{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T21:40:25Z","timestamp":1784065225730,"version":"3.55.0"},"reference-count":100,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,6,26]],"date-time":"2024-06-26T00:00:00Z","timestamp":1719360000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,6,26]],"date-time":"2024-06-26T00:00:00Z","timestamp":1719360000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Smithsonian Institution, National Museum of Natural History, United States","award":["Pre-doctoral Fellowship"],"award-info":[{"award-number":["Pre-doctoral Fellowship"]}]},{"name":"National Science Foundation, United States","award":["NSF BCS-1643318"],"award-info":[{"award-number":["NSF BCS-1643318"]}]},{"name":"National Science Foundation, United States","award":["NSF BCS-1643318"],"award-info":[{"award-number":["NSF BCS-1643318"]}]},{"name":"National Science Foundation, United States","award":["NSF BCS-1643318"],"award-info":[{"award-number":["NSF BCS-1643318"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Dental calculus is a microbial biofilm that contains biomolecules from oral commensals and pathogens, including those potentially related to cause of death (CoD). To assess the utility of calculus as a diagnostically informative substrate, in conjunction with paleopathological analysis, calculus samples from 39 individuals in the Smithsonian Institution\u2019s Robert J. Terry Collection with CoDs of either syphilis or tuberculosis were assessed via shotgun metagenomic sequencing for the presence of <jats:italic>Treponema pallidum<\/jats:italic> subsp<jats:italic>. pallidum<\/jats:italic> and <jats:italic>Mycobacterium tuberculosis<\/jats:italic> complex (MTBC) DNA. Paleopathological analysis revealed that frequencies of skeletal lesions associated with these diseases were partially inconsistent with diagnostic criteria. Although recovery of <jats:italic>T. p. pallidum<\/jats:italic> DNA from individuals with a syphilis CoD was elusive, MTBC DNA was identified in at least one individual with a tuberculosis CoD. The authenticity of MTBC DNA was confirmed using targeted quantitative PCR assays, MTBC genome enrichment, and in silico bioinformatic analyses; however, the lineage of the MTBC strain present could not be determined. Overall, our study highlights the utility of dental\u00a0calculus for molecular detection of tuberculosis in the archaeological record and underscores the effect of museum preparation techniques and extensive handling on pathogen DNA preservation in skeletal collections.<\/jats:p>","DOI":"10.1038\/s41598-024-64818-7","type":"journal-article","created":{"date-parts":[[2024,6,26]],"date-time":"2024-06-26T10:05:59Z","timestamp":1719396359000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool"],"prefix":"10.1038","volume":"14","author":[{"given":"Rita M.","family":"Austin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanvi P.","family":"Honap","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allison E.","family":"Mann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"H\u00fcbner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cassandra M. S.","family":"DeGaglia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina","family":"Warinner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Molly K.","family":"Zuckerman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Courtney A.","family":"Hofman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,6,26]]},"reference":[{"key":"64818_CR1","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1002\/ajpa.21613","volume":"146","author":"KN Harper","year":"2011","unstructured":"Harper, K. N., Zuckerman, M. K., Harper, M. L., Kingston, J. D. & Armelagos, G. J. The origin and antiquity of syphilis revisited: An appraisal of Old World pre-Columbian evidence for treponemal infection. Am. J. Phys. Anthropol. 146, 99\u2013133 (2011).","journal-title":"Am. J. Phys. Anthropol."},{"key":"64818_CR2","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1002\/ajpa.21185","volume":"140","author":"AC Stone","year":"2009","unstructured":"Stone, A. C., Wilbur, A. K., Buikstra, J. E. & Roberts, C. A. Tuberculosis and leprosy in perspective. Am. J. Phys. Anthropol. 140, 66\u201394 (2009).","journal-title":"Am. J. Phys. Anthropol."},{"key":"64818_CR3","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1038\/nrg3664","volume":"15","author":"JE Galagan","year":"2014","unstructured":"Galagan, J. E. Genomic insights into tuberculosis. Nat. Rev. Genet. 