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Kharlamova N, Ogarkov O, Berdnikov I, Berdnikova N, Galeev R, Mokrousov I. Bioarchaeological and molecular evidence of tuberculosis in human skeletal remains from 18th-19th century orthodox cemeteries in Irkutsk, Eastern Siberia. Tuberculosis (Edinb) 2023; 143S:102368. [PMID: 38012918 DOI: 10.1016/j.tube.2023.102368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 11/29/2023]
Abstract
In this study, we tested the skeletal human remains from the 18th - early 19th century Orthodox cemeteries in Irkutsk, Eastern Siberia, for tuberculosis-associated morphological alterations and Mycobacterium tuberculosis DNA. The morphologically studied bone collection included 591 individuals of mainly Caucasian origin. The molecular methods (IS6110-PCR and spoligotyping) suggested that at least four individuals (out of 15 TB-suspected, DNA-tested) were positive for the presence of M. tuberculosis DNA. All of them were males (3 maturus, 1 maturus senilis). Two of them date back to the second and third quarters of the 18th century, another to the last quarter of the 18th century, and the last one to the second half of the 19th century. The combined molecular analysis cautiously suggested presence of different strains and at least some of them represented not the currently predominant in Siberia Beijing genotype (M. tuberculosis East-Asian lineage) but strains of European origin. In conclusion, this study presented bioarchaeological and molecular evidence of tuberculosis in human skeletal remains from 18th-19th century Orthodox cemeteries in Irkutsk, Eastern Siberia. The samples are not M. bovis and represent human M. tuberculosis sensu stricto. Their precise phylogenetic identity is elusive but evokes the European/Russian origin of at least some isolates.
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Affiliation(s)
- Natalia Kharlamova
- Center for Physical Anthropology, N.N. Mikloukho-Maklay Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | - Oleg Ogarkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, 664003, Russia
| | - Ivan Berdnikov
- Scientific Research Center "Baikal Region", Irkutsk State University, Irkutsk, 664003, Russia
| | - Natalia Berdnikova
- Scientific Research Center "Baikal Region", Irkutsk State University, Irkutsk, 664003, Russia
| | - Ravil Galeev
- Laboratory of Facial Reconstruction, N.N. Mikloukho-Maklay Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, 197101, Russia.
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Lee OYC, Wu HHT, Besra GS, Minnikin DE, Jaeger HY, Maixner F, Zink A, Gasparik M, Pap I, Bereczki Z, Pálfi G. Sensitive lipid biomarker detection for tuberculosis in late Neanderthal skeletons from Subalyuk Cave, Hungary. Tuberculosis (Edinb) 2023; 143S:102420. [PMID: 38012927 DOI: 10.1016/j.tube.2023.102420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/29/2023]
Abstract
Skeletal remains of two Neanderthal individuals, a 25-35 year-old woman and a 3-4 year-old child, were discovered in a Subalyuk Cave in North-Eastern Hungary. Radiocarbon dating of the female and child remains revealed an age of 39,732-39,076 and 36,117-35,387 cal BP, respectively. Paleopathological studies of these Neanderthal remains revealed probable evidence of skeletal mycobacterial infection, including in the sacrum of the adult specimen and the endocranial surface of the child's skull. Application of PCR amplification to the juvenile cranium and a vertebra gave a positive result (IS6110) for tuberculosis, backed up by spoligotyping. Lipid biomarker analyses of the same two specimens revealed definitive signals for C32 mycoserosates, a very characteristic component of the Mycobacterium tuberculosis complex (MTBC). A vertebra from the adult provided weak evidence for mycocerosate biomarkers. The correlation of probable skeletal lesions with characteristic amplified DNA fragments and a proven lipid biomarker points to the presence of tuberculosis in these Neanderthals. In particular, the closely similar biomarker profiles, for two distinct juvenile cranial and vertebral bones, strengthen this diagnosis.
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Affiliation(s)
- Oona Y-C Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Houdini H T Wu
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK.
| | - David E Minnikin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Heidi Y Jaeger
- Institute for Mummy Studies, Eurac Research, Bolzano, Italy
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, Bolzano, Italy
| | - Albert Zink
- Institute for Mummy Studies, Eurac Research, Bolzano, Italy
| | - Mihály Gasparik
- Department of Palaeontology and Geology, Hungarian Natural History Museum, Hungary
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Hungary; Department of Anthropology, Eötvös Loránd University, Budapest, Hungary; Department of Biological Anthropology, University of Szeged, Hungary
| | - Zsolt Bereczki
- Department of Biological Anthropology, University of Szeged, Hungary
| | - György Pálfi
- Department of Biological Anthropology, University of Szeged, Hungary
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Zink A, Maixner F, Jäger HY, Szikossy I, Pálfi G, Pap I. Tuberculosis in mummies - New findings, perspectives and limitations. Tuberculosis (Edinb) 2023; 143S:102371. [PMID: 38012931 DOI: 10.1016/j.tube.2023.102371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 06/29/2023] [Accepted: 07/02/2023] [Indexed: 11/29/2023]
Abstract
The molecular analysis of ancient pathogen DNA represents a unique opportunity for the study of infectious diseases in ancient human remains. Among other diseases, paleogenetic studies have been successful in detecting tuberculous DNA in ancient human remains. In the beginning of ancient DNA (aDNA) studies, the presence of tuberculosis (TB) DNA was assessed using a PCR-based assay targeting specific regions of the Mycobacterium tuberculosis (MTB) complex, such as the repetitive element IS6110. The advent of high-throughput sequencing has enabled the reconstruction of full ancient TB genomes in the field of paleomicrobiology. However, despite the numerous paleopathological and PCR-based studies on the presence of tuberculosis in historic human remains, full genome wide reconstructions are still limited to well-preserved specimens with low environmental contamination and connected with extensive screening efforts. This has led to some controversies regarding the evolutionary history of its causative agent Mycobacterium tuberculosis. In this context, mummies have been shown to be a good source for the detection of MTB complex DNA due to a low exposure to environmental influences and the overall good state of preservation of hard and soft tissues in the human remains. Here, we present the major findings on the presence of TB infections in the 18th century naturally mummified human remains from Vác, Hungary and the current status of the detection of MTB complex DNA in mummified human remains. The future perspectives of detecting tuberculosis in mummies will be discussed in the light of methodological aspects, as well as ethical and curational challenges.
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Affiliation(s)
- Albert Zink
- Institute for Mummy Studies, Eurac Research, Bolzano, Italy.
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, Bolzano, Italy
| | | | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - György Pálfi
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary; Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary; Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
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Papa V, Galassi FM, Varotto E, Gori A, Vaccarezza M. The Evolution of Diagnostic Techniques in the Paleopathology of Tuberculosis: A Scoping Review. Pathog Immun 2023; 8:93-116. [PMID: 37900966 PMCID: PMC10603826 DOI: 10.20411/pai.v8i1.597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/21/2023] [Indexed: 10/31/2023] Open
Abstract
Tuberculosis (TB) is an ancient chronic infectious disease that remains a global health concern. In human remains, the most common and characteristic clinical signs are the skeletal modifications involving the spine, such as in Pott's disease. Diagnosing TB in ancient human remains is challenging. Therefore, in this systematic review, the authors investigated the studies assessing molecular diagnosis of Pott's disease in ancient human remains with the intention to survey the literature, map the evidence, and identify gaps and future perspectives on TB in paleopathology. Our systematic review offers a full contextualization of the history of Pott's disease in ancient times. Our search strategy was performed between August 2022 and March 2023. The authors initially identified 340 records, and 74 studies were finally included and assessed for qualitative analysis. Due to non-specific clinical signs associated with TB, how best to diagnose tuberculosis in human remains still represents a central point. Nevertheless, ancient DNA (aDNA) analysis, lipid biomarkers, and spoligotyping might be extremely useful tools in the study of TB in human remains. Moreover, we propose the extraction and study of immune response genes involved in innate and adaptive immunity versus Mycobacterium spp. as an innovative and vastly overlooked approach in TB paleopathology. Complementary methodologies should be integrated to provide the best approach to the study of TB in human remains.
