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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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2
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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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3
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Jäger HY, Maixner F, Pap I, Szikossy I, Pálfi G, Zink AR. Metagenomic analysis reveals mixed Mycobacterium tuberculosis infection in a 18th century Hungarian midwife. Tuberculosis (Edinb) 2022; 137:102181. [PMID: 35210171 DOI: 10.1016/j.tube.2022.102181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/12/2022] [Accepted: 02/03/2022] [Indexed: 01/24/2023]
Abstract
The Vác Mummy Collection comprises 265 well documented mummified individuals from the late 16th to the early 18th century that were discovered in 1994 inside a crypt in Vác, Hungary. This collection offers a unique opportunity to study the relationship between humans and pathogens in the pre-antibiotic era, as previous studies have shown a high proportion of tuberculosis (TB) infections among the individuals. In this study, we recovered ancient DNA with shotgun sequencing from a rib bone sample of a 18th century midwife. This individual is part of the collection and shows clear skeletal changes that are associated with tuberculosis and syphilis. To provide molecular proof, we applied a metagenomic approach to screen for ancient pathogen DNA. While we were unsuccessful to recover any ancient Treponema pallidum DNA, we retrieved high coverage ancient TB DNA and identified a mixed infection with two distinct TB strains by detailed single-nucleotide polymorphism and phylogenetic analysis. Thereby, we have obtained comprehensive results demonstrating the long-time prevalence of mixed infections with the sublineages L4.1.2.1/Haarlem and L4.10/PGG3 within the local community in preindustrial Hungary and put them in context of sociohistorical factors.
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Affiliation(s)
- Heidi Y Jäger
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Ildikó Pap
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary; Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika tér 2-6, Hungary; Department of Biological Anthropology, Eötvös Loránd University, Faculty of Science, 1117, Budapest, Pázmány Péter sétány 1/c, Hungary.
| | - Ildikó Szikossy
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary; Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika tér 2-6, Hungary.
| | - György Pálfi
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary.
| | - Albert R Zink
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
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Nerlich AG, Kirchhoff SM, Panzer S, Lehn C, Bachmeier BE, Bayer B, Anslinger K, Röcker P, Peschel OK. Chronic active non-lethal human-type tuberculosis in a high royal Bavarian officer of Napoleonic times-a mummy study. PLoS One 2021; 16:e0249955. [PMID: 33945536 PMCID: PMC8096010 DOI: 10.1371/journal.pone.0249955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/26/2021] [Indexed: 11/24/2022] Open
Abstract
In paleopathology, morphological and molecular evidence for infection by mycobacteria of the M. tuberculosis complex (MTC) is frequently associated with early death. In the present report, we describe a multidisciplinary study of a well-preserved mummy from Napoleonic times with a long-standing tuberculous infection by M. tuberculosis senso stricto who died at the age of 88 years of focal and non-MTB related bronchopneumonia. The well-preserved natural mummy of the Royal Bavarian General, Count Heinrich LII Reuss-Köstritz (1763–1851 CE), was extensively investigated by macro- and histomorphology, whole body CT scans and organ radiography, various molecular tissue analyses, including stable isotope analysis and molecular genetic tests. We identified signs for a long-standing, but terminally inactive pulmonary tuberculosis, tuberculous destruction of the second lumbar vertebral body, and a large tuberculous abscess in the right (retroperitoneal) psoas region (a cold abscess). This cold abscess harboured an active tuberculous infection as evidenced by histological and molecular tests. Radiological and histological analysis further revealed extensive arteriosclerosis with (non-obliterating) coronary and significant carotid arteriosclerosis, healthy bone tissue without evidence of age-related osteopenia, evidence for diffuse idiopathic skeletal hyperostosis and mild osteoarthrosis of few joints. This suggests excellent living conditions correlating well with his diet indicated by stable isotope results and literary evidence. Despite the clear evidence of a tuberculous cold abscess with bacterioscopic and molecular proof for a persisting MTC infection of a human-type M. tuberculosis strain, we can exclude the chronic MTC infection as cause of death. The detection of MTC in historic individuals should therefore be interpreted with great caution and include further data, such as their nutritional status.
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Affiliation(s)
- Andreas G. Nerlich
- Institute of Pathology, Academic Clinic München-Bogenhausen, Munich, Germany
- * E-mail:
| | - Sonja M. Kirchhoff
- Department of Radiology, Ludwig-Maximilians University (LMU), Munich, Germany
| | - Stephanie Panzer
- Department of Radiology, Trauma Center Murnau, Murnau, Germany
- Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Christine Lehn
- Institute of Legal Medicine, Ludwig-Maximilians University (LMU), Munich, Germany
| | - Beatrice E. Bachmeier
- Institute of Laboratory Medicine, University Hospital, Ludwig-Maximilians University (LMU), Munich, Germany
| | - Birgit Bayer
- Institute of Legal Medicine, Ludwig-Maximilians University (LMU), Munich, Germany
| | - Katja Anslinger
- Institute of Legal Medicine, Ludwig-Maximilians University (LMU), Munich, Germany
| | - Pascale Röcker
- Institute of Pathology, Academic Clinic München-Bogenhausen, Munich, Germany
| | - Oliver K. Peschel
- Institute of Legal Medicine, Ludwig-Maximilians University (LMU), Munich, Germany
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Henneberg M, Holloway-Kew K, Lucas T. Human major infections: Tuberculosis, treponematoses, leprosy-A paleopathological perspective of their evolution. PLoS One 2021; 16:e0243687. [PMID: 33630846 PMCID: PMC7906324 DOI: 10.1371/journal.pone.0243687] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/01/2021] [Indexed: 01/17/2023] Open
Abstract
The key to evolution is reproduction. Pathogens can either kill the human host or can invade the host without causing death, thus ensuring their own survival, reproduction and spread. Tuberculosis, treponematoses and leprosy are widespread chronic infectious diseases whereby the host is not immediately killed. These diseases are examples of the co-evolution of host and pathogen. They can be well studied as the paleopathological record is extensive, spanning over 200 human generations. The paleopathology of each disease has been well documented in the form of published synthetic analyses recording each known case and case frequencies in the samples they were derived from. Here the data from these synthetic analyses were re-analysed to show changes in the prevalence of each disease over time. A total of 69,379 skeletons are included in this study. There was ultimately a decline in the prevalence of each disease over time, this decline was statistically significant (Chi-squared, p<0.001). A trend may start with the increase in the disease’s prevalence before the prevalence declines, in tuberculosis the decline is monotonic. Increase in skeletal changes resulting from the respective diseases appears in the initial period of host-disease contact, followed by a decline resulting from co-adaptation that is mutually beneficial for the disease (spread and maintenance of pathogen) and host (less pathological reactions to the infection). Eventually either the host may become immune or tolerant, or the pathogen tends to be commensalic rather than parasitic.