15, 307\u2013320 (2014).","journal-title":"Nat. Rev. Genet."},{"key":"64818_CR4","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1038\/nature13591","volume":"514","author":"KI Bos","year":"2014","unstructured":"Bos, K. I. et al. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature 514, 494\u2013497 (2014).","journal-title":"Nature"},{"key":"64818_CR5","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/j.meegid.2011.12.001","volume":"12","author":"D \u0160majs","year":"2012","unstructured":"\u0160majs, D., Norris, S. J. & Weinstock, G. M. Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws. Infect. Genet. Evol. 12, 191\u2013202 (2012).","journal-title":"Infect. Genet. Evol."},{"key":"64818_CR6","first-page":"4","volume":"7","author":"M Tampa","year":"2014","unstructured":"Tampa, M., Sarbu, I., Matei, C., Benea, V. & Georgescu, S. R. Brief history of syphilis. J. Med. Life 7, 4 (2014).","journal-title":"J. Med. Life"},{"key":"64818_CR7","first-page":"E9","volume":"58","author":"I Barberis","year":"2017","unstructured":"Barberis, I., Bragazzi, N. L., Galluzzo, L. & Martini, M. The history of tuberculosis: From the first historical records to the isolation of Koch\u2019s bacillus. J. Prevent. Med. Hyg. 58, E9 (2017).","journal-title":"J. Prevent. Med. Hyg."},{"key":"64818_CR8","first-page":"28","volume":"45","author":"SR Mercuri","year":"2022","unstructured":"Mercuri, S. R. et al. Syphilis: A mini review of the history, epidemiology and focus on microbiota. New Microbiologica 45, 28\u201334 (2022).","journal-title":"New Microbiologica"},{"key":"64818_CR9","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1097\/OLQ.0000000000000899","volume":"46","author":"TA Peterman","year":"2019","unstructured":"Peterman, T. A. & Kidd, S. E. Trends in Deaths due to Syphilis, United States, 1968\u20132015. Sexually Transmit. Dis. 46, 37 (2019).","journal-title":"Sexually Transmit. Dis."},{"key":"64818_CR10","doi-asserted-by":"publisher","first-page":"592","DOI":"10.1046\/j.1365-2672.2001.01494.x","volume":"91","author":"AM Sefton","year":"2001","unstructured":"Sefton, A. M. The Great Pox that was\u2026 syphilis. J. Appl. Microbiol. 91, 592\u2013596 (2001).","journal-title":"J. Appl. Microbiol."},{"key":"64818_CR11","doi-asserted-by":"publisher","first-page":"954","DOI":"10.1093\/clinids\/23.5.954","volume":"23","author":"KA Sepkowitz","year":"1996","unstructured":"Sepkowitz, K. A. How contagious is tuberculosis?. Clin. Infect. Dis. 23, 954\u2013962 (1996).","journal-title":"Clin. Infect. Dis."},{"key":"64818_CR12","unstructured":"World Health Organization. Global Tuberculosis Report 2020. (2020)."},{"key":"64818_CR13","unstructured":"World Health Organization. Global Tuberculosis Report 2023. (2023)."},{"key":"64818_CR14","unstructured":"World Health Organization. Syphilis Fact Sheets. World Health Organization https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/syphilis#:~:text=Key%20facts,cases%20with%20adverse%20birth%20outcomes. (2024)."},{"key":"64818_CR15","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1128\/CMR.12.2.187","volume":"12","author":"AE Singh","year":"1999","unstructured":"Singh, A. E. & Romanowski, B. Syphilis: review with emphasis on clinical, epidemiologic, and some biologic features. Clin. Microbiol. Rev. 12, 187\u2013209 (1999).","journal-title":"Clin. Microbiol. Rev."},{"key":"64818_CR16","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1097\/DAD.0b013e3181e8b587","volume":"33","author":"JA Carlson","year":"2011","unstructured":"Carlson, J. A., Dabiri, G., Cribier, B. & Sell, S. The immunopathobiology of syphilis: the manifestations and course of syphilis are determined by the level of delayed-type hypersensitivity. Am. J. Dermatopathol. 33, 433 (2011).","journal-title":"Am. J. Dermatopathol."},{"key":"64818_CR17","volume-title":"The Myth of Syphilis The Natural History of Treponematosis in North America","author":"ML Powell","year":"2005","unstructured":"Powell, M. L. & Cook, D. C. The Myth of Syphilis The Natural History of Treponematosis in North America (University Press of Florida, 2005)."