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Affiliation(s)
- Veronica Papa
- Forensic Anthropology, Paleopathology and Bioarchaeology (FAPAB) Research Center, Avola, Italy
- Department of Economics, Law, Cybersecurity, and Sports Sciences, University of Naples “Parthenope,” Naples, Italy
- School of Science, Engineering and Health, University of Naples “Parthenope,” Naples, Italy
| | - Francesco M. Galassi
- Forensic Anthropology, Paleopathology and Bioarchaeology (FAPAB) Research Center, Avola, Italy
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237, Lodz, Poland
| | - Elena Varotto
- Forensic Anthropology, Paleopathology and Bioarchaeology (FAPAB) Research Center, Avola, Italy
- Archaeology, College of Humanities, Arts and Social Sciences, Flinders University, Adelaide, SA, Australia
| | - Andrea Gori
- I Division of Infectious Diseases, “Luigi Sacco” Hospital, ASST Fatebenefratelli Sacco, Milan, Italy; Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Mauro Vaccarezza
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, Perth, 6102 Western Australia, Australia
- Curtin Health Innovation Research Institute (CHIRI), Faculty of Health Sciences, Curtin University, Bentley, Perth, 6102 Western Australia, Australia
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Mokrousov I, Vinogradova T, Dogonadze M, Zabolotnykh N, Vyazovaya A, Vitovskaya M, Solovieva N, Ariel B. A multifaceted interplay between virulence, drug resistance, and the phylogeographic landscape of Mycobacterium tuberculosis. Microbiol Spectr 2023; 11:e0139223. [PMID: 37768091 PMCID: PMC10581221 DOI: 10.1128/spectrum.01392-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/06/2023] [Indexed: 09/29/2023] Open
Abstract
Latin-American Mediterranean (LAM) family is one of the most significant and global genotypes of Mycobacterium tuberculosis. Here, we used the murine model to study the virulence and lethality of the genetically and epidemiologically distinct LAM strains. The pathobiological characteristics of the four LAM strains (three drug resistant and one drug susceptible) and the susceptible reference strain H37Rv were studied in the C57BL/6 mouse model. The whole-genome sequencing was performed using the HiSeq Illumina platform, followed by bioinformatics and phylogenetic analysis. The susceptible strain H37Rv showed the highest virulence. Drug-susceptible LAM strain (spoligotype SIT264) was more virulent than three multidrug-resistant (MDR) strains (SIT252, SIT254, and SIT266). All three MDR isolates were low lethal, while the susceptible isolate and H37Rv were moderately/highly lethal. Putting the genomic, phenotypic, and virulence features of the LAM strains/spoligotypes in the context of their dynamic phylogeography over 20 years reveals three types of relationships between virulence, resistance, and transmission. First, the most virulent and more lethal drug-susceptible SIT264 increased its circulation in parts of Russia. Second, moderately virulent and pre-XDR SIT266 was prevalent in Belarus and continues to be visible in North-West Russia. Third, the low virulent and MDR strain SIT252 previously considered as emerging has disappeared from the population. These findings suggest that strain virulence impacts the transmission, irrespective of drug resistance properties. The increasing circulation of susceptible but more virulent and lethal strains implies that personalized TB treatment should consider not only resistance but also the virulence of the infecting M. tuberculosis strains. IMPORTANCE The study is multidisciplinary and investigates the epidemically/clinically important and global lineage of Mycobacterium tuberculosis, named Latin-American-Mediterranean (LAM), yet insufficiently studied with regard to its pathobiology. We studied different LAM strains (epidemic vs endemic and resistant vs susceptible) in the murine model and using whole-genome analysis. We also collected long-term, 20-year data on their prevalence in Eurasia. The findings are both expected and unexpected. (i) We observe that a drug-susceptible but highly virulent strain increased its prevalence. (ii) By contrast, the multidrug-resistant (MDR) but low-virulent, low-lethal strain (that we considered as emerging 15 years ago) has almost disappeared. (iii) Finally, an intermediate case is the MDR strain with moderate virulence that continues to circulate. We conclude that (i) the former and latter strains are the most hazardous and require close epidemiological monitoring, and (ii) personalized TB treatment should consider not only drug resistance but also the virulence of the infecting strains and development of anti-virulence drugs is warranted.
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Affiliation(s)
- Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Tatiana Vinogradova
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Marine Dogonadze
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Natalia Zabolotnykh
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Anna Vyazovaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Maria Vitovskaya
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Boris Ariel
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
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Hider J, Duggan AT, Klunk J, Eaton K, Long GS, Karpinski E, Giuffra V, Ventura L, Fornaciari A, Fornaciari G, Golding GB, Prowse TL, Poinar HN. Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2022; 39:20-34. [PMID: 36174312 DOI: 10.1016/j.ijpp.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 08/05/2022] [Accepted: 08/13/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVE To investigate variation in ancient DNA recovery of Brucella melitensis, the causative agent of brucellosis, from multiple tissues belonging to one individual MATERIALS: 14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 th century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis. METHODS Shotgun sequencing data from was examined to determine the presence of Brucella DNA. RESULTS Three of the 14 samples contained authentic ancient DNA, identified as belonging to B. melitensis. A genome (23.81X depth coverage, 0.98 breadth coverage) was recovered from a kidney stone. Nine of the samples contained reads classified as B. melitensis (7-169), but for many the data quality was insufficient to withstand our identification and authentication criteria. CONCLUSIONS We identified significant variation in the preservation and abundance of B. melitensis DNA present across multiple tissues, with calcified nodules yielding the highest number of authenticated reads. This shows how greatly sample selection can impact pathogen identification. SIGNIFICANCE Our results demonstrate variation in the preservation and recovery of pathogen DNA across tissues. This study highlights the importance of sample selection in the reconstruction of infectious disease burden and highlights the importance of a holistic approach to identifying disease. LIMITATIONS Study focuses on pathogen recovery in a single individual. SUGGESTIONS FOR FURTHER RESEARCH Further analysis of how sampling impacts aDNA recovery will improve pathogen aDNA recovery and advance our understanding of disease in past peoples.
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Affiliation(s)
- Jessica Hider
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada.
| | - Ana T Duggan
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Daicel Arbor Biosciences, 5840 Interface Drive, Suite 101, Ann Arbor, MI 48103, USA
| | - Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - George S Long
- Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Valentina Giuffra
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, Medical School, via Roma 57, 56126 Pisa, PI, Italy
| | - Luca Ventura
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Italy; Division of Pathology, San Salvatore Hospital, University of L'Aquila, Coppito, 67100 L'Aquila, AQ, Italy
| | - Antonio Fornaciari
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, Medical School, via Roma 57, 56126 Pisa, PI, Italy
| | - Gino Fornaciari
- Maria Luisa di Borbone Academy, Villa Borbone, viale dei Tigli 32, 55049 Viareggio, LU, Italy
| | - G Brian Golding
- Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Tracy L Prowse
- Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biochemistry, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L9, Canada
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7
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Rayo E, Ferrari G, Neukamm J, Akgül G, Breidenstein AM, Cooke M, Phillips C, Bouwman AS, Rühli FJ, Schuenemann VJ. Non-destructive extraction of DNA from preserved tissues in medical collections. Biotechniques 2022; 72:60-64. [PMID: 35037474 DOI: 10.2144/btn-2021-0014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Museum specimens and histologically fixed material are valuable samples for the study of historical soft tissues and represent a possible pathogen-specific source for retrospective molecular investigations. However, current methods for molecular analysis are inherently destructive, posing a dilemma between performing a study with the available technology, thus damaging the sample, and conserving the material for future investigations. Here the authors present the first tests of a non-destructive alternative that facilitates genetic analysis of fixed wet tissues while avoiding tissue damage. The authors extracted DNA from the fixed tissues as well as their embedding fixative solution, to quantify the DNA that was transferred to the liquid component. The results show that human historical DNA can be retrieved from the fixative material of medical specimens and provide new options for sampling valuable collections.
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Affiliation(s)
- Enrique Rayo
- Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland.,Plant Ecology Genomics Group, Institute of Integrative Biology (IBZ), ETH Zürich, CH-8092, Switzerland
| | - Giada Ferrari
- Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland.,Royal Botanical Garden Edinburgh, Edinburgh, EH3 5NZ, UK
| | - Judith Neukamm
- Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, DE-72074, Germany
| | - Gülfirde Akgül
- Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland
| | - Abagail M Breidenstein
- Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland
| | - Martyn Cooke
- Museums & Archives, The Royal College of Surgeons of England, London, WC2A 3PE, UK
| | - Carina Phillips
- Museums & Archives, The Royal College of Surgeons of England, London, WC2A 3PE, UK
| | - Abigail S Bouwman
- Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland
| | - Frank J Rühli
- Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine (IEM), University of Zürich, Zürich, CH-8050, Switzerland
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Gresky J, Dorn J, Teßmann B, Petiti E. How rare is rare? A literature survey of the last 45 years of paleopathological research on ancient rare diseases. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2021; 33:94-102. [PMID: 33813348 DOI: 10.1016/j.ijpp.2021.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
OBJECTIVE This paper aims to provide a quantitative estimation of the representation of diseases defined as rare today in the bioarchaeological literature and to outline the reasons for this. MATERIALS A 45-year bibliometric study of publications in seven bioarchaeological journals, along with two journals and editorial groups of broader scientific focus. METHODS Analyses of distribution patterns of the search hits and diachronic trends for achondroplasia, autosomal-dominant osteopetrosis, osteogenesis imperfecta, and osteopoikilosis, compared to those for tuberculosis as control measure of coverage. RESULTS Studies of ancient rare diseases (ARD) are mostly published as case reports in specialized journals and their number did not benefit from the introduction of biomolecular studies. The higher frequency of cases of achondroplasia suggests that not all rare diseases are equally under-represented. CONCLUSIONS Rare diseases are still largely under-represented in bioarchaeological literature. Their marginality likely results from a combination of taphonomic, methodological and public visibility factors. SIGNIFICANCE This article is the first attempt to provide a quantitative assessment of the under-representation of ARD and to outline the factors behind it. LIMITATIONS Rare diseases are an etiologically heterogeneous group. The number of surveyed journals and articles, as well as targeted diseases might be limiting factors. SUGGESTIONS FOR FURTHER RESEARCH Increasing collection and dissemination of data on ARD; opening a wide-ranging debate on their definition; implementation of biomolecular studies.
