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

TL;DR

This study found that carbapenem-resistant Klebsiella pneumoniae in a South African hospital is dominated by local clones rather than global strains, highlighting the need for region-specific infection control.

Contribution

The study identifies unique local CRKP clones in South Africa, distinct from international lineages, and emphasizes local acquisition and spread of resistance genes.

Findings

CRKP isolates in the hospital were dominated by ST2621 and ST39, which were associated with specific carbapenemase genes.

These clones were primarily found in adult and neonatal/pediatric patients, suggesting local acquisition and institutional spread.

The findings indicate that local CRKP clones differ from global epidemic lineages, requiring tailored infection control strategies.

Abstract

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.

Carbapenem resistant K. pneumoniae (CRKP) have emerged as a cause of hospital and community acquired infections, posing a significant threat to public health, and have hence been listed as a priority pathogen by the World Health Organization (WHO). In this study we investigated the molecular epidemiology of CRKP and found that local endemic CRKP was dominated by two sequence types which had both been present since 2016. These may be local clones that have acquired carbapenemase genes and become disseminated in our setting, a marked difference from the intercontinental spread observed for other successful CRKP lineages. Our findings will assist in improved monitoring and identification of local CRKP, which will aid in preventing nosocomial infections in vulnerable patients by contributing to guidelines for infection prevention and control practises. Furthermore, this implies that in other understudied locations, CRKP also need to be investigated, to determine how local clones may differ and how they arise. This can in turn teach us about patterns of evolution of successful clones, especially with respect to particular plasmid types or carbapenemase genes.

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