},{"key":"64818_CR18","doi-asserted-by":"crossref","unstructured":"Majander, K. et al. Redefining the treponemal history through pre-Columbian genomes from Brazil. Nature 1\u20137 (2024).","DOI":"10.1038\/s41586-023-06965-x"},{"key":"64818_CR19","doi-asserted-by":"publisher","first-page":"842","DOI":"10.1258\/095646207782716901","volume":"18","author":"R Castro","year":"2007","unstructured":"Castro, R. et al. Detection of Treponema pallidum sp pallidum DNA in latent syphilis. Int. J. STD AIDS 18, 842\u2013845 (2007).","journal-title":"Int. J. STD AIDS"},{"key":"64818_CR20","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01153-18","author":"DG Edmondson","year":"2018","unstructured":"Edmondson, D. G., Hu, B. & Norris, S. J. Long-term in vitro culture of the syphilis spirochete Treponema pallidum subsp. pallidum. MBio https:\/\/doi.org\/10.1128\/mBio.01153-18 (2018).","journal-title":"MBio"},{"key":"64818_CR21","doi-asserted-by":"publisher","first-page":"2091","DOI":"10.1016\/j.jas.2007.02.007","volume":"34","author":"TE Von Hunnius","year":"2007","unstructured":"Von Hunnius, T. E., Yang, D., Eng, B., Waye, J. S. & Saunders, S. R. Digging deeper into the limits of ancient DNA research on syphilis. J. Archaeol. Sci. 34, 2091\u20132100 (2007).","journal-title":"J. Archaeol. Sci."},{"key":"64818_CR22","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1016\/j.jas.2004.11.014","volume":"32","author":"AS Bouwman","year":"2005","unstructured":"Bouwman, A. S. & Brown, T. A. The limits of biomolecular palaeopathology: Ancient DNA cannot be used to study venereal syphilis. J. Archaeol. Sci. 32, 703\u2013713 (2005).","journal-title":"J. Archaeol. Sci."},{"key":"64818_CR23","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0006447","volume":"12","author":"VJ Schuenemann","year":"2018","unstructured":"Schuenemann, V. J. et al. Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains. PLoS Neglect. Trop. Dis. 12, e0006447 (2018).","journal-title":"PLoS Neglect. Trop. Dis."},{"key":"64818_CR24","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1099\/jmm.0.000978","volume":"68","author":"A Meffray","year":"2019","unstructured":"Meffray, A. et al. Molecular detection of Treponema pallidum subspecies pallidum in 150-year-old foetal remains, southeastern France. J. Med. Microbiol. 68, 761\u2013769 (2019).","journal-title":"J. Med. Microbiol."},{"key":"64818_CR25","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1007\/s12024-020-00243-2","volume":"16","author":"JS Henkel","year":"2020","unstructured":"Henkel, J. S., Davis, J. & Farley, N. Anatomical and biochemical evidence for Treponema pallidum in a 19th to early twentieth century skeletal cadaver. Forensic Sci. Med. Pathol. 16, 557\u2013561 (2020).","journal-title":"Forensic Sci. Med. Pathol."},{"key":"64818_CR26","doi-asserted-by":"publisher","first-page":"3788","DOI":"10.1016\/j.cub.2020.07.058","volume":"30","author":"K Majander","year":"2020","unstructured":"Majander, K. et al. Ancient bacterial genomes reveal a high diversity of Treponema pallidum strains in early modern Europe. Curr. Biol. 30, 3788\u20133803 (2020).","journal-title":"Curr. Biol."},{"key":"64818_CR27","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1016\/j.cub.2020.04.002","volume":"30","author":"R Barquera","year":"2020","unstructured":"Barquera, R. et al. Origin and health status of first-generation Africans from early colonial Mexico. Curr. Biol. 30, 2078\u20132091 (2020).","journal-title":"Curr. Biol."},{"key":"64818_CR28","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1146\/annurev.immunol.19.1.93","volume":"19","author":"JL Flynn","year":"2001","unstructured":"Flynn, J. L. & Chan, J. Immunology of tuberculosis. Ann. Rev. Immunol. 19, 93 (2001).","journal-title":"Ann. Rev. Immunol."},{"key":"64818_CR29","doi-asserted-by":"publisher","first-page":"e1006687","DOI":"10.1371\/journal.ppat.1006687","volume":"13","author":"TJ Scriba","year":"2017","unstructured":"Scriba, T. J. et al. Sequential inflammatory processes define human progression from M. tuberculosis infection to tuberculosis disease. PLoS pathogens 13, e1006687 (2017).","journal-title":"PLoS pathogens"},{"key":"64818_CR30","volume-title":"Ortner\u2019s Identification of Pathological Conditions in Human Skeletal Remains","author":"JE Buikstra","year":"2019","unstructured":"Buikstra, J. E. Ortner\u2019s Identification of Pathological Conditions in Human Skeletal Remains (Academic Press, 2019)."},{"key":"64818_CR31","volume-title":"Identification of Pathological Conditions in Human Skeletal Remains","author":"DJ Ortner","year":"2003","unstructured":"Ortner, D. J. Identification of Pathological Conditions in Human Skeletal Remains (Academic Press, 2003)."},{"key":"64818_CR32","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/j.ijpp.2019.01.001","volume":"27","author":"D Dangvard Pedersen","year":"2019","unstructured":"Dangvard Pedersen, D., Milner, G. R., Kolmos, H. J. & Boldsen, J. L. The association between skeletal lesions and tuberculosis diagnosis using a probabilistic approach. Int. J. Paleopathol. 