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Affiliation(s)
- Maciej Henneberg
- Biological and Comparative Anatomy Research Unit, Adelaide Medical School, University of Adelaide, Adelaide, Australia
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Department of Archaeology, Flinders University, Adelaide, Australia
- * E-mail:
| | - Kara Holloway-Kew
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, Australia
| | - Teghan Lucas
- Department of Archaeology, Flinders University, Adelaide, Australia
- School of Medical Sciences, Anatomy, University of New South Wales, Sydney, New South Wales, Australia
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Váradi OA, Rakk D, Spekker O, Terhes G, Urbán E, Berthon W, Pap I, Szikossy I, Maixner F, Zink A, Vágvölgyi C, Donoghue HD, Minnikin DE, Szekeres A, Pálfi G. Verification of tuberculosis infection among Vác mummies (18th century CE, Hungary) based on lipid biomarker profiling with a new HPLC-HESI-MS approach. Tuberculosis (Edinb) 2020; 126:102037. [PMID: 33338873 DOI: 10.1016/j.tube.2020.102037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 11/19/2022]
Abstract
Tuberculosis (TB) was a large burden of infections that peaked during the 19th century in Europe. Mummies from the 18th century CE, discovered in the crypt of a church at Vác, Hungary, had high TB prevalence, as revealed by amplification of key fragments of TB DNA and genome-wide TB analysis. Complementary methods are needed to confirm these diagnoses and one approach uses the identification of specific lipid biomarkers, such as TB mycocerosic acids (MCs). Previously, MC derivatives were profiled by specialised gas chromatography-mass spectrometry (GC-MS), so an alternative more direct approach has been developed. Underivatized MCs are extracted and analysed by high-performance liquid chromatography linked to a mass spectrometer, in heated electrospray ionisation mode (HPLC-HESI-MS). The method was validated using representatives of the Mycobacterium tuberculosis complex and other mycobacteria and tested on six Vác mummy cases, previously considered positive for TB infection. Analysing both rib and soft tissue samples, four out of six cases gave profiles of main C32 and major C29 and C39 mycocerosates correlating well with those of M. tuberculosis. Multidisciplinary methods are needed in the diagnosis of ancient tuberculosis; this new protocol accesses important confirmatory evidence, as demonstrated by the confirmation of TB in the Vác mummies.
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Affiliation(s)
- Orsolya Anna Váradi
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary; Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
| | - Dávid Rakk
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
| | - Olga Spekker
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
| | - Gabriella Terhes
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Hungary. Postal address: P.O.B. 427, H-6701, Szeged, Hungary.
| | - Edit Urbán
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Hungary. Postal address: Szigeti út 12, H-7624 Pécs, Hungary; Institute of Translational Medicine, Medical School, University of Pécs, Hungary. Postal address: Szigeti út 12, H-7624, Pécs, Hungary.
| | - William Berthon
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Hungary. Postal address: Ludovika tér 2-6, H-1083, Budapest, Hungary.
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, Hungary. Postal address: Ludovika tér 2-6, H-1083, Budapest, Hungary.
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, Bolzano, Italy. Postal address: Viale Druso, 1, I-39100, Bolzano, Italy.
| | - Albert Zink
- Institute for Mummy Studies, Eurac Research, Bolzano, Italy. Postal address: Viale Druso, 1, I-39100, Bolzano, Italy.
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
| | - Helen D Donoghue
- Centre for Clinical Microbiology, University College London, London, UK. Postal address: Gower Street, London, WC1E 6BT, UK.
| | - David E Minnikin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK. Postal Address: B15 2TT Birmingham, UK.
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
| | - György Pálfi
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
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Arning N, Wilson DJ. The past, present and future of ancient bacterial DNA. Microb Genom 2020; 6:mgen000384. [PMID: 32598277 PMCID: PMC7478633 DOI: 10.1099/mgen.0.000384] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.
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Affiliation(s)
- Nicolas Arning
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
| | - Daniel J. Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
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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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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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10
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Sirous M, Khosravi AD, Tabandeh MR, Salmanzadeh S, Ahmadkhosravi N, Amini S. Molecular detection of rifampin, isoniazid, and ofloxacin resistance in Iranian isolates of Mycobacterium tuberculosis by high-resolution melting analysis. Infect Drug Resist 2018; 11:1819-1829. [PMID: 30425535 PMCID: PMC6202043 DOI: 10.2147/idr.s178831] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Background The emergence of drug resistance among Mycobacterium tuberculosis (MTB) strains is a serious health concern worldwide. The development of rapid molecular diagnostic methods in recent years has a significant impact on the early detection of resistance to major anti-TB drugs in MTB isolates, which helps in employing appropriate treatment regimen and prevents the spread of drug-resistant strains. This study was designed to evaluate the efficacy of real-time PCR and high-resolution melting (HRM) curve analysis for the determination of resistance to rifampin (RIF), isoniazid (INH), and ofloxacin (OFX) in MTB isolates and to investigate their resistance-related mutations. Methods HRM analysis was performed to screen 52 (32 drug-resistant and 20 fully susceptible) MTB clinical isolates for mutations in rpoB, katG, mab-inhA, and gyrA genes. The HRM results were then confirmed by DNA sequencing. Results In total, 32 phenotypically resistant isolates, comprising 18 RIF-, 16 INH-, and five OFX- resistant strains, were investigated. HRM analysis successfully identified 15 out of 18 mutations in rpoB, 14 out of 16 mutations in katG and mab-inhA, and four out of five mutations in gyrA conferring resistance to RIF, INH, and OFX, respectively. The obtained sensitivity and specificity, respectively, for HRM in comparison with phenotypic susceptibility testing were found to be 83.3% and 100% for RIF, 87.5% and 100% for INH, and 80% and 100% for OFX. In five resistant strains (12.8%), no mutation was detected by using HRM and DNA sequencing. Conclusion HRM assay is a rapid, accurate, and cost-effective method possessing high sensitivity and specificity for the determination of antibiotic resistance among MTB clinical isolates and screening of their associated mutations. This method can generate results in a shorter period of time than taken by the phenotypic susceptibility testing and also allows for timely treatment and prevention of the emergence of possible MDR strains.
