دورية أكاديمية
Population structure, biogeography and transmissibility of mycobacterium tuberculosis
العنوان: | Population structure, biogeography and transmissibility of mycobacterium tuberculosis |
---|---|
المؤلفون: | 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, Dean, Anna S., Zignol, Matteo, Farhat, Maha Reda |
بيانات النشر: | Nature Research |
سنة النشر: | 2021 |
المجموعة: | University of Pretoria: UPSpace |
مصطلحات موضوعية: | Lineages, Human, Tuberculosis (TB), Mycobacterium tuberculosis (MTB) |
الوصف: | 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. ; http://www.nature.com/naturecommunicationsTest ; am2022 ; Medical Microbiology |
نوع الوثيقة: | article in journal/newspaper |
اللغة: | English |
تدمد: | 2041-1723 |
العلاقة: | https://repository.up.ac.za/handle/2263/88067Test; 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. |
DOI: | 10.1038/s41467-021-26248-1 |
الإتاحة: | https://doi.org/10.1038/s41467-021-26248-1Test https://repository.up.ac.za/handle/2263/88067Test |
حقوق: | © The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License. |
رقم الانضمام: | edsbas.C268124D |
قاعدة البيانات: | BASE |
ResultId |
1 |
---|---|
Header |
edsbas BASE edsbas.C268124D 927 3 Academic Journal academicJournal 926.820373535156 |
PLink |
https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&scope=site&db=edsbas&AN=edsbas.C268124D&custid=s6537998&authtype=sso |
FullText |
Array
(
[Availability] => 0
)
Array ( [0] => Array ( [Url] => https://doi.org/10.1038/s41467-021-26248-1# [Name] => EDS - BASE [Category] => fullText [Text] => View record in BASE [MouseOverText] => View record in BASE ) [1] => Array ( [Url] => https://resolver.ebscohost.com/openurl?custid=s6537998&groupid=main&authtype=ip,guest&sid=EBSCO:edsbas&genre=article&issn=20411723&ISBN=&volume=&issue=&date=20210101&spage=&pages=&title=Population structure, biogeography and transmissibility of mycobacterium tuberculosis&atitle=Population%20structure%2C%20biogeography%20and%20transmissibility%20of%20mycobacterium%20tuberculosis&id=DOI:10.1038/s41467-021-26248-1 [Name] => Full Text Finder (s6537998api) [Category] => fullText [Text] => Full Text Finder [Icon] => https://imageserver.ebscohost.com/branding/images/FTF.gif [MouseOverText] => Full Text Finder ) ) |
Items |
Array
(
[Name] => Title
[Label] => Title
[Group] => Ti
[Data] => Population structure, biogeography and transmissibility of mycobacterium tuberculosis
)
Array ( [Name] => Author [Label] => Authors [Group] => Au [Data] => <searchLink fieldCode="AR" term="%22Freschi%2C+Luca%22">Freschi, Luca</searchLink><br /><searchLink fieldCode="AR" term="%22Vargas+Jr%2E%2C+Roger%22">Vargas Jr., Roger</searchLink><br /><searchLink fieldCode="AR" term="%22Husain%2C+Ashaque%22">Husain, Ashaque</searchLink><br /><searchLink fieldCode="AR" term="%22Kamal%2C+S%2EM%2E+Mostofa%22">Kamal, S.M. Mostofa</searchLink><br /><searchLink fieldCode="AR" term="%22Skrahina%2C+Alena%22">Skrahina, Alena</searchLink><br /><searchLink fieldCode="AR" term="%22Tahseen%2C+Sabira%22">Tahseen, Sabira</searchLink><br /><searchLink fieldCode="AR" term="%22Ismail%2C+Nazir+Ahmed%22">Ismail, Nazir Ahmed</searchLink><br /><searchLink fieldCode="AR" term="%22Barbova%2C+Anna%22">Barbova, Anna</searchLink><br /><searchLink fieldCode="AR" term="%22Niemann%2C+Stefan%22">Niemann, Stefan</searchLink><br /><searchLink fieldCode="AR" term="%22Cirillo%2C+Daniela+Maria%22">Cirillo, Daniela Maria</searchLink><br /><searchLink fieldCode="AR" term="%22Dean%2C+Anna+S%2E%22">Dean, Anna S.