Epidemiological investigation of an Acinetobacter baumannii outbreak using Core Genome Multilocus Sequence Typing

Abstract Obiectives Carbapenem-resistant (CR) Acinetobacter baumannii is a serious nosocomial pathogen able to cause a variety of serious, often life-threatening infections and outbreaks. We aimed to investigate the molecular epidemiology of clinical isolates of CR A. baumannii from an outbreak that occurred in the intensive care unit (ICU) of our hospital. Methods From January to April 2017, 13 CR A. baumannii isolates were collected from 7 patients treated in the ICU at the “L. Spallanzani” hospital, Rome, Italy. Typing was performed by the repetitive extragenic palindromic sequence (rep)-PCR-based DiversiLab system. Whole Genome Sequencing (WGS) data were used for in silico analysis of traditional Multi Locus Sequence Typing (MLST) results, for identifying resistance genes, and for core genome MLST (cgMLST) analysis. Epidemiological data were obtained from hospital records. Results All isolates showed a carbapenem-resistant profile, and carried the bla OXA-23 carbapenemase gene. Typing performed by rep-PCR and MLST showed that the isolates clustered into one group while the cgMLST approach, which uses 2390 gene targets to characterize the gene-by-gene allelic profile, highlighted the presence of two cluster types. These results allowed us to identify two patients who were likely to be the source of two separate transmission chains. Conclusion Our results show that whole-genome-DNA sequencing by cgMLST is a valuable tool, better suited for prompt epidemiological investigations than traditional typing methods because of its higher discriminatory ability in determining clonal relatedness.