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Affiliation(s)
- Mehrandokht Sirous
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran, .,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Azar Dokht Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran, .,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Mohammad Reza Tabandeh
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Shokrollah Salmanzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Nazanin Ahmadkhosravi
- Khuzestan Tuberculosis Regional Reference Laboratory, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sirus Amini
- Tehran Tuberculosis Regional Reference Laboratory, Tehran University of Medical Sciences, Tehran, Iran
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11
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Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 2018; 66:e1-e29. [PMID: 28173586 PMCID: PMC5410953 DOI: 10.1093/sysbio/syw059] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/02/2022] Open
Abstract
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
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Affiliation(s)
- Michela Leonardi
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, Toulouse, France
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12
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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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13
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Abstract
Epidemic typhus caused by Rickettsia prowazekii is one of the oldest pestilential diseases of humankind. The disease is transmitted to human beings by the body louse Pediculus humanus corporis and is still considered a major threat by public health authorities, despite the efficacy of antibiotics, because poor sanitary conditions are conducive to louse proliferation. Epidemic typhus has accompanied disasters that impact humanity and has arguably determined the outcome of more wars than have soldiers and generals. The detection, identification, and characterization of microorganisms in ancient remains by paleomicrobiology has permitted the diagnosis of past epidemic typhus outbreaks through the detection of R. prowazekii. Various techniques, including microscopy and immunodetection, can be used in paleomicrobiology, but most of the data have been obtained by using PCR-based molecular techniques on dental pulp samples. Paleomicrobiology enabled the identification of the first outbreak of epidemic typhus in the 18th century in the context of a pan-European great war in the city of Douai, France, and supported the hypothesis that typhus was imported into Europe by Spanish soldiers returning from America. R. prowazekii was also detected in the remains of soldiers of Napoleon's Grand Army in Vilnius, Lithuania, which indicates that Napoleon's soldiers had epidemic typhus. The purpose of this article is to underscore the modern comprehension of clinical epidemic typhus, focus on the historical relationships of the disease, and examine the use of paleomicrobiology in the detection of past epidemic typhus outbreaks.
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14
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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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15
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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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16
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Arjomandzadegan M, Titov L, Farnia P, Owlia P, Ranjbar R, Sheikholeslami F, Surkova L. Molecular detection of fluoroquinolone resistance-associated gyrA mutations in ofloxacin-resistant clinical isolates of Mycobacterium tuberculosis from Iran and Belarus. Int J Mycobacteriol 2016; 5:299-305. [PMID: 27847014 DOI: 10.1016/j.ijmyco.2016.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 04/27/2016] [Accepted: 06/28/2016] [Indexed: 10/21/2022] Open
Abstract
OBJECTIVE/BACKGROUND Detection of mutations in the quinolone resistance-determining region (QRDR) of the gyrA gene could determine resistance to fluoroquinolone antituberculosis drugs. The aim of this study was to detect mutations in QRDRs. METHODS From 184 clinical isolates of Mycobacterium tuberculosis, ofloxacin resistance was proven in 42 isolates using the proportion method. The molecular basis of resistance to ofloxacin were investigated by the determination of mutations in the QRDR region of the gyrA gene. Extracted DNA fragments of 194bp from the gyrA gene were amplified and an automatic DNA sequencer was used for the sequencing process. RESULTS Molecular genetic analysis of 42 resistant M. tuberculosis strains demonstrated that they belong to Principal Genetic Group (PGG) 1 in 19 cases (45.2±10.9%), to PGG2 in 15 cases (35.7±10.5%), and to PGG3 in eight cases (19.0±8.4%). Isolates from PGG1 were dominant among resistant isolates (P<.05). It was found that 24 (57%) resistant isolates carried mutations at codon 94 with five different amino acid changes: D94A (n=11), D94G (n=3), D94T (n=4), D94A (n=4), and D94Y (n=2). The remaining 18 (43%) isolates had mutations in codon A90V (GCG→GTG) and S91P (TCG→CCG). Five isolates had two mutations in codons 90 and 94. There was no difference between mutations at these two codons in resistant isolates of the two countries (P<.001). There was no polymorphism observed in codon 95 in any of the ofloxacin-susceptible isolates. CONCLUSION It was concluded that the determination of nucleotide sequences of QRDRs can be used as a molecular test for the rapid detection of ofloxacin resistance. Furthermore, frequencies in gyrA codons in Belarus and Iran were similar, therefore it is not of geographical concern for the two countries.
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Affiliation(s)
| | - Leonid Titov
- Research Institute for Epidemiology and Microbiology, Minsk, Belarus
| | - Parissa Farnia
- Mycobacteriology Research Centre (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parviz Owlia
- Molecular Microbiology Research Center, Shahed University, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Fatemeh Sheikholeslami
- Mycobacteriology Research Centre (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
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17
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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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18
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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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19
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Feldman M, Hershkovitz I, Sklan EH, Kahila Bar-Gal G, Pap I, Szikossy I, Rosin-Arbesfeld R. Detection of a Tumor Suppressor Gene Variant Predisposing to Colorectal Cancer in an 18th Century Hungarian Mummy. PLoS One 2016; 11:e0147217. [PMID: 26863316 PMCID: PMC4749341 DOI: 10.1371/journal.pone.0147217] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/30/2015] [Indexed: 01/23/2023] Open
Abstract
Mutations of the Adenomatous polyposis coli (APC) gene are common and strongly associated with the development of colorectal adenomas and carcinomas. While extensively studied in modern populations, reports on visceral tumors in ancient populations are scarce. To the best of our knowledge, genetic characterization of mutations associated with colorectal cancer in ancient specimens has not yet been described. In this study we have sequenced hotspots for mutations in the APC gene isolated from 18th century naturally preserved human Hungarian mummies. While wild type APC sequences were found in two mummies, we discovered the E1317Q missense mutation, known to be a colorectal cancer predisposing mutation, in a large intestine tissue of an 18th century mummy. Our data suggests that this genetic predisposition to cancer already existed in the pre-industrialization era. This study calls for similar investigations of ancient specimens from different periods and geographical locations to be conducted and shared for the purpose of obtaining a larger scale analysis that will shed light on past cancer epidemiology and on cancer evolution.
