Whole genome sequencing of clinical methicillin-resistant Staphylococcus aureus isolates across hospitals in Mwanza, Tanzania

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of both healthcare-associated and community-acquired infections, characterized by limited treatment options and substantial morbidity and mortality, particularly in low- and middle-income countries such as Tanzania. However, genomic data which provides valuable insights into the pathogen’s genetic landscape, remains scarce. This study utilized whole-genome sequencing (WGS) to examine local molecular epidemiological profiles of 14 MRSA isolates isolated from blood, urine, and pus samples during (n=6; June 2019 – June 2020) and after (n=8; March – August 2023) the implementation of the National Action Plan on Antimicrobial Resistance (NAP-AMR) in Mwanza, Tanzania. All isolates belonged to sequence type 8 (ST8), and 92.9% (13/14) were spa type t1476. Phenotypic and genotypic antimicrobial resistance results were consistent for all antibiotics tested, with the exception of tetracycline. Pairwise single-nucleotide polymorphism (SNP) analysis revealed genetic diversity, with SNP differences ranging from 0 to 99. Maximum likelihood phylogeny analysis based on SNP data identified two closely related MRSA pairs, one from multiple wards while the other confined within the same ward within the same hospital. In conclusion, WGS revealed that all MRSA isolates belonged to ST8 with substantial genetic diversity and phylogenetic analysis revealed two closely related MRSA pairs, suggesting transmission event, acquisition from a shared source, or circulation of a closely related lineage. These findings highlight the importance of genomic surveillance for uncovering MRSA transmission patterns and guiding infection prevention efforts.