A genomic infection control study for Staphylococcus aureus in two Ghanaian hospitals

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 hospital outbreaks in Ghana and describe genomic features of the isolates sampled in the outbreaks. The study was carried out at Korle-Bu Teaching Hospital and Lekma Hospital where the suspected outbreaks occurred in 2012 and 2015, respectively. The isolates collected from the two hospitals were from three sources including carriage, invasive disease, and the environment. Whole genome sequencing of the isolates was performed and the sequence reads were mapped to the 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. The isolates belonged to diverse sequence types (STs) with ST15 and ST152 most common. All isolates carried the gene, with low prevalence of and genes also observed. All isolates were negative. The genes were common and observed in distinct lineages that revealed diverse phages. At Korle-Bu Teaching Hospital, the genomics data indicated several transmission events of ST15 involving contamination of various surfaces in the pediatric emergency ward where the outbreak occurred. 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 genes among the isolates.