27, 88\u2013100 (2019).","journal-title":"Int. J. Paleopathol."},{"key":"64818_CR33","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1134\/S0006297922030051","volume":"87","author":"AB Malyarchuk","year":"2022","unstructured":"Malyarchuk, A. B. et al. Genomics of ancient pathogens: First advances and prospects. Biochemistry (Moscow) 87, 242\u2013258 (2022).","journal-title":"Biochemistry (Moscow)"},{"key":"64818_CR34","doi-asserted-by":"publisher","DOI":"10.1016\/j.tube.2023.102392","volume":"143","author":"HY J\u00e4ger","year":"2023","unstructured":"J\u00e4ger, H. Y. et al. Hit or miss-A metagenomic evaluation of intra-bone variability of host pathogen load in tuberculosis-infected human remains. Tuberculosis 143, 102392 (2023).","journal-title":"Tuberculosis"},{"key":"64818_CR35","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1016\/j.ijpp.2019.12.006","volume":"29","author":"EA Nelson","year":"2020","unstructured":"Nelson, E. A., Buikstra, J. E., Herbig, A., Tung, T. A. & Bos, K. I. Advances in the molecular detection of tuberculosis in pre-contact Andean South America. Int. J. Paleopathol. 29, 128\u2013140 (2020).","journal-title":"Int. J. Paleopathol."},{"key":"64818_CR36","doi-asserted-by":"publisher","first-page":"1195","DOI":"10.1038\/s41467-022-28562-8","volume":"13","author":"\u00c5J V\u00e5gene","year":"2022","unstructured":"V\u00e5gene, \u00c5. J. et al. Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations. Nat. Commun. 13, 1195 (2022).","journal-title":"Nat. Commun."},{"key":"64818_CR37","doi-asserted-by":"publisher","first-page":"1176","DOI":"10.1038\/ng.2744","volume":"45","author":"I Comas","year":"2013","unstructured":"Comas, I. et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat. Gen. 45, 1176\u20131182 (2013).","journal-title":"Nat. Gen."},{"key":"64818_CR38","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000160","volume":"4","author":"T Wirth","year":"2008","unstructured":"Wirth, T. et al. Origin, spread and demography of the Mycobacterium tuberculosis complex. PLoS Pathog. 4, e1000160 (2008).","journal-title":"PLoS Pathog."},{"key":"64818_CR39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-020-02112-1","volume":"21","author":"S Sabin","year":"2020","unstructured":"Sabin, S. et al. A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. Genome Biol. 21, 1\u201324 (2020).","journal-title":"Genome Biol."},{"key":"64818_CR40","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1008067","volume":"15","author":"F Menardo","year":"2019","unstructured":"Menardo, F., Duch\u00eane, S., Brites, D. & Gagneux, S. The molecular clock of Mycobacterium tuberculosis. PLoS Pathogens 15, e1008067 (2019).","journal-title":"PLoS Pathogens"},{"key":"64818_CR41","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1146\/annurev-micro-090817-062436","volume":"73","author":"KI Bos","year":"2019","unstructured":"Bos, K. I. et al. Paleomicrobiology: Diagnosis and evolution of ancient pathogens. Ann. Rev. Microbiol. 73, 639\u2013666 (2019).","journal-title":"Ann. Rev. Microbiol."},{"key":"64818_CR42","doi-asserted-by":"publisher","first-page":"6717","DOI":"10.1038\/ncomms7717","volume":"6","author":"GL Kay","year":"2015","unstructured":"Kay, G. L. et al. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nat. Commun. 6, 6717 (2015).","journal-title":"Nat. Commun."},{"key":"64818_CR43","doi-asserted-by":"publisher","first-page":"767","DOI":"10.1111\/j.1475-4754.2012.00707.x","volume":"55","author":"C de la Fuente","year":"2013","unstructured":"de la Fuente, C., Flores, S. & Moraga, M. DNA from human ancient bacteria: a novel source of genetic evidence from archaeological dental calculus. Archaeometry 55, 767\u2013778 (2013).","journal-title":"Archaeometry"},{"key":"64818_CR44","doi-asserted-by":"publisher","first-page":"eaau7126","DOI":"10.1126\/sciadv.aau7126","volume":"5","author":"A Radini","year":"2019","unstructured":"Radini, A. et al. Medieval women\u2019s early involvement in manuscript production suggested by lapis lazuli identification in dental calculus. Sci. Adv. 5, eaau7126 (2019).","journal-title":"Sci. Adv."},{"key":"64818_CR45","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1038\/ng.2536","volume":"45","author":"CJ Adler","year":"2013","unstructured":"Adler, C. J. et al. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat. Genet. 45, 450\u2013455 (2013).","journal-title":"Nat. Genet."