Evidence map›Paper›PMID 26923111›Full record

ReviewNature reviews. Microbiology2016

The genomic signatures of Shigella evolution, adaptation and geographical spread.

Hao Chung The, Duy Pham Thanh, Kathryn E Holt, Nicholas R Thomson, Stephen Baker

Abstract readReview
PubMed Publisher
In one paragraph

Review in Nature reviews. Microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 108 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
108citing papers in PubMed, 1 pooled it
–field-weighted citation impact
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

108 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Trial
  3. Standardization and evaluation of artificial intelligence-driven Fourier-transform infrared bio-typing for the discrimination of Escherichia coli and Shigella spp. on genus, species and serogroup level.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026
    Article
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  5. bioRxiv : the preprint server for biology · 2026
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  6. GlobalMicrobiology spectrum · 2026
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  7. Review
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  13. Genomic and epidemiological characteristics ofPathogens and global health · 2025
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  19. Article
  20. Genomic epidemiology and public health implications of zoonotic monophasicFrontiers in cellular and infection microbiology · 2025
    Article

48 more citing papers are in PubMed but not listed here.

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

5 authors.

Hao Chung TheThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.
Duy Pham ThanhThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.
Kathryn E HoltCentre for Systems Genomics, University of Melbourne.
Nicholas R ThomsonBacterial Genomics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
Stephen BakerThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.

Funding

Wellcome Trust 098051Wellcome Trust 100087
6 · The paper itself

Abstract

Shigella spp. are some of the key pathogens responsible for the global burden of diarrhoeal disease. These facultative intracellular bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Escherichia coli and Salmonella spp. The genus Shigella comprises four different species, each consisting of several serogroups, all of which show phenotypic similarity, including invasive pathogenicity. DNA sequencing suggests that this similarity results from the convergent evolution of different Shigella spp. founders. Here, we review the evolutionary relationships between Shigella spp. and E . coli, and we highlight how the genomic plasticity of these bacteria and their acquisition of a distinctive virulence plasmid have enabled the development of such highly specialized pathogens. Furthermore, we discuss the insights that genotyping and whole-genome sequencing have provided into the phylogenetics and intercontinental spread of Shigella spp.

Indexed as

Evolution, MolecularGenome, BacterialAdaptation, PhysiologicalEscherichia coliGenomicsPhylogenyPlasmidsSequence Analysis, DNAShigellaVirulence FactorsVirulence Factors

Identifiers

What OpenQuestion holds

Textmetadata
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.