Molecular characterization of Panton-Valentine leukocidin-encoding bacteriophage types detected in Staphylococcus aureus isolates from South Africa and Nigeria

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Background: Panton-Valentine leukocidin (PVL) which has been associated with necrotizing pneumonia and fasciitis is carried by staphylococcal bacteriophages. This study aimed to characterize bacteriophage morphology and diversity in PVL positive S. aureus isolates from South Africa and Nigeria. Methods: Seventy PVL positive S. aureus isolates from South Africa (24 MRSA and 25 MSSA) and Nigeria (21 MRSA) were investigated using a three-part PCR-based bacteriophage typing scheme; followed by transmission electron microscopy (TEM) and whole genome sequencing (WGS) on selected isolates. Results: Icosahedral head group II was the most prevalent (South Africa: MRSA 92%; MSSA: 96% and Nigeria MRSA: 92%). Only icosahedral head groups I and elongated head groups were detected with both PCR and TEM. Results were inconclusive for part II of the PCR-typing scheme, therefore the seven bacteriophage types identified in part III were referred to as “bacteriophage-like.” Bacteriophage ΦPVL-like was the most prevalent (67%) among the South African MRSA isolates and ΦSa2USA-like was the most prevalent among the South African MSSA isolates (72%) and the Nigerian MRSA isolates (47%). WGS confirmed three variant PVL-encoding bacteriophages, one incomplete lukS/F -encoding phage and four complete lukE/D -encoding bacteriophage types. The Bengal Bay clone (ST772/CC1- SCCmec V) and another outbreak associated strain ST152 (CC152) were also detected. Conclusion: The PCR-based typing scheme detected and characterized PVL-encoding bacteriophages in the majority of the study isolates. However, there is a need for the improvement of the current typing scheme, specifically in resource-limited countries that cannot afford WGS.

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