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.
