Whole genome sequencing reveals methicillin-resistant Staphylococcus aureus strains' clonality across hospitals in Mwanza, Tanzania

Antimicrobial resistance (AMR) is a critical global health threat, with methicillin-resistant Staphylococcus aureus (MRSA) posing a significant challenge. However, comprehensive genomic data on MRSA remains scarce in low- and middle-income countries, particularly on whole-genome sequencing (WGS), which provides valuable insights into the pathogen’s genetic landscape. This study utilized WGS to examine local molecular epidemiological profiles of MRSA strains isolated from clinical samples during and after the implementation of the National Action Plan on Antimicrobial Resistance (NAP-AMR) in Mwanza, Tanzania. A total of 14 MRSA strains isolated from patients with bloodstream, urinary, and skin and soft tissue infections from five hospitals during NAP-AMR (June 2019 – June 2020) and after NAP-AMR (March–August 2023), were sequenced. All isolates belonged to sequence type 8 (ST8), and 92.9% (13/14) were spa type t1476. All resistance and virulence genes were chromosomally encoded, and phenotypic antimicrobial resistance profiles demonstrated perfect concordance with genotypic predictions, except for tetracycline. Pairwise single-nucleotide polymorphism (SNP) analysis revealed limited genetic diversity, with SNP differences ranging from 4 to 140. Maximum likelihood phylogeny analysis based on SNP data identified two distinct clonal clusters of MRSA strains, one comprising isolates from multiple hospital wards and the other confined to strains within the same ward. The sequenced MRSA strains exhibited a highly clonal population structure, predominated by ST8 spa type t1476, with chromosomally encoded resistance and virulence genes. The strong concordance between phenotypic and genotypic resistance, alongside limited genetic diversity and distinct clonal clustering, suggests local transmission, underscoring the need for strengthened infection control measures.