},{"key":"64818_CR46","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1038\/ng.2906","volume":"46","author":"C Warinner","year":"2014","unstructured":"Warinner, C. et al. Pathogens and host immunity in the ancient human oral cavity. Nat. Genet. 46, 336\u2013344 (2014).","journal-title":"Nat. Genet."},{"key":"64818_CR47","first-page":"1005","volume":"10","author":"A Linossier","year":"1995","unstructured":"Linossier, A., Gajardo, M. & Olavarria, J. Paleomicrobiological study in dental calculus: Streptococcus mutans. Scan. Microsc. 10, 1005\u20131013 (1995).","journal-title":"Scan. Microsc."},{"key":"64818_CR48","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1002\/ajpa.22960","volume":"160","author":"AT Ozga","year":"2016","unstructured":"Ozga, A. T. et al. Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. Am. J. Phys. Anthropol. 160, 220\u2013228 (2016).","journal-title":"Am. J. Phys. Anthropol."},{"key":"64818_CR49","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1038\/sj.bdj.2017.224","volume":"222","author":"T Dietrich","year":"2017","unstructured":"Dietrich, T. et al. Evidence summary: The relationship between oral and cardiovascular disease. Brit. Dent. J. 222, 381\u2013385 (2017).","journal-title":"Brit. Dent. J."},{"key":"64818_CR50","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/j.archger.2006.04.004","volume":"44","author":"Y Sumi","year":"2007","unstructured":"Sumi, Y., Miura, H., Michiwaki, Y., Nagaosa, S. & Nagaya, M. Colonization of dental plaque by respiratory pathogens in dependent elderly. Arch. Gerontol. Geriat. 44, 119\u2013124 (2007).","journal-title":"Arch. Gerontol. Geriat."},{"issue":"5","key":"64818_CR51","doi-asserted-by":"publisher","first-page":"563","DOI":"10.26719\/2010.16.5.563","volume":"16","author":"MM El Attar","year":"2010","unstructured":"El Attar, M. M., Zaghloul, M. Z. & El Menoufy, H. S. Role of periodontitis in hospital-acquired pneumonia. E Mediterr. Health J. 16(5), 563\u2013569 (2010).","journal-title":"E Mediterr. Health J."},{"key":"64818_CR52","doi-asserted-by":"publisher","first-page":"S62","DOI":"10.1111\/j.1834-7819.2009.01144.x","volume":"54","author":"M Cullinan","year":"2009","unstructured":"Cullinan, M., Ford, P. & Seymour, G. Periodontal disease and systemic health: current status. Austr. Dental J. 54, S62\u2013S69 (2009).","journal-title":"Austr. Dental J."},{"key":"64818_CR53","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s42003-021-02997-z","volume":"5","author":"RM Austin","year":"2022","unstructured":"Austin, R. M. et al. Remembering St. Louis individual\u2014structural violence and acute bacterial infections in a historical anatomical collection. Commun. Biol. 5, 1\u201310 (2022).","journal-title":"Commun. Biol."},{"key":"64818_CR54","doi-asserted-by":"publisher","first-page":"20190584","DOI":"10.1098\/rstb.2019.0584","volume":"375","author":"AK Fotakis","year":"2020","unstructured":"Fotakis, A. K. et al. Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus. Philos. Trans. R. Soc. B 375, 20190584 (2020).","journal-title":"Philos. Trans. R. Soc. B"},{"key":"64818_CR55","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1038\/ng.590","volume":"42","author":"I Comas","year":"2010","unstructured":"Comas, I. et al. Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat. Genet. 42, 498 (2010).","journal-title":"Nat. Genet."},{"key":"64818_CR56","unstructured":"Young, S. Please Forget to Floss: Developing an Assay for Identifying Tuberculosis in Dental Calculus from the Smithsonian\u2019s Huntington Collection (1893\u20131921). (Syracuse University, 2017)."},{"key":"64818_CR57","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1038\/nmeth.1650","volume":"8","author":"D Knights","year":"2011","unstructured":"Knights, D. et al. Bayesian community-wide culture-independent microbial source tracking. Nat. Methods 8, 761\u2013763 (2011).","journal-title":"Nat. Methods"},{"key":"64818_CR58","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-28091-9","author":"AE Mann","year":"2018","unstructured":"Mann, A. E. et al. Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Sci. Rep. https:\/\/doi.org\/10.1038\/s41598-018-28091-9 (2018).","journal-title":"Sci. Rep."},{"key":"64818_CR59","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-019-1903-0","volume":"20","author":"R H\u00fcbler","year":"2019","unstructured":"H\u00fcbler, R. et al. HOPS: Automated detection and authentication of pathogen DNA in archaeological remains. Genome Biol. 20, 1\u201313 (2019).","journal-title":"Genome Biol."