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Austin RM, Honap TP, Mann AE, Hübner A, DeGaglia CMS, Warinner C, Zuckerman MK, Hofman CA. Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool. Sci Rep 2024; 14:14720. [PMID: 38926415 PMCID: PMC11208530 DOI: 10.1038/s41598-024-64818-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Dental calculus is a microbial biofilm that contains biomolecules from oral commensals and pathogens, including those potentially related to cause of death (CoD). To assess the utility of calculus as a diagnostically informative substrate, in conjunction with paleopathological analysis, calculus samples from 39 individuals in the Smithsonian Institution's Robert J. Terry Collection with CoDs of either syphilis or tuberculosis were assessed via shotgun metagenomic sequencing for the presence of Treponema pallidum subsp. pallidum and Mycobacterium tuberculosis complex (MTBC) DNA. Paleopathological analysis revealed that frequencies of skeletal lesions associated with these diseases were partially inconsistent with diagnostic criteria. Although recovery of T. p. pallidum DNA from individuals with a syphilis CoD was elusive, MTBC DNA was identified in at least one individual with a tuberculosis CoD. The authenticity of MTBC DNA was confirmed using targeted quantitative PCR assays, MTBC genome enrichment, and in silico bioinformatic analyses; however, the lineage of the MTBC strain present could not be determined. Overall, our study highlights the utility of dental calculus for molecular detection of tuberculosis in the archaeological record and underscores the effect of museum preparation techniques and extensive handling on pathogen DNA preservation in skeletal collections.
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Affiliation(s)
- Rita M Austin
- Frontiers in Evolutionary Zoology Research Group, Natural History Museum of Oslo, University of Oslo, Oslo, 0562, Norway.
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA.
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, 73019, USA.
| | - Tanvi P Honap
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, 73019, USA
| | - Allison E Mann
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Alexander Hübner
- Department Archaeogenetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | | | - Christina Warinner
- Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA
| | - Molly K Zuckerman
- Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Mississippi State, MS, 39762, USA.
| | - Courtney A Hofman
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA.
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, 73019, USA.
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2
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Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, D’Aleo F, Saegeman V, Franceschetti L, Novati S, Fernández-Rodríguez A, Verzeletti A, Farina C, Bandi C. Forensic Microbiology: When, Where and How. Microorganisms 2024; 12:988. [PMID: 38792818 PMCID: PMC11123702 DOI: 10.3390/microorganisms12050988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.
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Affiliation(s)
- Riccardo Nodari
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Milena Arghittu
- Analysis Laboratory, ASST Melegnano e Martesana, 20077 Vizzolo Predabissi, Italy
| | - Paolo Bailo
- Section of Legal Medicine, School of Law, University of Camerino, 62032 Camerino, Italy
| | - Cristina Cattaneo
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Roberta Creti
- Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesco D’Aleo
- Microbiology and Virology Laboratory, GOM—Grande Ospedale Metropolitano, 89124 Reggio Calabria, Italy
| | - Veroniek Saegeman
- Microbiology and Infection Control, Vitaz Hospital, 9100 Sint-Niklaas, Belgium
| | - Lorenzo Franceschetti
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Stefano Novati
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy
| | - Amparo Fernández-Rodríguez
- Microbiology Department, Biology Service, Instituto Nacional de Toxicología y Ciencias Forenses, 41009 Madrid, Spain
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, 25123 Brescia, Italy
| | - Claudio Farina
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Claudio Bandi
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biosciences, University of Milan, 20133 Milan, Italy
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3
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Putrino A, Marinelli E, Galeotti A, Ferrazzano GF, Ciribè M, Zaami S. A Journey into the Evolution of Human Host-Oral Microbiome Relationship through Ancient Dental Calculus: A Scoping Review. Microorganisms 2024; 12:902. [PMID: 38792733 PMCID: PMC11123932 DOI: 10.3390/microorganisms12050902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/26/2024] Open
Abstract
One of the most promising areas of research in palaeomicrobiology is the study of the human microbiome. In particular, ancient dental calculus helps to reconstruct a substantial share of oral microbiome composition by mapping together human evolution with its state of health/oral disease. This review aims to trace microbial characteristics in ancient dental calculus to describe the evolution of the human host-oral microbiome relationship in oral health or disease in children and adults. Following the PRISMA-Extension for Scoping Reviews guidelines, the main scientific databases (PubMed, Scopus, Lilacs, Cochrane Library) have been drawn upon. Eligibility criteria were established, and all the data collected on a purpose-oriented collection form were analysed descriptively. From the initial 340 records, only 19 studies were deemed comprehensive enough for the purpose of this review. The knowledge of the composition of ancient oral microbiomes has broadened over the past few years thanks to increasingly well-performing decontamination protocols and additional analytical avenues. Above all, metagenomic sequencing, also implemented by state-of-the-art bioinformatics tools, allows for the determination of the qualitative-quantitative composition of microbial species associated with health status and caries/periodontal disease. Some microbial species, especially periodontal pathogens, do not appear to have changed in history, while others that support caries disease or oral health could be connected to human evolution through lifestyle and environmental contributing factors.
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Affiliation(s)
- Alessandra Putrino
- Dentistry Unit, Management Innovations, Diagnostics and Clinical Pathways, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (A.G.); (M.C.)
| | - Enrico Marinelli
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100 Latina, Italy;
| | - Angela Galeotti
- Dentistry Unit, Management Innovations, Diagnostics and Clinical Pathways, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (A.G.); (M.C.)
- U.N.-E.U. INTERNATIONAL RESEARCH PROJECT ON HUMAN HEALTH-ORAL HEALTH SECTION, 1200 Géneve, Switzerland;
| | - Gianmaria Fabrizio Ferrazzano
- U.N.-E.U. INTERNATIONAL RESEARCH PROJECT ON HUMAN HEALTH-ORAL HEALTH SECTION, 1200 Géneve, Switzerland;
- UNESCO Chair in Health Education and Sustainable Development, Dentistry Section, University of Naples “Federico II”, 80138 Naples, Italy
- East-Asian-Pacific International Academic Consortium
| | - Massimiliano Ciribè
- Dentistry Unit, Management Innovations, Diagnostics and Clinical Pathways, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (A.G.); (M.C.)
| | - Simona Zaami
- Department of Anatomical, Histological, Forensic and Orthopedic Sciences, Sapienza University of Rome, 00161 Rome, Italy;
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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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5
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Honap TP, Monroe CR, Johnson SJ, Jacobson DK, Abin CA, Austin RM, Sandberg P, Levine M, Sankaranarayanan K, Lewis CM. Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:542-556. [PMID: 37002784 DOI: 10.1002/ajpa.24735] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
OBJECTIVES Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA. MATERIALS AND METHODS Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted. RESULTS Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains. DISCUSSION We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.
