Genetic and phenotypic diversity of bloodstream associated Staphylococcus epidermidis isolates obtained from private and public hospitals in South Africa

Abstract

Staphylococcus epidermidis is a commensal bacterium commonly implicated in bloodstream infections. Most S. epidermidis infections are acquired in hospitals and are associated with the use of medical devices. In contrast to its more virulent relative Staphylococcus aureus, S. epidermidis is often overlooked and regarded as a contaminant in diagnostic laboratories. As a result, limited information reporting on the prevalence of antibiotic resistance, virulence genes and clonality of S. epidermidis is available. In attempts to bridge this information gap, this study used phenotypic and genotypic methods to investigate the genetic diversity and genetic relatedness of bloodstream associated S. epidermidis isolates collected from private and public hospitals in Gauteng.

A total of 161 bloodstream associated S. epidermidis isolates were collected from private and public hospitals over a period of eight months. The isolates were identified and characterised for the presence of antibiotic resistance and virulence genes using multiplex polymerase chain reaction (M-PCR) assays. The pathogenicity of S. epidermidis was further investigated using the microtitre plate assay to quantify biofilm formation. The genetic relatedness of the isolates was characterised using the staphylococcal cassette chromosome methicillin (SCCmec), pulsed field gel electrophoresis (PFGE) and whole genome sequencing (WGS).

All 161 isolates (98 from private and 63 from public hospitals) were identified as S. epidermidis, with 91.9% (148/161) of the isolates being resistant to methicillin (i.e MRSE). The high prevalence of the mecA gene is concerning as this gene can easily be transferred to more pathogenic bacteria such as S. aureus.

The most prevalent antibiotic resistance genes in isolates from public and private hospitals were the aac, tetK and msrA genes conferring resistance to tetracyclines, aminoglycosides and macrolides. The following virulence genes were prevalent among the private hospital isolates; EMBP [97.9% (96/98)], agrA, and aae [all at 95.9% (94/98)]. Among public hospitals isolates, the agrA [93.7% (59/63)], EMBP [84.1% (53/63)] and aae [73% (46/63] were the most prevalent genes. These virulence genes are known to play an important role in the pathogenicity of S. epidermidis through strengthening biofilm formation. Using the biofilm quantification method, all [100% (5/5)] the representative isolates from private hospitals were characterised as strong biofilm formers while the isolates from public hospitals were characterised as either weak biofilm formers [60% (3/5)] or non-biofilm formers [40% (2/5)].

A community based SCCmec type, SCCmec type IV was found to be dominant in both the private [11.8% (11/93)] and public [18.2% (10/55)] hospitals. This indicates the possible introduction of community-based strains of S. epidermidis into the hospitals. The PFGE showed a high genetic diversity among the S. epidermidis isolates, with a total of 16 Pulsotypes defined. Whole genome sequencing on selected representative isolates gave the sequence types, ST2, ST5, ST7, ST23 and ST28. The three sequence types, ST2, ST5 and ST23 were reported by other researchers to be endemic and predominantly associated with complicated bloodstream infections in S. epidermidis.

The high prevalence of antibiotic resistance and virulence genes in this study supports the notion that S. epidermidis serves as a reservoir for more pathogenic bacteria such as S. aureus. The isolation of endemic strains warrants for comprehensive surveillance of S. epidermidis in South African hospitals.