1
|
Zuckerman MK, Hofman CA. Lessons from ancient pathogens. Science 2024; 385:490-492. [PMID: 39088602 DOI: 10.1126/science.adk0584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
Ancient infectious diseases and microbes can be used to address contemporary disease.
Collapse
Affiliation(s)
- Molly K Zuckerman
- Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Mississippi State, MS, USA
- Cobb Institute of Archaeology, Mississippi State University, Mississippi State, MS, USA
- The Department of Anthropology, National Museum of Natural History, Washington, DC, USA
| | - Courtney A Hofman
- Cobb Institute of Archaeology, Mississippi State University, Mississippi State, MS, USA
- The Department of Anthropology, National Museum of Natural History, Washington, DC, USA
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
| |
Collapse
|
2
|
Gröschel MI, Pérez-Llanos FJ, Diel R, Vargas R, Escuyer V, Musser K, Trieu L, Meissner JS, Knorr J, Klinkenberg D, Kouw P, Homolka S, Samek W, Mathema B, van Soolingen D, Niemann S, Ahuja SD, Farhat MR. Differential rates of Mycobacterium tuberculosis transmission associate with host-pathogen sympatry. Nat Microbiol 2024:10.1038/s41564-024-01758-y. [PMID: 39090390 DOI: 10.1038/s41564-024-01758-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 06/12/2024] [Indexed: 08/04/2024]
Abstract
Several human-adapted Mycobacterium tuberculosis complex (Mtbc) lineages exhibit a restricted geographical distribution globally. These lineages are hypothesized to transmit more effectively among sympatric hosts, that is, those that share the same geographical area, though this is yet to be confirmed while controlling for exposure, social networks and disease risk after exposure. Using pathogen genomic and contact tracing data from 2,279 tuberculosis cases linked to 12,749 contacts from three low-incidence cities, we show that geographically restricted Mtbc lineages were less transmissible than lineages that have a widespread global distribution. Allopatric host-pathogen exposure, in which the restricted pathogen and host are from non-overlapping areas, had a 38% decrease in the odds of infection among contacts compared with sympatric exposures. We measure tenfold lower uptake of geographically restricted lineage 6 strains compared with widespread lineage 4 strains in allopatric macrophage infections. We conclude that Mtbc strain-human long-term coexistence has resulted in differential transmissibility of Mtbc lineages and that this differs by human population.
Collapse
Affiliation(s)
- Matthias I Gröschel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Francy J Pérez-Llanos
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- West German Genome Center, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Human Genetics, The University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Roland Diel
- Institute for Epidemiology, University Medical Hospital Schleswig-Holstein, Kiel, Germany
- Lungenclinic Grosshansdorf, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Vincent Escuyer
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Kimberlee Musser
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Lisa Trieu
- New York City Department of Health and Mental Hygiene, New York, NY, USA
| | | | - Jillian Knorr
- New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Don Klinkenberg
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Peter Kouw
- Department of Tuberculosis, Public Health Service, Amsterdam, The Netherlands
| | - Susanne Homolka
- Diagnostic Mycobacteriology, National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Wojciech Samek
- Department of Electrical Engineering and Computer Science, Technical University Berlin, Berlin, Germany
- Department of Artificial Intelligence, Fraunhofer Heinrich Hertz Institute, Berlin, Germany
| | - Barun Mathema
- Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Dick van Soolingen
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Shama Desai Ahuja
- New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA.
| |
Collapse
|
3
|
Srivatsav AT, Liang K, Jaworek MW, Dong W, Matsuo T, Grélard A, Peters J, Winter R, Duan M, Kapoor S. Residual Membrane Fluidity in Mycobacterial Cell Envelope Layers under Extreme Conditions Underlines Membrane-Centric Adaptation. J Phys Chem B 2024; 128:6838-6852. [PMID: 38960927 DOI: 10.1021/acs.jpcb.4c02469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
One of the routes for adaptation to extreme environments is via remodeling of cell membrane structure, composition, and biophysical properties rendering a functional membrane. Collective studies suggest some form of membrane feedback in mycobacterial species that harbor complex lipids within the outer and inner cell wall layers. Here, we study the homeostatic membrane landscape of mycobacteria in response to high hydrostatic pressure and temperature triggers using high pressure fluorescence, mass and infrared spectroscopies, NMR, SAXS, and molecular dynamics simulations. Our findings reveal that mycobacterial membrane possesses unique and lipid-specific pressure-induced signatures that attenuate progression to highly ordered phases. Both inner and outer membrane layers exhibit phase coexistence of nearly identical lipid phases keeping residual fluidity over a wide range of temperature and pressure, but with different sensitivities. Lipidomic analysis of bacteria grown under pressure revealed lipidome remodeling in terms of chain length, unsaturation, and specific long-chained characteristic mycobacterial lipids, rendering a fluid bacterial membrane. These findings could help understand how bacteria may adapt to a broad spectrum of harsh environments by modulating their lipidome to select lipids that enable the maintenance of a fluid functional cell envelope.
