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Urban C, Blom AA, Avanzi C, Walker-Meikle K, Warren AK, White-Iribhogbe K, Turle R, Marter P, Dawson-Hobbis H, Roffey S, Inskip SA, Schuenemann VJ. Ancient Mycobacterium leprae genome reveals medieval English red squirrels as animal leprosy host. Curr Biol 2024; 34:2221-2230.e8. [PMID: 38703773 DOI: 10.1016/j.cub.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/15/2024] [Accepted: 04/02/2024] [Indexed: 05/06/2024]
Abstract
Leprosy, one of the oldest recorded diseases in human history, remains prevalent in Asia, Africa, and South America, with over 200,000 cases every year.1,2 Although ancient DNA (aDNA) approaches on the major causative agent, Mycobacterium leprae, have elucidated the disease's evolutionary history,3,4,5 the role of animal hosts and interspecies transmission in the past remains unexplored. Research has uncovered relationships between medieval strains isolated from archaeological human remains and modern animal hosts such as the red squirrel in England.6,7 However, the time frame, distribution, and direction of transmissions remains unknown. Here, we studied 25 human and 12 squirrel samples from two archaeological sites in Winchester, a medieval English city well known for its leprosarium and connections to the fur trade. We reconstructed four medieval M. leprae genomes, including one from a red squirrel, at a 2.2-fold average coverage. Our analysis revealed a phylogenetic placement of all strains on branch 3 as well as a close relationship between the squirrel strain and one newly reconstructed medieval human strain. In particular, the medieval squirrel strain is more closely related to some medieval human strains from Winchester than to modern red squirrel strains from England, indicating a yet-undetected circulation of M. leprae in non-human hosts in the Middle Ages. Our study represents the first One Health approach for M. leprae in archaeology, which is centered around a medieval animal host strain, and highlights the future capability of such approaches to understand the disease's zoonotic past and current potential.
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Affiliation(s)
- Christian Urban
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland; Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Alette A Blom
- Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland; Department of Archaeology, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK; School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Charlotte Avanzi
- Department of Microbiology, Immunology and Pathology, Colorado State University, 401 W Pitkin St, Fort Collins, CO 80523, USA
| | - Kathleen Walker-Meikle
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland; Science Museum Group, Science Museum, Exhibition Road, South Kensington, London SW7 2DD, UK
| | - Alaine K Warren
- Department of Microbiology, Immunology and Pathology, Colorado State University, 401 W Pitkin St, Fort Collins, CO 80523, USA
| | - Katie White-Iribhogbe
- School of Oriental and African Studies (SOAS), University of London, 10 Thornaugh Street, London WC1H 0XG, UK
| | - Ross Turle
- Hampshire Cultural Trust, Chilcomb House, Chilcomb Lane, Winchester SO23 8RB, UK
| | - Phil Marter
- School of History, Archaeology and Philosophy, University of Winchester, Medecroft Building, Sparkford Road, Winchester SO22 4NH, UK
| | - Heidi Dawson-Hobbis
- School of History, Archaeology and Philosophy, University of Winchester, Medecroft Building, Sparkford Road, Winchester SO22 4NH, UK
| | - Simon Roffey
- School of History, Archaeology and Philosophy, University of Winchester, Medecroft Building, Sparkford Road, Winchester SO22 4NH, UK
| | - Sarah A Inskip
- School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK.
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland; Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
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2
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Taylor GM, White-Iribhogbe K, Cole G, Ashby D, Stewart GR, Dawson-Hobbis H. Bioarchaeological investigation of individuals with suspected multibacillary leprosy from the mediaeval leprosarium of St Mary Magdalen, Winchester, Hampshire, UK. J Med Microbiol 2024; 73. [PMID: 38362924 DOI: 10.1099/jmm.0.001806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
Introduction. We have examined four burials from the St Mary Magdalen mediaeval leprosarium cemetery in Winchester, Hampshire, UK. One (Sk.8) was a male child, two (Sk.45 and Sk.52) were adolescent females and the fourth (Sk.512) was an adult male. The cemetery was in use between the 10th and 12th centuries. All showed skeletal lesions of leprosy. Additionally, one of the two females (Sk.45) had lesions suggestive of multi-cystic tuberculosis and the second (Sk.52) of leprogenic odontodysplasia (LO), a rare malformation of the roots of the permanent maxillary incisors.Gap statement. Relatively little is known of the manifestations of lepromatous leprosy (LL) in younger individuals from the archaeological record.Aims and Methodology. To address this, we have used ancient DNA testing and osteological examination of the individuals, supplemented with X-ray and microcomputed tomography (micro-CT) scan as necessary to assess the disease status.Results and Conclusions. The presence of Mycobacterium leprae DNA was confirmed in both females, and genotyping showed SNP type 3I-1 strains but with a clear genotypic variation. We could not confirm Mycobacterium tuberculosis complex DNA in the female individual SK.45. High levels of M. leprae DNA were found within the pulp cavities of four maxillary teeth from the male child (Sk.8) with LO, consistent with the theory that the replication of M. leprae in alveolar bone may interfere with root formation at key stages of development. We report our biomolecular findings in these individuals and review the evidence this site has contributed to our knowledge of mediaeval leprosy.
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Affiliation(s)
- G Michael Taylor
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, GU2 7XH, Surrey, UK
| | - Katie White-Iribhogbe
- Centre of African Studies, School of Oriental and African Studies (SOAS), University of London, Thornhaugh Street, Russell Square, London, WC1H 0XG, UK
| | - Garrard Cole
- UCL Institute of Archaeology, 31-34 Gordon Square, London, WC1H 0PY, UK
| | - David Ashby
- School of History, Archaeology and Philosophy, University of Winchester, Sparkford Road, Winchester, Hampshire, SO22 4NR, UK
| | - Graham R Stewart
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, GU2 7XH, Surrey, UK
| | - Heidi Dawson-Hobbis
- School of History, Archaeology and Philosophy, University of Winchester, Sparkford Road, Winchester, Hampshire, SO22 4NR, UK
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3
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van der Kuyl AC. Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens. EPIDEMIOLOGIA (BASEL, SWITZERLAND) 2022; 3:443-464. [PMID: 36547255 PMCID: PMC9778136 DOI: 10.3390/epidemiologia3040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022]
Abstract
Since life on earth developed, parasitic microbes have thrived. Increases in host numbers, or the conquest of a new species, provide an opportunity for such a pathogen to enjoy, before host defense systems kick in, a similar upsurge in reproduction. Outbreaks, caused by "endemic" pathogens, and epidemics, caused by "novel" pathogens, have thus been creating chaos and destruction since prehistorical times. To study such (pre)historic epidemics, recent advances in the ancient DNA field, applied to both archeological and historical remains, have helped tremendously to elucidate the evolutionary trajectory of pathogens. These studies have offered new and unexpected insights into the evolution of, for instance, smallpox virus, hepatitis B virus, and the plague-causing bacterium Yersinia pestis. Furthermore, burial patterns and historical publications can help in tracking down ancient pathogens. Another source of information is our genome, where selective sweeps in immune-related genes relate to past pathogen attacks, while multiple viruses have left their genomes behind for us to study. This review will discuss the sources available to investigate (pre)historic diseases, as molecular knowledge of historic and prehistoric pathogens may help us understand the past and the present, and prepare us for future epidemics.
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Affiliation(s)
- Antoinette C. van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; ; Tel.: +31-205-666-778
- Amsterdam Institute for Infection and Immunity, 1100 DD Amsterdam, The Netherlands
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4
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Filipek KL, Roberts CA, Montgomery J, Gowland RL, Moore J, Tucker K, Evans JA. Creating communities of care: Sex estimation and mobility histories of adolescents buried in the cemetery of St. Mary Magdalen leprosarium (Winchester, England). AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022. [PMCID: PMC9306906 DOI: 10.1002/ajpa.24498] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Objectives This study examines the biological sex and geographical origins of adolescents buried at the St Mary Magdalen leprosarium (Winchester, UK). The data are combined with archaeological and palaeopathological evidence to broaden the understanding of mobility and its relationship to leprosy and leprosaria in Medieval England. Materials and Methods Nineteen individuals (~10–25 at death) with skeletal lesions diagnostic of leprosy were analyzed using standard osteological methods. Amelogenin peptides were extracted from five individuals whose biological sex could not be assessed from macroscopic methods. Enamel samples were analyzed to produce 87Sr/86Sr and δ18O values to explore mobility histories. Results Amelogenin peptides revealed three males and two females. Tooth enamel samples provided an 87Sr/86Sr ratio range from 0.7084 to 0.7103 (mean 0.7090, ±0.0012, 2σ). δ18OP values show a wide range of 15.6‰–19.3‰ (mean 17.8 ± 1.6‰ 2σ), with corresponding δ18ODW values ranging from −9.7‰ to −4.1‰ (mean −6.3 ± 2.4‰ 2σ). Discussion Amelogenin peptide data reveal the presence of adolescent females with bone changes of leprosy, making them the youngest confirmed females with leprosy in the archaeological record. Results also show at least 12 adolescents were local, and seven were from further afield, including outside Britain. Since St. Mary Magdalen was a leprosarium, it is possible that these people traveled there specifically for care. Archaeological and palaeopathological data support the notion that care was provided at this facility and that leprosy stigma, as we understand it today, may not have existed in this time and place.