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Affiliation(s)
- Tanvi P Honap
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Cara R Monroe
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Center for the Ethics of Indigenous Genomics Research (CEIGR), University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Sarah J Johnson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - David K Jacobson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Christopher A Abin
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Rita M Austin
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Paul Sandberg
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Marc Levine
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
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6
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Hodgins HP, Chen P, Lobb B, Wei X, Tremblay BJM, Mansfield MJ, Lee VCY, Lee PG, Coffin J, Duggan AT, Dolphin AE, Renaud G, Dong M, Doxey AC. Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains. Nat Commun 2023; 14:5475. [PMID: 37673908 PMCID: PMC10482840 DOI: 10.1038/s41467-023-41174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/23/2023] [Indexed: 09/08/2023] Open
Abstract
The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, we analyze metagenomic datasets from 38 human archaeological samples and identify bacterial genomic sequences related to modern-day Clostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. These genomic assemblies had varying levels of completeness, and a subset of them displayed hallmarks of ancient DNA damage. Phylogenetic analyses revealed known C. tetani clades as well as potentially new Clostridium lineages closely related to C. tetani. The genomic assemblies encode 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from an ancient Chilean mummy sample and found that it induced tetanus muscle paralysis in mice, with potency comparable to modern TeNT. Thus, our ancient DNA analysis identifies DNA from neurotoxigenic C. tetani in archaeological human samples, and a novel variant of TeNT that can cause disease in mammals.
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Affiliation(s)
- Harold P Hodgins
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Pengsheng Chen
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Briallen Lobb
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Xin Wei
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Benjamin J M Tremblay
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Michael J Mansfield
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Victoria C Y Lee
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Pyung-Gang Lee
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Jeffrey Coffin
- Department of Anthropology, University of Waterloo, Waterloo, ON, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Alexis E Dolphin
- Department of Anthropology, University of Waterloo, Waterloo, ON, Canada
| | - Gabriel Renaud
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, MA, USA.
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA.
| | - Andrew C Doxey
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada.
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Bauer IL. The oral repellent - science fiction or common sense? Insects, vector-borne diseases, failing strategies, and a bold proposition. Trop Dis Travel Med Vaccines 2023; 9:7. [PMID: 37381000 DOI: 10.1186/s40794-023-00195-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/09/2023] [Indexed: 06/30/2023] Open
Abstract
Over the last decades, unimaginable amounts of money have gone into research and development of vector control measures, repellents, treatment, and vaccines for vector borne diseases. Technological progress and scientific breakthroughs allowed for ever more sophisticated and futuristic strategies. Yet, each year, millions of people still die or suffer from potentially serious consequences of malaria or dengue to more recent infections, such as zika or chikungunya, or of debilitating consequences of neglected tropical diseases. This does not seem value for money. In addition, all current vector control strategies and personal protection methods have shortcomings, some serious, that are either destructive to non-target species or unsatisfactory in their effectiveness. On the other hand, the rapid decline in insect populations and their predators reflects decades-long aggressive and indiscriminate vector control. This major disruption of biodiversity has an impact on human life not anticipated by the well-meaning killing of invertebrates. The objective of this paper is to re-examine current control methods, their effectiveness, their impact on biodiversity, human and animal health, and to call for scientific courage in the pursuit of fresh ideas. This paper brings together topics that are usually presented in isolation, thereby missing important links that offer potential solutions to long-standing problems in global health. First, it serves as a reminder of the importance of insects to human life and discusses the few that play a role in transmitting disease. Next, it examines critically the many currently employed vector control strategies and personal protection methods. Finally, based on new insights into insect chemo-sensation and attractants, this perspective makes a case for revisiting a previously abandoned idea, the oral repellent, and its use via currently successful methods of mass-application. The call is out for focused research to provide a powerful tool for public health, tropical medicine, and travel medicine.
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Affiliation(s)
- Irmgard L Bauer
- College of Healthcare Sciences, Academy - Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia.
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Vassallo A, Modi A, Quagliariello A, Bacci G, Faddetta T, Gallo M, Provenzano A, La Barbera A, Lombardo G, Maggini V, Firenzuoli F, Zaccaroni M, Gallo G, Caramelli D, Aleo Nero C, Baldi F, Fani R, Palumbo Piccionello A, Pucciarelli S, Puglia AM, Sineo L. Novel Sources of Biodiversity and Biomolecules from Bacteria Isolated from a High Middle Ages Soil Sample in Palermo (Sicily, Italy). Microbiol Spectr 2023; 11:e0437422. [PMID: 37071008 PMCID: PMC10269861 DOI: 10.1128/spectrum.04374-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/26/2023] [Indexed: 04/19/2023] Open
Abstract
The urban plan of Palermo (Sicily, Italy) has evolved throughout Punic, Roman, Byzantine, Arab, and Norman ages until it stabilized within the borders that correspond to the current historic center. During the 2012 to 2013 excavation campaign, new remains of the Arab settlement, directly implanted above the structures of the Roman age, were found. The materials investigated in this study derived from the so-called Survey No 3, which consists of a rock cavity of subcylindrical shape covered with calcarenite blocks: it was probably used to dispose of garbage during the Arabic age and its content, derived from daily activities, included grape seeds, scales and bones of fish, small animal bones, and charcoals. Radiocarbon dating confirmed the medieval origin of this site. The composition of the bacterial community was characterized through a culture-dependent and a culture-independent approach. Culturable bacteria were isolated under aerobic and anaerobic conditions and the total bacterial community was characterized through metagenomic sequencing. Bacterial isolates were tested for the production of compounds with antibiotic activity: a Streptomyces strain, whose genome was sequenced, was of particular interest because of its inhibitory activity, which was due to the Type I polyketide aureothin. Moreover, all strains were tested for the production of secreted proteases, with those belonging to the genus Nocardioides having the most active enzymes. Finally, protocols commonly used for ancient DNA studies were applied to evaluate the antiquity of isolated bacterial strains. Altogether these results show how paleomicrobiology might represent an innovative and unexplored source of novel biodiversity and new biotechnological tools. IMPORTANCE One of the goals of paleomicrobiology is the characterization of the microbial community present in archaeological sites. These analyses can usually provide valuable information about past events, such as occurrence of human and animal infectious diseases, ancient human activities, and environmental changes. However, in this work, investigations about the composition of the bacterial community of an ancient soil sample (harvested in Palermo, Italy) were carried out aiming to screen ancient culturable strains with biotechnological potential, such as the ability to produce bioactive molecules and secreted hydrolytic enzymes. Besides showing the biotechnological relevance of paleomicrobiology, this work reports a case of germination of putatively ancient bacterial spores recovered from soil rather than extreme environments. Moreover, in the case of spore-forming species, these results raise questions about the accuracy of techniques usually applied to estimate antiquity of DNA, as they could lead to its underestimation.