</searchLink><br /><searchLink fieldCode="AR" term="%22Zignol%2C+Matteo%22">Zignol, Matteo</searchLink><br /><searchLink fieldCode="AR" term="%22Farhat%2C+Maha+Reda%22">Farhat, Maha Reda</searchLink> ) Array ( [Name] => Publisher [Label] => Publisher Information [Group] => PubInfo [Data] => Nature Research ) Array ( [Name] => DatePubCY [Label] => Publication Year [Group] => Date [Data] => 2021 ) Array ( [Name] => Subset [Label] => Collection [Group] => HoldingsInfo [Data] => University of Pretoria: UPSpace ) Array ( [Name] => Subject [Label] => Subject Terms [Group] => Su [Data] => <searchLink fieldCode="DE" term="%22Lineages%22">Lineages</searchLink><br /><searchLink fieldCode="DE" term="%22Human%22">Human</searchLink><br /><searchLink fieldCode="DE" term="%22Tuberculosis+%28TB%29%22">Tuberculosis (TB)</searchLink><br /><searchLink fieldCode="DE" term="%22Mycobacterium+tuberculosis+%28MTB%29%22">Mycobacterium tuberculosis (MTB)</searchLink> ) Array ( [Name] => Abstract [Label] => Description [Group] => Ab [Data] => 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. ; http://www.nature.com/naturecommunications ; am2022 ; Medical Microbiology ) Array ( [Name] => TypeDocument [Label] => Document Type [Group] => TypDoc [Data] => article in journal/newspaper ) Array ( [Name] => Language [Label] => Language [Group] => Lang [Data] => English ) Array ( [Name] => ISSN [Label] => ISSN [Group] => ISSN [Data] => 2041-1723 ) Array ( [Name] => NoteTitleSource [Label] => Relation [Group] => SrcInfo [Data] => https://repository.up.ac.za/handle/2263/88067; 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. ) Array ( [Name] => DOI [Label] => DOI [Group] => ID [Data] => 10.1038/s41467-021-26248-1 ) Array ( [Name] => URL [Label] => Availability [Group] => URL [Data] => https://doi.org/10.1038/s41467-021-26248-1<br />https://repository.up.ac.za/handle/2263/88067 ) Array ( [Name] => Copyright [Label] => Rights [Group] => Cpyrght [Data] => © The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License. ) Array ( [Name] => AN [Label] => Accession Number [Group] => ID [Data] => edsbas.C268124D ) |
RecordInfo |
Array
(
[BibEntity] => Array
(
[Identifiers] => Array
(
[0] => Array
(
[Type] => doi
[Value] => 10.1038/s41467-021-26248-1
)
)
[Languages] => Array
(
[0] => Array
(
[Text] => English
)
)
[Subjects] => Array
(
[0] => Array
(
[SubjectFull] => Lineages
[Type] => general
)
[1] => Array
(
[SubjectFull] => Human
[Type] => general
)
[2] => Array
(
[SubjectFull] => Tuberculosis (TB)
[Type] => general
)
[3] => Array
(
[SubjectFull] => Mycobacterium tuberculosis (MTB)
[Type] => general
)
)
[Titles] => Array
(
[0] => Array
(
[TitleFull] => Population structure, biogeography and transmissibility of mycobacterium tuberculosis
[Type] => main
)
)
)
[BibRelationships] => Array
(
[HasContributorRelationships] => Array
(
[0] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Freschi, Luca
)
)
)
[1] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Vargas Jr., Roger
)
)
)
[2] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Husain, Ashaque
)
)
)
[3] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Kamal, S.M. Mostofa
)
)
)
[4] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Skrahina, Alena
)
)
)
[5] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Tahseen, Sabira
)
)
)
[6] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Ismail, Nazir Ahmed
)
)
)
[7] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Barbova, Anna
)
)
)
[8] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Niemann, Stefan
)
)
)
[9] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Cirillo, Daniela Maria
)
)
)
[10] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Dean, Anna S.
)
)
)
[11] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Zignol, Matteo
)
)
)
[12] => Array
(
[PersonEntity] => Array
(
[Name] => Array
(
[NameFull] => Farhat, Maha Reda
)
)
)
)
[IsPartOfRelationships] => Array
(
[0] => Array
(
[BibEntity] => Array
(
[Dates] => Array
(
[0] => Array
(
[D] => 01
[M] => 01
[Type] => published
[Y] => 2021
)
)
[Identifiers] => Array
(
[0] => Array
(
[Type] => issn-print
[Value] => 20411723
)
[1] => Array
(
[Type] => issn-locals
[Value] => edsbas
)
[2] => Array
(
[Type] => issn-locals
[Value] => edsbas.oa
)
)
)
)
)
)
)
|
IllustrationInfo |