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Affiliation(s)
- Kori Lea Filipek
- Department of Archaeology Durham University Durham UK
- Human Sciences Research Centre, School of Human Sciences University of Derby Derby UK
| | | | | | | | - Joanna Moore
- Department of Archaeology Durham University Durham UK
| | - Katie Tucker
- Department of Archaeology University of Winchester Winchester UK
| | - Jane A. Evans
- National Environmental Isotope Facility British Geological Survey Keyworth UK
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Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague. Proc Natl Acad Sci U S A 2022; 119:e2116722119. [PMID: 35412864 PMCID: PMC9169917 DOI: 10.1073/pnas.2116722119] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The bacterium Yersinia pestis has caused numerous historically documented outbreaks of plague and research using ancient DNA could demonstrate that it already affected human populations during the Neolithic. However, the pathogen’s genetic diversity, geographic spread, and transmission dynamics during this early period of Y. pestis evolution are largely unexplored. Here, we describe a set of ancient plague genomes up to 5,000 y old from across Eurasia. Our data demonstrate that two genetically distinct forms of Y. pestis evolved in parallel and were both distributed across vast geographic distances, potentially occupying different ecological niches. Interpreted within the archeological context, our results suggest that the spread of plague during this period was linked to increased human mobility and intensification of animal husbandry. The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague’s formative years in terms of its early evolution and ecology.
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Malyarchuk AB, Andreeva TV, Kuznetsova IL, Kunizheva SS, Protasova MS, Uralsky LI, Tyazhelova TV, Gusev FE, Manakhov AD, Rogaev EI. Genomics of Ancient Pathogens: First Advances and Prospects. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:242-258. [PMID: 35526849 PMCID: PMC8916790 DOI: 10.1134/s0006297922030051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/08/2022] [Accepted: 01/21/2022] [Indexed: 11/23/2022]
Abstract
Paleogenomics is one of the urgent and promising areas of interdisciplinary research in the today's world science. New genomic methods of ancient DNA (aDNA) analysis, such as next generation sequencing (NGS) technologies, make it possible not only to obtain detailed genetic information about historical and prehistoric human populations, but also to study individual microbial and viral pathogens and microbiomes from different ancient and historical objects. Studies of aDNA of pathogens by reconstructing their genomes have so far yielded complete sequences of the ancient pathogens that played significant role in the history of the world: Yersinia pestis (plague), Variola virus (smallpox), Vibrio cholerae (cholera), HBV (hepatitis B virus), as well as the equally important endemic human infectious agents: Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy), and Treponema pallidum (syphilis). Genomic data from these pathogens complemented the information previously obtained by paleopathologists and allowed not only to identify pathogens from the past pandemics, but also to recognize the pathogen lineages that are now extinct, to refine chronology of the pathogen appearance in human populations, and to reconstruct evolutionary history of the pathogens that are still relevant to public health today. In this review, we describe state-of-the-art genomic research of the origins and evolution of many ancient pathogens and viruses and examine mechanisms of the emergence and spread of the ancient infections in the mankind history.
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Affiliation(s)
- Alexandra B Malyarchuk
- Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Tatiana V Andreeva
- Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Irina L Kuznetsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Svetlana S Kunizheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Maria S Protasova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Lev I Uralsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Tatiana V Tyazhelova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Fedor E Gusev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Andrey D Manakhov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Evgeny I Rogaev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia.
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
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7
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Luo Y, Kiriya M, Tanigawa K, Kawashima A, Nakamura Y, Ishii N, Suzuki K. Host-Related Laboratory Parameters for Leprosy Reactions. Front Med (Lausanne) 2021; 8:694376. [PMID: 34746168 PMCID: PMC8568883 DOI: 10.3389/fmed.2021.694376] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 09/30/2021] [Indexed: 12/27/2022] Open
Abstract
Leprosy reactions are acute inflammatory episodes that complicate the course of a Mycobacterium leprae infection and are the major cause of leprosy-associated pathology. Two types of leprosy reactions with relatively distinct pathogenesis and clinical features can occur: type 1 reaction, also known as reversal reaction, and type 2 reaction, also known as erythema nodosum leprosum. These acute nerve-destructive immune exacerbations often cause irreversible disabilities and deformities, especially when diagnosis is delayed. However, there is no diagnostic test to detect or predict leprosy reactions before the onset of clinical symptoms. Identification of biomarkers for leprosy reactions, which impede the development of symptoms or correlate with early-onset, will allow precise diagnosis and timely interventions to greatly improve the patients' quality of life. Here, we review the progress of research aimed at identifying biomarkers for leprosy reactions, including its correlation with not only immunity but also genetics, transcripts, and metabolites, providing an understanding of the immune dysfunction and inflammation that underly the pathogenesis of leprosy reactions. Nevertheless, no biomarkers that can reliably predict the subsequent occurrence of leprosy reactions from non-reactional patients and distinguish type I reaction from type II have yet been found.
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Affiliation(s)
- Yuqian Luo
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital and Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, China.,Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Mitsuo Kiriya
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Kazunari Tanigawa
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Akira Kawashima
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Yasuhiro Nakamura
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Norihisa Ishii
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan.,National Sanatorium Tamazenshoen, Tokyo, Japan
| | - Koichi Suzuki
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
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8
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Urban C, Blom AA, Pfrengle S, Walker-Meikle K, Stone AC, Inskip SA, Schuenemann VJ. One Health Approaches to Trace Mycobacterium leprae's Zoonotic Potential Through Time. Front Microbiol 2021; 12:762263. [PMID: 34745073 PMCID: PMC8566891 DOI: 10.3389/fmicb.2021.762263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 09/16/2021] [Indexed: 11/25/2022] Open
Abstract
Hansen's disease (leprosy), mainly caused by infection with Mycobacterium leprae, has accompanied humanity for thousands of years. Although currently rare in Europe, there are over 200,000 new infections annually in South East Asia, Africa, and South America. Over the years many disciplines - palaeopathology, ancient DNA and other ancient biomolecules, and history - have contributed to a better understanding of leprosy's past, in particular its history in medieval Europe. We discuss their contributions and potential, especially in relation to the role of inter-species transmission, an unexplored phenomenon in the disease's history. Here, we explore the potential of interdisciplinary approaches that understand disease as a biosocial phenomenon, which is a product of both infection with M. leprae and social behaviours that facilitate transmission and spread. Genetic evidence of M. leprae isolated from archaeological remains combined with systematic zooarchaeological and historical analysis would not only identify when and in what direction transmission occurred, but also key social behaviours and motivations that brought species together. In our opinion, this combination is crucial to understand the disease's zoonotic past and current potential.
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Affiliation(s)
- Christian Urban
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Alette A. Blom
- Department of Archaeology, University of Cambridge, Cambridge, United Kingdom
| | - Saskia Pfrengle
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | | | - Anne C. Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, United States
| | - Sarah A. Inskip
- School of Archaeology and Ancient History, University of Leicester, Leicester, United Kingdom
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9
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Pfrengle S, Neukamm J, Guellil M, Keller M, Molak M, Avanzi C, Kushniarevich A, Montes N, Neumann GU, Reiter E, Tukhbatova RI, Berezina NY, Buzhilova AP, Korobov DS, Suppersberger Hamre S, Matos VMJ, Ferreira MT, González-Garrido L, Wasterlain SN, Lopes C, Santos AL, Antunes-Ferreira N, Duarte V, Silva AM, Melo L, Sarkic N, Saag L, Tambets K, Busso P, Cole ST, Avlasovich A, Roberts CA, Sheridan A, Cessford C, Robb J, Krause J, Scheib CL, Inskip SA, Schuenemann VJ. Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes. BMC Biol 2021; 19:220. [PMID: 34610848 PMCID: PMC8493730 DOI: 10.1186/s12915-021-01120-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/07/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period. RESULTS Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria. CONCLUSIONS Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.