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Affiliation(s)
- Alberto Vassallo
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
| | - Giovanni Bacci
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Teresa Faddetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Michele Gallo
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Venezia Mestre (VE), Italy
| | - Aldesia Provenzano
- Department of Clinical and Experimental Biomedical Sciences “Mario Serio,” University of Florence, Florence (FI), Italy
| | - Andrea La Barbera
- Unit of Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genoa (GE), Italy
| | - Giovanna Lombardo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Valentina Maggini
- Research and Innovation Center in Phytotherapy and Integrated Medicine, Tuscany Region, Careggi University Hospital, Florence (FI), Italy
| | - Fabio Firenzuoli
- Research and Innovation Center in Phytotherapy and Integrated Medicine, Tuscany Region, Careggi University Hospital, Florence (FI), Italy
| | - Marco Zaccaroni
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Giuseppe Gallo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Carla Aleo Nero
- Soprintendenza ai Beni culturali e ambientali di Palermo, Palermo (PA), Italy
| | - Franco Baldi
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Venezia Mestre (VE), Italy
| | - Renato Fani
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Antonio Palumbo Piccionello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Luca Sineo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
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Clavel P, Louis L, Sarkissian CD, Thèves C, Gillet C, Chauvey L, Tressières G, Schiavinato S, Calvière-Tonasso L, Telmon N, Clavel B, Jonvel R, Tzortzis S, Bouniol L, Fémolant JM, Klunk J, Poinar H, Signoli M, Costedoat C, Spyrou MA, Seguin-Orlando A, Orlando L. Improving the extraction of ancient Yersinia pestis genomes from the dental pulp. iScience 2023; 26:106787. [PMID: 37250315 PMCID: PMC10214834 DOI: 10.1016/j.isci.2023.106787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/11/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023] Open
Abstract
Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of ancient Yersinia pestis DNA release in solution during a pre-digestion of the dental pulp. We found that most of the ancient Y. pestis DNA is released within 60 min at 37°C in our experimental conditions. We recommend a simple pre-digestion as an economical procedure to obtain extracts enriched in ancient pathogen DNA, as longer digestion times release other types of templates, including host DNA. Combining this procedure with DNA capture, we characterized the genome sequences of 12 ancient Y. pestis bacteria from France dating to the second pandemic outbreaks of the 17th and 18th centuries Common Era.
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Affiliation(s)
- Pierre Clavel
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Lexane Louis
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Clio Der Sarkissian
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Catherine Thèves
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Claudia Gillet
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Lorelei Chauvey
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Gaétan Tressières
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Stéphanie Schiavinato
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Laure Calvière-Tonasso
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Norbert Telmon
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Benoît Clavel
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), CNRS-UMR7209, Muséum national d’histoire naturelle, 55 Rue Buffon, 75005 Paris, France
| | - Richard Jonvel
- Amiens Métropole Service Archéologie Préventive, 2 rue Colbert, 80000 Amiens, France
| | - Stéfan Tzortzis
- Service Régional de l’Archéologie, 21 allée Claude Forbin, 13100 Aix-en-Provence, France
| | - Laetitia Bouniol
- Service archéologique de la ville de Beauvais, 1 rue Desgroux, 60021 Beauvais, France
| | - Jean-Marc Fémolant
- Service archéologique de la ville de Beauvais, 1 rue Desgroux, 60021 Beauvais, France
| | | | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, ON L8S 4L9, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S, 4L9, Canada
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - Michel Signoli
- Aix-Marseille Université, CNRS, EFS, ADES, 13005 Marseille, France
| | | | - Maria A. Spyrou
- Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Andaine Seguin-Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
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10
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Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
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11
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Hider J, Duggan AT, Klunk J, Eaton K, Long GS, Karpinski E, Giuffra V, Ventura L, Fornaciari A, Fornaciari G, Golding GB, Prowse TL, Poinar HN. Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2022; 39:20-34. [PMID: 36174312 DOI: 10.1016/j.ijpp.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 08/05/2022] [Accepted: 08/13/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVE To investigate variation in ancient DNA recovery of Brucella melitensis, the causative agent of brucellosis, from multiple tissues belonging to one individual MATERIALS: 14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 th century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis. METHODS Shotgun sequencing data from was examined to determine the presence of Brucella DNA. RESULTS Three of the 14 samples contained authentic ancient DNA, identified as belonging to B. melitensis. A genome (23.81X depth coverage, 0.98 breadth coverage) was recovered from a kidney stone. Nine of the samples contained reads classified as B. melitensis (7-169), but for many the data quality was insufficient to withstand our identification and authentication criteria. CONCLUSIONS We identified significant variation in the preservation and abundance of B. melitensis DNA present across multiple tissues, with calcified nodules yielding the highest number of authenticated reads. This shows how greatly sample selection can impact pathogen identification. SIGNIFICANCE Our results demonstrate variation in the preservation and recovery of pathogen DNA across tissues. This study highlights the importance of sample selection in the reconstruction of infectious disease burden and highlights the importance of a holistic approach to identifying disease. LIMITATIONS Study focuses on pathogen recovery in a single individual. SUGGESTIONS FOR FURTHER RESEARCH Further analysis of how sampling impacts aDNA recovery will improve pathogen aDNA recovery and advance our understanding of disease in past peoples.
