Genomic comparison of Staphylococcus aureus isolates from patients with bacteraemia and infective endocarditis at public hospitals in Gauteng, South Africa

Abstract

<title>Abstract</title> <italic>Staphylococcus aureus</italic> ( <italic>S. aureus</italic> ) is a leading cause of bacteraemia and infective endocarditis worldwide, posing significant public health challenges in resource-limited low- and middle-income countries (LMICs). However, whether specific genomic factors influence <italic>S. aureus</italic> infective endocarditis (SAIE) development during <italic>S. aureus</italic> bacteraemia (SAB) remains unclear. Thus, the study aimed to determine whether clinical SAIE isolates were genomically distinguishable from SAB isolates originating from public hospitals in Gauteng, South Africa. Seventy-seven (54 SAB, 23 SAIE) bloodstream isolates were characterised to assess antimicrobial susceptibility (VITEK ^® 2 system), biofilm formation (crystal violet assay), virulence genes (multiplex-polymerase chain reactions) and genetic relatedness (pulsed-field gel electrophoresis). Twelve representative isolates underwent whole-genome sequencing to assess their mobilome, resistome, virulome and phylogenetic relatedness. A higher SAIE (29.9%) prevalence than previously reported in South Africa was observed, with cases linked to young male persons who inject drugs (P &lt; 0.01). While SAB and SAIE groups did not differ in virulence profiles, SAB cases demonstrated higher resistance rates to gentamicin and clindamycin compared to SAIE (P &lt; 0.05). The endemic Panton-Valentine leukocidin-positive sequence-type (ST) 152, clonal-complex (CC) 152 lineage predominated in SAIE isolates, while the pandemic CC8, encompassing ST239, ST508 and ST612, was exclusive to SAB isolates. The findings suggest that all SAB isolates may be capable of progressing to more severe SAIE forms with host risk factors as key predictors. Circulation of diverse, highly pathogenic <italic>S. aureus</italic> strains highlights the need for surveillance and targeted infection control.