Evidence map›Paper›PMID 30971707›Full record

ArticleScientific reports2019

High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139.

Matthew J Dorman, Daryl Domman, Muhammad Ikhtear Uddin, Salma Sharmin, Mokibul Hassan Afrad, Yasmin Ara Begum, Firdausi Qadri, Nicholas R Thomson

Open access · goldAbstract read
In one paragraph

Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
2.1field-weighted citation impact, top 15% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

14 citing papers in PubMed, 23 citations in OpenAlex.

  1. Trial
  2. Article
  3. Allelic variations and gene cluster modularity act as nonlinear bottlenecks for cholera emergence.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  4. Article
  5. Journal of bacteriology · 2024
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  6. Article
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  8. Microbial genomics · 2023
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 3 institutions in 2 countries.

Matthew J DormanWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom.ORCID http://orcid.org/0000-0001-7064-6163
Daryl DommanWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom.ORCID http://orcid.org/0000-0001-5389-9185
Muhammad Ikhtear UddinInfectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.
Salma SharminInfectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.
Mokibul Hassan AfradInfectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.ORCID http://orcid.org/0000-0002-9627-7877
Yasmin Ara BegumInfectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.
Firdausi QadriInfectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh. fqadri@icddrb.org.
Nicholas R ThomsonWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom. nrt@sanger.ac.uk.ORCID http://orcid.org/0000-0002-4432-8505
International Centre for Diarrhoeal Disease Research · BDWellcome Sanger Institute · GBUniversity of London · GB

Funding

Protecutive immunity to human cholera in BangladeshU01AI058935 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI CALDERWOOD, STEPHEN B., RYAN, EDWARD T. · 2003 to 2014
$7.8M
O-Specific Polysaccharide Responses and CholeraR37AI106878 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI Edward T. Ryan · 2020 to 2026
$5.1M
Innate and early B cell responses to V. choleraeR01AI103055 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI HARRIS, JASON B · 2014 to 2018
$3.9M
O-Specific Polysaccharide Responses and CholeraR01AI106878 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI RYAN, EDWARD T. · 2014 to 2018
$3.7M
O-Specific Polysaccharide Responses and CholeraR56AI106878 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI RYAN, EDWARD T. · 2013 to 2020
$843k
NIAID NIH HHS R01 AI103055NIAID NIH HHS R01 AI106878NIAID NIH HHS R37 AI106878NIAID NIH HHS R56 AI106878NIAID NIH HHS U01 AI058935Wellcome TrustWellcome Trust 098051Wellcome Trust 206194
6 · The paper itself

Abstract

Toxigenic Vibrio cholerae of the O139 serogroup have been responsible for several large cholera epidemics in South Asia, and continue to be of clinical and historical significance today. This serogroup was initially feared to represent a new, emerging V. cholerae clone that would lead to an eighth cholera pandemic. However, these concerns were ultimately unfounded. The majority of clinically relevant V. cholerae O139 isolates are closely related to serogroup O1, biotype El Tor V. cholerae, and comprise a single sublineage of the seventh pandemic El Tor lineage. Although related, these V. cholerae serogroups differ in several fundamental ways, in terms of their O-antigen, capsulation phenotype, and the genomic islands found on their chromosomes. Here, we present four complete, high-quality genomes for V. cholerae O139, obtained using long-read sequencing. Three of these sequences are from toxigenic V. cholerae, and one is from a bacterium which, although classified serologically as V. cholerae O139, lacks the CTXφ bacteriophage and the ability to produce cholera toxin. We highlight fundamental genomic differences between these isolates, the V. cholerae O1 reference strain N16961, and the prototypical O139 strain MO10. These sequences are an important resource for the scientific community, and will improve greatly our ability to perform genomic analyses of non-O1 V. cholerae in the future. These genomes also offer new insights into the biology of a V. cholerae serogroup that, from a genomic perspective, is poorly understood.

Indexed as

Genome, BacterialBacteriophagesCholera ToxinDrug Resistance, BacterialGenetic VariationO AntigensPhylogenySerogroupVibrio cholerae O139Cholera ToxinO Antigens

Identifiers

PMID30971707
PMCPMC6458141
OpenAlexW2936739024

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.