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Affiliation(s)
- Michal Feldman
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail:
| | - Israel Hershkovitz
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ella H. Sklan
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gila Kahila Bar-Gal
- Koret School of Veterinary Medicine, The Robert H. Smith faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - Rina Rosin-Arbesfeld
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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20
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Piombino-Mascali D, Jankauskas R, Tamošiūnas A, Valančius R, Gill-Frerking H, Spigelman M, Panzer S. Evidence of probable tuberculosis in Lithuanian mummies. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2015; 66:420-31. [DOI: 10.1016/j.jchb.2015.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 01/06/2015] [Indexed: 10/23/2022]
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21
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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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22
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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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23
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Szikossy I, Pálfi G, Molnár E, Karlinger K, Kovács BK, Korom C, Schultz M, Schmidt-Schultz TH, Spigelman M, Donoghue HD, Kustár Á, Pap I. Two positive tuberculosis cases in the late Nigrovits family, 18th century, Vác, Hungary. Tuberculosis (Edinb) 2015; 95 Suppl 1:S69-72. [DOI: 10.1016/j.tube.2015.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Gaul JS, Winter E, Grossschmidt K. Ancient pathogens in museal dry bone specimens: analysis of paleocytology and aDNA. Wien Med Wochenschr 2015; 165:133-9. [PMID: 25994097 DOI: 10.1007/s10354-015-0357-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/16/2015] [Indexed: 11/29/2022]
Abstract
Bone samples investigated in this study derive from the pathologic-anatomical collection of the Natural History Museum of Vienna. In order to explore the survival of treponemes and treponemal ancient DNA in museal dry bone specimens, we analyzed three individuals known to have been infected with Treponema pallidum pallidum. No reproducible evidence of surviving pathogen's ancient DNA (aDNA) was obtained, despite the highly sensitive extraction and amplification techniques (TPP15 and arp). Additionally, decalcification fluid of bone sections was smear stained with May-Gruenwald-Giemsa. The slides were examined using direct light microscope and dark field illumination. Remnants of spirochetal structures were detectable in every smear. Our results demonstrate that aDNA is unlikely to survive, but spirochetal remains are stainable and thus detectable.
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Affiliation(s)
- Johanna Sophia Gaul
- Department of Anthropology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria,
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25
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Kay GL, Sergeant MJ, Zhou Z, Chan JZM, Millard A, Quick J, Szikossy I, Pap I, Spigelman M, Loman NJ, Achtman M, Donoghue HD, Pallen MJ. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nat Commun 2015; 6:6717. [PMID: 25848958 PMCID: PMC4396363 DOI: 10.1038/ncomms7717] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/18/2015] [Indexed: 01/05/2023] Open
Abstract
Tuberculosis (TB) was once a major killer in Europe, but it is unclear how the strains and patterns of infection at ‘peak TB' relate to what we see today. Here we describe 14 genome sequences of M. tuberculosis, representing 12 distinct genotypes, obtained from human remains from eighteenth-century Hungary using metagenomics. All our historic genotypes belong to M. tuberculosis Lineage 4. Bayesian phylogenetic dating, based on samples with well-documented dates, places the most recent common ancestor of this lineage in the late Roman period. We find that most bodies yielded more than one M. tuberculosis genotype and we document an intimate epidemiological link between infections in two long-dead individuals. Our results suggest that metagenomic approaches usefully inform detection and characterization of historical and contemporary infections. Tuberculosis was once a major killer in Europe. Here the authors use metagenomics to obtain genomic sequences of Mycobacterium tuberculosis from human remains from eighteenth-century Hungary, revealing mixed infections within individuals as well as presence of the same strain in two individuals.
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Affiliation(s)
- Gemma L Kay
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Martin J Sergeant
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Zhemin Zhou
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jacqueline Z-M Chan
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Andrew Millard
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Joshua Quick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, Ludovika tér 2-6, 1083 Budapest, Hungary
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Ludovika tér 2-6, 1083 Budapest, Hungary
| | - Mark Spigelman
- 1] Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 9112102, Israel [2] Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark Achtman
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Helen D Donoghue
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Mark J Pallen
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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26
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Coqueugniot H, Dutailly B, Desbarats P, Boulestin B, Pap I, Szikossy I, Baker O, Montaudon M, Panuel M, Karlinger K, Kovács B, Kristóf LA, Pálfi G, Dutour O. Three-dimensional imaging of past skeletal TB: From lesion to process. Tuberculosis (Edinb) 2015; 95 Suppl 1:S73-9. [PMID: 25754340 DOI: 10.1016/j.tube.2015.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
3D imaging has become an essential tool in the field of biological anthropology, notably for human evolution purposes. High resolution virtual 3D reconstructions of original specimens contribute to their preservation and broaden the ability for research, teaching and exchanges. Paleopathology can get substantial benefit from these methods, among others for reconstructing infectious pathological processes on ancient bones. Tuberculosis is frequently diagnosed on ancient human remains; however, some osseous expressions are difficult to interpret using classical methods. We illustrate here the interest of 3D methods for reconstructing processes involved in pathological bone changes due to Mycobacterium tuberculosis infection. Four paleopathological specimens attributed to this infection, dating from different time periods and concerning diverse parts of the skeleton have been analyzed using a specific 3D digital chain we have previously developed. These 3D analyses allow to virtually reconstruct the initial location and aspect of the infectious process, its extension as well as its possible diffusion to the surrounding soft tissues. This possible virtual follow-up of the disease leads to the concept of processual paleopathology that we would like to introduce in the field. The 3D methodology can help to improve our knowledge of natural history and evolution of ancient human infections such as tuberculosis.
