Molecular epidemiology of Carbapenem-resistant gram-negative bacteria in a regional hospital in KwaZulu-Natal, South Africa.

Abstract

Introduction Carbapenem-resistant Enterobacterales (CRE) are becoming a serious public health threat in South Africa. This is especially true in KwaZulu-Natal (KZN), where regional hospitals are important for patient referrals. However, CREs in these hospitals are not well understood in terms of molecular characterisation. This study examined the burden and genetic basis of carbapenem-resistant Enterobacterales in a new regional hospital compared with higher-level facilities in KZN. Methods We reviewed laboratory surveillance data from three public hospitals: Inkosi Albert Luthuli Central Hospital (quaternary), Mahatma Gandhi Memorial Hospital (regional), and the recently opened Dr Pixley Ka Isaka Seme Memorial Hospital (regional) between 2016 and 2024. We screened a total of 720 carbapenem-resistant Enterobacterales isolates. Phenotypic methods were used to confirm identity and carbapenem resistance of the isolates, and while Polymerase Chain Reaction (PCR) was used to screen isolates for carbapenemase, extended-spectrum β-lactamase (ESBL), and ampC β-lactamase genes. Results CRE accounted for 11.7% of all Enterobacterales, with an increasing trend observed across all hospitals. The newly established regional hospital showed the most rapid increase. The distribution of species varied by hospital level. Klebsiella pneumoniae was most common at the quaternary centre, while Proteus mirabilis was more frequent in regional hospitals. The main carbapenemase genes found were blaOXA-48-like and blaNDM. However, 15.4% of CRE did not harbour detectable carbapenemases, suggesting possible non-enzymatic resistance mechanisms. Notably, 81.5% of isolates carried ESBL and/or ampC genes, and 96.4% harboured multiple β-lactamases (carbapenemases, ESBLs, and/or ampCs), with only 3.6% lacking any screened β- lactamase genes. Conclusion The increasing prevalence of CRE and the presence of various resistance mechanisms in KZN highlight the urgent need for coordinated molecular surveillance, improved infection prevention and control, and synchronised antimicrobial stewardship across all hospital levels.