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Affiliation(s)
- Julia Gresky
- German Archaeological Institute, Department of Natural Sciences, Berlin, Germany.
| | - Juliane Dorn
- German Archaeological Institute, Department of Natural Sciences, Berlin, Germany
| | - Barbara Teßmann
- Berlin Society of Anthropology, Ethnology and Prehistory, Berlin, Germany
| | - Emmanuele Petiti
- German Archaeological Institute, Department of Natural Sciences, Berlin, Germany
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9
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A case of childhood tuberculosis from late mediaeval Somerset, England. Tuberculosis (Edinb) 2021; 128:102088. [PMID: 34022508 DOI: 10.1016/j.tube.2021.102088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/04/2021] [Accepted: 05/09/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND The remains of a 3-5 year-old child from the late mediaeval cemetery serving the Priory of St. Peter and St. Paul, Taunton, Somerset, UK was the subject of an aDNA study. OBJECTIVE The aim was to distinguish between two differential diagnoses suggested by earlier osteological examination of the remains; either tuberculosis or Langerhans cell histiocytosis. FINDINGS The remains tested positive for MTB complex markers, corroborating this diagnosis reached on osteological grounds. Based on positivity for the mtp40 element and a deletion in the pks15/1 locus, we conclude that infection was due to a strain of the human pathogen M.tuberculosis belonging to lineage 4. Although DNA recovered from the case was heavily fragmented, sex determination by amelogenin PCR suggested these are the remains of a young male child. The findings are discussed considering additions to the literature since the original report. CONCLUSIONS Descriptions of tuberculosis in children from this period are rare and burial Sk2077 represents the first UK example of a pre-adolescent individual to have a molecular diagnosis combined with osteological pathology. This provides an important reference of childhood tuberculosis and insight into the likely presence of tuberculosis in the mediaeval adult population served by this cemetery.
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10
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Lentz DL, Hamilton TL, Dunning NP, Scarborough VL, Luxton TP, Vonderheide A, Tepe EJ, Perfetta CJ, Brunemann J, Grazioso L, Valdez F, Tankersley KB, Weiss AA. Molecular genetic and geochemical assays reveal severe contamination of drinking water reservoirs at the ancient Maya city of Tikal. Sci Rep 2020; 10:10316. [PMID: 32587274 PMCID: PMC7316703 DOI: 10.1038/s41598-020-67044-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/02/2020] [Indexed: 11/09/2022] Open
Abstract
Understanding civilizations of the past and how they emerge and eventually falter is a primary research focus of archaeological investigations because these provocative data sets offer critical insights into long-term human behavior patterns, especially in regard to land use practices and sustainable environmental interactions. The ancient Maya serve as an intriguing example of this research focus, yet the details of their spectacular emergence in a tropical forest environment followed by their eventual demise have remained enigmatic. Tikal, one of the foremost of the ancient Maya cities, plays a central role in this discussion because of its sharp population decline followed by abandonment during the late 9th century CE. Our results, based on geochemical and molecular genetic assays on sediments from four of the main reservoirs, reveal that two of the largest reservoirs at Tikal, essential for the survival of the city during the dry seasons, were contaminated with high levels of mercury, phosphate and cyanobacteria known to produce deadly toxins. Our observations demonstrate severe pollution problems at a time when episodes of climatic aridity were prevalent. This combination of catastrophic events clearly threatened the sustainability of the city and likely contributed to its abandonment.
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Affiliation(s)
- David L Lentz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA.
| | - Trinity L Hamilton
- Department of Plant and Microbial Biology and the BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
| | - Nicholas P Dunning
- Department of Geography, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Vernon L Scarborough
- Department of Anthropology, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Todd P Luxton
- National Risk Management Research Laboratory, US Environmental Protection Agency, Cincinnati, OH, 45224, USA
| | - Anne Vonderheide
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Eric J Tepe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Cory J Perfetta
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - James Brunemann
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Liwy Grazioso
- Museo Miraflores, 7 Calle 21-55, Guatemala City, Guatemala
| | - Fred Valdez
- Department of Anthropology, University of Texas, Austin, TX, 78212, USA
| | - Kenneth B Tankersley
- Department of Anthropology, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Alison A Weiss
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, OH, 45267, USA
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11
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Arriola LA, Cooper A, Weyrich LS. Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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12
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Zou X, He G, Wang M, Huo L, Chen X, Liu J, Wang S, Ye Z, Wang F, Wang Z, Hou Y. Genetic diversity and phylogenetic structure of four Tibeto-Burman-speaking populations in Tibetan-Yi corridor revealed by insertion/deletion polymorphisms. Mol Genet Genomic Med 2020; 8:e1140. [PMID: 32017463 PMCID: PMC7196475 DOI: 10.1002/mgg3.1140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/01/2020] [Accepted: 01/03/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Insertion/deletion polymorphisms (InDels), combined with all the desirable features of both short tandem repeat and single nucleotide polymorphism, have been used in archaeological and anthropological research, population genetics and forensic application. METHODS Thirty InDels in 530 individuals residing in the Tibetan-Yi corridor (142 Dujiangyan Tibetans, 164 Muli Tibetans, 187 Xichang Yis, and 37 Yanyuan Mosuos) were genotyped using the Investigator DIPplex. Forensic parameters and allele frequency spectrum were calculated. Genetic relationships between the investigated populations and worldwide and nationwide populations were assessed based on both the allele frequency distribution and genotype data. RESULTS The combined powers of exclusion were 0.9807 (Dujiangyan Tibetan), 0.9880 (Muli Tibetan), 0.9852 (Xichang Yi) and 0.9892 (Yanyuan Mosuo). The combined powers of discrimination were 0.999999999983 (Dujiangyan Tibetan), 0.999999999942 (Muli Tibetan), 0.999999999982 (Xichang Yi) and 0.999999999962 (Yanyuan Mosuo), respectively. The comprehensive population comparisons among worldwide and nationwide populations uniformly illustrated that the investigated populations have a genetically closer relationship with Tibeto-Burman-speaking populations and geographically adjacent populations. CONCLUSION These 30 loci can be regarded as an efficient genetic tool in forensic individual identification and as a supplementary tool in paternity testing in Dujiangyan Tibetan, Muli Tibetan, Xichang Yi, and Yanyuan Mosuo. The genetic proximity between the four populations in the Tibetan-Yi corridor and other populations is strongly correlated with the linguistic origin and geographical distance.
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Affiliation(s)
- Xing Zou
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Guanglin He
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Mengge Wang
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Liwen Huo
- Chongqing Hechuan District Public Security BureauChongqingChina
| | - Xu Chen
- Department of Clinical LaboratoryThe First People’s Hospital of Liangshan Yi Autonomous PrefectureXichangChina
| | - Jing Liu
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Shouyu Wang
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Ziwei Ye
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Fei Wang
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Zheng Wang
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Yiping Hou
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
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13
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Donoghue HD. Tuberculosis and leprosy associated with historical human population movements in Europe and beyond - an overview based on mycobacterial ancient DNA. Ann Hum Biol 2019; 46:120-128. [PMID: 31137975 DOI: 10.1080/03014460.2019.1624822] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Context: Tuberculosis and leprosy are readily recognised in human remains due to their typical palaeopathology. Both Mycobacterium tuberculosis (MTB) and Mycobacterium leprae (ML) are obligate pathogens and have been detected in ancient human populations. Objective: To demonstrate historical tuberculosis and leprosy cases in Europe and beyond using molecular methods, as human populations are associated with different mycobacterial genotypes. Methods: MTB and ML ancient DNA (aDNA) has been detected by DNA amplification using PCR, or by whole genome sequencing. Mycobacterial cell wall lipids also provide specific markers for identification. Results: In 18th century Hungary, the European indigenous MTB genotype 4 strains have been found. However, many individuals were co-infected with up to three MTB sub-genotypes. In 8th-14th century Europe significant differences in ML genotypes were found between northwest Europe compared with central, southern, or eastern Europe. In addition, several co-infections of MTB and ML were detected in historical samples. Conclusion: Both MTB and ML strain types differ between geographically separate populations. This is associated with ancient human migration after an evolutionary bottleneck and clonal expansion. The absence of indigenous leprosy in Europe today may be due to the greater mortality of tuberculosis in individuals who are co-infected with both organisms.
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Affiliation(s)
- Helen D Donoghue
- a Centre for Clinical Microbiology , University College London (UCL) , London , UK
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14
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Borówka P, Pułaski Ł, Marciniak B, Borowska-Strugińska B, Dziadek J, Żądzińska E, Lorkiewicz W, Strapagiel D. Screening methods for detection of ancient Mycobacterium tuberculosis complex fingerprints in next-generation sequencing data derived from skeletal samples. Gigascience 2019; 8:5521156. [PMID: 31220249 PMCID: PMC6586198 DOI: 10.1093/gigascience/giz065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/07/2019] [Accepted: 05/10/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Recent advances in ancient DNA studies, especially in increasing isolated DNA yields and quality, have opened the possibility of analysis of ancient host microbiome. However, such pitfalls as spurious identification of pathogens based on fragmentary data or environmental contamination could lead to incorrect epidaemiological conclusions. Within the Mycobacterium genus, Mycobacterium tuberculosis complex members responsible for tuberculosis share up to ∼99% genomic sequence identity, while other more distantly related Mycobacteria other than M. tuberculosis can be causative agents for pulmonary diseases or soil dwellers. Therefore, reliable determination of species complex is crucial for interpretation of sequencing results. RESULTS Here we present a novel bioinformatical approach, used for screening of ancient tuberculosis in sequencing data, derived from 28 individuals (dated 4400-4000 and 3100-2900 BC) from central Poland. We demonstrate that cost-effective next-generation screening sequencing data (∼20M reads per sample) could yield enough information to provide statistically supported identification of probable ancient disease cases. CONCLUSIONS Application of appropriate bioinformatic tools, including an unbiased selection of genomic alignment targets for species specificity, makes it possible to extract valid data from full-sample sequencing results (without subjective targeted enrichment procedures). This approach broadens the potential scope of palaeoepidaemiology both to older, suboptimally preserved samples and to pathogens with difficult intrageneric taxonomy.