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Affiliation(s)
- Hélène Coqueugniot
- De la Préhistoire à l'Actuel: Culture, Environnement, Anthropologie (PACEA - UMR 5199, CNRS - Université de Bordeaux - Ministère de la Culture et de la Communication), Allée Geoffroy Saint-Hilaire, 33615 Pessac Cedex, France; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Bruno Dutailly
- De la Préhistoire à l'Actuel: Culture, Environnement, Anthropologie (PACEA - UMR 5199, CNRS - Université de Bordeaux - Ministère de la Culture et de la Communication), Allée Geoffroy Saint-Hilaire, 33615 Pessac Cedex, France
| | - Pascal Desbarats
- Laboratoire Bordelais de Recherche en Informatique (UMR 5800 LaBRI), Université de Bordeaux, 351 Cours de la Libération, 33405 Talence, France
| | - Bruno Boulestin
- De la Préhistoire à l'Actuel: Culture, Environnement, Anthropologie (PACEA - UMR 5199, CNRS - Université de Bordeaux - Ministère de la Culture et de la Communication), Allée Geoffroy Saint-Hilaire, 33615 Pessac Cedex, France
| | - Ildiko Pap
- National Museum of Natural History, Department of Anthropology, Budapest, Hungary
| | - Ildiko Szikossy
- National Museum of Natural History, Department of Anthropology, Budapest, Hungary
| | - Oussama Baker
- Laboratoire d'Anthropologie biologique Paul Broca, EPHE (Ecole Pratique des Hautes Etudes), Paris, France
| | - Michel Montaudon
- Service d'Imagerie médicale, Centre Hospitalo-Universitaire de Bordeaux, France
| | - Michel Panuel
- Service d'Imagerie médicale, Centre Hospitalo-Universitaire de Marseille, France
| | - Kinga Karlinger
- Department of Diagnostic Radiology and Oncotherapy, Semmelweis University, Budapest, Hungary
| | - Balázs Kovács
- Department of Diagnostic Radiology and Oncotherapy, Semmelweis University, Budapest, Hungary
| | | | - György Pálfi
- Department of Biological Anthropology, University of Szeged, Hungary
| | - Olivier Dutour
- De la Préhistoire à l'Actuel: Culture, Environnement, Anthropologie (PACEA - UMR 5199, CNRS - Université de Bordeaux - Ministère de la Culture et de la Communication), Allée Geoffroy Saint-Hilaire, 33615 Pessac Cedex, France; Laboratoire d'Anthropologie biologique Paul Broca, EPHE (Ecole Pratique des Hautes Etudes), Paris, France; Department of Anthropology, University of Western Ontario, Canada.
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27
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Spigelman M, Donoghue HD, Abdeen Z, Ereqat S, Sarie I, Greenblatt CL, Pap I, Szikossy I, Hershkovitz I, Bar-Gal GK, Matheson C. Evolutionary changes in the genome of Mycobacterium tuberculosis and the human genome from 9000 years BP until modern times. Tuberculosis (Edinb) 2015; 95 Suppl 1:S145-9. [PMID: 25771203 DOI: 10.1016/j.tube.2015.02.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The demonstration of Mycobacterium tuberculosis DNA in ancient skeletons gives researchers an insight into its evolution. Findings of the last two decades sketched the biological relationships between the various species of tubercle bacilli, the time scale involved, their possible origin and dispersal. This paper includes the available evidence and on-going research. In the submerged Eastern Mediterranean Neolithic village of Atlit Yam (9000 BP), a human lineage of M. tuberculosis, defined by the TbD1 deletion in its genome, was demonstrated. An infected infant at the site provides an example of active tuberculosis in a human with a naïve immune system. Over 4000 years later tuberculosis was found in Jericho. Urbanization increases population density encouraging M. tuberculosis/human co-evolution. As susceptible humans die of tuberculosis, survivors develop genetic resistance to disease. Thus in 18th century Hungarian mummies from Vác, 65% were positive for tuberculosis yet a 95-year-old woman had clearly survived a childhood Ghon lesion. Whole genome studies are in progress, to detect changes over the millennia both in bacterial virulence and also host susceptibility/resistance genes that determine the NRAMP protein and Killer Cell Immunoglobulin-like Receptors (KIRs). This paper surveys present evidence and includes initial findings.
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Affiliation(s)
- 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; Kuvin Center for the Study of Infectious & Tropical Diseases and Ancient DNA, Hadassah Medical School, The Hebrew University, Jerusalem, Israel.
| | - 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, London, UK.
| | - Ziad Abdeen
- Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University, Abu-Deis, P.O. Box 201760, West Bank, Palestine.
| | - Suheir Ereqat
- Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University, Abu-Deis, P.O. Box 201760, West Bank, Palestine.
| | - Issa Sarie
- Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University, Abu-Deis, P.O. Box 201760, West Bank, Palestine.
| | - Charles L Greenblatt
- Kuvin Center for the Study of Infectious & Tropical Diseases and Ancient DNA, Hadassah Medical School, The Hebrew University, Jerusalem, Israel.
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary.
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - 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, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Carney Matheson
- Paleo-DNA Laboratory, Departments of Anthropology and Biology, Lakehead University, Thunder Bay, Ontario, Canada.
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Müller R, Roberts CA, Brown TA. Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity. Proc Biol Sci 2014; 281:20133236. [PMID: 24573854 PMCID: PMC3953847 DOI: 10.1098/rspb.2013.3236] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second–nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth–nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis.