Collapse
Affiliation(s)
- Aswin T Srivatsav
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Kuan Liang
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Michel W Jaworek
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Dortmund D-44227, Germany
| | - Wanqian Dong
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Tatsuhito Matsuo
- University of Grenoble Alpes, CNRS, LIPhy, Grenoble 38044, France
- Institut Laue Langevin, Grenoble F-38042, Cedex 9, France
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Axelle Grélard
- Université de Bordeaux, CNRS, Bordeaux INP, Institut de Chimie & Biologie des Membranes & des Nano-objets, UMR5248, Institut Européen de Chimie et Biologie, Pessac F-33607, France
| | - Judith Peters
- University of Grenoble Alpes, CNRS, LIPhy, Grenoble 38044, France
- Institut Laue Langevin, Grenoble F-38042, Cedex 9, France
- Institut Universitaire de France (IUF), UFR de PhITEM, CS 10090, Grenoble 38044, France
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Dortmund D-44227, Germany
| | - Mojie Duan
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8528, Japan
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Duffy SC, Marais B, Kapur V, Behr MA. Zoonotic tuberculosis in the 21st century. THE LANCET. INFECTIOUS DISEASES 2024; 24:339-341. [PMID: 38307096 DOI: 10.1016/s1473-3099(24)00059-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Affiliation(s)
- Shannon C Duffy
- Department of Microbiology and Immunology, McGill University, Montreal, QC H4A 3J1, Canada; McGill International TB Centre, McGill University, Montreal, QC H4A 3J1, Canada; The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Ben Marais
- Sydney Infectious Diseases Institute, University of Sydney, NSW, Australia
| | - Vivek Kapur
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, QC H4A 3J1, Canada; McGill International TB Centre, McGill University, Montreal, QC H4A 3J1, Canada; Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada; The Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
| |
Collapse
|
6
|
Orgeur M, Sous C, Madacki J, Brosch R. Evolution and emergence of Mycobacterium tuberculosis. FEMS Microbiol Rev 2024; 48:fuae006. [PMID: 38365982 PMCID: PMC10906988 DOI: 10.1093/femsre/fuae006] [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: 11/09/2023] [Revised: 01/12/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases in human history, prevailing even in the 21st century. The causative agents of TB are represented by a group of closely related bacteria belonging to the Mycobacterium tuberculosis complex (MTBC), which can be subdivided into several lineages of human- and animal-adapted strains, thought to have shared a last common ancestor emerged by clonal expansion from a pool of recombinogenic Mycobacterium canettii-like tubercle bacilli. A better understanding of how MTBC populations evolved from less virulent mycobacteria may allow for discovering improved TB control strategies and future epidemiologic trends. In this review, we highlight new insights into the evolution of mycobacteria at the genus level, describing different milestones in the evolution of mycobacteria, with a focus on the genomic events that have likely enabled the emergence and the dominance of the MTBC. We also review the recent literature describing the various MTBC lineages and highlight their particularities and differences with a focus on host preferences and geographic distribution. Finally, we discuss on putative mechanisms driving the evolution of tubercle bacilli and mycobacteria in general, by taking the mycobacteria-specific distributive conjugal transfer as an example.
Collapse
Affiliation(s)
- Mickael Orgeur
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Camille Sous
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Jan Madacki
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Unit for Human Evolutionary Genetics, 75015 Paris, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| |
Collapse
|
7
|
Harrison LB, Kapur V, Behr MA. An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows. Microb Genom 2024; 10:001165. [PMID: 38175684 PMCID: PMC10868604 DOI: 10.1099/mgen.0.001165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Reference-based alignment of short-reads is a widely used technique in genomic analysis of the Mycobacterium tuberculosis complex (MTBC) and the choice of reference sequence impacts the interpretation of analyses. The most widely used reference genomes include the ATCC type strain (H37Rv) and the putative MTBC ancestral sequence of Comas et al. both of which are based on a lineage 4 sequence. As such, these reference sequences do not capture all of the structural variation known to be present in the ancestor of the MTBC. To better represent the base of the MTBC, we generated an imputed ancestral genomic sequence, termed MTBC0 from reference-free alignments of closed MTBC genomes. When used as a reference sequence in alignment workflows, MTBC0 mapped more short sequencing reads and called more pairwise SNPs relative to the Comas et al. sequence while exhibiting minimal impact on the overall phylogeny of MTBC. The results also show that MTBC0 provides greater fidelity in capturing genomic variation and allows for the inclusion of regions absent from H37Rv in standard MTBC workflows without additional steps. The use of MTBC0 as an ancestral reference sequence in standard workflows modestly improved read mapping, SNP calling and intuitively facilitates the study of structural variation and evolution in MTBC.