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Affiliation(s)
- Jessica Hider
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada.
| | - Ana T Duggan
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Daicel Arbor Biosciences, 5840 Interface Drive, Suite 101, Ann Arbor, MI 48103, USA
| | - Katherine Eaton
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - George S Long
- Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Emil Karpinski
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Valentina Giuffra
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, Medical School, via Roma 57, 56126 Pisa, PI, Italy
| | - Luca Ventura
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Italy; Division of Pathology, San Salvatore Hospital, University of L'Aquila, Coppito, 67100 L'Aquila, AQ, Italy
| | - Antonio Fornaciari
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, Medical School, via Roma 57, 56126 Pisa, PI, Italy
| | - Gino Fornaciari
- Maria Luisa di Borbone Academy, Villa Borbone, viale dei Tigli 32, 55049 Viareggio, LU, Italy
| | - G Brian Golding
- Department of Biology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Tracy L Prowse
- Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Anthropology, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L8, Canada; Department of Biochemistry, McMaster University, 1280 Main St W, Hamilton, ON L8S 4L9, Canada
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12
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van der Kuyl AC. Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens. EPIDEMIOLOGIA 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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022] Open
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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13
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Alt KW, Al-Ahmad A, Woelber JP. Nutrition and Health in Human Evolution-Past to Present. Nutrients 2022; 14:3594. [PMID: 36079850 PMCID: PMC9460423 DOI: 10.3390/nu14173594] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/23/2022] Open
Abstract
Anyone who wants to understand the biological nature of humans and their special characteristics must look far back into evolutionary history. Today's way of life is drastically different from that of our ancestors. For almost 99% of human history, gathering and hunting have been the basis of nutrition. It was not until about 12,000 years ago that humans began domesticating plants and animals. Bioarchaeologically and biochemically, this can be traced back to our earliest roots. Modern living conditions and the quality of human life are better today than ever before. However, neither physically nor psychosocially have we made this adjustment and we are paying a high health price for it. The studies presented allow us to reconstruct food supply, lifestyles, and dietary habits: from the earliest primates, through hunter-gatherers of the Paleolithic, farming communities since the beginning of the Anthropocene, to the Industrial Age and the present. The comprehensive data pool allows extraction of all findings of medical relevance. Our recent lifestyle and diet are essentially determined by our culture rather than by our millions of years of ancestry. Culture is permanently in a dominant position compared to natural evolution. Thereby culture does not form a contrast to nature but represents its result. There is no doubt that we are biologically adapted to culture, but it is questionable how much culture humans can cope with.
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Affiliation(s)
- Kurt W. Alt
- Center of Natural and Cultural Human History, Danube Private University, 3500 Krems, Austria
- Integrative Prehistory and Archaeological Science, University of Basel, 4055 Basel, Switzerland
| | - Ali Al-Ahmad
- Department of Operative Dentistry and Periodontology, Faculty of Medicine, University of Freiburg, 71906 Freiburg, Germany
| | - Johan Peter Woelber
- Department of Operative Dentistry and Periodontology, Faculty of Medicine, University of Freiburg, 71906 Freiburg, Germany
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14
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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15
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Li C, Lu C, Gong L, Liu J, Kan C, Zheng H, Wang S. SHP2/SPI1axis promotes glycolysis and the inflammatory response of macrophages in Helicobacter pylori-induced pediatric gastritis. Helicobacter 2022; 27:e12895. [PMID: 35437862 DOI: 10.1111/hel.12895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/14/2022] [Accepted: 03/20/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND Macrophages, as innate immune cells, were reported to participate in the pathogenesis of Helicobacter pylori (H. pylori)-induced gastritis. However, the role and mechanism of macrophage dysfunction in H. pylori-associated pediatric gastritis remain unclear. MATERIALS AND METHODS An RNA-sequencing assay was used to examine the differential gene expression in normal gastric antrum, non-H. pylori-infected tissue, and H. pylori-infected pediatric gastritis tissue. qPCR assays were applied to verify the expression of target genes. HE staining was performed to identify the occurrence of inflammation in the normal gastric antrum, non-H. pylori-infected tissue, and H. pylori-infected pediatric gastritis tissue. Western blotting was used to measure the expression of SHP2 in pediatric gastritis tissue. The metabolic profile of macrophages was determined via Seahorse metabolic analysis. Flow cytometry analysis was used to examine the level of reactive oxygen species (ROS). RESULTS We found that H. pylori -infected gastritis tissue exhibited many differentially expressed genes (DEGs) compared to gastritis tissue without H. pylori infection. Moreover, H. pylori -infected gastritis tissue showed many DEGs annotated with an overactive immune response. We identified that tyrosine-protein phosphatase nonreceptor type 11 (PTPN11), which encodes SHP2, was significantly increased in macrophages of H. pylori -infected gastritis tissue. Furthermore, we revealed that SHP2 could activate the glycolytic function of macrophages to promote H. pylori -induced inflammation. The transcription factor SPI1 , as the downstream molecule of SHP2, could be responsible for the regulation of metabolism-associated gene expression and inflammation. CONCLUSION Our study illustrated the molecular landscape of H. pylori-infected gastritis tissue in children and suggested that the SHP2/SPI1axis could be a novel therapeutic target in H. pylori-induced pediatric gastritis.
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Affiliation(s)
- Chuanying Li
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China.,Department of Gastroenterology, Children's Hospital of Anhui Medical University, Hefei, China
| | - Changyun Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Liangju Gong
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Jia Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Chen Kan
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Hong Zheng
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Siying Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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16
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Nishimura L, Fujito N, Sugimoto R, Inoue I. Detection of Ancient Viruses and Long-Term Viral Evolution. Viruses 2022; 14:v14061336. [PMID: 35746807 PMCID: PMC9230872 DOI: 10.3390/v14061336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.
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Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Naoko Fujito
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Correspondence: ; Tel.: +81-55-981-6795
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17
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Yarlagadda K, Zachwieja AJ, de Flamingh A, Phungviwatnikul T, Rivera-Colón AG, Roseman C, Shackelford L, Swanson KS, Malhi RS. Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes. Proc Biol Sci 2022; 289:20220052. [PMID: 35506233 PMCID: PMC9065982 DOI: 10.1098/rspb.2022.0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Canine microbiome studies are often limited in the geographic and temporal scope of samples studied. This results in a paucity of data on the canine microbiome around the world, especially in contexts where dogs may not be pets or human associated. Here, we present the shotgun sequences of fecal microbiomes of pet dogs from South Africa, shelter and stray dogs from India, and stray village dogs in Laos. We additionally performed a dietary experiment with dogs housed in a veterinary medical school, attempting to replicate the diet of the sampled dogs from Laos. We analyse the taxonomic diversity in these populations and identify the underlying functional redundancy of these microbiomes. Our results show that diet alone is not sufficient to recapitulate the higher diversity seen in the microbiome of dogs from Laos. Comparisons to previous studies and ancient dog fecal microbiomes highlight the need for greater population diversity in studies of canine microbiomes, as modern analogues can provide better comparisons to ancient microbiomes. We identify trends in microbial diversity and industrialization in dogs that mirror results of human studies, suggesting future research can make use of these companion animals as substitutes for humans in studying the effects of industrialization on the microbiome.
