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

Authors :
Thomas R Connor
Clare R Barker
Kate S Baker
François-Xavier Weill
Kaisar Ali Talukder
Anthony M Smith
Stephen Baker
Malika Gouali
Duy Pham Thanh
Ishrat Jahan Azmi
Wanderley Dias da Silveira
Torsten Semmler
Lothar H Wieler
Claire Jenkins
Alejandro Cravioto
Shah M Faruque
Julian Parkhill
Dong Wook Kim
Karen H Keddy
Nicholas R Thomson
Source :
eLife, Vol 4 (2015)
Publication Year :
2015
Publisher :
eLife Sciences Publications Ltd, 2015.

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.

Details

Language :
English
ISSN :
2050084X
Volume :
4
Database :
Directory of Open Access Journals
Journal :
eLife
Publication Type :
Academic Journal
Accession number :
edsdoj.65b978008c26433d8d4a442b3f947616
Document Type :
article
Full Text :
https://doi.org/10.7554/eLife.07335