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Affiliation(s)
- Saskia Pfrengle
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Meriam Guellil
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia
| | - Marcel Keller
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia
| | - Martyna Molak
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097, Warsaw, Poland
| | - Charlotte Avanzi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, USA
- Swiss and Tropical Public Health Institute, Basel, Switzerland
| | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia
| | - Núria Montes
- Unitat d'Antropologia Biològica, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Gunnar U Neumann
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Rezeda I Tukhbatova
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
- Laboratory of Structural Biology, Kazan Federal University, Kazan, Russian Federation, 420008
| | - Nataliya Y Berezina
- Research Institute and Museum of Anthropology, Moscow State University, 125009, Mokhovaya str. 11, Moscow, Russian Federation
| | - Alexandra P Buzhilova
- Research Institute and Museum of Anthropology, Moscow State University, 125009, Mokhovaya str. 11, Moscow, Russian Federation
| | - Dmitry S Korobov
- The Institute of Archaeology of the Russian Academy of Sciences, 117292, Dm. Uljanova str. 19, Moscow, Russian Federation
| | - Stian Suppersberger Hamre
- Department of Archaeology, History, Cultural studies and religion, University of Bergen, 5020, Bergen, Norway
| | - Vitor M J Matos
- Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Maria T Ferreira
- Laboratory of Forensic Anthropology, Department of Life Sciences, University of Coimbra, Centre for Functional Ecology, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
- Área de Antropología Física, Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana, 24071, León, Spain
| | - Laura González-Garrido
- Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
- Área de Antropología Física, Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Campus de Vegazana, 24071, León, Spain
- Institute of Biomedicine (IBIOMED), Universidad de León, Campus de Vegazana, 24071, León, Spain
| | - Sofia N Wasterlain
- Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Célia Lopes
- Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
- Laboratory of Biological Anthropology, Department of Biology; School of Science and Technology, University of Évora, Évora, Portugal
| | - Ana Luisa Santos
- Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Nathalie Antunes-Ferreira
- Laboratório de Ciências Forenses e Psicológicas Egas Moniz (LCFPEM), Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Egas Moniz CRL, Monte de Caparica, Portugal
- Laboratory of Biological Anthropology and Human Osteology (LABOH), CRIA/FCSH, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Vitória Duarte
- Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Ana Maria Silva
- Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
- Laboratory of Forensic Anthropology, Department of Life Sciences, University of Coimbra, Centre for Functional Ecology, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
- UNIARQ - University of Lisbon, Lisbon, Portugal
| | - Linda Melo
- Department of Life Sciences, University of Coimbra, Research Centre for Anthropology and Health, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Natasa Sarkic
- OSTEO Research, Camino de la Iglesia 1, Barrio de mata, Santiuste De Pedraza, 40171, Segovia, Spain
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia
| | - Philippe Busso
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, 25-28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Alexei Avlasovich
- Department of Archeology, History of Belarus and Special Historical Disciplines, Mogilev State A. Kuleshov University, Str Kosmonavtov 1, Mogilev, 212022, Republic of Belarus
| | - Charlotte A Roberts
- Department of Archaeology, Durham University, South Road, Durham, DH1 3 LE, UK
| | - Alison Sheridan
- Department of Scottish History and Archaeology, National Museums Scotland, Chambers Street, Edinburgh, EH1 1JF, UK
| | - Craig Cessford
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK
| | - John Robb
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
- Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia.
- St John's College, University of Cambridge, Cambridge, CB2 1TP, UK.
| | - Sarah A Inskip
- School of Archaeology and Ancient History, University of Leicester, Leicester, LE1 7RH, UK.
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.
- Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.
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10
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Fotakis AK, Denham SD, Mackie M, Orbegozo MI, Mylopotamitaki D, Gopalakrishnan S, Sicheritz-Pontén T, Olsen JV, Cappellini E, Zhang G, Christophersen A, Gilbert MTP, Vågene ÅJ. Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190584. [PMID: 33012227 PMCID: PMC7702802 DOI: 10.1098/rstb.2019.0584] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of sixteenth-century human dental calculus from an individual from Trondheim, Norway. When phylogenetically placed, this genome falls in branch 3I among the diversity of other contemporary ancient strains from Northern Europe. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. Mycobacterium leprae can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual's dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early-stage leprosy. This study is the first known example of successful multi-omics retrieval of M. leprae from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing M. leprae in individuals from the archaeological record. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Affiliation(s)
- Anna K Fotakis
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Sean D Denham
- Museum of Archaeology, University of Stavanger, Stavanger, Norway
| | - Meaghan Mackie
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway.,Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Miren Iraeta Orbegozo
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Dorothea Mylopotamitaki
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Thomas Sicheritz-Pontén
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Jesper V Olsen
- Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.,BGI-Shenzhen, 518083 Shenzhen, People's Republic of China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, People's Republic of China.,Centre for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, People's Republic of China
| | | | - M Thomas P Gilbert
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway.,NTNU University Museum, Trondheim, Norway
| | - Åshild J Vågene
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
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11
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Avanzi C, Singh P, Truman RW, Suffys PN. Molecular epidemiology of leprosy: An update. INFECTION GENETICS AND EVOLUTION 2020; 86:104581. [PMID: 33022427 DOI: 10.1016/j.meegid.2020.104581] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/27/2020] [Accepted: 10/01/2020] [Indexed: 12/27/2022]
Abstract
Molecular epidemiology investigations are notoriously challenging in the leprosy field mainly because the inherent characteristics of the disease as well as its yet uncultivated causative agents, Mycobacterium leprae and M. lepromatosis. Despite significant developments in understanding the biology of leprosy bacilli through genomic approaches, the exact mechanisms of transmission is still unclear and the factors underlying pathological variation of the disease in different patients remain as major gaps in our knowledge about leprosy. Despite these difficulties, the last two decades have seen the development of genotyping procedures based on PCR-sequencing of target loci as well as by the genome-wide analysis of an increasing number of geographically diverse isolates of leprosy bacilli. This has provided a foundation for molecular epidemiology studies that are bringing a better understanding of strain evolution associated with ancient human migrations, and phylogeographical insights about the spread of disease globally. This review discusses the advantages and drawbacks of the main tools available for molecular epidemiological investigations of leprosy and summarizes various methods ranging from PCR-based genotyping to genome-typing techniques. We also describe their main applications in analyzing the short-range and long-range transmission of the disease. Finally, we summarise the current gaps and challenges that remain in the field of molecular epidemiology of leprosy.
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Affiliation(s)
- Charlotte Avanzi
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA; Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Pushpendra Singh
- Indian Council of Medical Research - National Institute of Research in Tribal Health, Jabalpur, India
| | - Richard W Truman
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, LO, USA
| | - Philip N Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria - Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil.
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12
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Neukamm J, Pfrengle S, Molak M, Seitz A, Francken M, Eppenberger P, Avanzi C, Reiter E, Urban C, Welte B, Stockhammer PW, Teßmann B, Herbig A, Harvati K, Nieselt K, Krause J, Schuenemann VJ. 2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals. BMC Biol 2020; 18:108. [PMID: 32859198 PMCID: PMC7456089 DOI: 10.1186/s12915-020-00839-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/29/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging. RESULTS The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed. CONCLUSIONS The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.
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Affiliation(s)
- Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Saskia Pfrengle
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland.,Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097, Warsaw, Poland
| | - Alexander Seitz
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Michael Francken
- Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Paleoanthropology, Dept. of Geosciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Partick Eppenberger
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Charlotte Avanzi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, USA
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Christian Urban
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Beatrix Welte
- Institute of Pre- and Protohistory and Medieval Archaeology, Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Philipp W Stockhammer
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, 80799, Munich, Germany.,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Barbara Teßmann
- Berlin Society of Anthropology, Ethnology and Prehistory, 10117, Berlin, Germany.,Museum of Prehistory and Early History, SMPK Berlin, 10117, Berlin, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Katerina Harvati
- Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Paleoanthropology, Dept. of Geosciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,DFG Centre for Advanced Studies Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Kay Nieselt
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.
