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

Abstract

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.