S aureus Characterization from milk sample and humans in eastern Tanzania

Background. S. aureus is a common environmental organism and is found in a wide variety of sources, including dairy farms. Whole genome sequencing provides insight into which specific genes, mutations, and genetic variations are present in the different strains, allowing a better understanding of the strains' diversity. Aim: To investigate the distribution of sequence types circulating in different dairy herds using MLST, screen the isolates for antimicrobial resistance and virulence genes, and evaluate the genetic relatedness of S aureus isolated recovered from humans working in close contact with animals. Methods and results: A total of 43 S. aureus from cow milk samples of local milk-supplying farms in different Tanzanian regions were whole genome sequenced together with 12 S. aureus from healthy human skin swabs using NextSeq550 at KCRI-Biotechnology laboratory. Multilocus sequence typing revealed 14 different sequence types among all 55 isolates, including 5 novel sequence types: ST 7840, 7841, 7845, 7846, 7847, and 7848 and ST5477which was previously reported once in Rwanda. ResFinder analysis revealed a limited number of antibiotic resistance genes among the S. aureus including tet(K), blaZ, dfrG, erm(C), str and qacG, and fosB encoding for different antibiotics and multidrug efflux pumps. mecA was discovered in one of the 55 isolates included in the study. The SPN tree is composed of several different clusters of closely related isolates. A cluster of ST152 strains was a stand-alone cluster composed of 8 isolates from both human and animal origin. Conclusion: The diversity of S. aureus strains from local milk-supplying dairy farms in this study is highly variable with different clonal complexes predominated, namely CC152, CC5477, and CC97. CC152 has seemingly recently emerged especially in Africa and this is only the second report of isolates of CC5477.