Whole-genome sequencing and epidemiological analysis do not provide evidence for cross-transmission of mycobacterium abscessus in a cohort of pediatric cystic fibrosis patients

Clin Infect Dis. 2015 Apr 1;60(7):1007-16. doi: 10.1093/cid/ciu967. Epub 2014 Dec 1.


Background: Mycobacterium abscessus has emerged as a major pathogen in cystic fibrosis (CF) patients and has been associated with poor clinical outcomes, particularly following lung transplant. We investigated the acquisition of this bacterium in a cohort of pediatric CF patients.

Methods: Demographic and patient location data were used to uncover epidemiological links between patients with genetically related strains of M. abscessus that had been previously typed by variable-number tandem repeat profiling. Whole-genome sequencing was applied to 27 M. abscessus isolates from the 20 patients in this cohort to provide definitive data on the genetic relatedness of strains.

Results: Whole-genome sequencing data demonstrated that M. abscessus isolates from 16 patients were unrelated, differing by at least 34 single-nucleotide polymorphisms (SNPs) from any other isolate, suggesting that independent acquisition events have occurred. Only 2 clusters of very closely related (<25 SNPs) isolates from different patients were seen. The first cluster contained 8 isolates, differing by a maximum of 17 SNPs, from a sibling pair who had intense exposure to each other both inside and outside the hospital. The second cluster contained 3 isolates, differing by a maximum of 24 SNPs, from 2 individuals with no apparent epidemiological links.

Conclusions: We have not demonstrated cross-transmission of M. abscessus within our hospital, except between 1 sibling pair. Alternative routes of acquisition of M. abscessus infection, in particular the environment, require further investigation.

Keywords: Mycobacterium abscessus; VNTR; cross-transmission; cystic fibrosis; whole-genome sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Child
  • Child, Preschool
  • Cluster Analysis
  • Cohort Studies
  • Cystic Fibrosis / complications*
  • Epidemiologic Methods*
  • Female
  • Hospitals, Pediatric
  • Humans
  • Male
  • Molecular Typing
  • Mycobacterium / classification*
  • Mycobacterium / genetics
  • Mycobacterium / isolation & purification
  • Mycobacterium Infections, Nontuberculous / epidemiology*
  • Mycobacterium Infections, Nontuberculous / microbiology
  • Mycobacterium Infections, Nontuberculous / transmission*
  • Respiratory Tract Infections / epidemiology*
  • Respiratory Tract Infections / microbiology
  • Respiratory Tract Infections / transmission*
  • Sequence Homology