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Affiliation(s)
- K Yarlagadda
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - A J Zachwieja
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, Minnesota, USA
| | - A de Flamingh
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - T Phungviwatnikul
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - A G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - C Roseman
- School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - L Shackelford
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - K S Swanson
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - R S Malhi
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Department of Evolution, Ecology, and Behavior, University of Illinois Urbana-Champaign, Urbana, IL, USA.,School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
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18
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Bendrey R, Martin D. Zoonotic diseases: New directions in human-animal pathology. INTERNATIONAL JOURNAL OF OSTEOARCHAEOLOGY 2022; 32:548-552. [PMID: 33821116 PMCID: PMC8014110 DOI: 10.1002/oa.2975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
Zoonotic diseases-human diseases of animal origin-represent one of the world's greatest health challenges, both today and in the past. Since the Neolithic, zoonotic diseases have been one of the major factors shaping and influencing human adaptation. Archaeology is ideally situated to provide the long view on human-animal-pathogen relationships through combining cultural, environmental and biological datasets, yet long-term studies of linked human and animal records have often been overlooked and undertheorized. The seven papers in this special issue "Zoonotic diseases: New directions in human-animal pathology" cover a range of diseases caused by bacterial, viral, and parasitic pathogens, from case studies drawn from across Europe, Asia, Africa and the Americas. They speak to the diversity of human-animal-environment interactions that shaped disease emergence and transmission. They also review methodological advancements relating to disease identification and interpretation and discuss interdisciplinary approaches to effectively investigate these complex processes in the past. This introduction highlights their key themes and outcomes and identifies research priorities moving forward.
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Affiliation(s)
- Robin Bendrey
- School of History, Classics and ArchaeologyUniversity of EdinburghEdinburghUK
| | - Debra Martin
- Department of AnthropologyUniversity of NevadaLas VegasUSA
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19
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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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20
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Calvignac-Spencer S, Düx A, Gogarten JF, Patrono LV. Molecular archeology of human viruses. Adv Virus Res 2021; 111:31-61. [PMID: 34663498 DOI: 10.1016/bs.aivir.2021.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The evolution of human-virus associations is usually reconstructed from contemporary patterns of genomic diversity. An intriguing, though still rarely implemented, alternative is to search for the genetic material of viruses in archeological and medical archive specimens to document evolution as it happened. In this chapter, we present lessons from ancient DNA research and incorporate insights from virology to explore the potential range of applications and likely limitations of archeovirological approaches. We also highlight the numerous questions archeovirology will hopefully allow us to tackle in the near future, and the main expected roadblocks to these avenues of research.
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Affiliation(s)
- Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany.
| | - Ariane Düx
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany
| | - Jan F Gogarten
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany
| | - Livia V Patrono
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany
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21
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Kocher A, Papac L, Barquera R, Key FM, Spyrou MA, Hübler R, Rohrlach AB, Aron F, Stahl R, Wissgott A, van Bömmel F, Pfefferkorn M, Mittnik A, Villalba-Mouco V, Neumann GU, Rivollat M, van de Loosdrecht MS, Majander K, Tukhbatova RI, Musralina L, Ghalichi A, Penske S, Sabin S, Michel M, Gretzinger J, Nelson EA, Ferraz T, Nägele K, Parker C, Keller M, Guevara EK, Feldman M, Eisenmann S, Skourtanioti E, Giffin K, Gnecchi-Ruscone GA, Friederich S, Schimmenti V, Khartanovich V, Karapetian MK, Chaplygin MS, Kufterin VV, Khokhlov AA, Chizhevsky AA, Stashenkov DA, Kochkina AF, Tejedor-Rodríguez C, de Lagrán ÍGM, Arcusa-Magallón H, Garrido-Pena R, Royo-Guillén JI, Nováček J, Rottier S, Kacki S, Saintot S, Kaverzneva E, Belinskiy AB, Velemínský P, Limburský P, Kostka M, Loe L, Popescu E, Clarke R, Lyons A, Mortimer R, Sajantila A, de Armas YC, Hernandez Godoy ST, Hernández-Zaragoza DI, Pearson J, Binder D, Lefranc P, Kantorovich AR, Maslov VE, Lai L, Zoledziewska M, Beckett JF, Langová M, Danielisová A, Ingman T, Atiénzar GG, de Miguel Ibáñez MP, Romero A, Sperduti A, Beckett S, Salter SJ, Zilivinskaya ED, Vasil'ev DV, von Heyking K, Burger RL, Salazar LC, Amkreutz L, Navruzbekov M, Rosenstock E, Alonso-Fernández C, Slavchev V, Kalmykov AA, Atabiev BC, Batieva E, Calmet MA, Llamas B, Schultz M, Krauß R, Jiménez-Echevarría J, Francken M, Shnaider S, de Knijff P, Altena E, Van de Vijver K, Fehren-Schmitz L, Tung TA, Lösch S, Dobrovolskaya M, Makarov N, Read C, Van Twest M, Sagona C, Ramsl PC, Akar M, Yener KA, Ballestero EC, Cucca F, Mazzarello V, Utrilla P, Rademaker K, Fernández-Domínguez E, Baird D, Semal P, Márquez-Morfín L, Roksandic M, Steiner H, Salazar-García DC, Shishlina N, Erdal YS, Hallgren F, Boyadzhiev Y, Boyadzhiev K, Küßner M, Sayer D, Onkamo P, Skeates R, Rojo-Guerra M, Buzhilova A, Khussainova E, Djansugurova LB, Beisenov AZ, Samashev Z, Massy K, Mannino M, Moiseyev V, Mannermaa K, Balanovsky O, Deguilloux MF, Reinhold S, Hansen S, Kitov EP, Dobeš M, Ernée M, Meller H, Alt KW, Prüfer K, Warinner C, Schiffels S, Stockhammer PW, Bos K, Posth C, Herbig A, Haak W, Krause J, Kühnert D. Ten millennia of hepatitis B virus evolution. Science 2021; 374:182-188. [PMID: 34618559 DOI: 10.1126/science.abi5658] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Arthur Kocher
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Florian van Bömmel
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Maria Pfefferkorn
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France
| | | | - Kerttu Majander
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Medicine (IEM), University of Zürich, 8057 Zürich, Switzerland
| | - Rezeda I Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russia
| | - Lyazzat Musralina
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Institute of Genetics and Physiology, 050060 Almaty, Kazakhstan
| | - Ayshin Ghalichi
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Megan Michel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joscha Gretzinger
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Departmento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cody Parker
