Genomic epidemiology of shigellosis in South Africa

Shigellosis is a leading cause of mortality and morbidity from moderate to severe diarrhoea globally, predominantly affecting children under the age of five years living in low- and middle-income nations. Emerging and widespread multidrug resistance (MDR) to recommended antimicrobials threaten to reverse hard-won reductions in shigellosis mortality. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance (AMR) determinants, and Shigella (the aetiological bacteria) transmission, ultimately aiding effective public healthcare policy, it has been under-utilised in sub-Saharan Africa. This study used WGSA of a large, representative sub-sample of isolates from South Africa, collected as part of public healthcare surveillance from 2011 to 2015. We focused on Shigella flexneri 2a and Shigella sonnei as these serotypes caused nearly 70% of all shigellosis cases in South Africa during the study period.