The present study was conducted from July to August 2018 on milk samples taken at dairy farms in the Northern Province and Kigali District of Rwanda in order to identify Staphylococcus spp. associated with bovine intramammary
infection. A total of 161 staphylococcal isolates originating from quarter milk samples of 112 crossbred dairy cattle were included in the study. Antimicrobial susceptibility testing was performed and isolates were examined for the presence of various resistance genes. Staphylococcus aureus isolates were also analyzed for the presence of
virulence factors, genotyped by spa typing and further phenotypically subtyped for
capsule expression using Fourier Transform Infrared (FTIR) spectroscopy. Selected S. aureus were characterized using
DNA microarray technology, multi-locus sequence typing (MLST) and whole-genome sequencing. All
mecA-positive staphylococci were further genotyped using dru typing. In total, 14 different staphylococcal species were detected, with S. aureus being most prevalent (26.7%), followed by S. xylosus (22.4%) and S. haemolyticus (14.9%). A high number of isolates was resistant to
penicillin and
tetracycline. Various antimicrobial and
biocide resistance genes were detected. Among S. aureus, the
Panton-Valentine leukocidin (PVL) genes, as well as bovine
leukocidin (LukM/LukF-P83) genes, were detected in two and three isolates, respectively, of which two also carried the
toxic shock syndrome toxin gene
tsst-1 bovine variant. t1236 was the predominant spa type. FTIR-based
capsule serotyping revealed a high prevalence of non-encapsulated S. aureus isolates (89.5%). The majority of the selected S. aureus isolates belonged to clonal complex (CC) 97 which was determined using
DNA microarray based assignment. Three new MLST sequence types were detected.