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Arizona State University School of Human Evolution and Social Change, Tempe Arizona, USA
| | - Marcel Keller
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Evelyn K Guevara
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Michal Feldman
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Stefanie Eisenmann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Guido Alberto Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | | | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Marina K Karapetian
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Vladimir V Kufterin
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Andrey A Chizhevsky
- Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan, Russia
| | - Dmitry A Stashenkov
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Anna F Kochkina
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Cristina Tejedor-Rodríguez
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | | | | | - Rafael Garrido-Pena
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Autonomous University of Madrid, Spain
| | | | - Jan Nováček
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany.,University Medical School Göttingen, Institute of Anatomy and Cell Biology, 37075 Göttingen, Germany
| | | | - Sacha Kacki
- Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France.,Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Sylvie Saintot
- INRAP, ARAR UMR 5138, Maison de l'Orient et de la Méditerranée, Lyon, France
| | | | | | - Petr Velemínský
- Department of Anthropology, The National Museum, Prague, Czech Republic
| | - Petr Limburský
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Louise Loe
- Oxford Archaeology South, Janus House, Osney Mead, Oxford, OX2 0ES, UK
| | | | - Rachel Clarke
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | - Alice Lyons
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | | | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.,Forensic Medicine Unit, Finnish Institute of Health and Welfare, Helsinki, Finland
| | | | - Silvia Teresita Hernandez Godoy
- Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.,Universidad de Matanzas, Matanzas, Cuba
| | - Diana I Hernández-Zaragoza
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.,Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Jessica Pearson
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Didier Binder
- Université Côte d'Azur, CNRS, CEPAM UMR 7264, Nice, France
| | - Philippe Lefranc
- Université de Strasbourg, CNRS, Archimède UMR 7044, Strasbourg, France
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Vladimir E Maslov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Luca Lai
- Department of Anthropology, University of South Florida, Tampa, FL, USA.,Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | | | - Michaela Langová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alžběta Danielisová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tara Ingman
- Koç University, Research Center for Anatolian Civilizations, Istanbul 34433, Turkey
| | - Gabriel García Atiénzar
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Maria Paz de Miguel Ibáñez
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Alejandro Romero
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain.,Departamento de Biotecnología, Facultad de Ciencias, Universidad de Alicante, 03690, Alicante, Spain
| | - Alessandra Sperduti
- Bioarchaeology Service, Museum of Civilizations, Rome, Italy.,Dipartimento Asia Africa e Mediterraneo, Università di Napoli L'Orientale, Napoli, Italy
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Melbourne Dental School, University of Melbourne, Victoria 3010 Australia.,Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, College Road, Cranfield, MK43 0AL, UK
| | - Susannah J Salter
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Emma D Zilivinskaya
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Kristin von Heyking
- SNSB, State Collection for Anthropology and Palaeoanatomy, 80333 Munich, Germany
| | - Richard L Burger
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Lucy C Salazar
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Luc Amkreutz
- National Museum of Antiquities, 2301 EC Leiden, Netherlands
| | | | - Eva Rosenstock
- Freie Universität Berlin, Einstein Center Chronoi, 14195 Berlin, Germany
| | | | | | | | - Biaslan Ch Atabiev
- Institute for Caucasus Archaeology, 361401 Nalchik, Republic Kabardino-Balkaria, Russia
| | - Elena Batieva
- Azov History, Archaeology and Palaeontology Museum-Reserve, Azov 346780, Russia
| | | | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia.,Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia.,National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
| | - Michael Schultz
- University Medical School Göttingen, Institute of Anatomy and Embryology, 37075 Göttingen, Germany.,Institute of Biology, University of Hildeshein, Germany
| | - Raiko Krauß
- Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany
| | | | - Michael Francken
- State Office for Cultural Heritage Baden-Württemberg, 78467 Konstanz, Germany
| | - Svetlana Shnaider
- ArchaeoZoology in Siberia and Central Asia-ZooSCAn, CNRS-IAET SB RAS International Research Laboratory, IRL 2013, Novosibirsk, Russia
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Katrien Van de Vijver
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Center for Archaeological Sciences, University of Leuven, Belgium.,Dienst Archeologie-Stad Mechelen, Belgium
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Laboratory, Department of Anthropology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tiffiny A Tung
- Department of Anthropology, Vanderbilt University, Nashville, TN 37235, USA
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Maria Dobrovolskaya
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Nikolaj Makarov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Chris Read
- Applied Archaeology School of Science, Institute of Technology Sligo, Ireland
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK
| | - Claudia Sagona
- School of Historical and Philosophical Studies, University of Melbourne, Victoria 3010, Australia
| | - Peter C Ramsl
- Institute of Prehistoric and Historical Archaeology, University of Vienna, Austria
| | - Murat Akar
- Department of Archaeology, Hatay Mustafa Kemal University, Alahan-Antakya, Hatay 31060, Turkey
| | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY 10028, USA
| | - Eduardo Carmona Ballestero
- Territorial Service of Culture and Tourism from Valladolid, Castilla y León Regional Government, C/ San Lorenzo, 5, 47001, Valladolid, Spain.,Department of History, Geography and Comunication, University of Burgos, Paseo de Comendadores, s/n 09001 Burgos (Burgos), Spain
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica-CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | | | - Pilar Utrilla
- Área de Prehistoria, P3A DGA Research Group, IPH, University of Zaragoza, C/ Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Douglas Baird
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Lourdes Márquez-Morfín
- Osteology Laboratory, Post Graduate Studies Division, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada.,Caribbean Research Institute, Univeristy of Winnipeg, Winnipeg, MB, Canada.,DFG Center for Advanced Studies "Words, Bones, Genes, Tools," University of Tübingen, Tübingen, Germany