},{"key":"64818_CR60","doi-asserted-by":"publisher","first-page":"20130622","DOI":"10.1098\/rstb.2013.0622","volume":"370","author":"KM Harkins","year":"2015","unstructured":"Harkins, K. M. et al. Screening ancient tuberculosis with qPCR: Challenges and opportunities. PhilosT R Soc. B 370, 20130622 (2015).","journal-title":"PhilosT R Soc. B"},{"key":"64818_CR61","doi-asserted-by":"publisher","first-page":"1292","DOI":"10.1093\/molbev\/msu074","volume":"31","author":"JM Enk","year":"2014","unstructured":"Enk, J. M. et al. Ancient whole genome enrichment using baits built from modern DNA. Mol. Biol. Evol. 31, 1292\u20131294 (2014).","journal-title":"Mol. Biol. Evol."},{"key":"64818_CR62","unstructured":"Buikstra, J. E. & Ubelaker, D. H. Standards for recording human remains. Ark Archaeol Sur Res (1994)."},{"key":"64818_CR63","doi-asserted-by":"publisher","first-page":"275","DOI":"10.5312\/wjo.v14.i5.275","volume":"14","author":"W Leowattana","year":"2023","unstructured":"Leowattana, W., Leowattana, P. & Leowattana, T. Tuberculosis of the spine. World J. Orthoped. 14, 275 (2023).","journal-title":"World J. Orthoped."},{"key":"64818_CR64","doi-asserted-by":"publisher","first-page":"1749","DOI":"10.1513\/AnnalsATS.201509-632PS","volume":"12","author":"JF Murray","year":"2015","unstructured":"Murray, J. F., Schraufnagel, D. E. & Hopewell, P. C. Treatment of tuberculosis. A historical perspective. Ann. Am. Thor. Soc. 12, 1749\u20131759 (2015).","journal-title":"Ann. Am. Thor. Soc."},{"key":"64818_CR65","volume-title":"Human osteology method statement","author":"N Powers","year":"2012","unstructured":"Powers, N. Human osteology method statement (Museum of London, 2012)."},{"key":"64818_CR66","unstructured":"Steckel, R. H., Larsen, C. S., Sciulli, P. W., Walker, P. L., & others. Data collection codebook. The global history of health project 2006, 1\u201341 (2006)."},{"key":"64818_CR67","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1002\/ajpa.20160","volume":"130","author":"AL Santos","year":"2006","unstructured":"Santos, A. L. & Roberts, C. A. Anatomy of a serial killer: differential diagnosis of tuberculosis based on rib lesions of adult individuals from the Coimbra Identified Skeletal Collection Portugal. American Journal of Physical Anthropology 130, 38\u201349 (2006).","journal-title":"American Journal of Physical Anthropology"},{"key":"64818_CR68","doi-asserted-by":"crossref","unstructured":"Hackett, C. J. Diagnostic Criteria of Syphilis, Yaws and Treponarid (Treponematoses) and of Some Other Diseases in Dry Bones (for Use in Osteo-Archaeology). (Springer-Verlag, Heidelberger Platz 3, D-1 Berlin 33, 1976).","DOI":"10.1007\/978-3-662-06583-9"},{"key":"64818_CR69","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1002\/ajpa.20839","volume":"137","author":"DA Weston","year":"2008","unstructured":"Weston, D. A. Investigating the specificity of periosteal reactions in pathology museum specimens. Am. J. Phys. Anthropol. 137, 48\u201359 (2008).","journal-title":"Am. J. Phys. Anthropol."},{"key":"64818_CR70","doi-asserted-by":"crossref","unstructured":"Weston, D. A. Nonspecific Infection in Paleopathology: Interpreting Periosteal Reactions. in A Companion to Paleopathology (2012).","DOI":"10.1002\/9781444345940.ch27"},{"key":"64818_CR71","doi-asserted-by":"crossref","unstructured":"Crespo, F. Reconstructing immune competence in skeletal samples: A theoretical and methodological approach. Theoretical Approaches in Bioarchaeology 76\u201392 (2020).","DOI":"10.4324\/9780429262340-6"},{"key":"64818_CR72","doi-asserted-by":"publisher","DOI":"10.1016\/j.jas.2020.105102","volume":"116","author":"MA Pilloud","year":"2020","unstructured":"Pilloud, M. A. & Schwitalla, A. W. Re-evaluating traditional markers of stress in an archaeological sample from central California. J. Archaeol. Sci. 116, 105102 (2020).","journal-title":"J. Archaeol. Sci."},{"key":"64818_CR73","unstructured":"Resnick, D. & Niwayama, G. Infectious Diseases. in Diagnosis of Bone and Joint Disorders 2323\u20132448 (W.B. Saunders, 1995)."