Population structure, biogeography and transmissibility of mycobacterium tuberculosis
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Date
Authors
Freschi, Luca
Vargas Jr., Roger
Husain, Ashaque
Kamal, S.M. Mostofa
Skrahina, Alena
Tahseen, Sabira
Ismail, Nazir Ahmed
Barbova, Anna
Niemann, Stefan
Cirillo, Daniela Maria
Journal Title
Journal ISSN
Volume Title
Publisher
Nature Research
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.
Description
Keywords
Lineages, Human, Tuberculosis (TB), Mycobacterium tuberculosis (MTB)
Sustainable Development Goals
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.