Collapse
Affiliation(s)
- Luke B. Harrison
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
- Bacterial Symbionts Evolution, INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec H7V 1B7, Canada
| | - Vivek Kapur
- Department of Animal Science, The Pennsylvania State University, State College, PA 16802-3500, USA
| | - Marcel A. Behr
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec H4A 3S5, Canada
| |
Collapse
|
8
|
Alba P, Caprioli A, Cocumelli C, Eleni C, Diaconu EL, Donati V, Ianzano A, Sorbara L, Stravino F, Cerini N, Boniotti MB, Zanoni M, Franco A, Battisti A. Genomics insights into a Mycobacterium pinnipedii isolate causing tuberculosis in a captive South American sea lion ( Otaria flavescens) from Italy. Front Microbiol 2023; 14:1303682. [PMID: 38188565 PMCID: PMC10768177 DOI: 10.3389/fmicb.2023.1303682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Tuberculosis (TB) affects humans and other animals, and it is caused by bacteria within the Mycobacterium tuberculosis complex (MTBC). In this study, we report the characterisation of Mycobacterium pinnipedii that caused a TB case in a sea lion (Otaria flavescens) kept in an Italian zoo. The animal died due to severe, progressive disorders involving the respiratory and gastro-enteric systems and the skin. At necropsy, typical gross lesions referable to a TB generalised form were found. In particular, nodular granulomatous lesions were detected in the lungs and several lymph nodes, and colonies referable to Mycobacterium spp. were isolated from lung, mesenteric, and mediastinal lymph nodes. The isolate was identified by PCR as a MTBC, had a spoligotype SB 1480 ("seal lineage"), and was characterised and characterised by whole-genome sequencing analysis confirming that the MTBC involved was M. pinnipedii. The analysis of the resistome and virulome indicated the presence of macrolide and aminoglycoside resistance genes intrinsic in M. tuberculosis [erm-37 and aac(2')-Ic] and confirmed the presence of the region of difference 1 (RD1), harbouring the esxA and esxB virulence genes, differently from its closest taxon, M. microti. As for other MTCB members, M. pinnipedii infection can spill over into non-pinniped mammalian species; therefore, zoological gardens, veterinary practitioners, and public health officers should be aware of the hazard posed by tuberculosis from marine mammals. Since the isolate under study, as well as all available genomes of M. pinnipedii investigated in this study retains almost all the M. tuberculosis virulence genes, it could indeed cause infection, lesions, and disease in other animal species, including humans.
Collapse
Affiliation(s)
- Patricia Alba
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Andrea Caprioli
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Cristiano Cocumelli
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Claudia Eleni
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Elena Lavinia Diaconu
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Valentina Donati
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Angela Ianzano
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Luigi Sorbara
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Fiorentino Stravino
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Natalino Cerini
- Azienda Sanitaria Locale Roma 6, Servizi Veterinari, Rome, Italy
| | | | - Mariagrazia Zanoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, Brescia, Italy
| | - Alessia Franco
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| | - Antonio Battisti
- Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Rome, Italy
| |
Collapse
|
9
|
Duchene S. Tracing the origin of virulence. Science 2023; 382:1245-1246. [PMID: 38096277 DOI: 10.1126/science.adl6094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Microbial genomes from ancient chickens uncover the drivers of pathogenicity.
