Genomic epidemiology of multiple Acinetobacter baumannii outbreaks in a veterinary intensive care unit

Acinetobacter baumannii is a pathogen primarily found in health-care associated settings. Its potential to acquire and control a large reservoir of antimicrobial resistance genes and its ability to survive for extended periods in the environment makes it a threat and challenge for hospitals. Identifying transmission chains in repeated outbreaks of A. baumannii is difficult because existing typing methods lack resolution. Whole genome sequencing (WGS) forms an attractive alternative to investigate outbreaks events. We investigated two outbreaks of A. baumannii in a companion animal intensive care unit (caICU) at the faculty of Veterinary Medicine of Utrecht University in 2012 and 2014. Multi Locus Sequence Typing (MLST) of the isolates revealed that all animal isolates from both outbreaks in the caICU belonged to sequence type 2. Isolates from the outbreaks had identical resistance phenotypes, which suggested that the outbreak events were linked. Using genome sequencing we investigated if these outbreaks were part of a protracted outbreak or were independent events. Time-measured phylogenetic reconstruction on WGS data of the clinical isolates, reference isolates and public genome sequences revealed that the outbreaks were two independent events and that isolates from both outbreaks diverged at approximately 30 years before. Our study shows the benefit of WGS combined with molecular clock investigations in outbreak management in a clinical setting.