Genomic characterization of sporadic isolates of the dominant clone of Mycobacterium abscessus subspecies massiliense

Sci Rep. 2021 Jul 28;11(1):15336. doi: 10.1038/s41598-021-94789-y.

Abstract

Recent studies have characterized a dominant clone (Clone 1) of Mycobacterium abscessus subspecies massiliense (M. massiliense) associated with high prevalence in cystic fibrosis (CF) patients, pulmonary outbreaks in the United States (US) and United Kingdom (UK), and a Brazilian epidemic of skin infections. The prevalence of Clone 1 in non-CF patients in the US and the relationship of sporadic US isolates to outbreak clones are not known. We surveyed a reference US Mycobacteria Laboratory and a US biorepository of CF-associated Mycobacteria isolates for Clone 1. We then compared genomic variation and antimicrobial resistance (AMR) mutations between sporadic non-CF, CF, and outbreak Clone 1 isolates. Among reference lab samples, 57/147 (39%) of patients with M. massiliense had Clone 1, including pulmonary and extrapulmonary infections, compared to 11/64 (17%) in the CF isolate biorepository. Core and pan genome analyses revealed that outbreak isolates had similar numbers of single nucleotide polymorphisms (SNPs) and accessory genes as sporadic US Clone 1 isolates. However, pulmonary outbreak isolates were more likely to have AMR mutations compared to sporadic isolates. Clone 1 isolates are present among non-CF and CF patients across the US, but additional studies will be needed to resolve potential routes of transmission and spread.

Publication types

  • Multicenter Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • Antitubercular Agents / pharmacology
  • Child
  • Clone Cells
  • Cystic Fibrosis / complications
  • Cystic Fibrosis / diagnosis*
  • Cystic Fibrosis / microbiology
  • Cystic Fibrosis / pathology
  • DNA, Bacterial / genetics*
  • Drug Resistance, Bacterial / genetics
  • Genetic Variation
  • Genome, Bacterial*
  • Humans
  • Middle Aged
  • Mycobacterium Infections, Nontuberculous / complications
  • Mycobacterium Infections, Nontuberculous / diagnosis*
  • Mycobacterium Infections, Nontuberculous / microbiology
  • Mycobacterium Infections, Nontuberculous / pathology
  • Mycobacterium abscessus / classification
  • Mycobacterium abscessus / drug effects
  • Mycobacterium abscessus / genetics*
  • Mycobacterium abscessus / isolation & purification
  • Phylogeny
  • Polymorphism, Single Nucleotide
  • United States / epidemiology

Substances

  • Antitubercular Agents
  • DNA, Bacterial