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

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 (blaNDM-1, blaOXA-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 sample from a sink drain, which is likely a major reservoir in this setting and highlights the need for targeted environmental remediation. Using a phylogenetically informed approach, we also identified diagnostic genes that distinguish this outbreak clone. These markers hold the potential to provide a low-cost method for tracking future CRAb isolates related to this outbreak. IMPORTANCE : Carbapenem-resistant Acinetobacter baumannii is an increasingly significant cause of hospital-acquired bloodstream infections, particularly in low- and middle-income countries where limited resources often prevent the use of advanced outbreak investigation methods. This study leveraged whole genome sequencing to uncover transmission patterns of these antibiotic-resistant infections which were occurring more frequently in a referral hospital in Botswana. By linking clinical and environmental samples collected over an 18-month period, we identified a cluster of infections genetically linked to samples collected from the environment, including a sample taken from a sink drain in the neonatal unit. Furthermore, the study identified key genes specific to outbreak strains that could be used as diagnostic markers to track future outbreaks, even in the absence of genomic sequencing. These findings demonstrate how combining genomic sequencing with targeted gene identification can guide infection prevention and control efforts, helping to curb the spread of antibiotic resistance in resource-limited settings.