Phylogenomic and genomic analysis reveals unique and shared genetic signatures of <i>Mycobacterium kansasii </i>complex species
Creators: name: Machado, Edson
name: Vasconcellos, Sidra
name: Gomes, Lia
name: Catanho, Marcos
name: Ramos, Jesus
name: Carvalho, Luciana de
name: Goldenberg, Telma
name: Dalcolmo, Margareth
name: Redner, Paulo
name: Caldas, Paulo
name: Campos, Carlos
name: Lourenço, Maria Cristina
name: Lasunskaia, Elena
name: Mussi, Vinicius
name: Spinasse, Lizania
name: Vinhas, Solange
name: Rigouts, Leen
name: Cogneau, Sari
name: de Rijk, Pim
name: Utpatel, Christian
name: Kaustova, Jarmila
name: van der Laan, Tridia
name: de Neeling, Han
name: Rastogi, Nalin
name: Levina, Klavdia
name: Kütt, Marge
name: Mokrousov, Igor
name: Zhuravlev, Viacheslav
name: Makhado, Ndivhu
name: Žolnir-Dovč, Manca
name: Jankovic, Vera
name: de Waard, Jacobus
name: Sisco, Maria
name: Soolingen, Dick van
name: Niemann, Stefan
name: C. de Jong, Bouke
name: Meehan, Conor
name: Suffys, Philip
Publisher: name: Microbiology Society
Year: 2024
Subjects: classificationCode: 320211
subject: Infectious diseases
classificationCode: 310204
subject: Genomics and transcriptomics
classificationCode: 310203
subject: Computational ecology and phylogenetics
classificationCode: 310410
subject: Phylogeny and comparative analysis
classificationCode: 310704
subject: Microbial genetics
classificationCode: 310799
subject: Microbiology not elsewhere classified

description: <br>Supplementary Material/Supporting data/code for Phylogenomic and genomic analysis reveals unique and shared genetic signatures of <i>Mycobacterium kansasii</i> complex species, as described on Microbial Genomics.<b>Species belonging to the </b><b><i>Mycobacterium kansasii</i></b><b> 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 </b><b><i>M. kansasii</i></b><b> (</b><b><i>stricto sensu</i></b><b>), 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 defense systems and show that the MKC species harbors unique and shared genomic signatures. High frequency of presence of prophages and different types of defense systems was observed. We found that the </b><b><i>M. kansasii</i></b><b> 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 </b><b><i>M. kansasii</i></b><b> lineage emerged during the 20th century. Further analysis of the </b><b><i>M. kansasii</i></b><b> genomes revealed almost 300 regions of difference contributing to genomic diversity, as well as fixed mutations that may explain the </b><b><i>M. kansasii</i></b><b>'s increased virulence and drug resistance.</b>