Collapse
Affiliation(s)
- Sebastian Duchene
- Department of Computational Biology, Institut Pasteur, Paris, France
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| |
Collapse
|
10
|
Jäger HY, Atz Zanotelli D, Maixner F, Nicklisch N, Alt KW, Meller H, Pap I, Szikossy I, Pálfi G, Zink AR. Hit or miss - A metagenomic evaluation of intra-bone variability of host pathogen load in tuberculosis-infected human remains. Tuberculosis (Edinb) 2023; 143S:102392. [PMID: 38012935 DOI: 10.1016/j.tube.2023.102392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 11/29/2023]
Abstract
Many sampling protocols have been established to successfully retrieve human DNA from archaeological remains, however the systematic detection of ancient pathogens remains challenging. Here, we present a first assessment of the intra-bone variability of metagenomic composition in human skeletal remains and its effect on the sampling success for Mycobacterium tuberculosis (MTB) and human endogenous DNA. For this purpose, four bone samples from published peer-reviewed studies with PCR-based evidence for ancient MTB DNA were selected. Two bone samples of a Neolithic individual from Halberstadt, Germany and two ribs of two 18th-century Hungarian church mummies were sampled at multiple locations for equal amounts, followed by DNA extraction and library construction. Shotgun sequencing data was generated for taxonomic profiling as well as quantitative and qualitative evaluation of MTB and human endogenous DNA. Despite low variance in microbial diversity within and across samples, intra-bone variability of up to 36.45- and 62.88-fold for authentic ancient MTB and human reads, respectively, was detected. This study demonstrates the variable sampling success for MTB and human endogenous DNA within single skeletal samples despite relatively consistent microbial composition and highlights how a multisampling approach can facilitate the detection of hotspots with highly concentrated pathogen and human endogenous DNA.
Collapse
Affiliation(s)
- Heidi Y Jäger
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Daniel Atz Zanotelli
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Nicole Nicklisch
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria; State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany.
| | - Kurt W Alt
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria; State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany.
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany.
| | - Ildikó Pap
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary; Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika Tér 2-6, Hungary; Department of Biological Anthropology, Eötvös Loránd University, Faculty of Science, 1117, Budapest, Pázmány Péter Sétány 1/c, Hungary.
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika Tér 2-6, Hungary; Department of Biological Anthropology, Eötvös Loránd University, Faculty of Science, 1117, Budapest, Pázmány Péter Sétány 1/c, Hungary.
| | - György Pálfi
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary.
| | - Albert R Zink
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| |
Collapse
|
11
|
Zink A, Maixner F, Jäger HY, Szikossy I, Pálfi G, Pap I. Tuberculosis in mummies - New findings, perspectives and limitations. Tuberculosis (Edinb) 2023; 143S:102371. [PMID: 38012931 DOI: 10.1016/j.tube.2023.102371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 06/29/2023] [Accepted: 07/02/2023] [Indexed: 11/29/2023]
Abstract
The molecular analysis of ancient pathogen DNA represents a unique opportunity for the study of infectious diseases in ancient human remains. Among other diseases, paleogenetic studies have been successful in detecting tuberculous DNA in ancient human remains. In the beginning of ancient DNA (aDNA) studies, the presence of tuberculosis (TB) DNA was assessed using a PCR-based assay targeting specific regions of the Mycobacterium tuberculosis (MTB) complex, such as the repetitive element IS6110. The advent of high-throughput sequencing has enabled the reconstruction of full ancient TB genomes in the field of paleomicrobiology. However, despite the numerous paleopathological and PCR-based studies on the presence of tuberculosis in historic human remains, full genome wide reconstructions are still limited to well-preserved specimens with low environmental contamination and connected with extensive screening efforts. This has led to some controversies regarding the evolutionary history of its causative agent Mycobacterium tuberculosis. In this context, mummies have been shown to be a good source for the detection of MTB complex DNA due to a low exposure to environmental influences and the overall good state of preservation of hard and soft tissues in the human remains. Here, we present the major findings on the presence of TB infections in the 18th century naturally mummified human remains from Vác, Hungary and the current status of the detection of MTB complex DNA in mummified human remains. The future perspectives of detecting tuberculosis in mummies will be discussed in the light of methodological aspects, as well as ethical and curational challenges.
Collapse
Affiliation(s)
- Albert Zink
- Institute for Mummy Studies, Eurac Research, Bolzano, Italy.
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, Bolzano, Italy
| | | | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - György Pálfi
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary; Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary; Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| |
Collapse
|
12
|
Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
Collapse
Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Ávila-Arcos MC, Raghavan M, Schlebusch C. Going local with ancient DNA: A review of human histories from regional perspectives. Science 2023; 382:53-58. [PMID: 37797024 DOI: 10.1126/science.adh8140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.
