Carbapenem resistant Klebsiella pneumoniae isolates at a tertiary hospital in Cape Town, South Africa, are dominated by specific local clones rather than previously described international lineages

Carbapenem-resistant K. pneumoniae (CRKP) are increasingly prevalent pathogens in hospital settings worldwide. In early 2019, an outbreak of carbapenem-resistant Enterobacterales (CRE) at a tertiary hospital in South Africa triggered a retrospective investigation to determine local CRKP molecular epidemiology. The evolution of CRE at the institution progressed from sporadic cases in 2016-2017 to establishment of CRKP as an endemic pathogen by 2020. Of 778 clinical and carriage CRKP isolates (2016-2020), 413 (53%) were collected and sequenced. Sequence type (ST) 2621 (164, 40%) and ST39 (164, 40%) predominated with several minor STs making up the remainder. The majority of ST2621 associated with blaOXA-181 were isolated from adult patients (59%) and clinical samples (84%). ST39 with blaNDM-1 was predominantly identified in carriage isolates (76%) from neonatal (57%) and paediatric (38%) patients. The establishment of these unique CRKP clones distinct from the globally dominant epidemic lineages suggests local acquisition of carbapenemase genes with subsequent institutional propagation. Strengthening of infection prevention practices and antibiotic stewardship programmes at this institution is critical to reduce CRKP transmission and curtail evolution of future antimicrobial resistant clones.