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13
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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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14
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Arriola LA, Cooper A, Weyrich LS. Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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15
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Tió-Coma M, Avanzi C, Verhard EM, Pierneef L, van Hooij A, Benjak A, Roy JC, Khatun M, Alam K, Corstjens P, Cole ST, Richardus JH, Geluk A. Genomic Characterization of Mycobacterium leprae to Explore Transmission Patterns Identifies New Subtype in Bangladesh. Front Microbiol 2020; 11:1220. [PMID: 32612587 PMCID: PMC7308449 DOI: 10.3389/fmicb.2020.01220] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/13/2020] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium leprae, the causative agent of leprosy, is an unculturable bacterium with a considerably reduced genome (3.27 Mb) compared to homologues mycobacteria from the same ancestry. In 2001, the genome of M. leprae was first described and subsequently four genotypes (1-4) and 16 subtypes (A-P) were identified providing means to study global transmission patterns for leprosy. In order to understand the role of asymptomatic carriers we investigated M. leprae carriage as well as infection in leprosy patients (n = 60) and healthy household contacts (HHC; n = 250) from Bangladesh using molecular detection of the bacterial element RLEP in nasal swabs (NS) and slit skin smears (SSS). In parallel, to study M. leprae genotype distribution in Bangladesh we explored strain diversity by whole genome sequencing (WGS) and Sanger sequencing. In the studied cohort in Bangladesh, M. leprae DNA was detected in 33.3% of NS and 22.2% of SSS of patients with bacillary index of 0 whilst in HHC 18.0% of NS and 12.3% of SSS were positive. The majority of the M. leprae strains detected in this study belonged to genotype 1D (55%), followed by 1A (31%). Importantly, WGS allowed the identification of a new M. leprae genotype, designated 1B-Bangladesh (14%), which clustered separately between the 1A and 1B strains. Moreover, we established that the genotype previously designated 1C, is not an independent subtype but clusters within the 1D genotype. Intraindividual differences were present between the M. leprae strains obtained including mutations in hypermutated genes, suggesting mixed colonization/infection or in-host evolution. In summary, we observed that M. leprae is present in asymptomatic contacts of leprosy patients fueling the concept that these individuals contribute to the current intensity of transmission. Our data therefore emphasize the importance of sensitive and specific tools allowing post-exposure prophylaxis targeted at M. leprae-infected or -colonized individuals.
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Affiliation(s)
- Maria Tió-Coma
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Charlotte Avanzi
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Els M. Verhard
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Louise Pierneef
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Anouk van Hooij
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Johan Chandra Roy
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Marufa Khatun
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Khorshed Alam
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Paul Corstjens
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
| | - Jan Hendrik Richardus
- Department of Public Health, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
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16
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Miura S, Tamura K, Tao Q, Huuki LA, Kosakovsky Pond SL, Priest J, Deng J, Kumar S. A new method for inferring timetrees from temporally sampled molecular sequences. PLoS Comput Biol 2020; 16:e1007046. [PMID: 31951607 PMCID: PMC7018096 DOI: 10.1371/journal.pcbi.1007046] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 02/13/2020] [Accepted: 12/09/2019] [Indexed: 12/11/2022] Open
Abstract
Pathogen timetrees are phylogenies scaled to time. They reveal the temporal history of a pathogen spread through the populations as captured in the evolutionary history of strains. These timetrees are inferred by using molecular sequences of pathogenic strains sampled at different times. That is, temporally sampled sequences enable the inference of sequence divergence times. Here, we present a new approach (RelTime with Dated Tips [RTDT]) to estimating pathogen timetrees based on a relative rate framework underlying the RelTime approach that is algebraic in nature and distinct from all other current methods. RTDT does not require many of the priors demanded by Bayesian approaches, and it has light computing requirements. In analyses of an extensive collection of computer-simulated datasets, we found the accuracy of RTDT time estimates and the coverage probabilities of their confidence intervals (CIs) to be excellent. In analyses of empirical datasets, RTDT produced dates that were similar to those reported in the literature. In comparative benchmarking with Bayesian and non-Bayesian methods (LSD, TreeTime, and treedater), we found that no method performed the best in every scenario. So, we provide a brief guideline for users to select the most appropriate method in empirical data analysis. RTDT is implemented for use via a graphical user interface and in high-throughput settings in the newest release of cross-platform MEGA X software, freely available from http://www.megasoftware.net. Pathogen timetrees trace the origins and evolutionary histories of strains in populations, hosts, and outbreaks. The tips of these molecular phylogenies often contain sampling time information because the sequences were generally obtained at different times during the disease outbreaks and propagation. We have developed a new method for inferring divergence times and confidence intervals for phylogenies with tip dates. The new Relative Times with Dated Tips (RTDT) methods showed excellent performance in the analysis of computer-simulated datasets, producing similar or better results in several evolutionary scenarios as compared to other fast, non-Bayesian methods. The new method is available in the cross-platform MEGA software package (version 10.1 and higher) that provides a graphical user interface and allows usage via a command line in scripting and high throughput analysis (www.megasoftware.net).
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Affiliation(s)
- Sayaka Miura
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Koichiro Tamura
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Louise A. Huuki
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Sergei L. Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Jessica Priest
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Jiamin Deng
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail:
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17
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Crespo F, White J, Roberts C. Revisiting the tuberculosis and leprosy cross-immunity hypothesis: Expanding the dialogue between immunology and paleopathology. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2019; 26:37-47. [PMID: 31185376 DOI: 10.1016/j.ijpp.2019.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 05/08/2019] [Accepted: 05/26/2019] [Indexed: 06/09/2023]
Abstract
OBJECTIVE Our primary objective is to re-visit the tuberculosis and leprosy cross-immunity. hypothesis through the careful integration of immunology and paleopathology. METHODS Using an integrated theoretical analysis that evaluates clinical literature on human innate immunological responses, paleomicrobiology, bioarchaeology, and paleopathology, we develop a multifactorial model. RESULTS Past populations do not represent homogeneous immunological landscapes, and therefore it is likely that leprosy in Medieval Europe did not uniformly decline due to cross-immunity. CONCLUSIONS We recommend that bioarchaeological reconstructions of past disease experience take into consideration models that include variation in immune function based on past environments and social contexts. This provides a unique opportunity to conduct comprehensive analyses on complex immunological processes. SIGNIFICANCE Extrapolating results from experimental immunology to larger populations elucidates complexities of disease cross-immunity and highlights the importance of synthesizing archaeological, social, paleopathological and biological data as a means of understanding disease in the past. LIMITATIONS All extrapolations from data produced from in vitro studies to past populations, using living donors, pose significant limitations where, among other factors, the full reconstruction of past environmental and social contexts can frequently be sparse or incomplete. SUGGESTIONS FOR FUTURE RESEARCH To reduce the limitations of integrating experimental immunology with bioarchaeological reconstructions (i.e. how to use skeletal samples to reconstruct inflammatory phenotypes), we propose that osteoimmunology, or the study of the interplay between immune cells and bone cells, should be considered a vital discipline and perhaps the foundation for the expansion of paleoimmunology.
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Affiliation(s)
- Fabian Crespo
- Department of Anthropology, University of Louisville, Louisville, KY, 40292, USA.
| | - Jacob White
- Department of Anthropology, University of Louisville, Louisville, KY, 40292, USA
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18
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Abstract
Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.
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19
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Bos KI, Kühnert D, Herbig A, Esquivel-Gomez LR, Andrades Valtueña A, Barquera R, Giffin K, Kumar Lankapalli A, Nelson EA, Sabin S, Spyrou MA, Krause J. Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens. Annu Rev Microbiol 2019; 73:639-666. [PMID: 31283430 DOI: 10.1146/annurev-micro-090817-062436] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.
