Population genomics, resistome and plasmidome of invasive Klebsiella pneumoniae isolates in adults hospitalised in Johannesburg, South Africa

Abstract Klebsiella pneumoniae (KPn) is a leading cause of healthcare-associated infections in adults in low- and middle-income countries. We conducted laboratory-based surveillance between 2023 and 2024 in Johannesburg, South Africa, and analysed 508 KPn whole genomes isolated from blood and cerebrospinal fluid cultures of hospitalised adults. We investigated the key antimicrobial resistance (AMR) profiles in invasive KPn isolates, and plasmid-mediated AMR. Overall, 79.1% of the KPn isolates harboured genes conferring a multidrug-resistant (MDR) phenotype. The prevalence of genotypic AMR compared to phenotypic AMR was higher for aminoglycosides and carbapenems, similar for third generation cephalosporins, and lower for colistin, respectively. Three plasmid types, IncX3, IncFII and IncFIB, were most frequently associated with harbouring beta-lactamase genes bla CTX, bla TEM, bla NDM, and bla OXA. On multiple regression modelling, ST2497 was associated with increased risk of death. Overall, our findings contribute to the genomic characterisation of drug-resistant KPn invasive disease in the WHO African Region. Klebsiella pneumoniae (KPn) has emerged as a leading cause of community-associated infections (CAIs) and healthcare-associated infections (HAIs) in adults, 1, 2 with the highest burden of disease in low- and middle-income countries (LMICs). 3 According to a predictive statistical modelling study on the global burden of bacterial antimicrobial resistance (AMR) in 2019, KPn invasive disease (KPn-ID) accounted for 50,000 deaths attributable to AMR in Africa. 3 Due to the rising global public health crisis of bacterial AMR, third-generation-cephalosporin (3GC)- and carbapenem-resistant strains of KPn have been included in the critical group of the World Health Organisation (WHO) Bacterial Priority Pathogens List since 2017, 4 underscoring the need for novel therapeutic agents and preventive strategies. Notably, carbapenem-resistant KPn (CRKp) rose from fifth in 2017 to become the top WHO priority pathogen in 2024, due to limited treatment options, high associated mortality, and rapidly increasing AMR rates across the majority of WHO regions. 4 In a recent meta-analysis, the estimated global prevalence of hospital-acquired CRKp was 28.7% (95% CI, 26.5%–30.9%), with rates exceeding 50.0% in some regions. 5 In addition to AMR, convergence of AMR with hypervirulence genes has been reported in KPn, and poses a new diagnostic and therapeutic challenge. 6 Genomic-based surveillance of KPn, with a particular focus on accurately identifying CRKp and hypervirulent (hvKp) strains, integrated with clinical data, is needed to accurately determine the burden of KPn disease and guide targeted public health interventions aimed at reducing KPn-associated morbidity and mortality in vulnerable populations. 2, 7 Key interventions include the implementation of robust infection prevention and control (IPC) measures, development of novel antimicrobial therapies, and advancement of preventive strategies such as vaccination. 8-10 Despite the growing global threat posed by CRKp and hvKp, molecular surveillance in the WHO African region remains limited, resulting in underestimation of the disease burden and delays in timely, evidence-based responses to emerging threats. 6, 7 We previously reported on the clinical and microbiological epidemiology of KPn-ID in African adults, 11 and now we add to that the detailed genomic epidemiology of KPn infections in hospitalised adults in Johannesburg, South Africa to address the knowledge gap of key AMR and virulence profiles in invasive KPn isolates.