ArticlePLOS global public health2026
Integrated epidemiologic investigation and genomic confirmation of a Klebsiella pneumoniae neonatal sepsis outbreak in Botswana.
Article in PLOS global public health, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Klebsiella pneumoniae (Kpn) is a major cause of infant mortality worldwide, with most transmission occurring among hospitalized neonates in low- and middle-income countries where infections caused by multidrug-resistant Kpn (MDR-Kpn) are increasingly common. We hypothesized that integrating laboratory surveillance for neonatal colonization and infection, real-time epidemiologic investigations, and whole-genome sequencing (WGS) could identify transmission pathways to guide targeted infection prevention and control (IPC) strategies. We conducted Kpn surveillance in a 36-bed neonatal unit in Botswana over 12 months (2022-2023). WGS was performed on Kpn isolates from bloodstream infections (BSIs), and MDR-Kpn isolates collected from environmental sampling during outbreaks and twice-monthly colonization screenings (skin and perirectal swabs) using culture media selective for MDR-Kpn (CHROMagar Extended-spectrum beta-lactamase [ESBL]/SuperCarba). WGS data were analyzed using multilocus sequence typing (MLST), pangenome and reference-based single-nucleotide polymorphism (SNP) analyses, and Bayesian phylogenetics. We identified 55 Kpn BSIs during the 12-month surveillance period and the median prevalence of MDR-Kpn colonization was 28%. Kpn was recovered from multi-use intravenous (IV) fluid bags during a Kpn outbreak (41 BSIs, 10 deaths), which was controlled by implementing a 24-hour discard policy for IV medications. Among 270 Kpn isolates available (28 BSI, 232 colonizing, 10 environmental [six IV fluid, four sink drain]), WGS confirmed over half of BSI genomes (n = 17) and all six IV fluid isolates belonged to ST1414 and were closely related (<25 SNPs). The ST1414 clone was susceptible to third-generation cephalosporins and was therefore not detected during MDR-Kpn colonization screening. This study reinforces the value of integrating WGS with real-time epidemiologic investigations to understand transmission dynamics and guide IPC. Colonization surveillance focused solely on MDR-Kpn may overlook drug-susceptible but outbreak-prone strains.
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