First look: Whole genome sequence analysis of Shigella from South Africa

Bacteria of the genus Shigella are the leading bacterial cause of diarrhoeal illness in children in low-and-middle income nations, but there is no licensed vaccine and they are increasingly antimicrobial resistant. Understanding this disease and its AMR in endemic areas is of global concern as shigellosis also occurs in high-income nations, frequently contracted through travel and onward transmission. In addition to the direct morbidity and mortality of shigellosis cases, childhood diarrhoeal illness is linked with life-long sequelae including stunted growth and impaired cognitive development. Whole Genome Sequence Analysis (WGSA) of Shigella is currently transforming our understanding of the epidemiology, AMR and biology of shigellosis, but this approach has yet to be applied in many of the regions where the disease is most common, resulting in critical knowledge and surveillance gaps. One such under-sampled endemic region is Africa.
In this bioinformatics project, we are working with whole genome sequence data from over 500 isolates of Shigella collected in South Africa. South Africa is a demographically-diverse nation that is particularly relevant to the study of global infectious diseases spread through travel as it acts as an African, and international, transport hub. As such, the student is working with a large molecular dataset including phylogenetic and gene-content analyses, as well as epidemiological approaches to integrate patient metadata.
In doing so, we will determine what WGSA subtypes of Shigella are responsible for most disease, as well as evaluate the antimicrobial resistance in Shigella in this area of importance, but poor surveillance. This will directly inform treatment recommendations for people in South Africa as well as returning travellers, and contribute to public health surveillance on a global scale, particularly for countries that have transitioned to WGSA for public health microbiology, such as the United Kingdom.