Phenotypic and genotypic characterisation of clinically relevant Staphylococcus aureus isolates from cystic fibrosis patients from private clinics in South Africa

Abstract

Introduction. Cystic fibrosis is a hereditary disease that results in ineffective mucocilliary clearance of secretions, creating an environment that allows Staphylococcus aureus to thrive. The aim of this study was to determine the phenotypic and genotypic characteristics of S. aureus isolates obtained from cystic fibrosis patients attending private clinics in South Africa.

Materials and Methods. A total of 87 S. aureus isolates were collected. Phenotypic susceptibility testing was performed using the Vitek®2 automated system (bioMérieux, France) according to EUCAST guidelines. Multiplex-PCR assays were used to target antibiotic resistance genes and a selection of biofilm formation, haemolysins and cytoxin genes. Pulsed-field gel electrophoresis was conducted and a dendrogram constructed to assess the genetic relatedness of isolates. Whole genome sequencing was performed on four isolates to determine sequence types, the resistome and virulome of the isolates.

Results. Phenotypic antibiotic susceptibility testing showed the highest resistance against erythromycin in 62.1% (54/87) of isolates. Multiplex-PCR assay results showed 11.4% (10/87) of the S. aureus isolates were MRSA; and the most prevalent macrolide and tetracycline resistance genes was ermC 36.8% (32/87) and tetK 2.3% (2/87). The biocide resistance gene, qacC was detected in 4.5% (4/87) of the isolates. The most prevalent virulence gene was: hla 48.2% (42/87). Sequence types detected were pandemic strains ST5 and ST36, and livestock associated strain ST398 as well as a novel ST.

The S. aureus isolates from CF patients in this study were highly diverse, indicating limited spread from clinical settings. Multidrug resistant isolates were detected which limits treatment options for these patients; the isolates also harbour virulence genes that can increase the severity of the disease and potentially increase the morbidity and mortality among these patients.