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Affiliation(s)
- Kirsten I Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Luis Roger Esquivel-Gomez
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Aditya Kumar Lankapalli
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; .,Faculty of Biological Sciences, Friedrich Schiller University, 07737 Jena, Germany
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20
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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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21
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The Evolution of Genotyping Strategies To Detect, Analyze, and Control Transmission of Tuberculosis. Microbiol Spectr 2019; 6. [PMID: 30338753 DOI: 10.1128/microbiolspec.mtbp-0002-2016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The introduction of genotypic tools to analyze Mycobacterium tuberculosis isolates has transformed our knowledge of the transmission dynamics of this pathogen. We discuss the development of the laboratory methods that have been applied in recent years to study the epidemiology of M. tuberculosis. This review integrates two approaches: on the one hand, it considers how genotyping techniques have evolved over the years; and on the other, it looks at how the way we think these techniques should be applied has changed. We begin by examining the application of fingerprinting tools to suspected outbreaks only, before moving on to universal genotyping schemes, and finally we describe the latest real-time strategies used in molecular epidemiology. We also analyze refined approaches to obtaining epidemiological data from patients and to increasing the discriminatory power of genotyping by techniques based on genomic characterization. Finally, we review the development of integrative solutions to reconcile the speed of PCR-based methods with the high discriminatory power of whole-genome sequencing in easily implemented formats adapted to low-resource settings. Our analysis of future considerations highlights the need to bring together the three key elements of high-quality surveillance of transmission in tuberculosis, namely, speed, precision, and ease of implementation.
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22
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Taylor GM, Murphy EM, Mendum TA, Pike AWG, Linscott B, Wu H, O’Grady J, Richardson H, O’Donovan E, Troy C, Stewart GR. Leprosy at the edge of Europe-Biomolecular, isotopic and osteoarchaeological findings from medieval Ireland. PLoS One 2018; 13:e0209495. [PMID: 30586394 PMCID: PMC6306209 DOI: 10.1371/journal.pone.0209495] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/06/2018] [Indexed: 11/18/2022] Open
Abstract
Relatively little is known of leprosy in Medieval Ireland; as an island located at the far west of Europe it has the potential to provide interesting insights in relation to the historical epidemiology of the disease. To this end the study focuses on five cases of probable leprosy identified in human skeletal remains excavated from inhumation burials. Three of the individuals derived from the cemetery of St Michael Le Pole, Golden Lane, Dublin, while single examples were also identified from Ardreigh, Co. Kildare, and St Patrick’s Church, Armoy, Co. Antrim. The individuals were radiocarbon dated and examined biomolecularly for evidence of either of the causative pathogens, M. leprae or M. lepromatosis. Oxygen and strontium isotopes were measured in tooth enamel and rib samples to determine where the individuals had spent their formative years and to ascertain if they had undertaken any recent migrations. We detected M. leprae DNA in the three Golden Lane cases but not in the probable cases from either Ardreigh Co. Kildare or Armoy, Co. Antrim. M. lepromatosis was not detected in any of the burals. DNA preservation was sufficiently robust to allow genotyping of M. leprae strains in two of the Golden Lane burials, SkCXCV (12-13th century) and SkCCXXX (11-13th century). These strains were found to belong on different lineages of the M. leprae phylogenetic tree, namely branches 3 and 2 respectively. Whole genome sequencing was also attempted on these two isolates with a view to gaining further information but poor genome coverage precluded phylogenetic analysis. Data from the biomolecular study was combined with osteological, isotopic and radiocarbon dating to provide a comprehensive and multidisciplinary study of the Irish cases. Strontium and oxygen isotopic analysis indicate that two of the individuals from Golden Lane (SkCXLVIII (10-11th century) and SkCXCV) were of Scandinavian origin, while SkCCXXX may have spent his childhood in the north of Ireland or central Britain. We propose that the Vikings were responsible for introducing leprosy to Ireland. This work adds to our knowledge of the likely origins of leprosy in Medieval Ireland and will hopefully stimulate further research into the history and spread of this ancient disease across the world.
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Affiliation(s)
- G. Michael Taylor
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Eileen M. Murphy
- Archaeology and Palaeoecology, School of Natural and Built Environment, Queen’s University Belfast, Belfast, Northern Ireland
- * E-mail:
| | - Tom A. Mendum
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Alistair W. G. Pike
- Department of Archaeology, University of Southampton, Highfield Road, Southampton, United Kingdom
| | - Bethan Linscott
- Department of Archaeology, University of Southampton, Highfield Road, Southampton, United Kingdom
| | - Huihai Wu
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Justin O’Grady
- Norwich Medical School, University of East Anglia, Norwich, England, United Kingdom
| | - Hollian Richardson
- Norwich Medical School, University of East Anglia, Norwich, England, United Kingdom
| | - Edmond O’Donovan
- Edmond O’Donovan & Associates, Archaeological Consultant, Bray, Co. Wicklow, Republic of Ireland
| | - Carmelita Troy
- Rubicon Heritage Services Ltd, Unit 2, Europa Enterprise Park, Midleton, Co. Cork, Republic of Ireland
| | - Graham R. Stewart
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
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23
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Geluk A. Correlates of immune exacerbations in leprosy. Semin Immunol 2018; 39:111-118. [PMID: 29950273 DOI: 10.1016/j.smim.2018.06.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 01/13/2023]
Abstract
Leprosy is still a considerable health threat in pockets of several low and middle income countries worldwide where intense transmission is witnessed, and often results in irreversible disabilities and deformities due to delayed- or misdiagnosis. Early detection of leprosy represents a substantial hurdle in present-day leprosy health care. The dearth of timely diagnosis has, however, particularly severe consequences in the case of inflammatory episodes, designated leprosy reactions, which represent the major cause of leprosy-associated irreversible neuropathy. There is currently no accurate, routine diagnostic test to reliably detect leprosy reactions, or to predict which patients will develop these immunological exacerbations. Identification of host biomarkers for leprosy reactions, particularly if correlating with early onset prior to development of clinical symptoms, will allow timely interventions that contribute to decreased morbidity. Development of a point-of-care (POC) test based on such correlates would be a definite game changer in leprosy health care. In this review, proteomic-, transcriptomic and metabolomic research strategies aiming at identification of host biomarker-based correlates of leprosy reactions are discussed, next to external factors associated with occurrence of these episodes. The vast diversity in research strategies combined with the variability in patient- and control cohorts argues for harmonisation of biomarker discovery studies with geographically overarching study sites. This will improve identification of specific correlates associated with risk of these damaging inflammatory episodes in leprosy and subsequent application to rapid field tests.
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Affiliation(s)
- Annemieke Geluk
- Dept. of Infectious Diseases, LUMC, PO Box 9600, 2300 RC Leiden, The Netherlands.
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24
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Schuenemann VJ, Avanzi C, Krause-Kyora B, Seitz A, Herbig A, Inskip S, Bonazzi M, Reiter E, Urban C, Dangvard Pedersen D, Taylor GM, Singh P, Stewart GR, Velemínský P, Likovsky J, Marcsik A, Molnár E, Pálfi G, Mariotti V, Riga A, Belcastro MG, Boldsen JL, Nebel A, Mays S, Donoghue HD, Zakrzewski S, Benjak A, Nieselt K, Cole ST, Krause J. Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe. PLoS Pathog 2018; 14:e1006997. [PMID: 29746563 PMCID: PMC5944922 DOI: 10.1371/journal.ppat.1006997] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/28/2018] [Indexed: 11/19/2022] Open
Abstract
Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.
