The genomic epidemiology of shigellosis in South Africa

George E. Stenhouse (), Karen H. Keddy, Rebecca J. Bengtsson, Neil Hall, Anthony M. Smith, Juno Thomas, Miren Iturriza-Gómara and Kate S. Baker ()
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George E. Stenhouse: University of Liverpool
Karen H. Keddy: 2Independent Consultant
Rebecca J. Bengtsson: University of Liverpool
Neil Hall: Norwich Research Park
Anthony M. Smith: National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS)
Juno Thomas: National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS)
Miren Iturriza-Gómara: University of Liverpool
Kate S. Baker: University of Liverpool

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-43345-5

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