Whole genome sequencing to analyse patient-to-patient transmission of Mycobacterium abscessus in cystic fibrosis patients.

Background:Mycobacterium abscessus is an extensively drug resistant pathogen that causes pulmonary disease particularly in cystic fibrosis patients. Identifying direct patient-to-patient transmission of M. abscessus is critically important in infection control and the management of these high-risk patients. While clinical laboratories use molecular epidemiology to understand transmission it is only recently that laboratories have begun adopting whole-genome sequencing (WGS) for these studies. However there is still conflicting evidence as to how M. abscessus is acquired and transmitted within these patient cohorts.Methods:We sequenced the whole genomes of 145 M. abscessus isolates from 62 patients seen at four hospitals in two countries over 16 years.Results:We have shown that WGS of M. abscessus isolates can provide enough information to replace multiple existing molecular assays used routinely in clinical microbiology laboratories. We found only one episode of direct patient-to-patient transmission. In contrast, we found many instances where patients acquired unique M. abscessus strains even after spending considerable time on the same wards with other M. abscessus positive patients. We have also shown that a comparison of a fixed number of core single nucleotide variants (SNVs) cannot be used to infer cross-transmission across all M. abscessus isolates and propose analysing samples within clonal complexes separately.Conclusions:This novel analysis has demonstrated that the majority of patients in this study have not acquired M. abscessus through direct patient-patient transmission. Tracking transmission using WGS will only realise its full potential with proper environmental screening as well as patient sampling.