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Affiliation(s)
- Paulina Borówka
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland
| | - Łukasz Pułaski
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland.,Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Street, 93-232 Łódź, Poland
| | - Błażej Marciniak
- Biobank Lab, Faculty of Biology and Environmental Protection, Department of Molecular Biophysics, University of Lodz, 14 Pilarskiego Street, 90-231 Łódź, Poland.,BBMRI.pl Consortium, 147 Stabłowicka Street, 54-066 Wrocław, Poland
| | - Beata Borowska-Strugińska
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Street, 93-232 Łódź, Poland
| | - Elżbieta Żądzińska
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland
| | - Wiesław Lorkiewicz
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland
| | - Dominik Strapagiel
- Biobank Lab, Faculty of Biology and Environmental Protection, Department of Molecular Biophysics, University of Lodz, 14 Pilarskiego Street, 90-231 Łódź, Poland.,BBMRI.pl Consortium, 147 Stabłowicka Street, 54-066 Wrocław, Poland
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15
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Flammer PG, Dellicour S, Preston SG, Rieger D, Warren S, Tan CKW, Nicholson R, Přichystalová R, Bleicher N, Wahl J, Faria NR, Pybus OG, Pollard M, Smith AL. Molecular archaeoparasitology identifies cultural changes in the Medieval Hanseatic trading centre of Lübeck. Proc Biol Sci 2018; 285:rspb.2018.0991. [PMID: 30282648 PMCID: PMC6191690 DOI: 10.1098/rspb.2018.0991] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/07/2018] [Indexed: 01/16/2023] Open
Abstract
Throughout history, humans have been afflicted by parasitic worms, and eggs are readily detected in archaeological deposits. This study integrated parasitological and ancient DNA methods with a large sample set dating between Neolithic and Early Modern periods to explore the utility of molecular archaeoparasitology as a new approach to study the past. Molecular analyses provided unequivocal species-level parasite identification and revealed location-specific epidemiological signatures. Faecal–oral transmitted nematodes (Ascaris lumbricoides and Trichuris trichiura) were ubiquitous across time and space. By contrast, high numbers of food-associated cestodes (Diphyllobothrium latum and Taenia saginata) were restricted to medieval Lübeck. The presence of these cestodes and changes in their prevalence at approximately 1300 CE indicate substantial alterations in diet or parasite availability. Trichuris trichiura ITS-1 sequences grouped into two clades; one ubiquitous and one restricted to medieval Lübeck and Bristol. The high sequence diversity of T.t.ITS-1 detected in Lübeck is consistent with its importance as a Hanseatic trading centre. Collectively, these results introduce molecular archaeoparasitology as an artefact-independent source of historical evidence.
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Affiliation(s)
- Patrik G Flammer
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK.,Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Simon Dellicour
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK.,Rega Institute for Medical Research, Clinical and Epidemiological Virology, Department of Microbiology and Immunology, KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Stephen G Preston
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Dirk Rieger
- Archäologie und Denkmalpflege der Hansestadt Lübeck, 23566 Lübeck, Germany
| | - Sylvia Warren
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Cedric K W Tan
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Rebecca Nicholson
- Oxford Archaeology Ltd., Janus House, Osney Mead, Oxford OX2 0ES, UK
| | | | - Niels Bleicher
- Hochbauamt der Stadt Zürich, Abteilung Unterwasserarchäologie, 8008 Zürich, Switzerland
| | - Joachim Wahl
- Universität Tübingen, 72070 Tübingen, Germany.,Regierungspräsidium Stuttgart, Landesamt für Denkmalpflege, 78467 Konstanz, Germany
| | - Nuno R Faria
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Oliver G Pybus
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Mark Pollard
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Adrian L Smith
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
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16
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Gruzdev DA, Musiyak VV, Levit GL, Krasnov VP, Charushin VN. Purine derivatives with antituberculosis activity. RUSSIAN CHEMICAL REVIEWS 2018. [DOI: 10.1070/rcr4772] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The review summarizes the data published over the last 10 – 15 years concerning the key groups of purine derivatives with antituberculosis activity. The structures of purines containing heteroatoms (S, O, N), fragments of heterocycles, amino acids and peptides, in the 6-position, as well as of purine nucleosides are presented. The possible targets for the action of such compounds and structure – activity relationship are discussed. Particular attention is paid to the most active compounds, which are of considerable interest as a basis for the development of efficient antituberculosis drugs.
The bibliography includes 99 references.
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17
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Margaryan A, Hansen HB, Rasmussen S, Sikora M, Moiseyev V, Khoklov A, Epimakhov A, Yepiskoposyan L, Kriiska A, Varul L, Saag L, Lynnerup N, Willerslev E, Allentoft ME. Ancient pathogen DNA in human teeth and petrous bones. Ecol Evol 2018; 8:3534-3542. [PMID: 29607044 PMCID: PMC5869295 DOI: 10.1002/ece3.3924] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 01/11/2018] [Accepted: 01/23/2018] [Indexed: 01/21/2023] Open
Abstract
Recent ancient DNA (aDNA) studies of human pathogens have provided invaluable insights into their evolutionary history and prevalence in space and time. Most of these studies were based on DNA extracted from teeth or postcranial bones. In contrast, no pathogen DNA has been reported from the petrous bone which has become the most desired skeletal element in ancient DNA research due to its high endogenous DNA content. To compare the potential for pathogenic aDNA retrieval from teeth and petrous bones, we sampled these elements from five ancient skeletons, previously shown to be carrying Yersinia pestis. Based on shotgun sequencing data, four of these five plague victims showed clearly detectable levels of Y. pestis DNA in the teeth, whereas all the petrous bones failed to produce Y. pestis DNA above baseline levels. A broader comparative metagenomic analysis of teeth and petrous bones from 10 historical skeletons corroborated these results, showing a much higher microbial diversity in teeth than petrous bones, including pathogenic and oral microbial taxa. Our results imply that although petrous bones are highly valuable for ancient genomic analyses as an excellent source of endogenous DNA, the metagenomic potential of these dense skeletal elements is highly limited. This trade‐off must be considered when designing the sampling strategy for an aDNA project.
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Affiliation(s)
- Ashot Margaryan
- Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark.,Institute of Molecular Biology National Academy of Sciences Yerevan Armenia
| | - Henrik B Hansen
- Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Simon Rasmussen
- Department of Bio and Health Informatics Technical University of Denmark Kongens Lyngby Denmark
| | - Martin Sikora
- Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RASSt Petersburg Russia
| | - Alexandr Khoklov
- Samara State University of Social Sciences and Education Samara Russia
| | - Andrey Epimakhov
- Institute of History and Archaeology RAS (South Ural Department) South Ural State University Chelyabinsk Russia
| | - Levon Yepiskoposyan
- Institute of Molecular Biology National Academy of Sciences Yerevan Armenia.,Russian-Armenian University Yerevan Armenia
| | - Aivar Kriiska
- School of Humanities Tallinn University Tallinn Estonia
| | - Liivi Varul
- School of Humanities Tallinn University Tallinn Estonia
| | - Lehti Saag
- Department of Evolutionary Biology Institute of Molecular and Cell Biology University of Tartu Tartu Estonia.,Estonian Biocentre Institute of Genomics University of Tartu Tartu Estonia
| | - Niels Lynnerup
- Department of Forensic Medicine Section of Forensic Pathology University of Copenhagen Copenhagen East Denmark
| | - Eske Willerslev
- Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark.,Department of Zoology University of Cambridge Cambridge UK.,Wellcome Trust Sanger Institute Hinxton Cambridgeshire CB10 1SA UK
| | - Morten E Allentoft
- Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
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18
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Mokrousov I, Shitikov E, Skiba Y, Kolchenko S, Chernyaeva E, Vyazovaya A. Emerging peak on the phylogeographic landscape of Mycobacterium tuberculosis in West Asia: Definitely smoke, likely fire. Mol Phylogenet Evol 2017; 116:202-212. [DOI: 10.1016/j.ympev.2017.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 12/16/2022]
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19
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Positive Diagnosis of Ancient Leprosy and Tuberculosis Using Ancient DNA and Lipid Biomarkers. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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20
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Staphylococcus aureus Sequences from Osteomyelitic Specimens of a Pathological Bone Collection from Pre-Antibiotic Times. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Abstract
Tuberculosis is a significant global disease today, so understanding its origins and history is important. It is primarily a lung infection and is transmitted by infectious aerosols from person to person, so a high population density encourages its spread. The causative organism is Mycobacterium tuberculosis, an obligate pathogen in the M. tuberculosis complex that also contains closely related species, such as Mycobacterium bovis, that primarily infect animals. Typical bone lesions occur in about 5% of untreated infections. These can be recognized in historical and archaeological material, along with nonspecific paleopathology such as new bone formation (periostitis), especially on ribs. Based on such lesions, tuberculosis has been found in ancient Egypt, pre-Columbian America, and Neolithic Europe. The detection of M. tuberculosis ancient DNA (aDNA) by using PCR led to the development of the new field of paleomicrobiology. As a result, a large number of tuberculosis cases were recognized in mummified tissue and bones with nonspecific or no lesions. In parallel with these developments, M. tuberculosis cell wall lipid biomarkers have detected tuberculosis suggested by paleopathology and confirmed aDNA findings. In well-preserved cases, molecular typing has identified M. tuberculosis lineages and genotypes. The current interest in targeted enrichment, shotgun sequencing, and metagenomic analysis reveals ancient mixed infections with different M. tuberculosis strains and other pathogens. Identification of M. tuberculosis lineages from samples of known age enables the date of the emergence of strains and lineages to be calculated directly rather than by making assumptions on the rate of evolutionary change.
