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Stenhouse, George E., Keddy, Karen H., Bengtsson, Rebecca J., Hall, Neil 
ORCID: https://orcid.org/0000-0003-2808-0009, Smith, Anthony M., Thomas, Juno, Iturriza-Gómara, Miren and Baker, Kate S.
(2023)
The genomic epidemiology of shigellosis in South Africa.
Nature Communications, 14.
ISSN 2041-1723
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Abstract
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.
| Item Type: | Article |
|---|---|
| Additional Information: | Data availability The study isolates’ raw sequences have been deposited in the European Nucleotide Archive under project accession PRJEB55173 and individual isolate accession numbers can be found in the Supplementary Data 1. Accession numbers for reference isolates used in the study are also provided in the supplementary table. All patient metadata, and all data generated from the analysis of this metadata, used in this study are provided in the Supplementary Data 1 and Source Data files, respectively. Source data are provided with this paper. Funding Information: 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.). Rights Retention Statement: 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. |
| Uncontrolled Keywords: | chemistry(all),biochemistry, genetics and molecular biology(all),physics and astronomy(all),sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1600 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 25 Oct 2024 14:30 |
| Last Modified: | 01 Nov 2024 13:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97217 |
| DOI: | 10.1038/s41467-023-43345-5 |
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