Genetic Variation among Panton-Valentine Leukocidin-Encoding Bacteriophages in Staphylococcus aureusClonal Complex 30 Strains

ABSTRACTClonal complex 30 (CC30), one of the major Staphylococcus aureuslineages, has caused extensive hospital-acquired and community-acquired infections worldwide. Recent comparative genomics studies have demonstrated that three CC30 clones—phage type 80/81, Southwest Pacific (SWP), and contemporary EMRSA-16 associated (Con) strains—shared a recent common ancestor more than 100 years ago. Panton-Valentine leukocidin (PVL), a bacteriophage encoded toxin that has been epidemiologically linked with community-associated methicillin-resistant S. aureus(CA-MRSA), has frequently been identified in CC30 clones, although the pvlgene variation and distribution of PVL-encoding phages are poorly understood. We determined here the distribution of PVL phages, PVL gene sequences, and chromosomal phage insertion sites in 52 S. aureusCC30 PVL-harboring isolates, collected from four continents over a 75-year period. Our results indicate that PVL phages with icosahedral heads, including F108PVL and FPVL, were mainly associated with phage 80/81 strains, whereas phages with elongated heads were predominantly found in SWP (FSa2958 and FTCH60) and Con (FSa2USA) strains. Nine single-nucleotide polymorphisms were identified in the lukSF-PVgene, with six isolates harboring the R variant that has been previously associated with CA-MRSA strains. Interestingly, all six R variant strains belonged to the same Con CC30 clone and carried a FSa2USA-like phage. Similar chromosomal phage insertion sites were also identified in all 52 PVL-harboring CC30 strains. These analyses provide important insights into the microepidemiology of PVL-harboring CC30 strains, while the discovery of FSa2USA-associated R variant strains sheds further light on the evolution of PVL-positive CA-MRSA.