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22
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Philips A, Stolarek I, Kuczkowska B, Juras A, Handschuh L, Piontek J, Kozlowski P, Figlerowicz M. Comprehensive analysis of microorganisms accompanying human archaeological remains. Gigascience 2017; 6:1-13. [PMID: 28609785 PMCID: PMC5965364 DOI: 10.1093/gigascience/gix044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/09/2017] [Accepted: 06/11/2017] [Indexed: 02/01/2023] Open
Abstract
Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains. DNA samples were isolated from the teeth of human skeletons dated from 100 AD to 1200 AD. The skeletons were collected from 7 archaeological sites in Central Europe and stored under different conditions. The majority of identified microbes were ubiquitous environmental bacteria that most likely contaminated the host remains not long ago. We observed that the composition of microbial communities was sample-specific and not correlated with its temporal or geographical origin. Additionally, traces of bacteria and archaea typical for human oral/gut flora, as well as potential pathogens, were identified in two-thirds of the samples. The genetic material of human-related species, in contrast to the environmental species that accounted for the majority of identified bacteria, displayed DNA damage patterns comparable with endogenous human ancient DNA, which suggested that these microbes might have accompanied the individual before death. Our study showed that the microbiome observed in an individual sample is not reliant on the method or duration of sample storage. Moreover, shallow sequencing of DNA extracted from ancient specimens and subsequent bioinformatics analysis allowed both the identification of ancient microbial species, including potential pathogens, and their differentiation from contemporary species that colonized human remains more recently.
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Affiliation(s)
- Anna Philips
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Ireneusz Stolarek
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Bogna Kuczkowska
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty
of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland
| | - Luiza Handschuh
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Department of Hematology and Bone Marrow Transplantation, University of
Medical Sciences, Poznan, 60-569, Poland
- Institute of Technology and Chemical Engineering, Poznan University of
Technology, Poznan, 60-965, Poland
| | - Janusz Piontek
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty
of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland
| | - Piotr Kozlowski
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Institute of Technology and Chemical Engineering, Poznan University of
Technology, Poznan, 60-965, Poland
| | - Marek Figlerowicz
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan,
60-965, Poland
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23
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Donoghue HD. Insights gained from ancient biomolecules into past and present tuberculosis—a personal perspective. Int J Infect Dis 2017; 56:176-180. [DOI: 10.1016/j.ijid.2016.11.413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/17/2016] [Accepted: 11/20/2016] [Indexed: 01/24/2023] Open
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24
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Hühns M, Erbersdobler A, Obliers A, Röpenack P. Identification of HPV Types and Mycobacterium Tuberculosis Complex in Historical Long-Term Preserved Formalin Fixed Tissues in Different Human Organs. PLoS One 2017; 12:e0170353. [PMID: 28114406 PMCID: PMC5256871 DOI: 10.1371/journal.pone.0170353] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/03/2017] [Indexed: 01/18/2023] Open
Abstract
University anatomical-pathological collections represent huge sources of human tissues and preparations from a variety of different diseases. With the help of modern genetic and histological methods, preserved fixed tissues from pathological collections can be used to re-evaluate former diagnoses. We analysed 25 specimens from our pathological collection with ages ranging from 78 to 112 years. The tissues originated from the oral cavity, lip, tongue, lung, bone, kidney, spleen, thymus, larynx, lymph node, penis and uterine cervix with an original diagnosis of epithelial cancers or tuberculosis. Amplifiable DNA was extracted and in epithelial cancers, potential HPV infection was investigated. Specimens with an original diagnosis of tuberculosis were examined for mycobacterial infection. The tissues were also examined using modern histological methods. Our data showed that in 24/25 specimens the histological structure was preserved and in 10/11 specimens the diagnosis of squamous cell carcinoma could be confirmed. Additionally, HPV type 16 was detected in 8 specimens. The histological pattern of tuberculosis was found in 11/14 specimens and the Mycobacterium tuberculosis complex was ascertained in four specimens. Our study showed that pathogens such as HPV or Mycobacterium tuberculosis can be detected in historical pathological preparations, and that these collections are suitable for further epidemiological research.
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Affiliation(s)
- Maja Hühns
- Institute of Pathology, University Medicine of Rostock, Rostock, Germany
- * E-mail:
| | | | - Annette Obliers
- Institute of Pathology, University Medicine of Rostock, Rostock, Germany
| | - Paula Röpenack
- Institute of Pathology, University Medicine of Rostock, Rostock, Germany
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25
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Abstract
The recent Ebola epidemic provides a dramatic example of the devastation and fear generated by epidemics, particularly those caused by new emerging or reemerging diseases. A focus on the control and prevention of diseases in living populations dominates most epidemic disease research. However, research on epidemics in the past provides a temporal depth to our understanding of the context and consequences of diseases and is crucial for predicting how diseases might shape human biology and demography in the future. This article reviews recent research on historic epidemics of plague and tuberculosis, both of which have affected human populations for millennia. Research on these diseases demonstrates the range (and differential availability) of various lines of evidence (e.g., burial context, diagnostic skeletal lesions, molecular data) that inform about past disease in general. I highlight how research on past epidemics may be informative in ways that benefit living populations.
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Affiliation(s)
- Sharon N. DeWitte
- Department of Anthropology and Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208
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26
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Forst J, Brown TA. Inability of 'Whole Genome Amplification' to Improve Success Rates for the Biomolecular Detection of Tuberculosis in Archaeological Samples. PLoS One 2016; 11:e0163031. [PMID: 27654468 PMCID: PMC5031403 DOI: 10.1371/journal.pone.0163031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 09/01/2016] [Indexed: 11/30/2022] Open
Abstract
We assessed the ability of whole genome amplification (WGA) to improve the efficiency of downstream polymerase chain reactions (PCRs) directed at ancient DNA (aDNA) of members of the Mycobacterium tuberculosis complex (MTBC). Using extracts from a variety of bones and a tooth from human skeletons with or without lesions indicative of tuberculosis, from multiple time periods, we obtained inconsistent results. We conclude that WGA does not provide any advantage in studies of MTBC aDNA. The sporadic nature of our results are probably due to the fact that WGA is itself a PCR-based procedure which, although designed to deal with fragmented DNA, might be inefficient with the low concentration of templates in an aDNA extract. As such, WGA is subject to similar, if not the same, restrictions as PCR when applied to aDNA.
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Affiliation(s)
- Jannine Forst
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester, United Kingdom
| | - Terence A. Brown
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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Andam CP, Worby CJ, Chang Q, Campana MG. Microbial Genomics of Ancient Plagues and Outbreaks. Trends Microbiol 2016; 24:978-990. [PMID: 27618404 DOI: 10.1016/j.tim.2016.08.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 07/29/2016] [Accepted: 08/16/2016] [Indexed: 01/22/2023]
Abstract
The recent use of next-generation sequencing methods to investigate historical disease outbreaks has provided us with an unprecedented ability to address important and long-standing questions in epidemiology, pathogen evolution, and human history. In this review, we present major findings that illustrate how microbial genomics has provided new insights into the nature and etiology of infectious diseases of historical importance, such as plague, tuberculosis, and leprosy. Sequenced isolates collected from archaeological remains also provide evidence for the timing of historical evolutionary events as well as geographic spread of these pathogens. Elucidating the genomic basis of virulence in historical diseases can provide relevant information on how we can effectively understand the emergence and re-emergence of infectious diseases today and in the future.
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Affiliation(s)
- Cheryl P Andam
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA; University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Durham, NH 03824, USA.
| | - Colin J Worby
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA
| | - Qiuzhi Chang
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA
| | - Michael G Campana
- Smithsonian Conservation Biology Institute, Center for Conservation Genomics, 3001 Connecticut Avenue NW, Washington, DC 20008, USA.
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Abstract
ABSTRACT
With the advent of next-generation sequencing technology, the genotyping of clinical
Mycobacterium tuberculosis
strains went through a major breakup that dramatically improved the field of molecular epidemiology but also revolutionized our deep understanding of the
M. tuberculosis
complex evolutionary history. The intricate paths of the pathogen and its human host are reflected by a common geographical origin in Africa and strong biogeographical associations that largely reflect the past migration waves out of Africa. This long coevolutionary history is cardinal for our understanding of the host-pathogen dynamic, including past and ongoing demographic components, strains’ genetic background, as well as the immune system genetic architecture of the host. Coalescent- and Bayesian-based analyses allowed us to reconstruct population size changes of
M. tuberculosis
through time, to date the most recent common ancestor and the several phylogenetic lineages. This information will ultimately help us to understand the spread of the Beijing lineage, the rise of multidrug-resistant sublineages, or the fall of others in the light of socioeconomic events, antibiotic programs, or host population densities. If we leave the present and go through the looking glass, thanks to our ability to handle small degraded molecules combined with targeted capture, paleomicrobiology covering the Pleistocene era will possibly unravel lineage replacements, dig out extinct ones, and eventually ask for major revisions of the current model.
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Schnorr SL, Sankaranarayanan K, Lewis CM, Warinner C. Insights into human evolution from ancient and contemporary microbiome studies. Curr Opin Genet Dev 2016; 41:14-26. [PMID: 27507098 DOI: 10.1016/j.gde.2016.07.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 12/11/2022]
Abstract
Over the past decade, human microbiome research has energized the study of human evolution through a complete shift in our understanding of what it means to be human. The microbiome plays a pivotal role in human biology, performing key functions in digestion, mood and behavior, development and immunity, and a range of acute and chronic diseases. It is therefore critical to understand its evolution and changing ecology through time. Here we review recent findings on the microbiota of diverse human populations, non-human primates, and past human populations and discuss the implications of this research in formulating a deeper evolutionary understanding of the human holobiont.
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Affiliation(s)
- Stephanie L Schnorr
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA
| | | | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA.
