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Elife. 2015 Aug 4;4:e07335. doi: 10.7554/eLife.07335.

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri.

Author information

1
Cardiff School of Biosciences, Cardiff, United Kingdom.
2
Pathogen Genomics, Wellcome Trust Sanger Centre, Cambridge, United Kingdom.
3
Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France.
4
Centre for Food and Water Borne Diseases, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.
5
Centre for Enteric Diseases, National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
6
The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
7
Department of Genetics, Evolution, and Bioagents, Institute of Biology, University of Campinas, São Paulo, Brazil.
8
Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie University, Berlin, Germany.
9
Gastrointestinal Bacteria Reference Unit, Public Health England, London, United Kingdom.
10
Global Evaluative Sciences, Inc., Seattle, United States.
11
Department of Pharmacy, School of Pharmacy, Hanyang University, Ansan, Republic of Korea.

Abstract

Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago. Here we combine whole genome sequencing with geographical and temporal data to examine the natural history of the species. Our analysis subdivides S. flexneri into seven phylogenetic groups (PGs); each containing two-or-more serotypes and characterised by distinct virulence gene complement and geographic range. Within the S. flexneri PGs we identify geographically restricted sub-lineages that appear to have persistently colonised regions for many decades to over 100 years. Although we found abundant evidence of antimicrobial resistance (AMR) determinant acquisition, our dataset shows no evidence of subsequent intercontinental spread of antimicrobial resistant strains. The pattern of colonisation and AMR gene acquisition suggest that S. flexneri has a distinct life-cycle involving local persistence.

KEYWORDS:

E. coli; Shigella; dysentery; epidemiology; genomics; global health; infectious disease; microbiology; pathogen evolution

PMID:
26238191
PMCID:
PMC4522646
DOI:
10.7554/eLife.07335
[Indexed for MEDLINE]
Free PMC Article

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