Infection and Drug Resistance (Oct 2018)
A genomic infection control study for Staphylococcus aureus in two Ghanaian hospitals
Abstract
Eric S Donkor,1 Dorota Jamrozy,2 Richael O Mills,3,4 Thomas Dankwah,3 Philip K Amoo,5 Beverly Egyir,6 Ebenezer V Badoe,7 Joana Twasam,8 Stephen D Bentley2 1Department of Medical Microbiology, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra, Ghana; 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; 3Central Laboratory, Korle-Bu Teaching Hospital, Accra, Ghana; 4Department of Biomedical Sciences, University of Cape Coast, Cape Coast Ghana; 5Public Health Unit, Korle-Bu Teaching Hospital, Accra, Ghana; 6Bacteriology Unit, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana; 7Department of Child Health, School of Medicine and Dentistry, University of Ghana, Accra, Ghana; 8Laboratory Unit, Lekma Hospital, Accra, Ghana Background: Whole genome sequencing analysis (WGSA) provides the best resolution for typing of bacterial isolates and has the potential for identification of transmission pathways. The aim of the study was to apply WGSA to elucidate the possible transmission events involved in two suspected Staphylococcus aureus hospital outbreaks in Ghana and describe genomic features of the S. aureus isolates sampled in the outbreaks. Methods: The study was carried out at Korle-Bu Teaching Hospital and Lekma Hospital where the suspected outbreaks occurred in 2012 and 2015, respectively. The S. aureus isolates collected from the two hospitals were from three sources including carriage, invasive disease, and the environment. Whole genome sequencing of the S. aureus isolates was performed and the sequence reads were mapped to the S. aureus reference genome of strain USA300_FPR3757. A maximum-likelihood phylogenetic tree was reconstructed. Multilocus sequence typing together with the analysis of antimicrobial resistance and virulence genes were performed by short read mapping using the SRST2. Results: The S. aureus isolates belonged to diverse sequence types (STs) with ST15 and ST152 most common. All isolates carried the blaZ gene, with low prevalence of tetK and dfrG genes also observed. All isolates were mecA negative. The pvl genes were common and observed in distinct lineages that revealed diverse Sa2int phages. At Korle-Bu Teaching Hospital, the genomics data indicated several transmission events of S. aureus ST15 involving contamination of various surfaces in the pediatric emergency ward where the outbreak occurred. Conclusion: The pattern of dissemination of the ST15 clone in the emergency ward of Korle-Bu Teaching Hospital highlights a basic problem with disinfection of environmental surfaces at the hospital. Diverse phage population rather than a single highly transmissible phage type likely mediates the high prevalence of pvl genes among the S. aureus isolates. Keywords: Staphylococcus aureus, sequencing, transmission, outbreak, Ghana