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31
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Gogarten JF, Düx A, Schuenemann VJ, Nowak K, Boesch C, Wittig RM, Krause J, Calvignac-Spencer S, Leendertz FH. Tools for opening new chapters in the book of Treponema pallidum evolutionary history. Clin Microbiol Infect 2016; 22:916-921. [PMID: 27498082 DOI: 10.1016/j.cmi.2016.07.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/04/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
Abstract
Treponema pallidum infections causing yaws disease and venereal syphilis are globally widespread in human populations, infecting hundreds of thousands and millions annually respectively; endemic syphilis is much less common, and pinta has not been observed in decades. We discuss controversy surrounding the origin, evolution and history of these pathogens in light of available molecular and anthropological evidence. These bacteria (or close relatives) seem to affect many wild African nonhuman primate (NHP) species, though to date only a single NHP Treponema pallidum genome has been published, hindering detection of spillover events and our understanding of potential wildlife reservoirs. Similarly, only ten genomes of Treponema pallidum infecting humans have been published, impeding a full understanding of their diversity and evolutionary history. Research efforts have been hampered by the difficulty of culturing and propagating Treponema pallidum. Here we highlight avenues of research recently opened by the coupling of hybridization capture and next-generation sequencing. We present data generated with such an approach suggesting that asymptomatic bones from NHP occasionally contain enough treponemal DNA to recover large fractions of their genomes. We expect that these methods, which naturally can be applied to modern biopsy samples and ancient human bones, will soon considerably improve our understanding of these enigmatic pathogens and lay rest to old yet unresolved controversies.
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Affiliation(s)
- J F Gogarten
- Epidemiology of Highly Pathogenic Microorganisms, Germany; Primatology Department, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Department of Biology, McGill University, Montreal, Quebec, Canada
| | - A Düx
- Epidemiology of Highly Pathogenic Microorganisms, Germany; Viral Evolution, Robert Koch Institute, Berlin, Germany
| | - V J Schuenemann
- Institute for Archeological Sciences, University of Tübingen, Tübingen, Germany
| | - K Nowak
- Epidemiology of Highly Pathogenic Microorganisms, Germany
| | - C Boesch
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - R M Wittig
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Taï Chimpanzee Project, CSRS, Abidjan, Cote d'Ivoire
| | - J Krause
- Institute for Archeological Sciences, University of Tübingen, Tübingen, Germany; Max Planck Institute for the Science of Human History, Jena, Germany
| | - S Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms, Germany; Viral Evolution, Robert Koch Institute, Berlin, Germany.
| | - F H Leendertz
- Epidemiology of Highly Pathogenic Microorganisms, Germany.
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Rivera-Perez JI, Santiago-Rodriguez TM, Toranzos GA. Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology. Microbiol Spectr 2016; 4:10.1128/microbiolspec.EMF-0006-2015. [PMID: 27726770 PMCID: PMC5287379 DOI: 10.1128/microbiolspec.emf-0006-2015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Indexed: 01/14/2023] Open
Abstract
Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.
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Archaeogenetics in evolutionary medicine. J Mol Med (Berl) 2016; 94:971-7. [PMID: 27289479 DOI: 10.1007/s00109-016-1438-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 05/22/2016] [Accepted: 06/03/2016] [Indexed: 12/24/2022]
Abstract
Archaeogenetics is the study of exploration of ancient DNA (aDNA) of more than 70 years old. It is an important part of the wider studies of many different areas of our past, including animal, plant and pathogen evolution and domestication events. Hereby, we address specifically the impact of research in archaeogenetics in the broader field of evolutionary medicine. Studies on ancient hominid genomes help to understand even modern health patterns. Human genetic microevolution, e.g. related to abilities of post-weaning milk consumption, and specifically genetic adaptation in disease susceptibility, e.g. towards malaria and other infectious diseases, are of the upmost importance in contributions of archeogenetics on the evolutionary understanding of human health and disease. With the increase in both the understanding of modern medical genetics and the ability to deep sequence ancient genetic information, the field of archaeogenetic evolutionary medicine is blossoming.
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34
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Roberts CA. Palaeopathology and its relevance to understanding health and disease today: the impact of the environment on health, past and present. ANTHROPOLOGICAL REVIEW 2016. [DOI: 10.1515/anre-2016-0001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
This paper considers the discipline of palaeopathology, how it has developed, how it is studied, and what limitations present challenges to analysis. The study of disease has a long history and has probably most rapidly developed over the last 40-50 years with the development of methods, and particularly ancient pathogen DNA analysis. While emphasizing that palaeopathology has close synergies to evolutionary medicine, it focuses then on three ‘case studies’ that illustrate the close interaction people have had with their environments and how that has impacted their health. Upper and lower respiratory tract disease has affected sinuses and ribs, particularly in urban contexts, and tuberculosis in particular has been an ever present disease throughout thousands of years of our existence. Ancient DNA methods are now allowing us to explore how strains of the bacteria causing TB have changed through time. Vitamin D deficiency and ‘phossy jaw’ are also described, both potentially related to polluted environments, and possibly to working conditions in the industrial period. Access to UV light is emphasized as a preventative factor for rickets and where a person lives is important (latitude). The painful stigmatizing ‘phossy jaw’ appears to be a condition related to the match making industries. Finally, thoughts for the future are outlined, and two key concerns: a close consideration of ethical issues and human remains, especially with destructive analyses, and thinking more about how palaeopathological research can impact people beyond academia.
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Bianucci R, Araujo A, Pusch CM, Nerlich AG. The identification of malaria in paleopathology-An in-depth assessment of the strategies to detect malaria in ancient remains. Acta Trop 2015; 152:176-180. [PMID: 26366472 DOI: 10.1016/j.actatropica.2015.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 07/19/2015] [Accepted: 09/01/2015] [Indexed: 01/07/2023]
Abstract
The comprehensive analyses of human remains from various places and time periods, either by immunological or molecular approaches, provide circumstantial evidence that malaria tropica haunted humankind at least since dynastic ancient Egypt. Here we summarize the "actual state-of-the-art" of these bio-molecular investigations and offer a solid basis for the discussion of the paleopathology of malaria in human history.
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Affiliation(s)
- Raffaella Bianucci
- Department of Public Health and Paediatric Sciences, Laboratory of Physical Anthropology, University of Turin, Italy; Centre for Ecological and Evolutionary Synthesis (CEES), Department Biosciences, University of Oslo, Norway; UMR 7568, Laboratoire d'Anthropologie bio-culturelle, Droit, Etique & Santé (Adés), Faculté de Médecine de Marseille, France
| | - Adauto Araujo
- Laboratório de Paleoparasitologia, Escola Nacional de Saúde Pública Sérgio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carsten M Pusch
- Institute of Anthropology and Human Genetics, Division of Molecular Genetics, University of Tübingen, Germany
| | - Andreas G Nerlich
- Institute of Pathology, Klinikum München-Bogenhausen, Munich, Germany.
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36
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Han SJ, Song T, Cho YJ, Kim JS, Choi SY, Bang HE, Chun J, Bai GH, Cho SN, Shin SJ. Complete genome sequence of Mycobacterium tuberculosis K from a Korean high school outbreak, belonging to the Beijing family. Stand Genomic Sci 2015; 10:78. [PMID: 26473025 PMCID: PMC4606834 DOI: 10.1186/s40793-015-0071-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 10/08/2015] [Indexed: 01/04/2023] Open
Abstract
Mycobacterium tuberculosis K, a member of the Beijing family, was first identified in 1999 as the most prevalent genotype in South Korea among clinical isolates of M. tuberculosis from high school outbreaks. M. tuberculosis K is an aerobic, non-motile, Gram-positive, and non-spore-forming rod-shaped bacillus. A transmission electron microscopy analysis displayed an abundance of lipid bodies in the cytosol. The genome of the M. tuberculosis K strain was sequenced using two independent sequencing methods (Sanger and Illumina). Here, we present the genomic features of the 4,385,518-bp-long complete genome sequence of M. tuberculosis K (one chromosome, no plasmid, and 65.59 % G + C content) and its annotation, which consists of 4194 genes (3447 genes with predicted functions), 48 RNA genes (3 rRNA and 45 tRNA) and 261 genes with peptide signals.
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Affiliation(s)
- Seung Jung Han
- Department of Microbiology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Taeksun Song
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Yong-Joon Cho
- ChunLab Inc., Seoul National University, Seoul, South Korea
| | - Jong-Seok Kim
- Department of Microbiology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Soo Young Choi
- Department of Microbiology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Hye-Eun Bang
- ChunLab Inc., Seoul National University, Seoul, South Korea
| | - Jongsik Chun
- ChunLab Inc., Seoul National University, Seoul, South Korea
| | - Gill-Han Bai
- Korean Institute of Tuberculosis, Korean National Tuberculosis Association, Osong, South Korea
| | - Sang-Nae Cho
- Department of Microbiology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
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Witas HW, Donoghue HD, Kubiak D, Lewandowska M, Gładykowska-Rzeczycka JJ. Molecular studies on ancient M. tuberculosis and M. leprae: methods of pathogen and host DNA analysis. Eur J Clin Microbiol Infect Dis 2015. [PMID: 26210385 PMCID: PMC4545183 DOI: 10.1007/s10096-015-2427-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Humans have evolved alongside infectious diseases for millennia. Despite the efforts to reduce their incidence, infectious diseases still pose a tremendous threat to the world population. Fast development of molecular techniques and increasing risk of new epidemics have resulted in several studies that look to the past in order to investigate the origin and evolution of infectious diseases. Tuberculosis and leprosy have become frequent targets of such studies, owing to the persistence of their molecular biomarkers in ancient material and the characteristic skeletal lesions each disease may cause. This review examines the molecular methods used to screen for the presence of M. tuberculosis and M. leprae ancient DNA (aDNA) and their differentiation in ancient human remains. Examples of recent studies, mainly from Europe, that employ the newest techniques of molecular analysis are also described. Moreover, we present a specific approach based on assessing the likely immunological profile of historic populations, in order to further elucidate the influence of M. tuberculosis and M. leprae on historical human populations.