},{"key":"64818_CR74","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1177\/00027162211008815","volume":"694","author":"MK Zuckerman","year":"2021","unstructured":"Zuckerman, M. K., Austin, R. M. & Hofman, C. A. Historical anatomical collections of human remains: Exploring their reinterpretation as representations of racial violence. Ann. Am. Acad. Polit. SS 694, 39\u201347 (2021).","journal-title":"Ann. Am. Acad. Polit. SS"},{"key":"64818_CR75","doi-asserted-by":"crossref","unstructured":"Zuckerman, M. K. Recovering the lived body from bodies of evidence: Interrogation of diagnostic criteria and parameters for disease ecology reconstructed from skeletons within anatomical and medical anatomical collections. in Bioarchaeological Analyses and Bodies 89\u2013107 (Springer, 2018).","DOI":"10.1007\/978-3-319-71114-0_6"},{"key":"64818_CR76","unstructured":"Cova, C (2020). Making silenced voices speak. In: Theoretical Approaches in Bioarchaeology. Routledge: UK"},{"key":"64818_CR77","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1002\/ajpa.23104","volume":"162","author":"FA Crespo","year":"2017","unstructured":"Crespo, F. A., Klaes, C. K., Switala, A. E. & DeWitte, S. N. Do leprosy and tuberculosis generate a systemic inflammatory shift? Setting the ground for a new dialogue between experimental immunology and bioarchaeology. Am. J. Phys. Anthropol. 162, 143\u2013156 (2017).","journal-title":"Am. J. Phys. Anthropol."},{"key":"64818_CR78","first-page":"bcr2014204871","volume":"2014","author":"S Bezalely","year":"2014","unstructured":"Bezalely, S., Jacob, G., Flusser, G. & Ablin, J. Syphilis: an unusual manifestation?. Case Reports 2014, bcr2014204871 (2014).","journal-title":"Case Reports"},{"key":"64818_CR79","doi-asserted-by":"publisher","first-page":"1471","DOI":"10.1073\/pnas.1822038116","volume":"116","author":"RM Austin","year":"2019","unstructured":"Austin, R. M., Sholts, S. B., Williams, L., Kistler, L. & Hofman, C. A. Opinion: To curate the molecular past, museums need a carefully considered set of best practices. P. Natl. A Sci. 116, 1471\u20131474 (2019).","journal-title":"P. Natl. A Sci."},{"key":"64818_CR80","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/j.jhevol.2014.06.018","volume":"79","author":"LS Weyrich","year":"2015","unstructured":"Weyrich, L. S., Dobney, K. & Cooper, A. Ancient DNA analysis of dental calculus. J. Human Evol. 79, 119\u2013124 (2015).","journal-title":"J. Human Evol."},{"key":"64818_CR81","unstructured":"Kendra. Futures of Bioarchaeology and Personhood: Osteobiography of Two individuals from the Hamman-Todd Collection. (2023)."},{"key":"64818_CR82","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-020-66012-x","volume":"10","author":"K Giffin","year":"2020","unstructured":"Giffin, K. et al. A treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15th century Europe. Sci. Rep. 10, 1\u201313 (2020).","journal-title":"Sci. Rep."},{"key":"64818_CR83","doi-asserted-by":"publisher","first-page":"455","DOI":"10.2144\/btn-2020-0100","volume":"69","author":"A Furtw\u00e4ngler","year":"2020","unstructured":"Furtw\u00e4ngler, A. et al. Comparison of target enrichment strategies for ancient pathogen DNA. Biotechniques 69, 455\u2013459 (2020).","journal-title":"Biotechniques"},{"key":"64818_CR84","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1007\/978-3-319-71114-0_3","volume-title":"Bioarchaeological Analyses and Bodies","author":"R Watkins","year":"2018","unstructured":"Watkins, R. Anatomical collections as the anthropological other: Some considerations. In Bioarchaeological Analyses and Bodies 27\u201347 (Springer, 2018)."},{"key":"64818_CR85","doi-asserted-by":"publisher","first-page":"381","DOI":"10.4324\/9781003130994-24","volume-title":"The Routledge Handbook of Paleopathology","author":"C De Cova La","year":"2022","unstructured":"De Cova La, C. Ethical Considerations for Paleopathology. In The Routledge Handbook of Paleopathology 381\u2013396 (Routledge, 2022)."},{"key":"64818_CR86","unstructured":"Nichols, L. et al. Reclaiming Life Narratives: Reconstructing lived experiences of individuals in historical documented collections. (2023)."},{"key":"64818_CR87","unstructured":"DeGaglia, C. & Zuckerman, M. K. Ethical aspects of historical documented collections. (2022)."},{"key":"64818_CR88","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0290014","volume":"18","author":"C De La Cova","year":"2023","unstructured":"De La Cova, C., Mant, M. & Brickley, M. B. Structural violence and institutionalized individuals: A paleopathological perspective on a continuing issue. PLoS one 18, e0290014 (2023).","journal-title":"PLoS one"},{"key":"64818_CR89","doi-asserted-by":"publisher","first-page":"20130624","DOI":"10.1098\/rstb.2013.0624","volume":"370","author":"N Rohland","year":"2015","unstructured":"Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil\u2013DNA\u2013glycosylase treatment for screening of ancient DNA. Phil. Trans. R Soc. B 370, 20130624 (2015).","journal-title":"Phil. Trans. R Soc. B"},{"key":"64818_CR90","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13104-016-1900-2","volume":"9","author":"M Schubert","year":"2016","unstructured":"Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: Rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 1\u20137 (2016).","journal-title":"BMC Res. Notes"},{"key":"64818_CR91","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformat 25, 1754\u20131760 (2009).","journal-title":"Bioinformat"},{"key":"64818_CR92","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1186\/1471-2164-12-402","volume":"12","author":"N-F Alikhan","year":"2011","unstructured":"Alikhan, N.