Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species

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Machado, E, Vasconcellos, S, Gomes, L, Catanho, M, Ramos, J, de Carvalho, L, Goldenberg, T, Redner, P, Caldas, P, Campos, C, Dalcolmo, M, Lourenço, MC, Lasunskaia, E, Mussi, V, Spinassé, L, Vinhas, S, Rigouts, L, Cogneau, S, de Rijk, P, Utpatel, C, Kaustova, J, van der Laan, T, de Neeling, H, Rastogi, N, Levina, K, Kütt, M, Mokrousov, I, Zhuravlev, V, Makhado, N, Žolnir-Dovč, M, Jankovic, V, de Waard, J, Sisco, MC, van Soolingen, D, Niemann, S, de Jong, BC, Meehan, CJ ORCID: https://orcid.org/0000-0003-0724-8343 and Suffys, P, 2024. Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species. Microbial Genomics, 10 (7): 001266. ISSN 2057-5858

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Official URL: https://doi.org/10.1099/mgen.0.001266

Abstract

Species belonging to the Mycobacterium kansasii 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 M. kansasii (sensu stricto), 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 M. kansasii 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 M. kansasii lineage emerged during the twentieth century. Further analysis of the M. kansasii genomes revealed almost 300 regions of difference contributing to genomic diversity, as well as fixed mutations that may explain the M. kansasii’s increased virulence and drug resistance.

Item Type:	Journal article
Publication Title:	Microbial Genomics
Creators:	Machado, E., Vasconcellos, S., Gomes, L., Catanho, M., Ramos, J., de Carvalho, L., Goldenberg, T., Redner, P., Caldas, P., Campos, C., Dalcolmo, M., Lourenço, M.C., Lasunskaia, E., Mussi, V., Spinassé, L., Vinhas, S., Rigouts, L., Cogneau, S., de Rijk, P., Utpatel, C., Kaustova, J., van der Laan, T., de Neeling, H., Rastogi, N., Levina, K., Kütt, M., Mokrousov, I., Zhuravlev, V., Makhado, N., Žolnir-Dovč, M., Jankovic, V., de Waard, J., Sisco, M.C., van Soolingen, D., Niemann, S., de Jong, B.C., Meehan, C.J. and Suffys, P.
Publisher:	Microbiology Society
Date:	17 July 2024
Volume:	10
Number:	7
ISSN:	2057-5858
Identifiers:	Number Type 10.1099/mgen.0.001266 DOI 1916223 Other
Rights:	© 2024 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License
Divisions:	Schools > School of Science and Technology
Record created by:	Jeremy Silvester
Date Added:	19 Jul 2024 08:49
Last Modified:	19 Jul 2024 08:49
URI:	https://irep.ntu.ac.uk/id/eprint/51781