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Affiliation(s)
- Romy Müller
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, , 131 Princess Street, Manchester M1 7DN, UK, Department of Archaeology, Durham University, , South Road, Durham DH1 3LE, UK
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Chan JZM, Sergeant MJ, Lee OYC, Minnikin DE, Besra GS, Pap I, Spigelman M, Donoghue HD, Pallen MJ. Metagenomic analysis of tuberculosis in a mummy. N Engl J Med 2013; 369:289-90. [PMID: 23863071 DOI: 10.1056/nejmc1302295] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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30
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Hajdu T, Fóthi E, Kovári I, Merczi M, Molnár A, Maász G, Avar P, Marcsik A, Márk L. Bone tuberculosis in Roman Period Pannonia (western Hungary). Mem Inst Oswaldo Cruz 2013; 107:1048-53. [PMID: 23295757 DOI: 10.1590/s0074-02762012000800014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 09/10/2012] [Indexed: 11/21/2022] Open
Abstract
The purpose of this study was to analyse a skeleton (adult female, 25-30 years) that presented evidence of tuberculous spondylitis. The skeleton, dated from the Roman Period (III-VI centuries), was excavated near the town of Győr, in western Hungary. The skeleton was examined by gross observation supplemented with mycolic acid and proteomic analyses using MALDI-TOF/TOF tandem mass spectrometry. The biomolecular analyses supported the morphological diagnosis.
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Affiliation(s)
- Tamás Hajdu
- Department of Biological Anthropology, Institute of Biology, Faculty of Science, Eötvös Loránd University, Budapest, Hungary.
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31
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Anastasiou E, Mitchell PD. Palaeopathology and genes: investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations. Gene 2013; 528:33-40. [PMID: 23792062 DOI: 10.1016/j.gene.2013.06.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 05/23/2013] [Accepted: 06/01/2013] [Indexed: 01/11/2023]
Abstract
The aim of this paper is to review the use of genetics in palaeomicrobiology, and to highlight the importance of understanding past diseases. Palaeomicrobiology is the study of disease pathogens in skeletal and mummified remains from archaeological contexts. It has revolutionarised our understanding of health in the past by enabling a deeper knowledge of the origins and evolution of many diseases that have shaped us as a species. Bacterial diseases explored include tuberculosis, leprosy, bubonic plague, typhoid, syphilis, endemic and epidemic typhus, trench fever, and Helicobacter pylori. Viral diseases discussed include influenza, hepatitis B, human papilloma virus (HPV), human T-cell lymphotrophic virus (HTLV-1) and human immunodeficiency virus (HIV). Parasitic diseases investigated include malaria, leishmaniasis, Chagas' disease, roundworm, whipworm, pinworm, Chinese liver fluke, fleas and lice. Through a better understanding of disease origins and their evolution, we can place into context how many infectious diseases are changing over time, and so help us estimate how they may change in the future.
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Affiliation(s)
- Evilena Anastasiou
- Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge CB2 1QH, UK
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Nicklisch N, Maixner F, Ganslmeier R, Friederich S, Dresely V, Meller H, Zink A, Alt KW. Rib lesions in skeletons from early neolithic sites in Central Germany: On the trail of tuberculosis at the onset of agriculture. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 149:391-404. [DOI: 10.1002/ajpa.22137] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 08/01/2012] [Indexed: 12/19/2022]
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33
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Spoligotypes of Mycobacterium tuberculosis complex isolates from patients residents of 11 states of Brazil. INFECTION GENETICS AND EVOLUTION 2012; 12:649-56. [DOI: 10.1016/j.meegid.2011.08.027] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 08/26/2011] [Accepted: 08/28/2011] [Indexed: 11/23/2022]
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Djelouadji Z, Raoult D, Drancourt M. Palaeogenomics of Mycobacterium tuberculosis: epidemic bursts with a degrading genome. THE LANCET. INFECTIOUS DISEASES 2011; 11:641-50. [DOI: 10.1016/s1473-3099(11)70093-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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35
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Donoghue H. Insights gained from palaeomicrobiology into ancient and modern tuberculosis. Clin Microbiol Infect 2011; 17:821-9. [DOI: 10.1111/j.1469-0691.2011.03554.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Evinger S, Bernert Z, Fóthi E, Wolff K, Kovári I, Marcsik A, Donoghue HD, O'Grady J, Kiss KK, Hajdu T. New skeletal tuberculosis cases in past populations from Western Hungary (Transdanubia). HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2011; 62:165-83. [PMID: 21530965 DOI: 10.1016/j.jchb.2011.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 03/10/2011] [Indexed: 11/25/2022]
Abstract
The distribution, antiquity and epidemiology of tuberculosis (TB) have previously been studied in osteoarchaeological material in the eastern part of Hungary, mainly on the Great Plain. The purpose of this study is to map the occurrence of skeletal TB in different centuries in the western part of Hungary, Transdanubia, and to present new cases we have found. Palaeopathological analysis was carried out using macroscopic observation supported by radiographic and molecular methods. A large human osteoarchaeological sample (n=5684) from Transdanubian archaeological sites ranging from the 2nd to the 18th centuries served as a source of material. Spinal TB was observed in seven individuals (in three specimens with Pott's disease two of which also had cold abscess) and hip TB was assumed in one case. The results of DNA for Mycobacterium tuberculosis were positive in seven of the eight cases identified by paleopathology, and negative in the assumed case of hip TB. However, the molecular results are consistent with highly fragmented DNA, which limited further analysis. Based on the present study and previously published cases, osteotuberculosis was found in Transdanubia mainly during the 9th-13th centuries. However, there are no signs of TB in many other 9th-13th century sites, even in those that lie geographically close to those where osteotuberculous cases were found. This may be due to a true absence of TB caused by the different living conditions, way of life, or origin of these populations. An alternative explanation is that TB was present in some individuals with no typical paleopathology, but that death occurred before skeletal morphological features could develop.
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Affiliation(s)
- S Evinger
- Department of Anthropology, Hungarian Natural History Museum, Ludovika Square, Budapest, Hungary.
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37
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Stone AC, Wilbur AK, Buikstra JE, Roberts CA. Tuberculosis and leprosy in perspective. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 140 Suppl 49:66-94. [PMID: 19890861 DOI: 10.1002/ajpa.21185] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Two of humankind's most socially and psychologically devastating diseases, tuberculosis and leprosy, have been the subject of intensive paleopathological research due to their antiquity, a presumed association with human settlement and subsistence patterns, and their propensity to leave characteristic lesions on skeletal and mummified remains. Despite a long history of medical research and the development of effective chemotherapy, these diseases remain global health threats even in the 21st century, and as such, their causative agents Mycobacterium tuberculosis and M. leprae, respectively, have recently been the subject of molecular genetics research. The new genome-level data for several mycobacterial species have informed extensive phylogenetic analyses that call into question previously accepted theories concerning the origins and antiquity of these diseases. Of special note is the fact that all new models are in broad agreement that human TB predated that in other animals, including cattle and other domesticates, and that this disease originated at least 35,000 years ago and probably closer to 2.6 million years ago. In this work, we review current phylogenetic and biogeographic models derived from molecular biology and explore their implications for the global development of TB and leprosy, past and present. In so doing, we also briefly review the skeletal evidence for TB and leprosy, explore the current status of these pathogens, critically consider current methods for identifying ancient mycobacterial DNA, and evaluate coevolutionary models.
