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Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation

Mycobacterium avium is separated into four subspecies: M. avium subspecies avium (MAA), M. avium subspecies silvaticum (MAS), M. avium subspecies hominissuis (MAH), and M. avium subspecies paratuberculosis (MAP). Understanding the mechanisms of host and tissue adaptation leading to their clinical si...

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Autores principales: Mizzi, Rachel, Plain, Karren M., Whittington, Richard, Timms, Verlaine J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9121174/
https://www.ncbi.nlm.nih.gov/pubmed/35602010
http://dx.doi.org/10.3389/fmicb.2022.892333
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author Mizzi, Rachel
Plain, Karren M.
Whittington, Richard
Timms, Verlaine J.
author_facet Mizzi, Rachel
Plain, Karren M.
Whittington, Richard
Timms, Verlaine J.
author_sort Mizzi, Rachel
collection PubMed
description Mycobacterium avium is separated into four subspecies: M. avium subspecies avium (MAA), M. avium subspecies silvaticum (MAS), M. avium subspecies hominissuis (MAH), and M. avium subspecies paratuberculosis (MAP). Understanding the mechanisms of host and tissue adaptation leading to their clinical significance is vital to reduce the economic, welfare, and public health concerns associated with diseases they may cause in humans and animals. Despite substantial phenotypic diversity, the subspecies nomenclature is controversial due to high genetic similarity. Consequently, a set of 1,230 M. avium genomes was used to generate a phylogeny, investigate SNP hotspots, and identify subspecies-specific genes. Phylogeny reiterated the findings from previous work and established that Mycobacterium avium is a species made up of one highly diverse subspecies, known as MAH, and at least two clonal pathogens, named MAA and MAP. Pan-genomes identified coding sequences unique to each subspecies, and in conjunction with a mapping approach, mutation hotspot regions were revealed compared to the reference genomes for MAA, MAH, and MAP. These subspecies-specific genes may serve as valuable biomarkers, providing a deeper understanding of genetic differences between M. avium subspecies and the virulence mechanisms of mycobacteria. Furthermore, SNP analysis demonstrated common regions between subspecies that have undergone extensive mutations during niche adaptation. The findings provide insights into host and tissue specificity of this genetically conserved but phenotypically diverse species, with the potential to provide new diagnostic targets and epidemiological and therapeutic advances.
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spelling pubmed-91211742022-05-21 Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation Mizzi, Rachel Plain, Karren M. Whittington, Richard Timms, Verlaine J. Front Microbiol Microbiology Mycobacterium avium is separated into four subspecies: M. avium subspecies avium (MAA), M. avium subspecies silvaticum (MAS), M. avium subspecies hominissuis (MAH), and M. avium subspecies paratuberculosis (MAP). Understanding the mechanisms of host and tissue adaptation leading to their clinical significance is vital to reduce the economic, welfare, and public health concerns associated with diseases they may cause in humans and animals. Despite substantial phenotypic diversity, the subspecies nomenclature is controversial due to high genetic similarity. Consequently, a set of 1,230 M. avium genomes was used to generate a phylogeny, investigate SNP hotspots, and identify subspecies-specific genes. Phylogeny reiterated the findings from previous work and established that Mycobacterium avium is a species made up of one highly diverse subspecies, known as MAH, and at least two clonal pathogens, named MAA and MAP. Pan-genomes identified coding sequences unique to each subspecies, and in conjunction with a mapping approach, mutation hotspot regions were revealed compared to the reference genomes for MAA, MAH, and MAP. These subspecies-specific genes may serve as valuable biomarkers, providing a deeper understanding of genetic differences between M. avium subspecies and the virulence mechanisms of mycobacteria. Furthermore, SNP analysis demonstrated common regions between subspecies that have undergone extensive mutations during niche adaptation. The findings provide insights into host and tissue specificity of this genetically conserved but phenotypically diverse species, with the potential to provide new diagnostic targets and epidemiological and therapeutic advances. Frontiers Media S.A. 2022-05-06 /pmc/articles/PMC9121174/ /pubmed/35602010 http://dx.doi.org/10.3389/fmicb.2022.892333 Text en Copyright © 2022 Mizzi, Plain, Whittington and Timms. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Mizzi, Rachel
Plain, Karren M.
Whittington, Richard
Timms, Verlaine J.
Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation
title Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation
title_full Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation
title_fullStr Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation
title_full_unstemmed Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation
title_short Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation
title_sort global phylogeny of mycobacterium avium and identification of mutation hotspots during niche adaptation
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9121174/
https://www.ncbi.nlm.nih.gov/pubmed/35602010
http://dx.doi.org/10.3389/fmicb.2022.892333
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