Carbapenem-resistant Klebsiella pneumoniae South Africa

In late 2018, an outbreak of carbapenem resistant Enterobacterales (CRE) triggered an investigation into the molecular epidemiology and transmission dynamics of CRKP at Tygerberg Hospital (TBH), from sporadic cases in 2016-2017 to establishment as an endemic pathogen by 2020. A total of 414 CRKP were collected and sequenced between (2016 and 2020) including clinical and carriage samples. Sequence type (ST) 2621 (164, 40%) and ST39 (164, 40%) predominated, equally. The majority of ST2621 associated with blaOXA-181 were isolated from adult patients (59%) and clinical samples (84%). ST39 with blaNDM-1 was predominantly isolated from neonatal (57%) and paediatric (38%) isolates from carriage isolates. Diversity within both these lineages indicated circulation locally before introduction repeatedly into TBH occurred. The CRKP endemic at TBH also present a local problem rather than introduction of the dominant epidemic lineages described elsewhere. These may be local clones that acquired carbapenemase genes and became endemic in our setting, a marked difference from the intercontinental spread observed for other successful CRKP lineages.