Resistance, virulence and genetic relatedness of invasive Staphylococcus aureus isolates collected from private and public clinical settings in South Africa

Abstract

Staphylococcus aureus (S. aureus) is a leading cause of healthcare-associated infections (HAIs) and community-associated infections (CAIs) attributed to the harbouring of antibiotic resistance genes (ARGs) and virulence factors. New antibiotics are urgently required to treat the pathogen.

The two-tiered healthcare system in South Africa has elicited differences in antibiotic regimens among private and public clinical settings for treatment of bacterial infections resulting in different selective pressures among these settings. Information on molecular characteristics of S. aureus isolates from these settings remains limited. This study investigated the prevalence of ARGs, biocide resistance genes, virulence genes, staphylococcal cassette chromosome mec (SCCmec) types, accessory gene regulator (agr) groups and genetic relatedness of invasive S. aureus isolates collected from private and public clinical settings in South Africa to determine the molecular characteristics and genetic relatedness of invasive S. aureus isolates among these settings.

The study included a total of 183 invasive S. aureus isolates (110 isolates from private settings and 73 isolates from public settings). Multiplex polymerase chain reaction (M-PCR) assays were used for species confirmation and to characterise ARGs, biocide resistance genes, virulence genes, SCCmec types and agr groups. Pulsed-field gel electrophoresis (PFGE) was utilised to assess genetic relatedness. Based on M-PCR assay results and PFGE pulsotypes, 11 representative isolates were selected for whole-genome sequencing (WGS).

The S. aureus isolates harbouring tetracycline ARGs [20% (22/110) private isolates and 53.4% (39/73) public isolates] and biocide resistance genes [36.4% (40/110) private isolates and 61.6% (45/73) public isolates]; as well as containing at least two virulence genes, were detected by M-PCR assays. The SCCmec types II, IV and V were detected in private settings and SCCmec types I, III, IVd and V were detected in public settings by M-PCR assays and WGS. The agr groups I, II, III and IV were detected among the isolates.

The PFGE results revealed two major pulsotypes, 28 minor pulsotypes and 47 singletons, suggesting considerable genetic diversity among the isolates. Several minor pulsotypes clustered according to the clinical setting, however the largest major pulsotype (pulsotype O) contained isolates from both settings. Whole genome sequencing revealed additional ARGs, virulence genes, mobile genetic elements (MGEs), multi-drug resistance (MDR) efflux pumps and mutations detected at high frequencies, confirming the pathogenic significance of S. aureus. In addition, WGS also detected sequence types (STs) and staphylococcal protein A (spa) types. The identification of pulsotype O as ST152 as well as the identification of the epidemic strain ST5 in both settings indicated dominant strains circulating in both settings. The ST1 and epidemic strains ST8 and ST22 were identified in private settings; epidemic strain ST239 and ST2430 and novel STs-ST8011 and ST8012 identified in public settings; and several spa types were identified, indicating diverse strains circulating in each setting. The novel STs in public settings and novel spa types in both settings suggest new S. aureus strains emerging in each setting.

Dominant MDR, biocide resistant and virulent epidemic S. aureus strains are circulating in private and public settings in South Africa. The establishment of epidemic strains in these settings emphasises the importance of S. aureus strain surveillance monitoring.