| | - Hubert Steiner
- South Tyrol Provincial Heritage Service, South Tyrol, Italy
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Natalia Shishlina
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia.,State Historical Museum, Moscow, Russia
| | - Yilmaz Selim Erdal
- Human_G Laboratory, Department of Anthropology, Hacettepe University, Ankara 06800, Turkey
| | | | - Yavor Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Kamen Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany
| | - Duncan Sayer
- School of Natural Sciences, University of Central Lancashire, Preston, UK
| | - Päivi Onkamo
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland.,Department of Biology, University of Turku, 20500 Turku, Finland
| | - Robin Skeates
- Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Manuel Rojo-Guerra
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Arman Z Beisenov
- Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Zainolla Samashev
- Branch of Institute of Archaeology named after A.Kh. Margulan, 24 of 511 Nur-Sultan, Kazakhstan.,State Historical and Cultural Museum-Reserve "Berel," Katon-Karagay district, East Kazakhstan region, Kazakhstan
| | - Ken Massy
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Marcello Mannino
- Department of Archeology and Heritage Studies, Aarhus University, 8270 Højbjerg, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig Germany
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | | | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Egor P Kitov
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia.,Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Miroslav Dobeš
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Ernée
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | - Kurt W Alt
- Danube Private University, Center of Natural and Cultural Human History, A - 3500 Krems-Stein, Austria.,Integrative Prehistory and Archaeological Science, Spalenring 145, CH-4055 Basel, Switzerland.,Department of Biomedical Engineering (DBE), Universitätsspital Basel (HFZ), CH-4123 Allschwil, Switzerland
| | - Kay Prüfer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,European Virus Bioinformatics Center (EVBC), Jena, Germany
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22
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Boualam MA, Pradines B, Drancourt M, Barbieri R. Malaria in Europe: A Historical Perspective. Front Med (Lausanne) 2021; 8:691095. [PMID: 34277665 PMCID: PMC8277918 DOI: 10.3389/fmed.2021.691095] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/20/2021] [Indexed: 11/15/2022] Open
Abstract
Endemic malaria, which claimed 229 million new cases and 409,000 deaths in 2019 mainly in Africa, was eradicated from Europe by the mid-20th century. Historical descriptions of intermittent tertian and quartan fever reported in texts of Hippocrates in Greece and Celsus in Italy suggest malaria. A few paleomicrobiology investigations have confirmed the presence of malarial parasite Plasmodium falciparum in 1st, 2nd, and 5th century infected individuals in diverse regions of Italy, and Plasmodium sp. later in Bavaria. The causative Plasmodium pathogens, discovered in the 19th century in Algeria, were controversially used as therapeutic agents in the European pharmacopeia more than two centuries after effective quinine-based treatments had been introduced in Europe. How Europe managed to eradicate malaria and what the history of malaria was in Europe are of medical interest, and this review traces research pathways for a renewed understanding of malaria eradication in Europe through combined historical and paleomicrobiological investigations.
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Affiliation(s)
- Mahmoud A. Boualam
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Bruno Pradines
- IHU Méditerranée Infection, Marseille, France
- Unité parasitologie et entomologie, Département microbiologie et maladies infectieuses, Institut de recherche biomédicale des armées, Marseille, France
- Aix-Marseille University, IRD, SSA, AP-HM, VITROME, Marseille, France
- Centre national de référence du paludisme, Marseille, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Rémi Barbieri
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
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23
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Kilgore PB, Sha J, Andersson JA, Motin VL, Chopra AK. A new generation needle- and adjuvant-free trivalent plague vaccine utilizing adenovirus-5 nanoparticle platform. NPJ Vaccines 2021; 6:21. [PMID: 33514747 PMCID: PMC7846801 DOI: 10.1038/s41541-020-00275-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
A plague vaccine with a fusion cassette of YscF, F1, and LcrV encoding genes in an adenovirus-5 vector (rAd5-YFV) is evaluated for efficacy and immune responses in mice. Two doses of the vaccine provides 100% protection when administered intranasally against challenge with Yersinia pestis CO92 or its isogenic F1 mutant in short- or long- term immunization in pneumonic/bubonic plague models. The corresponding protection rates drop in rAd5-LcrV monovalent vaccinated mice in plague models. The rAd5-YFV vaccine induces superior humoral, mucosal and cell-mediated immunity, with clearance of the pathogen. Immunization of mice with rAd5-YFV followed by CO92 infection dampens proinflammatory cytokines and neutrophil chemoattractant production, while increasing Th1- and Th2-cytokine responses as well as macrophage/monocyte chemo-attractants when compared to the challenge control animals. This is a first study showing complete protection of mice from pneumonic/bubonic plague with a viral vector-based vaccine without the use of needles and the adjuvant.
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Affiliation(s)
- Paul B. Kilgore
- grid.176731.50000 0001 1547 9964Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX USA
| | - Jian Sha
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, USA. .,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
| | - Jourdan A. Andersson
- grid.176731.50000 0001 1547 9964Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX USA
| | - Vladimir L. Motin
- grid.176731.50000 0001 1547 9964Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX USA ,grid.176731.50000 0001 1547 9964Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX USA ,grid.176731.50000 0001 1547 9964Department of Pathology, University of Texas Medical Branch, Galveston, TX USA ,grid.176731.50000 0001 1547 9964Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX USA ,grid.176731.50000 0001 1547 9964Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX USA
| | - Ashok K. Chopra
- grid.176731.50000 0001 1547 9964Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX USA ,grid.176731.50000 0001 1547 9964Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX USA ,grid.176731.50000 0001 1547 9964Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX USA ,grid.176731.50000 0001 1547 9964Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX USA
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24
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Barbieri R, Signoli M, Chevé D, Costedoat C, Tzortzis S, Aboudharam G, Raoult D, Drancourt M. Yersinia pestis: the Natural History of Plague. Clin Microbiol Rev 2020; 34:e00044-19. [PMID: 33298527 PMCID: PMC7920731 DOI: 10.1128/cmr.00044-19] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.
