Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii

Nat Commun. 2021 May 3;12(1):2491. doi: 10.1038/s41467-021-22760-6.


Mycobacterium kansasii can cause serious pulmonary disease. It belongs to a group of closely-related species of non-tuberculous mycobacteria known as the M. kansasii complex (MKC). Here, we report a population genomics analysis of 358 MKC isolates from worldwide water and clinical sources. We find that recombination, likely mediated by distributive conjugative transfer, has contributed to speciation and on-going diversification of the MKC. Our analyses support municipal water as a main source of MKC infections. Furthermore, nearly 80% of the MKC infections are due to closely-related M. kansasii strains, forming a main cluster that apparently originated in the 1900s and subsequently expanded globally. Bioinformatic analyses indicate that several genes involved in metabolism (e.g., maintenance of the methylcitrate cycle), ESX-I secretion, metal ion homeostasis and cell surface remodelling may have contributed to M. kansasii's success and its ongoing adaptation to the human host.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Drinking Water / microbiology*
  • Energy Metabolism / genetics
  • Genetic Variation / genetics
  • Genetics, Population / methods
  • Genome, Bacterial / genetics*
  • Genomics
  • Humans
  • Lung Diseases / epidemiology*
  • Lung Diseases / microbiology
  • Mycobacterium Infections, Nontuberculous / epidemiology*
  • Mycobacterium Infections, Nontuberculous / microbiology
  • Mycobacterium kansasii / genetics*
  • Mycobacterium kansasii / isolation & purification
  • Virulence / genetics
  • Water Microbiology


  • Drinking Water