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Affiliation(s)
- H W Witas
- Department of Molecular Biology, Medical University of Łódź, Łódź, Poland,
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38
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Roberts CA. Old World tuberculosis: Evidence from human remains with a review of current research and future prospects. Tuberculosis (Edinb) 2015; 95 Suppl 1:S117-21. [DOI: 10.1016/j.tube.2015.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Lee OYC, Wu HHT, Besra GS, Rothschild BM, Spigelman M, Hershkovitz I, Bar-Gal GK, Donoghue HD, Minnikin DE. Lipid biomarkers provide evolutionary signposts for the oldest known cases of tuberculosis. Tuberculosis (Edinb) 2015; 95 Suppl 1:S127-32. [PMID: 25797611 DOI: 10.1016/j.tube.2015.02.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Studies on the evolution of tuberculosis, and the influence of this disease on human and animal development and interaction, require the accumulation of indisputable biomarker evidence. Ideally, the determination of full genomes would provide all the necessary information, but for very old specimens DNA preservation may be compromised and only limited DNA amplification may be a possibility. Mycobacterium tuberculosis is characterised by the presence of unusual cell envelope lipids, with specific biomarker potential. Lipid biomarker recognition has been decisive in pinpointing the oldest known cases of human and animal tuberculosis; the former are a woman and child from a pre-pottery settlement at Atlit-Yam, Israel (∼9,000 ka) and the latter is an extinct Bison antiquus from Natural Trap Cave, Wyoming (∼17,000 ka). Including some new data, it is demonstrated how analysis of a combination of mycolic, mycocerosic and mycolipenic acid and phthiocerol biomarkers provide incontrovertible evidence for tuberculosis in these landmark specimens.
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Affiliation(s)
- Oona Y-C Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Houdini H T Wu
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Bruce M Rothschild
- Biodiversity Institute and Departments of Anthropology and Geology, University of Kansas, Lawrence, KS 66045, USA.
| | - Mark Spigelman
- Kuvin Center for the Study of Infectious and Tropical Diseases and Ancient DNA, Hadassah Medical School, Hebrew University, Jerusalem, Israel.
| | - Israel Hershkovitz
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
| | - Gila Kahila Bar-Gal
- Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Rehovot, Israel.
| | - Helen D Donoghue
- Centres for Clinical Microbiology and the History of Medicine, University College London, UK.
| | - David E Minnikin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
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40
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Donoghue HD, Spigelman M, O'Grady J, Szikossy I, Pap I, Lee OYC, Wu HHT, Besra GS, Minnikin DE. Ancient DNA analysis - An established technique in charting the evolution of tuberculosis and leprosy. Tuberculosis (Edinb) 2015; 95 Suppl 1:S140-4. [PMID: 25773651 DOI: 10.1016/j.tube.2015.02.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Many tuberculosis and leprosy infections are latent or paucibacillary, suggesting a long time-scale for host and pathogen co-existence. Palaeopathology enables recognition of archaeological cases and PCR detects pathogen ancient DNA (aDNA). Mycobacterium tuberculosis and Mycobacterium leprae cell wall lipids are more stable than aDNA and restrict permeability, thereby possibly aiding long-term persistence of pathogen aDNA. Amplification of aDNA, using specific PCR primers designed for short fragments and linked to fluorescent probes, gives good results, especially when designed to target multi-copy loci. Such studies have confirmed tuberculosis and leprosy, including co-infections. Many tuberculosis cases have non-specific or no visible skeletal pathology, consistent with the natural history of this disease. M. tuberculosis and M. leprae are obligate parasites, closely associated with their human host following recent clonal distribution. Therefore genotyping based on single nucleotide polymorphisms (SNPs) can indicate their origins, spread and phylogeny. Knowledge of extant genetic lineages at particular times in past human populations can be obtained from well-preserved specimens where molecular typing is possible, using deletion analysis, microsatellite analysis and whole genome sequencing. Such studies have identified non-bovine tuberculosis from a Pleistocene bison from 17,500 years BP, human tuberculosis from 9000 years ago and leprosy from over 2000 years ago.
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Affiliation(s)
- Helen D Donoghue
- Centre for Clinical Microbiology, Division of Infection & Immunity, University College London, London, UK; Centre for the History of Medicine, Division of Biosciences, University College London, UK.
| | - Mark Spigelman
- Centre for Clinical Microbiology, Division of Infection & Immunity, University College London, London, UK; Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Justin O'Grady
- Centre for Clinical Microbiology, Division of Infection & Immunity, University College London, London, UK.
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural Science Museum, Budapest, Hungary.
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural Science Museum, Budapest, Hungary.
| | - Oona Y-C Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Houdini H T Wu
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - David E Minnikin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
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41
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Minnikin DE, Lee OYC, Wu HHT, Besra GS, Bhatt A, Nataraj V, Rothschild BM, Spigelman M, Donoghue HD. Ancient mycobacterial lipids: Key reference biomarkers in charting the evolution of tuberculosis. Tuberculosis (Edinb) 2015; 95 Suppl 1:S133-9. [PMID: 25736170 DOI: 10.1016/j.tube.2015.02.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Mycobacterium tuberculosis has a cell envelope incorporating a peptidoglycan-linked arabinogalactan esterified by long-chain mycolic acids. A range of "free" lipids are associated with the "bound" mycolic acids, producing an effective envelope outer membrane. The distribution of these lipids is discontinuous among mycobacteria and such lipids have proven potential for biomarker use in tracing the evolution of tuberculosis. A plausible evolutionary scenario involves progression from an environmental organism, such as Mycobacterium kansasii, through intermediate "smooth" tubercle bacilli, labelled "Mycobacterium canettii"; cell envelope lipid composition possibly correlates with such a progression. M. kansasii and "M. canettii" have characteristic lipooligosaccharides, associated with motility and biofilms, and glycosyl phenolphthiocerol dimycocerosates ("phenolic glycolipids"). Both these lipid classes are absent in modern M. tuberculosis sensu stricto, though simplified phenolic glycolipids remain in certain current biotypes. Dimycocerosates of the phthiocerol family are restricted to smaller phthiodiolone diesters in M. kansasii. Diacyl and pentaacyl trehaloses are present in "M. canettii" and M. tuberculosis, accompanied in the latter by related sulfated acyl trehaloses. In comparison with environmental mycobacteria, subtle modifications in mycolic acid structures in "M. canettii" and M. tuberculosis are notable. The probability of essential tuberculosis evolution taking place in Pleistocene megafauna, rather than Homo sapiens, is reemphasised.
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Affiliation(s)
- David E Minnikin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Oona Y-C Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Houdini H T Wu
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Apoorva Bhatt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Vijayashankar Nataraj
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Bruce M Rothschild
- Biodiversity Institute and Departments of Anthropology and Geology, University of Kansas, Lawrence, KS 66045, USA.
| | - Mark Spigelman
- Kuvin Center for the Study of Infectious and Tropical Diseases and Ancient DNA, Hadassah Medical School, Hebrew University, Jerusalem, Israel.
| | - Helen D Donoghue
- Centres for Clinical Microbiology and the History of Medicine, University College London, London, UK.
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42
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Hlavenková L, Teasdale M, Gábor O, Nagy G, Beňuš R, Marcsik A, Pinhasi R, Hajdu T. Childhood bone tuberculosis from Roman Pécs, Hungary. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2015; 66:27-37. [DOI: 10.1016/j.jchb.2014.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 10/06/2014] [Indexed: 12/17/2022]
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43
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Harkins KM, Buikstra JE, Campbell T, Bos KI, Johnson ED, Krause J, Stone AC. Screening ancient tuberculosis with qPCR: challenges and opportunities. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130622. [PMID: 25487341 PMCID: PMC4275897 DOI: 10.1098/rstb.2013.0622] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The field of ancient DNA (aDNA) has rapidly accelerated in recent years as a result of new methods in next-generation sequencing, library preparation and targeted enrichment. Such research is restricted, however, by the highly variable DNA preservation within different tissues, especially when isolating ancient pathogens from human remains. Identifying positive candidate samples via quantitative PCR (qPCR) for downstream procedures can reduce reagent costs, increase capture efficiency and maximize the number of sequencing reads of the target. This study uses four qPCR assays designed to target regions within the Mycobacterium tuberculosis complex (MTBC) to examine 133 human skeletal samples from a wide geographical and temporal range, identified by the presence of skeletal lesions typical of chronic disseminated tuberculosis. Given the inherent challenges working with ancient mycobacteria, strict criteria must be used and primer/probe design continually re-evaluated as new data from bacteria become available. Seven samples tested positive for multiple MTBC loci, supporting them as strong candidates for downstream analyses. Using strict and conservative criteria, qPCR remains a fast and effective screening tool when compared with screening by more expensive sequencing and enrichment technologies.
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Affiliation(s)
- Kelly M Harkins
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Jane E Buikstra
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Tessa Campbell
- Department of Archaeology, University of Cape Town, Cape Town, South Africa
| | - Kirsten I Bos
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Eric D Johnson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
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44
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Warinner C, Speller C, Collins MJ. A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130376. [PMID: 25487328 PMCID: PMC4275884 DOI: 10.1098/rstb.2013.0376] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.
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45
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Der Sarkissian C, Allentoft ME, Ávila-Arcos MC, Barnett R, Campos PF, Cappellini E, Ermini L, Fernández R, da Fonseca R, Ginolhac A, Hansen AJ, Jónsson H, Korneliussen T, Margaryan A, Martin MD, Moreno-Mayar JV, Raghavan M, Rasmussen M, Velasco MS, Schroeder H, Schubert M, Seguin-Orlando A, Wales N, Gilbert MTP, Willerslev E, Orlando L. Ancient genomics. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130387. [PMID: 25487338 PMCID: PMC4275894 DOI: 10.1098/rstb.2013.0387] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.
