Abstract
BACKGROUND: The molecular epidemiology of carbapenem-resistant Enterobacterales in Cape Town remains largely unknown. OBJECTIVES: This study aimed to describe the molecular epidemiology, resistome, virulome and mobilome of carbapenem-resistant Klebsiella pneumoniae (CRKP) within Cape Town to guide therapy, antimicrobial stewardship and infection prevention and control practices. METHODS: Eighty-five CRKP isolates from hospitalized patients underwent WGS as part of a prospective, multicentre, cross-sectional study, conducted between 1 November 2020 and 30 November 2022, across public-sector and private-sector hospitals in Cape Town, South Africa. RESULTS: MLST revealed three novel types, ST6785, ST6786 and ST6787, while the most common were ST219, ST307, ST17, ST13 and ST2497. Different predominant clones were noted in each hospital. The most common carbapenemase gene was bla(OXA-48-like), detected in 71% of isolates, with bla(NDM) detected in 5%. Notably, co-detection of two carbapenemase genes (bla(OXA-48-like) and bla(NDM)) occurred in 13% of isolates. The yersiniabactin siderophore was detected in 73% of isolates, and was most commonly associated with the ICEKp5 mobile element. All carbapenemases were located on plasmids. The genes bla(OXA-181) and bla(OXA-232) colocalized with a ColKP3 replicon type on assembled contigs in 83% and 100% of cases, respectively. CONCLUSIONS: CRKP epidemiology in Cape Town reflects institutionally dominant, rather than regional, clones. The most prevalent carbapenemase gene was bla(OXA-48-like), in keeping with CRKP epidemiology in South Africa in general. Emerging clones harbouring both bla(OXA-48-like) and bla(NDM), such as ST17, ST2497 and the novel ST6787, are a concern due to the limited availability of appropriate antimicrobial agents in South Africa.