We characterized invasive MRSA and MSSA isolates collected at the largest referral hospital of Southern Malawi between 1997 and 2016.

This is the first report describing the genetic population structure of Staphylococcus aureus in Malawi. We analysed 221 clinical isolates, of which 48 MRSA, collected over a two-decade period at the largest referral hospital in Southern Malawi. The proportion of S. aureus isolates from this hospital that are MRSA are steadily increasing with currently one in five isolates being MRSA. Our study shows this rise largely correlates with the introduction and expansion of the virulent hospital-associated MRSA strain ST612. Furthermore, we observed that the dominant strain type among MSSA was the PVL-producing strain ST152.