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Affiliation(s)
- Verena J. Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Charlotte Avanzi
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Seitz
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Sarah Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Marion Bonazzi
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Christian Urban
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Dorthe Dangvard Pedersen
- Unit of Anthropology (ADBOU), Department of Forensic Medicine, University of Southern Denmark, Odense S, Denmark
| | - G. Michael Taylor
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Pushpendra Singh
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Graham R. Stewart
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Petr Velemínský
- Department of Anthropology, National Museum, Prague, Czech Republic
| | - Jakub Likovsky
- Department of Archaeology of Landscape and Archaeobiology, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Antónia Marcsik
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - Erika Molnár
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - György Pálfi
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - Valentina Mariotti
- Department of Biological, Geological and Environmental Sciences, Bologna, Italy
- ADES AMU-CNRS- EFS: Anthropology and Health, Aix-Marseille Université, Marseille, France
| | - Alessandro Riga
- Department of Biology, University of Florence, Firenze, Italy
| | - M. Giovanna Belcastro
- Department of Biological, Geological and Environmental Sciences, Bologna, Italy
- ADES AMU-CNRS- EFS: Anthropology and Health, Aix-Marseille Université, Marseille, France
| | - Jesper L. Boldsen
- Unit of Anthropology (ADBOU), Department of Forensic Medicine, University of Southern Denmark, Odense S, Denmark
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Simon Mays
- Historic England, Portsmouth, United Kingdom
| | - Helen D. Donoghue
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Sonia Zakrzewski
- Department of Archaeology, University of Southampton, Southampton, United Kingdom
| | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kay Nieselt
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
- * E-mail: (KN); (STC); (JK)
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
- * E-mail: (KN); (STC); (JK)
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- * E-mail: (KN); (STC); (JK)
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25
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Krause-Kyora B, Nutsua M, Boehme L, Pierini F, Pedersen DD, Kornell SC, Drichel D, Bonazzi M, Möbus L, Tarp P, Susat J, Bosse E, Willburger B, Schmidt AH, Sauter J, Franke A, Wittig M, Caliebe A, Nothnagel M, Schreiber S, Boldsen JL, Lenz TL, Nebel A. Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans. Nat Commun 2018; 9:1569. [PMID: 29717136 PMCID: PMC5931558 DOI: 10.1038/s41467-018-03857-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 03/16/2018] [Indexed: 01/26/2023] Open
Abstract
Leprosy, a chronic infectious disease caused by Mycobacterium leprae (M. leprae), was very common in Europe till the 16th century. Here, we perform an ancient DNA study on medieval skeletons from Denmark that show lesions specific for lepromatous leprosy (LL). First, we test the remains for M. leprae DNA to confirm the infection status of the individuals and to assess the bacterial diversity. We assemble 10 complete M. leprae genomes that all differ from each other. Second, we evaluate whether the human leukocyte antigen allele DRB1*15:01, a strong LL susceptibility factor in modern populations, also predisposed medieval Europeans to the disease. The comparison of genotype data from 69 M. leprae DNA-positive LL cases with those from contemporary and medieval controls reveals a statistically significant association in both instances. In addition, we observe that DRB1*15:01 co-occurs with DQB1*06:02 on a haplotype that is a strong risk factor for inflammatory diseases today. Leprosy, caused by infection with Mycobacterium leprae, was common in Europe in the Middle Ages. Here, Krause-Kyora et al. analyze ancient DNA from a medieval Danish leprosarium to assemble 10 complete bacterial genomes and perform association analysis of the DRB1*15:01 allele with risk of leprosy infection.
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Affiliation(s)
- Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany. .,Max Planck Institute for the Science of Human History, Jena, 07745, Germany.
| | - Marcel Nutsua
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Lisa Boehme
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Federica Pierini
- Department of Evolutionary Ecology, Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
| | - Dorthe Dangvard Pedersen
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, 5260, Denmark
| | | | - Dmitriy Drichel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931, Germany
| | - Marion Bonazzi
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Lena Möbus
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Peter Tarp
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, 5260, Denmark
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Esther Bosse
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | | | | | | | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
| | - Amke Caliebe
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, 24105, Germany
| | - Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany.,Clinic for Internal Medicine, University Hospital of Schleswig-Holstein, Kiel, 24105, Germany
| | - Jesper L Boldsen
- Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, 5260, Denmark
| | - Tobias L Lenz
- Department of Evolutionary Ecology, Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, 24105, Germany
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26
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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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Phylogenomics and antimicrobial resistance of the leprosy bacillus Mycobacterium leprae. Nat Commun 2018; 9:352. [PMID: 29367657 PMCID: PMC5783932 DOI: 10.1038/s41467-017-02576-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/12/2017] [Indexed: 11/29/2022] Open
Abstract
Leprosy is a chronic human disease caused by the yet-uncultured pathogen Mycobacterium leprae. Although readily curable with multidrug therapy (MDT), over 200,000 new cases are still reported annually. Here, we obtain M. leprae genome sequences from DNA extracted directly from patients’ skin biopsies using a customized protocol. Comparative and phylogenetic analysis of 154 genomes from 25 countries provides insight into evolution and antimicrobial resistance, uncovering lineages and phylogeographic trends, with the most ancestral strains linked to the Far East. In addition to known MDT-resistance mutations, we detect other mutations associated with antibiotic resistance, and retrace a potential stepwise emergence of extensive drug resistance in the pre-MDT era. Some of the previously undescribed mutations occur in genes that are apparently subject to positive selection, and two of these (ribD, fadD9) are restricted to drug-resistant strains. Finally, nonsense mutations in the nth excision repair gene are associated with greater sequence diversity and drug resistance. Leprosy is caused by the yet-uncultured pathogen Mycobacterium leprae. Here, Benjak et al. obtain M. leprae genome sequences from DNA extracted from patients' skin biopsies and, by analysing 154 genomes from 25 countries, provide insight into the pathogen’s evolution and antimicrobial resistance.
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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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Staphylococcus aureus Sequences from Osteomyelitic Specimens of a Pathological Bone Collection from Pre-Antibiotic Times. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Sources of Materials for Paleomicrobiology. Microbiol Spectr 2017; 4. [PMID: 27726809 DOI: 10.1128/microbiolspec.poh-0016-2015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Paleomicrobiology establishes the diagnosis of ancient infectious diseases by studying ancient pathogens. This recent science also analyzes the evolution of these pathogens, virulence, and their adaptation to their habitat and their vectors. The DNA persists a long time after the death of an organism despite the chemical and enzymatic degradation. The possibility of sequencing bacterial, viral, parasitic and archaeal DNA molecules persists over time.Various sources are used for these studies: frozen tissue and particularly human tissue are a exceptional source for the analysis because at very low temperatures, all biological activity is suspended. The coprolites are a source of choice for studying the human microbiome. Other sources, the ancient bones are the most abundant, however, they may contain only small amounts of DNA due to natural leaching. When the use of the tooth is possible, is a particularly interesting source because of its highly mineralized structure, which gives greater persistence than bone. The calcified tartar deposited on teeth is a source of interest for the study of oral microbiome.All these sources are subject to precautions (gloves and masks hat) at the time of sampling to avoid cross contamination and also be listed in the most precise way because they are precious and rare.
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Abstract
Paleopathology studies the traces of disease on human and animal remains from ancient times. Infectious diseases have been, for over a century, one of its main fields of interest. The applications of paleogenetics methods to microbial aDNA, that started in the 90s combined to the recent development of new sequencing techniques allowing 'paleogenomics' approaches, have completely renewed the issue of the infections in the past. These advances open up new challenges in the understanding of the evolution of human-pathogen relationships, integrated in "One Health" concept.In this perspective, an integrative multidisciplinary approach combining data from ancient texts and old bones to those of old molecules is of great interest for reconstructing the past of human infections. Despite some too optimistic prediction of their eradication in the late 20th century, some of these ancient human diseases, such as plague, leprosy or tuberculosis, are still present and continue their evolution at the beginning of this 21rst century. Better know the past to predict a part of the future of human diseases remains, more than ever, the motto of the paleopathological science.
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Abstract
Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used. However, because of inherent problems with ancient DNA, its de novo assembly is highly complicated. In order to tackle the diversity in the length of the input reads, we propose a two-layer approach, where multiple assemblies are generated in the first layer, which are then combined in the second layer. We used this two-layer assembly to generate assemblies for two different ancient samples and compared the results to current de novo assembly approaches. We are able to improve the assembly with respect to the length of the contigs and can resolve more repetitive regions.