-F., Petty, N. K., Zakour, N. L. B. & Beatson, S. A. BLAST Ring Image Generator (BRIG): Simple prokaryote genome comparisons. BMC Genomics 12, 402 (2011).","journal-title":"BMC Genomics"},{"key":"64818_CR93","unstructured":"R Core Team. R: A Language and Environment for Statistical Computing. (Vienna, Austria, 2017)."},{"key":"64818_CR94","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. Journal of molecular biology 215, 403\u2013410 (1990).","journal-title":"Journal of molecular biology"},{"key":"64818_CR95","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The sequence alignment\/map format and SAMtools. Bioinformat 25, 2078\u20132079 (2009).","journal-title":"Bioinformat"},{"key":"64818_CR96","doi-asserted-by":"publisher","first-page":"568","DOI":"10.1101\/gr.129684.111","volume":"22","author":"DC Koboldt","year":"2012","unstructured":"Koboldt, D. C. et al. VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568\u2013576 (2012).","journal-title":"Genome Res."},{"key":"64818_CR97","doi-asserted-by":"publisher","first-page":"482","DOI":"10.3201\/eid2503.180894","volume":"25","author":"S Lipworth","year":"2019","unstructured":"Lipworth, S. et al. SNP-IT tool for identifying subspecies and associated lineages of Mycobacterium tuberculosis complex. Emerg. Infect. Dis. 25, 482 (2019).","journal-title":"Emerg. Infect. Dis."},{"key":"64818_CR98","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1093\/bioinformatics\/btw670","volume":"33","author":"G Renaud","year":"2017","unstructured":"Renaud, G., Hangh\u00f8j, K., Willerslev, E. & Orlando, L. gargammel: A sequence simulator for ancient DNA. Bioinformatics 33, 577\u2013579 (2017).","journal-title":"Bioinformatics"},{"key":"64818_CR99","doi-asserted-by":"publisher","first-page":"14616","DOI":"10.1073\/pnas.0704665104","volume":"104","author":"AW Briggs","year":"2007","unstructured":"Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Nat. Acad. Sci. 104, 14616\u201314621 (2007).","journal-title":"Proc. Nat. Acad. Sci."},{"key":"64818_CR100","first-page":"69","volume":"767","author":"H Li","year":"2012","unstructured":"Li, H. seqtk Toolkit for processing sequences in FASTA\/Q formats. GitHub 767, 69 (2012).","journal-title":"GitHub"}],"updated-by":[{"DOI":"10.1038\/s41598-024-69609-8","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2024,8,12]],"date-time":"2024-08-12T00:00:00Z","timestamp":1723420800000}}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-64818-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-64818-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-64818-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,12]],"date-time":"2024-08-12T19:08:43Z","timestamp":1723489723000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-64818-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,26]]},"references-count":100,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["64818"],"URL":"https:\/\/doi.org\/10.1038\/s41598-024-64818-7","relation":{"correction":[{"id-type":"doi","id":"10.1038\/s41598-024-69609-8","asserted-by":"object"}]},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,26]]},"assertion":[{"value":"27 January 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 June 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 June 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 August 2024","order":4,"name":"change_date","label":"Change Date","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Correction","order":5,"name":"change_type","label":"Change Type","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"A Correction to this paper has been published:","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"https:\/\/doi.org\/10.1038\/s41598-024-69609-8","URL":"https:\/\/doi.org\/10.1038\/s41598-024-69609-8","order":7,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"14720"}}