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Affiliation(s)
- Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ross Barnett
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ruth Fernández
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Rute da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Aurélien Ginolhac
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hákon Jónsson
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Michael D Martin
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval Velasco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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46
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Abstract
Biothreats are a high priority concern for public safety and national security. The field of microbial forensics was developed to analyze evidence associated with biological crimes in which microbes or their toxins are used as weapons. Microbial forensics is the scientific discipline dedicated to analyzing evidence from a bioterrorism act, biocrime, hoax, or inadvertent microorganism/toxin release for attribution purposes. Microbial forensics combines the practices of epidemiology with the characterization of microbial and microbial-related evidence to assist in determining the specific source of the sample, as individualizing as possible, and/or the methods, means, processes and locations involved to determine the identity of the perpetrator(s) of an attack.
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47
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Major transitions in human evolution revisited: a tribute to ancient DNA. J Hum Evol 2014; 79:4-20. [PMID: 25532800 DOI: 10.1016/j.jhevol.2014.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 06/06/2014] [Accepted: 06/19/2014] [Indexed: 11/23/2022]
Abstract
The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. These approaches promise to soon solve many pending controversies about our own origins that are indecipherable from modern patterns of genetic variation alone, and therefore provide an extremely powerful toolkit for a new generation of molecular anthropologists.
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48
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Ancient pathogen genomics: insights into timing and adaptation. J Hum Evol 2014; 79:137-49. [PMID: 25532802 DOI: 10.1016/j.jhevol.2014.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 09/08/2014] [Accepted: 11/05/2014] [Indexed: 12/15/2022]
Abstract
Disease is a major cause of natural selection affecting human evolution, whether through a sudden pandemic or persistent morbidity and mortality. Recent contributions in the field of ancient pathogen genomics have advanced our understanding of the antiquity and nature of human-pathogen interactions through time. Technical advancements have facilitated the recovery, enrichment, and high-throughput sequencing of pathogen and parasite DNA from archived and archaeological remains. These time-stamped genomes are crucial for calibrating molecular clocks to infer the timing of evolutionary events, while providing finer-grain resolution to phylogenetic reconstructions and complex biogeographical patterns. Additionally, genome scale data allow better identification of substitutions linked to adaptations of the pathogen to their human hosts. As methodology continues to improve, ancient genomes of humans and their diverse microbiomes from a range of eras and archaeological contexts will enable population-level ancient analyses in the near future and a better understanding of their co-evolutionary history.
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49
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Weyrich LS, Dobney K, Cooper A. Ancient DNA analysis of dental calculus. J Hum Evol 2014; 79:119-24. [PMID: 25476244 DOI: 10.1016/j.jhevol.2014.06.018] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 05/19/2014] [Accepted: 06/19/2014] [Indexed: 12/22/2022]
Abstract
Dental calculus (calcified tartar or plaque) is today widespread on modern human teeth around the world. A combination of soft starchy foods, changing acidity of the oral environment, genetic pre-disposition, and the absence of dental hygiene all lead to the build-up of microorganisms and food debris on the tooth crown, which eventually calcifies through a complex process of mineralisation. Millions of oral microbes are trapped and preserved within this mineralised matrix, including pathogens associated with the oral cavity and airways, masticated food debris, and other types of extraneous particles that enter the mouth. As a result, archaeologists and anthropologists are increasingly using ancient human dental calculus to explore broad aspects of past human diet and health. Most recently, high-throughput DNA sequencing of ancient dental calculus has provided valuable insights into the evolution of the oral microbiome and shed new light on the impacts of some of the major biocultural transitions on human health throughout history and prehistory. Here, we provide a brief historical overview of archaeological dental calculus research, and discuss the current approaches to ancient DNA sampling and sequencing. Novel applications of ancient DNA from dental calculus are discussed, highlighting the considerable scope of this new research field for evolutionary biology and modern medicine.
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Affiliation(s)
- Laura S Weyrich
- The Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, Australia
| | - Keith Dobney
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK
| | - Alan Cooper
- The Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, Australia.
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50
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Bos KI, Harkins KM, Herbig A, Coscolla M, Weber N, Comas I, Forrest SA, Bryant JM, Harris SR, Schuenemann VJ, Campbell TJ, Majander K, Wilbur AK, Guichon RA, Wolfe Steadman DL, Cook DC, Niemann S, Behr MA, Zumarraga M, Bastida R, Huson D, Nieselt K, Young D, Parkhill J, Buikstra JE, Gagneux S, Stone AC, Krause J. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature 2014; 514:494-7. [PMID: 25141181 PMCID: PMC4550673 DOI: 10.1038/nature13591] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/19/2014] [Indexed: 12/11/2022]
Abstract
Modern strains of Mycobacterium tuberculosis from the Americas are closely related to those from Europe, supporting the assumption that human tuberculosis was introduced post-contact. This notion, however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World. Comparative genomics of modern isolates suggests that M. tuberculosis attained its worldwide distribution following human dispersals out of Africa during the Pleistocene epoch, although this has yet to be confirmed with ancient calibration points. Here we present three 1,000-year-old mycobacterial genomes from Peruvian human skeletons, revealing that a member of the M. tuberculosis complex caused human disease before contact. The ancient strains are distinct from known human-adapted forms and are most closely related to those adapted to seals and sea lions. Two independent dating approaches suggest a most recent common ancestor for the M. tuberculosis complex less than 6,000 years ago, which supports a Holocene dispersal of the disease. Our results implicate sea mammals as having played a role in transmitting the disease to humans across the ocean.
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Affiliation(s)
- Kirsten I Bos
- 1] Department of Archaeological Sciences, University of Tübingen, Ruemelinstraße 23, 72070 Tübingen, Germany [2]
| | - Kelly M Harkins
- 1] School of Human Evolution and Social Change, Arizona State University, PO Box 872402, Tempe, Arizona 85287-2402, USA [2]
| | - Alexander Herbig
- 1] Department of Archaeological Sciences, University of Tübingen, Ruemelinstraße 23, 72070 Tübingen, Germany [2] Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany [3]
| | - Mireia Coscolla
- 1] Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland [2] University of Basel, Petersplatz 1, CH-4003 Basel, Switzerland [3]
| | - Nico Weber
- Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Iñaki Comas
- 1] Genomics and Health Unit, FISABIO-Public Health, Avenida Cataluña 21, 46020 Valencia, Spain [2] CIBER (Centros de Investigación Biomédica en Red) in Epidemiology and Public Health, Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Stephen A Forrest
- Department of Archaeological Sciences, University of Tübingen, Ruemelinstraße 23, 72070 Tübingen, Germany
| | - Josephine M Bryant
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Simon R Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Verena J Schuenemann
- Department of Archaeological Sciences, University of Tübingen, Ruemelinstraße 23, 72070 Tübingen, Germany
| | - Tessa J Campbell
- Department of Archaeology, University of Cape Town, Private Bag X1, Rondebosch, 7701, South Africa
| | - Kerttu Majander
- Department of Archaeological Sciences, University of Tübingen, Ruemelinstraße 23, 72070 Tübingen, Germany
| | - Alicia K Wilbur
- School of Human Evolution and Social Change, Arizona State University, PO Box 872402, Tempe, Arizona 85287-2402, USA
| | - Ricardo A Guichon
- CONICET, Laboratorio de Ecología Evolutiva Humana (FACSO, UNCPBA), Departamento de Biología (FCEyN, UNMDP), Calle 508 No. 881 (7631), Quequen, Argentina
| | - Dawnie L Wolfe Steadman
- Department of Anthropology, University of Tennessee, 250 South Stadium Hall, Knoxville, Tennessee 37996, USA
| | - Della Collins Cook
- Department of Anthropology, Indiana University, 701 East Kirkwood Avenue, Bloomington, Indiana 47405-7100, USA
| | - Stefan Niemann
- 1] Molecular Mycobacteriology, Forschungszentrum Borstel, Parkallee 1, 23845 Borstel, Germany [2] German Center for Infection Research, Forschungszentrum Borstel, Parkallee 1, 23845 Borstel, Germany
| | - Marcel A Behr
- McGill International TB Centre, McGill University, 1650 Cedar Avenue, Montreal H3G 1A4, Canada
| | - Martin Zumarraga
- Biotechnology Institute, CICVyA-INTA Castelar, Dr. Nicolás Repetto y De Los Reseros S/N, (B1686IGC) Hurlingham, Buenos Aires, Argentina
| | - Ricardo Bastida
- Instituto de Investigaciones Marinas y Costeras (CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, San Luis 1722, Mar del Plata 7600, Argentina
| | - Daniel Huson
- Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Kay Nieselt
- Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Douglas Young
- 1] Department of Medicine, Imperial College, London W2 1PG, UK [2] Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Julian Parkhill
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jane E Buikstra
- School of Human Evolution and Social Change, Arizona State University, PO Box 872402, Tempe, Arizona 85287-2402, USA
| | - Sebastien Gagneux
- 1] Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland [2] University of Basel, Petersplatz 1, CH-4003 Basel, Switzerland
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, PO Box 872402, Tempe, Arizona 85287-2402, USA
| | - Johannes Krause
- 1] Department of Archaeological Sciences, University of Tübingen, Ruemelinstraße 23, 72070 Tübingen, Germany [2] Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen 72070, Germany [3] Max Planck Institute for Science and History, Khalaische Straße 10, 07745 Jena, Germany
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