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

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A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. / Sabin, Susanna; Herbig, Alexander; Vågene, Åshild J.; Ahlström, Torbjörn; Bozovic, Gracijela; Arcini, Caroline; Kühnert, Denise; Bos, Kirsten I.

I: Genome Biology, Vol. 21, Nr. 1, 201, 10.08.2020.

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Sabin, Susanna ; Herbig, Alexander ; Vågene, Åshild J. ; Ahlström, Torbjörn ; Bozovic, Gracijela ; Arcini, Caroline ; Kühnert, Denise ; Bos, Kirsten I. / A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. I: Genome Biology. 2020 ; Vol. 21, Nr. 1.

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TY - JOUR

T1 - A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex

AU - Sabin, Susanna

AU - Herbig, Alexander

AU - Vågene, Åshild J.

AU - Ahlström, Torbjörn

AU - Bozovic, Gracijela

AU - Arcini, Caroline

AU - Kühnert, Denise

AU - Bos, Kirsten I.

PY - 2020/8/10

Y1 - 2020/8/10

N2 - 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.

AB - 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.

KW - Ancient DNA

KW - Metagenomics

KW - Molecular dating

KW - Mycobacterium tuberculosis

KW - Tuberculosis

U2 - 10.1186/s13059-020-02112-1

DO - 10.1186/s13059-020-02112-1

M3 - Article

C2 - 32778135

AN - SCOPUS:85089320876

VL - 21

JO - Genome Biology

JF - Genome Biology

SN - 1474-7596

IS - 1

M1 - 201

ER -