AST and genomic analysis of 42 S. aureus isolates collected at Fort Portal Regional Referral Hospital, by the hospital microbiology laboratory between 2017 and 2019; primarily derived from skin wounds or suspected urinary tract or bloodstream infections.

Tackling the major global threat of antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as parts of Sub-Saharan Africa where supplies and regulation of antibiotic treatments is compromised by poor investment in healthcare infrastructure. Specific local information about commonly circulating AMR profiles linked to treatment failures could better inform evidence-based training of health workers towards improved antibiotic stewardship measures. To that end, we have sequenced the genomes of 42 Staphylococcus aureus isolates from wound, bloodstream and urinary infections at Fort Portal Regional Referral Hospital (FPRRH), Uganda over a two-year period (2017-2019). We identified 27 different multi Locus sequence types (MLSTs), of which 33% (9/27) were classified as ST152, 26% (7/27) as ST1633 and 15% (4/27) as ST8. Antibiotic resistance phenotyping revealed 71.4% (30/42) of isolates were resistant to one or more antibiotics. 24% (10/42) were multi-drug resistant (MDR) and 4.8% (2/42) were considered to be pan-resistant (resistant to six different classes of antibiotics). Resistance phenotypes were largely explained by the presence of commonly known antibiotic resistance genes from the DNA sequencing data. Tetracycline resistance was (54%, 19/35) and largely accounted for by the presence of tetK and tetM genes encoding an efflux pump and ribosomal protection respectively in 50% (21/42) of isolates. Similarly, most isolates showing resistance to cefoxitin, gentamycin, erythromycin and ciprofloxacin harboured polymorphisms in blaZ, mecA, aph3 and aac genes respectively, which could account for these resistances. The most frequently detected resistance gene (dfrG/folA), encoding a dihydrofolate reductase and resistance to trimethoprim, was present in 100% of isolates, whilst only 48% showed resistance to co-trimoxazole (combination trimethoprim-sulfamethoxazole). This data has been used to validate hospital lab processes and develop local evidence-based training for hospital staff, as well as contributing towards the development of the hospitals first antibiogram.