A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

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Sabin, SusannaMax Planck Institute for the Science of Human History (author)

A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

Article/chapterEnglish2020

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2020-08-10
Springer Science and Business Media LLC,2020

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LIBRIS-ID:oai:lup.lub.lu.se:6562cbd5-1459-41a5-92e7-885b83a7545b
https://lup.lub.lu.se/record/6562cbd5-1459-41a5-92e7-885b83a7545bURI
https://doi.org/10.1186/s13059-020-02112-1DOI

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Language:English
Summary in:English

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Subject category:ref swepub-contenttype

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BACKGROUND: Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605-d. 1679). RESULTS: A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent. CONCLUSIONS: The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.

Subject headings and genre

MEDICIN OCH HÄLSOVETENSKAP Medicinska och farmaceutiska grundvetenskaper Medicinsk genetik hsv//swe
MEDICAL AND HEALTH SCIENCES Basic Medicine Medical Genetics hsv//eng
Ancient DNA
Metagenomics
Molecular dating
Mycobacterium tuberculosis
Tuberculosis

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Herbig, AlexanderMax Planck Institute for the Science of Human History (author)
Vågene, Åshild J.Max Planck Institute for the Science of Human History,University of Copenhagen (author)
Ahlström, TorbjörnLund University,Lunds universitet,Historisk osteologi,Institutionen för arkeologi och antikens historia,Institutioner,Humanistiska och teologiska fakulteterna,Historical Osteology,Department of Archaeology and Ancient History,Departments,Joint Faculties of Humanities and Theology(Swepub:lu)ark-tah (author)
Bozovic, GracijelaLund University,Lunds universitet,Diagnostisk radiologi, Lund,Sektion V,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Diagnostic Radiology, (Lund),Section V,Department of Clinical Sciences, Lund,Faculty of Medicine,Skåne University Hospital(Swepub:lu)med-gbz (author)
Arcini, CarolineThe Archaeologists, National Historical Museums(Swepub:lu)extLU-984 (author)
Kühnert, DeniseMax Planck Institute for the Science of Human History (author)
Bos, Kirsten I.Max Planck Institute for the Science of Human History (author)
Max Planck Institute for the Science of Human HistoryUniversity of Copenhagen (creator_code:org_t)

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In:Genome Biology: Springer Science and Business Media LLC21:11474-75961474-760X

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MEDICAL AND HEALTH SCIENCES: MEDICAL AND HEAL ...; and Basic Medicine; and Medical Genetics

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By the university: Lund University

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