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dc.contributor.author | Freschi, Luca![]() |
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dc.contributor.author | Vargas Jr., Roger![]() |
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dc.contributor.author | Husain, Ashaque![]() |
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dc.contributor.author | Kamal, S.M. Mostofa![]() |
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dc.contributor.author | Skrahina, Alena![]() |
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dc.contributor.author | Tahseen, Sabira![]() |
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dc.contributor.author | Ismail, Nazir Ahmed![]() |
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dc.contributor.author | Barbova, Anna![]() |
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dc.contributor.author | Niemann, Stefan![]() |
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dc.contributor.author | Cirillo, Daniela Maria![]() |
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dc.contributor.author | Dean, Anna S.![]() |
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dc.contributor.author | Zignol, Matteo![]() |
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dc.contributor.author | Farhat, Maha Reda![]() |
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dc.date.accessioned | 2022-11-01T13:22:38Z | |
dc.date.available | 2022-11-01T13:22:38Z | |
dc.date.issued | 2021-10-20 | |
dc.description.abstract | Mycobacterium tuberculosis is a clonal pathogen proposed to have co-evolved with its human host for millennia, yet our understanding of its genomic diversity and biogeography remains incomplete. Here we use a combination of phylogenetics and dimensionality reduction to reevaluate the population structure of M. tuberculosis, providing an in-depth analysis of the ancient Indo-Oceanic Lineage 1 and the modern Central Asian Lineage 3, and expanding our understanding of Lineages 2 and 4. We assess sub-lineages using genomic sequences from 4939 pan-susceptible strains, and find 30 new genetically distinct clades that we validate in a dataset of 4645 independent isolates. We find a consistent geographically restricted or unrestricted pattern for 20 groups, including three groups of Lineage 1. The distribution of terminal branch lengths across the M. tuberculosis phylogeny supports the hypothesis of a higher transmissibility of Lineages 2 and 4, in comparison with Lineages 3 and 1, on a global scale. We define an expanded barcode of 95 single nucleotide substitutions that allows rapid identification of 69 M. tuberculosis sub-lineages and 26 additional internal groups. Our results paint a higher resolution picture of the M. tuberculosis phylogeny and biogeography. | en_US |
dc.description.department | Medical Microbiology | en_US |
dc.description.librarian | am2022 | en_US |
dc.description.uri | http://www.nature.com/naturecommunications | en_US |
dc.identifier.citation | Freschi, L., Vargas Jr, R., Husain, A. et al. 2021, 'Population structure, biogeography and transmissibility of mycobacterium tuberculosis', Nature Communications, vol. 12, no. 6099, pp. 1-11, doi : 10.1038/s41467-021-26248-1. | en_US |
dc.identifier.issn | 2041-1723 | |
dc.identifier.other | 10.1038/s41467-021-26248-1 | |
dc.identifier.uri | https://repository.up.ac.za/handle/2263/88067 | |
dc.language.iso | en | en_US |
dc.publisher | Nature Research | en_US |
dc.rights | © The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License. | en_US |
dc.subject | Lineages | en_US |
dc.subject | Human | en_US |
dc.subject | Tuberculosis (TB) | en_US |
dc.subject | Mycobacterium tuberculosis (MTB) | en_US |
dc.title | Population structure, biogeography and transmissibility of mycobacterium tuberculosis | en_US |
dc.type | Article | en_US |