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Affiliation(s)
- Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA.
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38
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Paleopathology of human tuberculosis and the potential role of climate. Interdiscip Perspect Infect Dis 2009; 2009:437187. [PMID: 19360109 PMCID: PMC2665868 DOI: 10.1155/2009/437187] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2008] [Revised: 11/30/2008] [Accepted: 01/27/2009] [Indexed: 11/17/2022] Open
Abstract
Both origin and evolution of tuberculosis and its pathogens (Mycobacterium tuberculosis complex) are not fully understood. The paleopathological investigation of human remains offers a unique insight into the molecular evolution and spread including correlative data of the environment. The molecular analysis of material from Egypt (3000-500 BC), Sudan (200-600 AD), Hungary (600-1700 AD), Latvia (1200-1600 AD), and South Germany (1400-1800 AD) urprisingly revealed constantly high frequencies of tuberculosis in all different time periods excluding significant environmental influence on tuberculosis spread. The typing of various mycobacteria strains provides evidence for ancestral M. tuberculosis strains in Pre- to early Egyptian dynastic material (3500-2650 BC), while typical M. africanum signatures were detected in a Middle Kingdom tomb (2050-1650 BC). Samples from the New Kingdom to Late Period (1500-500 BC) indicated modern M. tuberculosis strains. No evidence was seen for M. bovis in Egyptian material while M. bovis signatures were first identified in Siberian biomaterial dating 2000 years before present. These results contraindicates the theory that M. tuberculosis evolved from M. bovis during early domestication in the region of the "Fertile Crescent," but supports the scenario that M. tuberculosis probably derived from an ancestral progenitor strain. The environmental influence of this evolutionary scenario deserves continuing intense evaluation.
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39
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Gibbon V, Paximadis M, Strkalj G, Ruff P, Penny C. Novel methods of molecular sex identification from skeletal tissue using the amelogenin gene. Forensic Sci Int Genet 2008; 3:74-9. [PMID: 19215875 DOI: 10.1016/j.fsigen.2008.10.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 09/22/2008] [Accepted: 10/15/2008] [Indexed: 11/24/2022]
Abstract
Sex identification from skeletal material is of vital importance in order to reconstruct the demographic variables of an individual in forensic genetics and ancient DNA (aDNA) analysis. When the use of conventional methods of sex identification are impossible, molecular analysis of the X and Y chromosomes provides an expedient solution. Two novel systems of molecular sex identification suitable for skeletal material using the amelogenin gene are described, beginning in intron 2-3, spanning exon 3 and ending in intron 3-4. This area was optimal for sexing, as it includes 14 sex-specific polymorphic regions in addition to an indel (insertion or deletion of nucleotides). Once optimised and working with 100% efficiency on the controls, these procedures were applied to a collection of miscellaneous archaeological skeletons (ex situ) sourced from the Raymond Dart Collection of Human Skeletons (Dart Collection). This collection was used to optimise these techniques for skeletal remains derived from an archaeological context. These methods produced 46.66% sex results for the ex situ sample, which is within the normal range for aDNA studies. These new techniques are optimal for sex identification, with both the inherent control of isolating many sex-specific features and combined with the use of sensitive micro-fluidic electrophoresis.
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Affiliation(s)
- Victoria Gibbon
- Department of Internal Medicine, University of the Witwatersrand, 7 York Rd, Johannesburg, 2193 Parktown, South Africa.
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40
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Lemma E, Zimhony O, Greenblatt CL, Koltunov V, Zylber MI, Vernon K, Spigelman M. Attempts to revive Mycobacterium tuberculosis from 300-year-old human mummies. FEMS Microbiol Lett 2008; 283:54-61. [PMID: 18399990 DOI: 10.1111/j.1574-6968.2008.01150.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Environmental persistence of Mycobacterium tuberculosis is subject to speculation. However, the reality that infected postmortem tissues can be a danger to pathologists and embalmers has worrisome implications. A few experimental studies have demonstrated the organism's ability to withstand exposure to embalming fluid and formalin. Recently, a failure was reported in an attempt to resuscitate an original isolate of Robert Koch to determine the lifetime of the tubercle bacillus. The present study also considers a historical approach to determine persistence under favorable environmental conditions. It asks whether acid-fast forms observed in tissues of 300-year-old Hungarian mummies can be resuscitated. Finding organisms before the advent of antibiotics and pasteurization may yield valuable genetic information. Using various media modifications, as well as guinea pig inoculation, an attempt was made to culture these tissues for M. tuberculosis. In addition, a resuscitation-promoting factor, known to increase colony counts in high G+C bacteria, was applied to the cultures. Although an occasional PCR-positive sample was detected, no colonies of M. tuberculosis were obtained. Our results may indicate that the life span of the tubercle bacillus is less than a few hundred years, even though in the short run it can survive harsh chemical treatment.
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Affiliation(s)
- Eshetu Lemma
- Infectious and Other Diseases Research Department, Ethiopian Health and Nutrition Research Institute, Addis Ababa, Ethiopia
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41
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Abstract
Mummies are human remains with preservation of nonbony tissue. Mummification by natural influences results in so-called natural mummies, whereas mummification induced by active (human) intervention results in so-called artificial mummies, although many cultures practiced burial rites, which to some degree involved both natural and artificial mummification. Since they are so uniquely well-preserved, mummies may give many insights into mortuary practices and burial rites. Specifically, the presence of soft tissues may expand the scope of paleopathological studies. Many recent mummy studies focus on the development and application of nondestructive methods for examining mummies, including radiography, CT-scanning with advanced three-dimensional visualizations, and endoscopic techniques, as well as minimally-destructive chemical, physical, and biological methods for, e.g., stable isotopes, trace metals, and DNA. This article discusses mummification and gives a presentation of various key mummy finds and a brief history of mummy studies. A description of the extant key technologies of natural and medical science that are applied in mummy studies is given; along with a discussion of some of the major results in terms of paleopathology. It is also shown how mummy studies have contributed much to the knowledge of the cultural habits and everyday life of past populations. Finally the impact of mummy studies on analyses of mortuary practices and cultural history is discussed.
