Carbapenem-resistant Acinetobacter baumannii at a hospital in Botswana: detecting a protracted outbreak using whole genome sequencing

作者：Jonathan Strysko, Tefelo Thela, Andries Feder, Janet Thubuka, Tichaona Machiya, Jack Mkubwa, Kagiso Mochankana, Celda Tiroyakgosi, Kgomotso Kgomanyane, Tlhalefo Dudu Ntereke, Tshiamo Zankere, Kwana Lechiile, Teresia Gatonye, Chimwemwe Viola Tembo, Moses Vurayai, Naledi Mannathoko, Margaret Mokomane, Ahmed M. Moustafa, David A. Goldfarb, Melissa Richard‐Greenblatt, Carolyn McGann, Susan Coffin, Britt Nakstad, Corrado Cancedda, Ebbing Lautenbach, Dineo Bogoshi, Anthony M. A. Smith, Paul J. Planet · 发表于：Microbiology Spectrum · 年份：2025 · DOI：10.1128/spectrum.01768-25 · 被引用次数：4 · 研究领域：Antibiotic Resistance in Bacteria、Evolution and Genetic Dynamics、Antibiotic Use and Resistance

ABSTRACT Carbapenem-resistant Acinetobacter baumannii (CRAb) has emerged as a major and often fatal cause of bloodstream infections among hospitalized patients in low- and middle-income countries (LMICs). CRAb outbreaks are hypothesized to arise from reservoirs in the hospital environment, but outbreak investigations in LMICs are often limited in scope due to lack of access to whole genome sequencing (WGS). We performed WGS on 43 stored isolates (blood cultures [ n = 23] and environmental swabs [ n = 20]) presumptively identified as A. baumannii collected during 2021–2022 from a 530-bed referral hospital in Gaborone, Botswana, where CRAb infection incidence was rising. Taxonomic assignment, multilocus sequence typing, antimicrobial resistance gene identification, K and O locus typing, and phylogenetic analyses were performed using publicly accessible analysis pipelines. All 23 blood and 25% (5/20) of environmental isolates were confirmed as A. baumannii, 79% ( n = 22) of which were sequence type 1 (ST1). All ST1 isolates harbored genes encoding carbapenemases ( bla NDM-1 , bla OXA-23 ). Phylogenetic analysis demonstrated that nearly identical ST1 isolates spanned wide ranges in time (>1 year), suggesting ongoing transmission from environmental sources. One highly similar clade (average difference of 2.3 single nucleotide polymorphisms) contained all eight neonatal blood isolates and three environmental isolates from the neonatal unit. Environmental isolates included a samp...