Journal article

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

Jane Hawkey, Kalani Paranagama, Kate S Baker, Rebecca J Bengtsson, Francois-Xavier Weill, Nicholas R Thomson, Stephen Baker, Louise Cerdeira, Zamin Iqbal, Martin Hunt, Danielle J Ingle, Timothy J Dallman, Claire Jenkins, Deborah A Williamson, Kathryn E Holt

NATURE COMMUNICATIONS | NATURE RESEARCH | Published : 2021

Abstract

Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S. sonnei outbreak investigation and surveillance, but comparison of data between studies and labs is challenging. Here, we present a genomic framework and genotyping scheme for S. sonnei to efficiently identify genotype and resistance determinants from WGS data. The scheme is implemented in the software package Mykrobe and tested on thousands of genomes. Applying this approach to analyse >4,000 S. sonnei isolates..

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Grants

Awarded by Bill and Melinda Gates Foundation, Seattle


Awarded by Wellcome Trust Clinical Research Career Development Fellowship


Awarded by UKRI MRC New Investigator Research Grant


Awarded by National Health and Medical Research Council (NHMRC) of Australia


Funding Acknowledgements

K.E.H. is supported by a Senior Medical Research Fellowship from the Viertel Foundation of Australia, and Bill and Melinda Gates Foundation, Seattle (grant #OPP1175797). K.S.B. is supported by a Wellcome Trust Clinical Research Career Development Fellowship (A/106690/A/14/Z) and RJB through a UKRI MRC New Investigator Research Grant (held by KSB, MR/R020787/1). K.S.B., T.J.D. and C.J. are affiliated to the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool in partnership with Public Health England (PHE), in collaboration with University of Warwick. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, the Department of Health and Social Care or Public Health England. D.A.W. is supported by an Investigator Grant from the National Health and Medical Research Council (NHMRC) of Australia (APP1174555).