Use of high-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak

Shared care of military trauma and civilian patients has resulted in transmission of multi-resistant Acinetobacter baumannii from military casualties to civilians. Current molecular typing technologies have proven useful in revealing phylogenetic relationships between A. baumannii isolates. However, they are unable to resolve differences between closely related isolates from small-scale outbreaks, where chains of transmission are often unclear. In a recent hospital outbreak in Birmingham, four military patients and two civilian patients were found to be colonized with isolates of multi-resistant A. baumannii that were indistinguishable using standard techniques. We have used high-throughput whole-genome sequencing to identify single nucleotide polymorphisms (SNPs) in these isolates. Our analyses show that closely related MDR-Aci lineages acquire SNPs rapidly enough to unravel some transmission events and to discriminate between alternative epidemiological hypotheses within a small-scale outbreak.