Genotypic profiles of emerging multidrug-resistant Staphylococcus capitis isolates from an ongoing outbreak in critically ill patients

Abstract

An increasing number of linezolid resistant (LZR), multidrug-resistant (MDR) Staphylococcus capitis infections have been observed in private hospitals in the greater Gauteng area since 2014. The aim of this study was to investigate the genotypic profiles of emerging LZR MDR S. capitis isolates from an ongoing outbreak in critically ill patients in South Africa’s private sectors. A total of 119 S. capitis isolates from 29 private hospitals were identified and reported as linezolid resistant. The antimicrobial resistance patterns of the LZR MDR S. capitis isolates were: erythromycin 99.2% (118/119), amoxycillin/clavulanate 98.3% (117/119), cloxacillin 98.3% (117/119), clindamycin 97.5% (116/119), fucidic acid 84% (100/119), gentamycin 74.8% (89/119), cotrimoxazole 27.2% (33/119), rifampicin 16.8% (20/119), daptomycin 2.5% (3/119), vancomycin 1.7% (2/119) and teicoplanin 0.8% (1/119). The cfr gene was found in one isolate, while the optrA and poxtA genes were not detected with multiplex (M)-PCR. The pulsed-field gel electrophoresis (PFGE) dendrogram showed 1 major pulsotype consisting of 76 isolates, 3 minor pulsotypes with nine, five and three isolates respectively and 10 singletons. Fifteen isolates were classified as untypeable. Whole genome sequencing analysis of five representative S. capitis isolates showed a less known point mutation at G2604T on the rRNA gene conferring resistance to linezolid. Antimicrobial resistant genes identified included: tetK, aac(6’)-le-aph(2”)-la, fusB, sepA, sdrM, mupA, mdeA, mecA, blaZ, ermC, dfrC. Phenotypic antibiotic susceptibility did not show expression of all the genotypic genes detected. The results showed that highly resistant LZR MDR S. capitis isolates are circulating in these private hospitals among adult patients in ICUs. This emphasizes the importance of continious surveillance (with the inclusion of molecular epidemiological investigations) to monitor the transmission and spread of these circulating LZR MDR S. capitis strains in clinical settings in South Africa.