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The genomic epidemiology of shigellosis in South Africa.

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Stenhouse, George E  ORCID logo
Bengtsson, Rebecca J 
Hall, Neil 


Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei. We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri, and that the HIV epidemic may have promoted Shigella population expansion.


Acknowledgements: We thank all participants of the NICD GERMS-SA Laboratory Surveillance Network for submission of clinical isolates of Shigella species to the NICD. The surveillance network includes laboratories belonging to the Department of Health (NHLS laboratories) and laboratories that form part of the private sector. Next-generation sequencing and library construction were delivered via the BBSRC National Capability in Genomics and Single Cell Analysis (BB/CCG1720/1, N.H.) at Earlham Institute, by members of the Genomics Pipelines Group. The project was supported by both a Global Challenges Research Fund (GCRF) data & resources grant BBS/OS/GC/000009D (N.H.) and the BBSRC Core Capability Grant to the Earlham Institute BB/CCG1720/1 (N.H.) and Core Strategic Programme Grant BBS/E/T/000PR9817 (N.H.). This work was also supported by Medical Research Council grant MR/R020787/1 (K.B.). For the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) licence to any Author Accepted Manuscript version arising from this submission.


Child, Humans, Child, Preschool, Dysentery, Bacillary, South Africa, Shigella, Shigella flexneri, Genomics, Anti-Infective Agents

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Nat Commun

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Springer Science and Business Media LLC
RCUK | MRC | Medical Research Foundation (MR/R020787/1)
RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) (BB/CCG1720/1, BBS/OS/GC/000009D, BB/CCG1720/1, BBS/E/T/000PR9817)