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Affiliation(s)
- Alexander Seitz
- Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Eberhard-Karls-Universität Tübingen , Tübingen , Germany
| | - Kay Nieselt
- Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Eberhard-Karls-Universität Tübingen , Tübingen , Germany
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Roffey S, Tucker K, Filipek-Ogden K, Montgomery J, Cameron J, O’Connell T, Evans J, Marter P, Taylor GM. Investigation of a Medieval Pilgrim Burial Excavated from the Leprosarium of St Mary Magdalen Winchester, UK. PLoS Negl Trop Dis 2017; 11:e0005186. [PMID: 28125649 PMCID: PMC5268360 DOI: 10.1371/journal.pntd.0005186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 11/15/2016] [Indexed: 01/10/2023] Open
Abstract
We have examined the remains of a Pilgrim burial from St Mary Magdalen, Winchester. The individual was a young adult male, aged around 18–25 years at the time of death. Radiocarbon dating showed the remains dated to the late 11th–early 12th centuries, a time when pilgrimages were at their height in Europe. Several lines of evidence in connection with the burial suggested this was an individual of some means and prestige. Although buried within the leprosarium cemetery, the skeleton showed only minimal skeletal evidence for leprosy, which was confined to the bones of the feet and legs. Nonetheless, molecular testing of several skeletal elements, including uninvolved bones all showed robust evidence of DNA from Mycobacterium leprae, consistent with the lepromatous or multibacillary form of the disease. We infer that in life, this individual almost certainly suffered with multiple soft tissue lesions. Genotyping of the M.leprae strain showed this belonged to the 2F lineage, today associated with cases from South-Central and Western Asia. During osteological examination it was noted that the cranium and facial features displayed atypical morphology for northern European populations. Subsequently, geochemical isotopic analyses carried out on tooth enamel indicated that this individual was indeed not local to the Winchester region, although it was not possible to be more specific about their geographic origin. This multidisciplinary research article, involving biomolecular analysis, osteology, strontium and oxygen isotopic analyses and archaeology, examines the remains of a Pilgrim burial excavated from the medieval leprosy hospital of St Mary Magdalen, Winchester, UK. Radiocarbon dating showed the remains dated to the late 11th–early 12th centuries, a time when pilgrimages were at their height in Europe. The leprosarium at Winchester is one of the earliest excavated examples from Western Europe and has been the subject of a series of recent academic papers. The site is remarkable for the high number of burials displaying skeletal lesions characteristic of leprosy (86%) and the state of preservation of biomolecular markers of the disease, including mycolipids and DNA. Genotyping of the M.leprae strain showed this belonged to the 2F lineage, today associated with cases from South-Central and Western Asia. Several aspects of the burial and dietary isotope analysis indicated this was an individual of some prestige and means; an unusual cranial morphology pointed to possible origin outside of the British Isles. Strontium and oxygen isotopic analyses confirmed he was not local to the Winchester area but were not able to pinpoint his precise origins. Overall these findings confirm the benefits of a multidisciplinary approach which allows investigation of the wider relationship between leprosy, medieval pilgrimage and M.leprae transmission.
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Affiliation(s)
- Simon Roffey
- Department of Archaeology, University of Winchester, Winchester, United Kingdom
- * E-mail:
| | - Katie Tucker
- Department of Archaeology, University of Winchester, Winchester, United Kingdom
| | | | - Janet Montgomery
- Department of Archaeology, Durham University, Durham United Kingdom
| | - Jamie Cameron
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, Oxford, United Kingdom
| | - Tamsin O’Connell
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Jane Evans
- NERC Isotope Geosciences Laboratory, Keyworth, Notts, United Kingdom
| | - Phil Marter
- Department of Archaeology, University of Winchester, Winchester, United Kingdom
| | - G. Michael Taylor
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, AX Building, University of Surrey, Guildford, Surrey, United Kingdom
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Das M, Chaitanya VS, Kanmani K, Rajan L, Ebenezer M. Genomic diversity in Mycobacterium leprae isolates from leprosy cases in South India. INFECTION GENETICS AND EVOLUTION 2016; 45:285-289. [PMID: 27642139 DOI: 10.1016/j.meegid.2016.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/12/2016] [Accepted: 09/14/2016] [Indexed: 01/25/2023]
Abstract
OBJECTIVE The Objective of this study was to identify the strain diversity of Mycobacterium leprae in terms of SNP types and subtypes stratified as per genomic single nucleotide polymorphisms, in clinical isolates of leprosy patients from a tertiary care leprosy center in South India. Further, the associations of SNP types with clinical outcomes in leprosy were also investigated. METHODS DNA was extracted from excisional skin biopsies of a total of 172 newly diagnosed untreated leprosy patients from a clinic in Tamil Nadu, in south India, that also serves patients from neighboring states. All the leprosy patients were those who voluntarily reported at the clinic during the study period of one year i.e., 2015. Clinical and histopathological details were collected at diagnosis and leprosy was confirmed through bacteriological smear examination and PCR for M. leprae specific RLEP region. SNP types and subtypes were determined by PCR amplification and Sanger sequencing of PCR products. RESULTS M. leprae specific RLEP gene amplification was achieved in 160 out of 172 patients. Among 160 specimens 118(73.75%) were type 1 and 42 (26.25%) were type 2 and on subtyping it was noted that 88/160 (55.00%) were 1D, 25/160 (15.62%) 1C, 5/160 (3.12%) 1A, 33/160 (20.62%) 2G and 9/160 (5.62%) were 2H. CONCLUSION Our results indicated that subtype 1D is predominant in the south Indian population. We also noted 2G, 1C and 1A in the patient sample tested. Additionally we identified subtype 2H for the first time in India.
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Affiliation(s)
- Madhusmita Das
- Molecular Biology Lab, Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC), Karigiri, Vellore, Tamil Nadu 632106, India.
| | - V Sundeep Chaitanya
- Molecular Biology Lab, Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC), Karigiri, Vellore, Tamil Nadu 632106, India
| | - K Kanmani
- Molecular Biology Lab, Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC), Karigiri, Vellore, Tamil Nadu 632106, India
| | - Lakshmi Rajan
- Molecular Biology Lab, Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC), Karigiri, Vellore, Tamil Nadu 632106, India
| | - Mannam Ebenezer
- Molecular Biology Lab, Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC), Karigiri, Vellore, Tamil Nadu 632106, India
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Andam CP, Worby CJ, Chang Q, Campana MG. Microbial Genomics of Ancient Plagues and Outbreaks. Trends Microbiol 2016; 24:978-990. [PMID: 27618404 DOI: 10.1016/j.tim.2016.08.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 07/29/2016] [Accepted: 08/16/2016] [Indexed: 01/22/2023]
Abstract
The recent use of next-generation sequencing methods to investigate historical disease outbreaks has provided us with an unprecedented ability to address important and long-standing questions in epidemiology, pathogen evolution, and human history. In this review, we present major findings that illustrate how microbial genomics has provided new insights into the nature and etiology of infectious diseases of historical importance, such as plague, tuberculosis, and leprosy. Sequenced isolates collected from archaeological remains also provide evidence for the timing of historical evolutionary events as well as geographic spread of these pathogens. Elucidating the genomic basis of virulence in historical diseases can provide relevant information on how we can effectively understand the emergence and re-emergence of infectious diseases today and in the future.
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Affiliation(s)
- Cheryl P Andam
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA; University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Durham, NH 03824, USA.
| | - Colin J Worby
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA
| | - Qiuzhi Chang
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA
| | - Michael G Campana
- Smithsonian Conservation Biology Institute, Center for Conservation Genomics, 3001 Connecticut Avenue NW, Washington, DC 20008, USA.
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Rivera-Perez JI, Santiago-Rodriguez TM, Toranzos GA. Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology. Microbiol Spectr 2016; 4:10.1128/microbiolspec.EMF-0006-2015. [PMID: 27726770 PMCID: PMC5287379 DOI: 10.1128/microbiolspec.emf-0006-2015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Indexed: 01/14/2023] Open
Abstract
Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.
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37
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Genomic Analysis of Bacterial Outbreaks. Evol Biol 2016. [DOI: 10.1007/978-3-319-41324-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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38
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Duchemin W, Daubin V, Tannier E. Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence. BMC Genomics 2015; 16 Suppl 10:S9. [PMID: 26450112 PMCID: PMC4603589 DOI: 10.1186/1471-2164-16-s10-s9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND We propose the computational reconstruction of a whole bacterial ancestral genome at the nucleotide scale, and its validation by a sequence of ancient DNA. This rare possibility is offered by an ancient sequence of the late middle ages plague agent. It has been hypothesized to be ancestral to extant Yersinia pestis strains based on the pattern of nucleotide substitutions. But the dynamics of indels, duplications, insertion sequences and rearrangements has impacted all genomes much more than the substitution process, which makes the ancestral reconstruction task challenging. RESULTS We use a set of gene families from 13 Yersinia species, construct reconciled phylogenies for all of them, and determine gene orders in ancestral species. Gene trees integrate information from the sequence, the species tree and gene order. We reconstruct ancestral sequences for ancestral genic and intergenic regions, providing nearly a complete genome sequence for the ancestor, containing a chromosome and three plasmids. CONCLUSION The comparison of the ancestral and ancient sequences provides a unique opportunity to assess the quality of ancestral genome reconstruction methods. But the quality of the sequencing and assembly of the ancient sequence can also be questioned by this comparison.
