Genomic and epidemiologic investigation of Mycobacterium abscessus isolates in a cystic fibrosis center to determine potential routes of transmission

BACKGROUND: Cystic Fibrosis (CF) Centers worldwide have reported healthcare-associated outbreaks of nontuberculous mycobacteria (NTM). We report a retrospective investigation of shared Mycobacterium abscessus strains among people with cystic fibrosis (pwCF) receiving care at Dell Children's/Ascension combined Pediatric and Adult CF Program (DCMC). METHODS: Whole genome sequencing (WGS) was used to identify genetically similar isolates among 167 NTM isolates from 57 pwCF. Epidemiological investigation, respiratory and environmental isolate comparisons, and watershed mapping were performed. RESULTS: WGS analysis revealed four M. abscessus clusters, two ssp. abscessus and two ssp. massiliense. One subject was infected with two distinct clustered M. abscessus (ssp. abscessus and ssp. massiliense). Epidemiologic investigation demonstrated opportunities for healthcare-associated transmission within all clusters. Two ssp. massiliense subject pairs had healthcare overlaps and high genomic relatedness, including one cohabitating sibling pair. M. abscessus recovered from DCMC revealed genetic similarity to a respiratory isolate from one patient who was never exposed to the hospital environment. CONCLUSIONS: We identified shared M. abscessus strains via genomic analysis among pwCF at DCMC. None of the clustered patient isolates matched hospital environmental isolates at the genomic level. One hospital environmental isolate had genomic similarity to a respiratory isolate of M. abscessus, but the epidemiologic investigation revealed no evidence of subject exposure to the hospital setting. One ssp. massiliense subject pair had the same level of pangenome relatedness as the sibling pair and epidemiological investigation revealed overlap in the clinic, supporting healthcare-associated person-to-person transmission among the pair within a cluster. One pwCF had polyclonal clustered infections, suggesting multiple environmental sources of acquisition outside the healthcare environment.