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.

Introduction: Pseudomonas aeruginosa AUST-03 (ST242) has been reported to cause epidemics in cystic fibrosis (CF) patients from Tasmania and Australia and has been associated with multidrug resistance and increased morbidity and mortality. Here, we report epidemic P. aeruginosa (AUST-03) strains in South African CF patients at a public academic hospital detected during a previous study and characterise the resistomes. Methods: The P. aeruginosa AUST-03 (ST242) strains were analysed with whole genome sequencing using the Illumina NextSeq2000 platform. Raw sequencing reads were processed using the Jekesa pipeline and multi-locus sequence typing and resistome characterisation was performed using public databases. Core single nucleotide polymorphism phylogenies were performed on P. aeruginosa ST242 strains from the study and from public databases. Antibiotic susceptibility testing was performed using the disk diffusion and broth microdilution techniques. Results: A total of 11 P. aeruginosa AUST-03 strains were isolated from two children with CF who had pulmonary exacerbations. The majority of the P. aeruginosa AUST-03 strains (8/11) were multidrug resistant (MDR) or extensively drug resistant; and the multidrug efflux pumps MexAB-OprM, MexCD-OprJ, MexEF-OprN, MexXY-OprM were the most clinically relevant antibiotic resistance determinants and were detected in all of the strains. The P. aeruginosa AUST-03 (ST242) study strains were most closely related to strains from Canada, China, Denmark and Slovenia. Conclusion: Epidemic MDR P. aeruginosa strains are present at South African public CF clinics and need to be considered when implementing patient segregation and infection control strategies to prevent further spread and outbreaks.