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Volume 10, Issue 7

Phylogenomic and genomic analysis reveals unique and shared genetic signatures of complex species Open Access

Abstract

Species belonging to the complex (MKC) are frequently isolated from humans and the environment and can cause serious diseases. The most common MKC infections are caused by the species (), leading to tuberculosis-like disease. However, a broad spectrum of virulence, antimicrobial resistance and pathogenicity of these non-tuberculous mycobacteria (NTM) are observed across the MKC. Many genomic aspects of the MKC that relate to these broad phenotypes are not well elucidated. Here, we performed genomic analyses from a collection of 665 MKC strains, isolated from environmental, animal and human sources. We inferred the MKC pangenome, mobilome, resistome, virulome and defence systems and show that the MKC species harbours unique and shared genomic signatures. High frequency of presence of prophages and different types of defence systems were observed. We found that the species splits into four lineages, of which three are lowly represented and mainly in Brazil, while one lineage is dominant and globally spread. Moreover, we show that four sub-lineages of this most distributed lineage emerged during the twentieth century. Further analysis of the genomes revealed almost 300 regions of difference contributing to genomic diversity, as well as fixed mutations that may explain the ’s increased virulence and drug resistance.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): lineages , Mycobacterium kansasii , pangenome , phylogenomics and virulence
Funding
This study was supported by the:
  • Deutsches Zentrum für Infektionsforschung
    • Principle Award Recipient: NotApplicable
  • Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (Award 26/210.877/2019)
    • Principle Award Recipient: PhilipSuffys
  • Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (Award 26/204.546/2021)
    • Principle Award Recipient: PhilipSuffys
  • Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (Award 26/201.115/2022)
    • Principle Award Recipient: PhilipSuffys
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (Award 207422/2014-1)
    • Principle Award Recipient: PhilipSuffys
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (Award 310418/2016-0)
    • Principle Award Recipient: PhilipSuffys
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (Award 307474/2020-8)
    • Principle Award Recipient: PhilipSuffys
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (Award 306344/2021-1)
    • Principle Award Recipient: ElenaLasunskaia
  • Academy of Medical Sciences (Award SBF006\1090)
    • Principle Award Recipient: ConorJ Meehan
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2024-07-17
2025-06-24
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Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species
M Gen 10, 001266 (2024); https://doi.org/10.1099/mgen.0.001266
/content/journal/mgen/10.1099/mgen.0.001266
/content/journal/mgen/10.1099/mgen.0.001266
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