Using Genomic and Traditional Epidemiologic Approaches to Define Complex Transmission Pathways of Klebsiella pneumoniae Infection in a Neonatal Unit in Botswana, 2022–2023

作者：Jonathan Strysko, Weiming Hu, Kagiso Mochankana, Janet Thubuka, Tshiamo Zankere, Boingotlo Gopolang, Erin Theiller, Steven M. Jones, Chimwemwe Viola Tembo, Tlhalefo Dudu Ntereke, Teresia Gatonye, Kwana Lechiile, Tapoloso Keatholetswe, Colleen Bianco, Susan Coffin, Carolyn McGann, Kyle Bittinger, Ebbing Lautenbach, Naledi Mannathoko, Margaret Mokomane, Mosepele Mosepele, Melissa Richard‐Greenblatt, Britt Nakstad, David A. Goldfarb, Paul J. Planet, Ahmed M. Moustafa · 发表于：medRxiv · 年份：2025 · DOI：10.1101/2025.11.06.25339637 · 被引用次数：3 · 研究领域：Antibiotic Resistance in Bacteria、Neonatal and Maternal Infections、Antibiotic Use and Resistance

Abstract Background 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. Methods and Findings 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 iso...