(s):

M. Dziejman ◽

D. Serruto ◽

V. C. Tam ◽

D. Sturtevant ◽

P. Diraphat ◽

...

Keyword(s):

Vibrio Cholerae ◽

Type Iii Secretion ◽

Type Iii Secretion System ◽

Secretion System ◽

Type Iii ◽

Genomic Characterization

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Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome

International Journal of Genomics ◽

10.1155/2017/8724304 ◽

2017 ◽

Vol 2017 ◽

pp. 1-14 ◽

Cited By ~ 7

Author(s):

Gary Xie ◽

Shannon L. Johnson ◽

Karen W. Davenport ◽

Mathumathi Rajavel ◽

Torsten Waldminghaus ◽

...

Keyword(s):

Vibrio Cholerae ◽

Large Scale ◽

Tandem Repeats ◽

Whole Genome Sequence ◽

Evolutionary Significance ◽

Single Chromosome ◽

Synonymous Mutations ◽

Naturally Occurring ◽

Genomic Characterization

The genetic make-up of most bacteria is encoded in a single chromosome while about 10% have more than one chromosome. Among these, Vibrio cholerae, with two chromosomes, has served as a model system to study various aspects of chromosome maintenance, mainly replication, and faithful partitioning of multipartite genomes. Here, we describe the genomic characterization of strains that are an exception to the two chromosome rules: naturally occurring single-chromosome V. cholerae. Whole genome sequence analyses of NSCV1 and NSCV2 (natural single-chromosome vibrio) revealed that the Chr1 and Chr2 fusion junctions contain prophages, IS elements, and direct repeats, in addition to large-scale chromosomal rearrangements such as inversions, insertions, and long tandem repeats elsewhere in the chromosome compared to prototypical two chromosome V. cholerae genomes. Many of the known cholera virulence factors are absent. The two origins of replication and associated genes are generally intact with synonymous mutations in some genes, as are recA and mismatch repair (MMR) genes dam, mutH, and mutL; MutS function is probably impaired in NSCV2. These strains are ideal tools for studying mechanistic aspects of maintenance of chromosomes with multiple origins and other rearrangements and the biological, functional, and evolutionary significance of multipartite genome architecture in general.

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