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Affiliation(s)
- Wandrille Duchemin
- Laboratoire de Biométrie et Biologie Évolutive, LBBE, UMR CNRS 5558, University of Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Vincent Daubin
- Laboratoire de Biométrie et Biologie Évolutive, LBBE, UMR CNRS 5558, University of Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Eric Tannier
- Laboratoire de Biométrie et Biologie Évolutive, LBBE, UMR CNRS 5558, University of Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne, France
- Institut National de Recherche en Informatique et en Automatique (INRIA) Grenoble Rhône-Alpes, 655 avenue de l'Europe, 38330 Montbonnot, France
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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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Inskip SA, Taylor GM, Zakrzewski SR, Mays SA, Pike AWG, Llewellyn G, Williams CM, Lee OYC, Wu HHT, Minnikin DE, Besra GS, Stewart GR. Osteological, biomolecular and geochemical examination of an early anglo-saxon case of lepromatous leprosy. PLoS One 2015; 10:e0124282. [PMID: 25970602 PMCID: PMC4430215 DOI: 10.1371/journal.pone.0124282] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/12/2015] [Indexed: 11/19/2022] Open
Abstract
We have examined a 5th to 6th century inhumation from Great Chesterford, Essex, UK. The incomplete remains are those of a young male, aged around 21-35 years at death. The remains show osteological evidence of lepromatous leprosy (LL) and this was confirmed by lipid biomarker analysis and ancient DNA (aDNA) analysis, which provided evidence for both multi-copy and single copy loci from the Mycobacterium leprae genome. Genotyping showed the strain belonged to the 3I lineage, but the Great Chesterford isolate appeared to be ancestral to 3I strains found in later medieval cases in southern Britain and also continental Europe. While a number of contemporaneous cases exist, at present, this case of leprosy is the earliest radiocarbon dated case in Britain confirmed by both aDNA and lipid biomarkers. Importantly, Strontium and Oxygen isotope analysis suggest that the individual is likely to have originated from outside Britain. This potentially sheds light on the origins of the strain in Britain and its subsequent spread to other parts of the world, including the Americas where the 3I lineage of M. leprae is still found in some southern states of America.
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Affiliation(s)
- Sarah A. Inskip
- Faculteit Archaeologie, Universiteit Leiden, 2311 BE, Leiden, The Netherlands
| | - G. Michael Taylor
- Department of Microbial and Cellular Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, GU2 7TE, United Kingdom
| | - Sonia R. Zakrzewski
- Department of Archaeology, University of Southampton, Avenue Campus, Highfield, Southampton, SO17 1BF, United Kingdom
| | - Simon A. Mays
- Ancient Monuments Laboratory, English Heritage Centre for Archaeology, Fort Cumberland, Fort Cumberland Road, Eastney, Portsmouth PO4 9LD, United Kingdom
| | - Alistair W. G. Pike
- Department of Archaeology, University of Southampton, Avenue Campus, Highfield, Southampton, SO17 1BF, United Kingdom
| | - Gareth Llewellyn
- EPSRC National Mass Spectrometry Facility, Institute of Mass Spectrometry, College of Medicine, Swansea University, Swansea, SA2 8PP, United Kingdom
| | - Christopher M. Williams
- EPSRC National Mass Spectrometry Facility, Institute of Mass Spectrometry, College of Medicine, Swansea University, Swansea, SA2 8PP, United Kingdom
| | - Oona Y-C Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Houdini H. T. Wu
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - David E. Minnikin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Graham R. Stewart
- Department of Microbial and Cellular Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, GU2 7TE, United Kingdom
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Donoghue HD, Michael Taylor G, Marcsik A, Molnár E, Pálfi G, Pap I, Teschler-Nicola M, Pinhasi R, Erdal YS, Velemínsky P, Likovsky J, Belcastro MG, Mariotti V, Riga A, Rubini M, Zaio P, Besra GS, Lee OYC, Wu HHT, Minnikin DE, Bull ID, O'Grady J, Spigelman M. A migration-driven model for the historical spread of leprosy in medieval Eastern and Central Europe. INFECTION GENETICS AND EVOLUTION 2015; 31:250-6. [PMID: 25680828 DOI: 10.1016/j.meegid.2015.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 02/01/2015] [Accepted: 02/03/2015] [Indexed: 11/26/2022]
Abstract
Leprosy was rare in Europe during the Roman period, yet its prevalence increased dramatically in medieval times. We examined human remains, with paleopathological lesions indicative of leprosy, dated to the 6th-11th century AD, from Central and Eastern Europe and Byzantine Anatolia. Analysis of ancient DNA and bacterial cell wall lipid biomarkers revealed Mycobacterium leprae in skeletal remains from 6th-8th century Northern Italy, 7th-11th century Hungary, 8th-9th century Austria, the Slavic Greater Moravian Empire of the 9th-10th century and 8th-10th century Byzantine samples from Northern Anatolia. These data were analyzed alongside findings published by others. M. leprae is an obligate human pathogen that has undergone an evolutionary bottleneck followed by clonal expansion. Therefore M. leprae genotypes and sub-genotypes give information about the human populations they have infected and their migration. Although data are limited, genotyping demonstrates that historical M. leprae from Byzantine Anatolia, Eastern and Central Europe resembles modern strains in Asia Minor rather than the recently characterized historical strains from North West Europe. The westward migration of peoples from Central Asia in the first millennium may have introduced different M. leprae strains into medieval Europe and certainly would have facilitated the spread of any existing leprosy. The subsequent decline of M. leprae in Europe may be due to increased host resistance. However, molecular evidence of historical leprosy and tuberculosis co-infections suggests that death from tuberculosis in leprosy patients was also a factor.
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Affiliation(s)
- Helen D Donoghue
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, UK.
| | - G Michael Taylor
- Department of Microbial and Cellular Science, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Antónia Marcsik
- University of Szeged, Mályva utca 23, H-6771 Szeged, Hungary
| | - Erika Molnár
- Department of Biological Anthropology, University of Szeged, Hungary
| | - Gyorgy Pálfi
- Department of Biological Anthropology, University of Szeged, Hungary
| | - Ildikó Pap
- Department of Anthropology, Natural History Museum, Budapest, Hungary
| | | | - Ron Pinhasi
- School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
| | - Yilmaz S Erdal
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Petr Velemínsky
- Department of Anthropology, National Museum, Prague, Czech Republic
| | - Jakub Likovsky
- Department of the Archaeology of Landscape and Archaeobiology, Institute of Archaeology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Maria Giovanna Belcastro
- Laboratorio di Bioarcheologia e Osteologia Forense, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Via Selmi 3, 40126 Bologna, Italy; Centro Fermi, Piazza del Viminale 1, 00184 Rome, Italy
| | - Valentina Mariotti
- Laboratorio di Bioarcheologia e Osteologia Forense, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Via Selmi 3, 40126 Bologna, Italy; ADES, UMR 7268 CNRS/Université de la Méditerranée/EFS, Université de la Méditerranée, CS80011, Bd Pierre Dramard,13344 Marseille Cedex 15, France
| | - Alessandro Riga
- Laboratorio di Bioarcheologia e Osteologia Forense, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Via Selmi 3, 40126 Bologna, Italy
| | - Mauro Rubini
- Department of Archaeology, Foggia University, Tivoli, Italy; Anthropological Service of S.B.A.L. (Ministry of Culture), Rome, Italy
| | - Paola Zaio
- Department of Archaeology, Foggia University, Tivoli, Italy
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Oona Y-C Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Houdini H T Wu
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - David E Minnikin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Ian D Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
| | - Justin O'Grady
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, UK
| | - Mark Spigelman
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, UK; Department of Anatomy and Anthropology Sackler Medical School, Tel Aviv University, Israel
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Ancient pathogen genomics: insights into timing and adaptation. J Hum Evol 2014; 79:137-49. [PMID: 25532802 DOI: 10.1016/j.jhevol.2014.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 09/08/2014] [Accepted: 11/05/2014] [Indexed: 12/15/2022]
Abstract
Disease is a major cause of natural selection affecting human evolution, whether through a sudden pandemic or persistent morbidity and mortality. Recent contributions in the field of ancient pathogen genomics have advanced our understanding of the antiquity and nature of human-pathogen interactions through time. Technical advancements have facilitated the recovery, enrichment, and high-throughput sequencing of pathogen and parasite DNA from archived and archaeological remains. These time-stamped genomes are crucial for calibrating molecular clocks to infer the timing of evolutionary events, while providing finer-grain resolution to phylogenetic reconstructions and complex biogeographical patterns. Additionally, genome scale data allow better identification of substitutions linked to adaptations of the pathogen to their human hosts. As methodology continues to improve, ancient genomes of humans and their diverse microbiomes from a range of eras and archaeological contexts will enable population-level ancient analyses in the near future and a better understanding of their co-evolutionary history.
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