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Affiliation(s)
- R Barbieri
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
| | - M Signoli
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - D Chevé
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - C Costedoat
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - S Tzortzis
- Ministère de la Culture, Direction Régionale des Affaires Culturelles de Provence-Alpes-Côte d'Azur, Service Régional de l'Archéologie, Aix-en-Provence, France
| | - G Aboudharam
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, Faculty of Odontology, Marseille, France
| | - D Raoult
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
| | - M Drancourt
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
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25
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Ferrari G, Neukamm J, Baalsrud HT, Breidenstein AM, Ravinet M, Phillips C, Rühli F, Bouwman A, Schuenemann VJ. Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190572. [PMID: 33012235 PMCID: PMC7702794 DOI: 10.1098/rstb.2019.0572] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2020] [Indexed: 12/15/2022] Open
Abstract
Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Helle T. Baalsrud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway
| | - Abagail M. Breidenstein
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Carina Phillips
- The Royal College of Surgeons of England, 35-43 Lincoln's Inn Fields, London WC2A 3PE, UK
| | - Frank Rühli
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Abigail Bouwman
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Verena J. Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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26
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Stone AC, Lewis CM, Schuenemann VJ. Insights into health and disease from ancient biomolecules. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190568. [PMID: 33012226 DOI: 10.1098/rstb.2019.0568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, 455 West Lindsey, Dale Hall Tower 521, Norman, OK 73019, USA
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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27
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Abstract
During the two World Wars, Bartonella quintana was responsible for trench fever and is now recognised as an agent of re-emerging infection. Many reports have indicated widespread B. quintana exposure since the 1990s. In order to evaluate its prevalence in ancient populations, we used real-time PCR to detect B. quintana DNA in 400 teeth collected from 145 individuals dating from the 1st to 19th centuries in nine archaeological sites, with the presence of negative controls. Fisher’s exact test was used to compare the prevalence of B. quintana in civil and military populations. B. quintana DNA was confirmed in a total of 28/145 (19.3%) individuals, comprising 78 citizens and 67 soldiers, 20.1% and 17.9% of which were positive for B. quintana bacteraemia, respectively. This study analysed previous studies on these ancient samples and showed that the presence of B. quintana infection followed the course of time in human history; a total of 14/15 sites from five European countries had a positive prevalence. The positive rate in soldiers was higher than those of civilians, with 20% and 18.8%, respectively, in the 18th and 19th centuries, but the difference in frequency was not significant. These results confirmed the role of dental pulp in diagnosing B. quintana bacteraemia in ancient populations and showed the incidence of B. quintana in both civilians and soldiers.
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28
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Morales-Arce AY, Sabin SJ, Stone AC, Jensen JD. The population genomics of within-host Mycobacterium tuberculosis. Heredity (Edinb) 2020; 126:1-9. [PMID: 33060846 DOI: 10.1038/s41437-020-00377-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 11/09/2022] Open
Abstract
Recent progress in genomic sequencing from patient samples has allowed for the first detailed insight into the within-host genetic diversity of Mycobacterium tuberculosis (M.TB), revealing remarkably low levels of variation. While this has often been attributed to low mutation rates, other factors have been described, including resistance evolution (i.e., selective sweeps), widespread purifying and background selection, and, more recently, progeny skew. Here we review recent findings pertaining to the processes governing the evolutionary dynamics of M.TB, discuss their implications for improving our understanding of this important human pathogen, and make recommendations for future work. Significantly, this emerging evolutionary framework involving the joint estimation of demographic, selective, and reproductive processes is forming a new paradigm for the study of within-host pathogen evolution that will be widely applicable across organisms.
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Affiliation(s)
- Ana Y Morales-Arce
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
| | - Susanna J Sabin
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Jeffrey D Jensen
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA. .,School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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29
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Amadei SS, Notario V. A Significant Question in Cancer Risk and Therapy: Are Antibiotics Positive or Negative Effectors? Current Answers and Possible Alternatives. Antibiotics (Basel) 2020; 9:E580. [PMID: 32899961 PMCID: PMC7558931 DOI: 10.3390/antibiotics9090580] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022] Open
Abstract
Cancer is predominantly considered as an environmental disease caused by genetic or epigenetic alterations induced by exposure to extrinsic (e.g., carcinogens, pollutants, radiation) or intrinsic (e.g., metabolic, immune or genetic deficiencies). Over-exposure to antibiotics, which is favored by unregulated access as well as inappropriate prescriptions by physicians, is known to have led to serious health problems such as the rise of antibiotic resistance, in particular in poorly developed countries. In this review, the attention is focused on evaluating the effects of antibiotic exposure on cancer risk and on the outcome of cancer therapeutic protocols, either directly acting as extrinsic promoters, or indirectly, through interactions with the human gut microbiota. The preponderant evidence derived from information reported over the last 10 years confirms that antibiotic exposure tends to increase cancer risk and, unfortunately, that it reduces the efficacy of various forms of cancer therapy (e.g., chemo-, radio-, and immunotherapy alone or in combination). Alternatives to the current patterns of antibiotic use, such as introducing new antibiotics, bacteriophages or enzybiotics, and implementing dysbiosis-reducing microbiota modulatory strategies in oncology, are discussed. The information is in the end considered from the perspective of the most recent findings on the tumor-specific and intracellular location of the tumor microbiota, and of the most recent theories proposed to explain cancer etiology on the notion of regression of the eukaryotic cells and systems to stages characterized for a lack of coordination among their components of prokaryotic origin, which is promoted by injuries caused by environmental insults.
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Affiliation(s)
| | - Vicente Notario
- Department of Radiation Medicine, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA;
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30
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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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31
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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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32
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Nelson EA, Buikstra JE, Herbig A, Tung TA, Bos KI. Advances in the molecular detection of tuberculosis in pre-contact Andean South America. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2020; 29:128-140. [PMID: 31964606 DOI: 10.1016/j.ijpp.2019.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 12/06/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
Andean paleopathological research has significantly enhanced knowledge about the geographical distribution and evolution of tuberculosis (TB) in pre-Columbian South America. In this paper, we review the history and progress of research on ancient tuberculosis (TB) in the Andean region, focusing on the strengths and limitations of current approaches for the molecular detection of ancient pathogens, with special attention to TB. As a case study, we describe a molecular screening approach for the detection of ancient Mycobacterium tuberculosis in individuals from Late Intermediate Period (1000-1400 CE) contexts at the site of Huari, Peru. We evaluate 34 commingled human vertebrae and combine morphological assessments of pathology with high throughput sequencing and a non-selective approach to ancient pathogen DNA screening. Our method enabled the simultaneous detection of ancient M. tuberculosis DNA and an evaluation of the environmental microbial composition of each sample. Our results show that despite the dominance of environmental DNA, molecular signatures of M. tuberculosis were identified in eight vertebrae, six of which had no observable skeletal pathology classically associated tuberculosis infection. This screening approach will assist in the identification of candidate samples for downstream genomic analyses. The method permits higher resolution disease identification in cases where pathology may be absent, or where the archaeological context may necessitate a broad differential diagnosis based on morphology alone.
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Affiliation(s)
- Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str 10, 07745 Jena, Germany; Eberhard Karls Universität Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany.
| | - Jane E Buikstra
- Center for Bioarchaeological Research, Arizona State University, 1151 S. Forest Ave., Tempe, AZ, 85281, USA.
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str 10, 07745 Jena, Germany.
| | - Tiffiny A Tung
- Department of Anthropology, Vanderbilt University, VU Station B #356050, Nashville, TN 37235, USA.
| | - Kirsten I Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str 10, 07745 Jena, Germany.
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