Background
Group A Streptococcus (GAS) infections disproportionately affect low- and middle-income countries, including Malawi. However, our understanding of molecular epidemiology remains limited. We investigated the genomic characteristics of invasive GAS isolates collected through hospital surveillance at the largest tertiary hospital in Malawi.
Methods
We performed whole genome sequencing on 178 presumed Streptococcus pyogenes blood, cerebrospinal fluid, and swab culture isolates from adult and pediatric patients admitted to Queen Elizabeth Central Hospital, Blantyre, Malawi, between 2012 and 2023. Genomic analyses included speciation, emm typing, core-genome phylogeny, and antimicrobial resistance gene profiling.
Results
Of the 178 isolates, 174 (97.8%) were confirmed as S. pyogenes genotypically, primarily from blood culture with 157/174 (90.2%) isolates, with patient ages ranging from 1 day to 96 years (median age: 7 years). Multi-locus sequence typing revealed 42.5% (74/174) of isolates belonged to novel sequence types. Additionally, a total of 56 distinct emmtypes were identified in 77.6% (135/174) of the isolates, also suggesting substantial diversity. Core-genome phylogenetic analysis confirmed extensive genetic diversity, with no predominance of emmtypes overall or clustering of emmtypes by year of isolation. Genotypic macrolide (3/174) and tetracycline (88/174) resistance was largely associated with specific emmtypes: emm8.3, emm11, emm26.3, emm56.2, emm63.3, emm65, emm71, emm77, emm119.2, emm179, emm124.1, emm165, emm177, emm183.2, and emm239.1.
Conclusion
The high diversity of emmtypes in Malawi has implications for the development of GAS vaccines with good coverage in the region. Expanded hospital and community surveillance is necessary to provide a comprehensive and high-resolution understanding of S. pyogenes population biology and dynamics.