Molecular Epidemiology of Staphylococcus epidermidis Implicated in Catheter-Related Bloodstream Infections at an Academic Hospital in Pretoria, South Africa

Abstract

Staphylococcus epidermidis is one of the most prevalent pathogens implicated in catheter-related bloodstream infections (CRBSI) at an academic hospital in Pretoria, South Africa. Little is known about the clonality and the prevalence of antibiotic resistance and virulence genes in S. epidermidis (e.g., icaAB, IS256, mecA, and qacA/B). A total of 508 intravascular catheters (IVCs) from 331 patients were submitted for culture from May to October 2013. Only 50% (n = 253/508) of the IVCs were accompanied by blood cultures (BCs) taken within 48 h. Forty-four percent (44%; n = 112/253) of IVCs were colonised, of which 26% (n = 65/253) were associated with a CRBSI. We identified S. epidermidis as the causal agent in 31% (n = 20/65) of the CRBSI cases. Fifty-nine S. epidermidis isolates were obtained, 23 isolates were cultured from 22 IVCs and 36 isolates were cultured from 36 BCs. All S. epidermidis isolates were resistant to β-lactams (100%; n = 59/59), followed by high levels of resistance toward erythromycin (86%; n = 51/59) and gentamicin (81%; n = 49/59). The mecA gene was prevalent in all the (100%, n = 59/59) isolates. Isolates contained the IS256 element (83%, n = 49/59), the icaAB gene (81%, n = 48/59) and, the qacA/B gene (81%, n = 48/59). All 48 isolates were qacA positive upon restriction enzyme digestion of the qacA/B amplicons. Phenotypic resistance toward 0.5% (m/v) chlorhexidine was not observed. Staphylococcal Cassette Chromosome (SCC) mec typing showed that SCCmec type IV (31%; n = 18/59) was the most prevalent. The remaining SCCmec elements were highly diverse. Pulsed-field gel electrophoresis (PFGE) showed that S. epidermidis isolates from individual patients were mostly clonal. Multilocus sequencing typing (MLST) of 10 sequenced isolates showed that sequence type (ST) 2 (40%; n = 4/10) was the most frequently detected, followed by ST54 (20%; n = 2/10), ST28 (10%; n = 1/10), ST59 (10%; n = 1/10) and ST490 (10%; 1/10). One isolate was newly assigned to ST596. These S. epidermidis infections can be attributed to patients' skin microflora or to poor infection control practices. Currently, S. epidermidis strains circulating in the studied hospital are multidrug-resistant and highly adaptive to environmental changes.

Keywords: MLST; PFGE; SCCmec typing; ST2; ST596; South Africa; Staphylococcus epidermidis; catheter-related bloodstream infections.

Figure 1

Antimicrobial susceptibility profiles of 59 S. epidermidis isolates as determined by the VITEK® 2 system (bioMérieux, France) (AST-P603) according to the CLSI guidelines (Clinical Laboratory Standards Institute, 2013).

Figure 2

Genetic relatedness of catheter and blood culture S. epidermidis isolates implicated in CRBSI events (with the blue blocks representing the major pulsotypes). AC, arterial catheter; BC, blood culture; CTSICU, cardiothoracic surgery ICU; CVP, central venous catheter; GSFW, general surgery female ward; HCM, high care, multidisciplinary; MPICU, medical and pulmonology ICU; MLST, multilocus sequence typing; NSW, neurosurgery ward; NT, not typeable; OW, oncology ward; PSW, paediatric surgery ward; POMW, plastic/maxillofacial ward; ST, sequence type; STICU, surgery and trauma ICU; VC, VasCath; VSW, vascular surgery ward. Banding patterns of the catheter culture and BC isolates showing ≥80% similarity were clonal. Please note that isolates 14.5, 20.1, 26.2, 28.5, and 42.5 were untypeable and not included in the dendrogram.

Figure 3

Comparative population snapshot of S. epidermidis STs detected in this study vs. STs in the S. epidermidis MLST database of clonal complex 2 as on the 16th of May 2017. Ten isolates were sequenced: ST2 (n = 4); ST54 (n = 2); ST28 (n = 1); ST59 (n = 1); ST490 (n = 1) and ST596 (n = 1). The sequence types (STs) found in this study are encircled, except for ST490 [not currently in the MLST database (last update 24-09-2015)]. The colour and meaning of each circle can be read according to the colour key.