Ward-specific clustering of methicillin-resistant Staphylococcus aureus spa-type t037 and t045 in two hospitals in South Africa: 2013 to 2017

Abstract

Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) is a highly clonal pathogen causing infections in various settings. The aim of this study was to determine if healthcare-associated (HA) MRSA isolates with the same spa-type originating from two geographically distinct hospitals in South Africa were genetically related based on PFGE. Furthermore, a small subset of MRSA isolates were characterised with WGS and then compared to PFGE to determine if PFGE is still a reliable method to define outbreaks and/or transmission chains.

Methods: Staphylococcus aureus isolated from blood cultures (BC) were submitted to the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM) as part of a laboratory-based surveillance programme (GERMS-SA). The identified HA-MRSA isolates underwent molecular characterisation [Staphylococcal Chromosome Cassette (SCC) mec and spa-typing]. Pulsed-field gel electrophoresis (PFGE) was performed on selected isolates with the same spa-type. Twenty-one MRSA isolates were selected for whole-genome sequencing (WGS) based on spa-type, PFGE clustering, time and place of isolation.

Results: Eighteen percent (n = 95/529) and 33% (n = 234/710) of isolates collected, from two public tertiary academic hospitals in the Gauteng (GAU) and the Western Cape (WC) provinces, were identified as MRSA, respectively. The most dominant clone in the GAU hospital was t037-III-MRSA (43.2%; n = 41/95). The most dominant clones in the WC hospital was t037-III-MRSA (23.9%, n = 56/234) and t045-I-MRSA (23.5%, n = 55/234). The GAU-t037-III-MRSA cases and WC-t045-I-MRSA cases occurred in the paediatric patient population, whereas the WC-t037-III-MRSA cases occurred in the adult patient population. A novel spa-type (t19935) was detected in the GAU hospital. PFGE showed that the GAU- and WC-t037-III-MRSA isolates were genetically indistinguishable, as well as most of the WC-t045-I-MRSA isolates. The Vienna/Hungarian/Brazilian clone and British EMRSA-3 clone were in circulation and a low frequency of single nucleotide polymorphisms (SNP) (≤20) differences was observed among isolates with the same spa-type.

Conclusion: The low number of SNP differences is suggestive of uninterrupted strain transmission and the persistence of t037-III-MRSA and t045-I-MRSA from 2013 to 2017 in the two studied hospitals. Alternative infection prevention and control strategies should be considered to supplement control efforts.

Fig 1. Dendrogram for t037-MRSA cases detected in the Gauteng and the Western Cape hospital.

• = Isolates underwent WGS; NICU = Neonatal ICU; SICU = Surgical ICU; PMICU = Paediatric medical ICU; PSW = Paediatric surgery ward; PW = Paediatric ward; WC = Western Cape; GAU = Gauteng.

Fig 2. Dendrogram for t045-MRSA cases detected in the Western Cape.

• = Isolates underwent WGS; NN = Neonatology, NHC = Neonatal high care; PHAE = Paediatrics haematology; PICU = Paediatric ICU; PW = Paediatric ward; WC = Western Cape.

Fig 3. Molecular and phylogenetic comparison of a selected set of MRSA strains (n = 21).

The phylogenetic tree and timeline was drawn with Microreact version 92.0.0 (https://microreact.org/project/sbBQtaWKnKdCHZ6L7bbQgJ/a639f664). NICU = Neonatal ICU; PMICU = Paediatric medical ICU; PSW = Paediatric surgery ward; PHAE = Paediatrics haematology; NN = Neonatology; PICU = Paediatric ICU; SICU = Surgical ICU. Reprinted from https://microreact.org/project/sbBQtaWKnKdCHZ6L7bbQgJ/a639f664 under a CC BY licence, with permission from the Centre for Genomic Pathogen Surveillance.