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PHYLOGENOMIC AND GENOMIC ANALYSIS REVEALS UNIQUE AND SHARED GENETIC SIGNATURES OF MYCOBACTERIUM KANSASII COMPLEX SPECIES
Produção científica do Laboratório de Genética Molecular de Microrganismos.
Impact Statement: Mycobacterium kansasii complex (MKC) is a group of closely related non-tuberculous mycobacteria species, recognized as a significant source of human infection. Species belonging to the MKC may present a broad spectrum of virulence, antimicrobial resistance and pathogenicity and there is a lack of knowledge about their genomic content related to these broad phenotypes. We have provided whole genomic sequencing DNA for 342 MKC isolates and, together with public data, investigated the MKC pangenome, mobilome, resistome, virulome and defence systems and show unique and shared genetic signatures within MKC species. Furthermore, with phylogenomic and Bayesian population analysis, we inferred the distribution and emergence of the Mycobacterium kansasii species lineages and sub-lineages. This study has considerably expanded the MKC available data, by providing genomic sequences of isolates from countries and global regions with unknown or poorly described MKC data until then.
Data Summary: Next generation sequencing (NGS) data generated in the study are available in the NCBI Sequence Read Archive (SRA) repository under the accession number PRJNA1048499 and the accession numbers for all data sets used are provided in Table S1 (available in the online version of this article).
Data Availability: All sequenced reads are available in BioProject PRJNA1048499. Supplementary tables 1 to 19 providing details of used data and results of this study are available on the Microbiology Figshare data repository platform: https://doi.org/10.6084/m9.figshare.26014465.v1.
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Affilliation
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 nontuberculous 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.
Publisher
Microbiology Society
Citation
MACHADO FILHO, Edson Silva et al. Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species. Microbial Genomics, v. 10, n. 7, p. 1-16, 17 July 2024.DOI
10.1099/mgen.0.001266ISSN
2057-5858Notes
Produção científica do Laboratório de Biologia Molecular Aplicada a Micobactérias.Produção científica do Laboratório de Genética Molecular de Microrganismos.
Impact Statement: Mycobacterium kansasii complex (MKC) is a group of closely related non-tuberculous mycobacteria species, recognized as a significant source of human infection. Species belonging to the MKC may present a broad spectrum of virulence, antimicrobial resistance and pathogenicity and there is a lack of knowledge about their genomic content related to these broad phenotypes. We have provided whole genomic sequencing DNA for 342 MKC isolates and, together with public data, investigated the MKC pangenome, mobilome, resistome, virulome and defence systems and show unique and shared genetic signatures within MKC species. Furthermore, with phylogenomic and Bayesian population analysis, we inferred the distribution and emergence of the Mycobacterium kansasii species lineages and sub-lineages. This study has considerably expanded the MKC available data, by providing genomic sequences of isolates from countries and global regions with unknown or poorly described MKC data until then.
Data Summary: Next generation sequencing (NGS) data generated in the study are available in the NCBI Sequence Read Archive (SRA) repository under the accession number PRJNA1048499 and the accession numbers for all data sets used are provided in Table S1 (available in the online version of this article).
Data Availability: All sequenced reads are available in BioProject PRJNA1048499. Supplementary tables 1 to 19 providing details of used data and results of this study are available on the Microbiology Figshare data repository platform: https://doi.org/10.6084/m9.figshare.26014465.v1.
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