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Affiliation(s)
- Niels Lynnerup
- Laboratory of Biological Anthropology, University of Copenhagen, Copenhagen, Denmark.
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42
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43
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Nair PNR. Abusing technology? Culture-difficult microbes and microbial remnants. ACTA ACUST UNITED AC 2007; 104:569-70. [PMID: 17625930 DOI: 10.1016/j.tripleo.2007.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Accepted: 06/01/2007] [Indexed: 10/23/2022]
Affiliation(s)
- P N R Nair
- Institute of Oral Biology, University of Zurich, Switzerland
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44
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Xiong L, Kong F, Yang Y, Cheng J, Gilbert GL. Use of PCR and reverse line blot hybridization macroarray based on 16S-23S rRNA gene internal transcribed spacer sequences for rapid identification of 34 mycobacterium species. J Clin Microbiol 2006; 44:3544-50. [PMID: 17021080 PMCID: PMC1594812 DOI: 10.1128/jcm.00633-06] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to develop a PCR and reverse line blot hybridization (PCR-RLB) macroarray assay based on 16S-23S rRNA gene internal transcribed spacer sequences for the identification and differentiation of 34 mycobacterial species or subspecies. The performance of the PCR-RLB assay was assessed and validated by using 78 reference strains belonging to 55 Mycobacterium species, 219 clinical isolates which had been identified as mycobacteria by high-performance liquid chromatography or gas chromatography, three skin biopsy specimens from patients with suspected leprosy which had been shown to contain acid-fast bacilli, and isolates of 14 nonmycobacterial species. All mycobacteria were amplified in the PCR and hybridized with a genus-specific probe (probe MYC). The 34 species-specific probes designed in this study hybridized only with the corresponding Mycobacterium species. The mycobacterial PCR-RLB assay is an efficient tool for the identification of clinical isolates of mycobacteria; it can reliably identify mixed mycobacterial cultures and M. leprae in skin biopsy specimens.
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Affiliation(s)
- Likuan Xiong
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, Darcy Rd., Westmead, New South Wales 2145, Australia
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45
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Donoghue HD, Spigelman M. Comment. Pathogenic microbial ancient DNA: a problem or an opportunity? Proc Biol Sci 2006; 273:641-2; discussion 643. [PMID: 16608680 PMCID: PMC1560079 DOI: 10.1098/rspb.2005.3261] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Accepted: 06/16/2005] [Indexed: 12/25/2022] Open
Affiliation(s)
- Helen D Donoghue
- Department of Infection, University College London Centre for Infectious Diseases and International Health 46, Cleveland Street, London W1T 4JF, UK.
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46
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Barnes I, Thomas MG. Evaluating bacterial pathogen DNA preservation in museum osteological collections. Proc Biol Sci 2006; 273:645-53. [PMID: 16608682 PMCID: PMC1560077 DOI: 10.1098/rspb.2005.3339] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 09/20/2005] [Indexed: 11/12/2022] Open
Abstract
Reports of bacterial pathogen DNA sequences obtained from archaeological bone specimens raise the possibility of greatly improving our understanding of the history of infectious diseases. However, the survival of pathogen DNA over long time periods is poorly characterized, and scepticism remains about the reliability of these data. In order to explore the survival of bacterial pathogen DNA in bone specimens, we analysed samples from 59 eighteenth and twentieth century individuals known to have been infected with either Mycobacterium tuberculosis or Treponema pallidum. No reproducible evidence of surviving pathogen DNA was obtained, despite the use of extraction and PCR-amplification methods determined to be highly sensitive. These data suggest that previous studies need to be interpreted with caution, and we propose that a much greater emphasis is placed on understanding how pathogen DNA survives in archaeological material, and how its presence can be properly verified and used.
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Affiliation(s)
- Ian Barnes
- Department of Biology, University College London, Gower Street, London WC1E 6BT, UK.
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47
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Spigelman M, Pap I, Donoghue HD. A death from Langerhans cell histiocytosis and tuberculosis in 18th Century Hungary – what palaeopathology can tell us today. Leukemia 2006; 20:740-2. [PMID: 16437150 DOI: 10.1038/sj.leu.2404103] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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48
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Willerslev E, Cooper A. Pathogenic microbial ancient DNA: a problem or an opportunity? Proc Biol Sci 2005. [DOI: 10.1098/rspb.2005.3262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Eske Willerslev
- Ancient DNA and Evolution Group, Niels Bohr Institute & Biological Institute, University of CopenhagenJuliane Maries vej 30, DK-2100, Denmark
| | - Alan Cooper
- University of AdelaideDarling Blg (DP 418), Rm G15b, North Terrace Campus, South Australia 5005, Australia
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49
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Abstract
In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.
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50
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Abstract
Palaeomicrobiology is an emerging field that is devoted to the detection, identification and characterization of microorganisms in ancient remains. Data indicate that host-associated microbial DNA can survive for almost 20,000 years, and environmental bacterial DNA preserved in permafrost samples has been dated to 400,000-600,000 years. In addition to frozen and mummified soft tissues, bone and dental pulp can also be used to search for microbial pathogens. Various techniques, including microscopy and immunodetection, can be used in palaeomicrobiology, but most data have been obtained using PCR-based molecular techniques. Infections caused by bacteria, viruses and parasites have all been diagnosed using palaeomicrobiological techniques. Additionally, molecular typing of ancient pathogens could help to reconstruct the epidemiology of past epidemics and could feed into current models of emerging infections, therefore contributing to the development of appropriate preventative measures.
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Affiliation(s)
- Michel Drancourt
- Unité des Rickettsies, CNRS UMR 6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, 27 Bd Jean Moulin, 13385 Marseille Cedex 05, France
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