Collapse
Affiliation(s)
- María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Maanasa Raghavan
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa
- SciLifeLab, Uppsala, Sweden
| |
Collapse
|
15
|
Klever AM, Alexander KA, Almeida D, Anderson MZ, Ball RL, Beamer G, Boggiatto P, Buikstra JE, Chandler B, Claeys TA, Concha AE, Converse PJ, Derbyshire KM, Dobos KM, Dupnik KM, Endsley JJ, Endsley MA, Fennelly K, Franco-Paredes C, Hagge DA, Hall-Stoodley L, Hayes D, Hirschfeld K, Hofman CA, Honda JR, Hull NM, Kramnik I, Lacourciere K, Lahiri R, Lamont EA, Larsen MH, Lemaire T, Lesellier S, Lee NR, Lowry CA, Mahfooz NS, McMichael TM, Merling MR, Miller MA, Nagajyothi JF, Nelson E, Nuermberger EL, Pena MT, Perea C, Podell BK, Pyle CJ, Quinn FD, Rajaram MVS, Mejia OR, Rothoff M, Sago SA, Salvador LCM, Simonson AW, Spencer JS, Sreevatsan S, Subbian S, Sunstrum J, Tobin DM, Vijayan KKV, Wright CTO, Robinson RT. The Many Hosts of Mycobacteria 9 (MHM9): A conference report. Tuberculosis (Edinb) 2023; 142:102377. [PMID: 37531864 PMCID: PMC10529179 DOI: 10.1016/j.tube.2023.102377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023]
Abstract
The Many Hosts of Mycobacteria (MHM) meeting series brings together basic scientists, clinicians and veterinarians to promote robust discussion and dissemination of recent advances in our knowledge of numerous mycobacterial diseases, including human and bovine tuberculosis (TB), nontuberculous mycobacteria (NTM) infection, Hansen's disease (leprosy), Buruli ulcer and Johne's disease. The 9th MHM conference (MHM9) was held in July 2022 at The Ohio State University (OSU) and centered around the theme of "Confounders of Mycobacterial Disease." Confounders can and often do drive the transmission of mycobacterial diseases, as well as impact surveillance and treatment outcomes. Various confounders were presented and discussed at MHM9 including those that originate from the host (comorbidities and coinfections) as well as those arising from the environment (e.g., zoonotic exposures), economic inequality (e.g. healthcare disparities), stigma (a confounder of leprosy and TB for millennia), and historical neglect (a confounder in Native American Nations). This conference report summarizes select talks given at MHM9 highlighting recent research advances, as well as talks regarding the historic and ongoing impact of TB and other infectious diseases on Native American Nations, including those in Southwestern Alaska where the regional TB incidence rate is among the highest in the Western hemisphere.
Collapse
Affiliation(s)
- Abigail Marie Klever
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Kathleen A Alexander
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA, USA; CARACAL/Chobe Research Institute Kasane, Botswana
| | - Deepak Almeida
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, MD, USA
| | - Matthew Z Anderson
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA; Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Gillian Beamer
- Host Pathogen Interactions and Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Paola Boggiatto
- Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Jane E Buikstra
- Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA
| | - Bruce Chandler
- Division of Public Health, Alaska Department of Health, AK, USA
| | - Tiffany A Claeys
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Aislinn E Concha
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Paul J Converse
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, MD, USA
| | - Keith M Derbyshire
- Division of Genetics, The Wadsworth Center, New York State Department of Health, Albany, NY, USA; Department of Biomedical Sciences, University at Albany, Albany, NY, USA
| | - Karen M Dobos
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA
| | - Kathryn M Dupnik
- Center for Global Health, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Janice J Endsley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Mark A Endsley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Kevin Fennelly
- Pulmonary Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | - Carlos Franco-Paredes
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA; Hospital Infantil de México Federico Gómez, México, USA
| | | | - Luanne Hall-Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Don Hayes
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Courtney A Hofman
- Department of Anthropology, University of Oklahoma, Norman, OK, USA; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA
| | - Jennifer R Honda
- Department of Cellular and Molecular Biology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Natalie M Hull
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Igor Kramnik
- Pulmonary Center, The Department of Medicine, Boston University Chobanian & Aveedisian School of Medicine, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Karen Lacourciere
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Ramanuj Lahiri
- United States Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen's Disease Program, Baton Rouge, LA, USA
| | - Elise A Lamont
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Michelle H Larsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Sandrine Lesellier
- French Agency for Food, Environmental & Occupational Health & Safety (ANSES), Laboratory for Rabies and Wildlife,Nancy, France
| | - Naomi R Lee
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ, USA
| | - Christopher A Lowry
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Najmus S Mahfooz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Temet M McMichael
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Marlena R Merling
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Michele A Miller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jyothi F Nagajyothi
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Elizabeth Nelson
- Microbial Paleogenomics Unit, Dept of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Eric L Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, MD, USA
| | - Maria T Pena
- United States Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen's Disease Program, Baton Rouge, LA, USA
| | - Claudia Perea
- Animal & Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Brendan K Podell
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA
| | - Charlie J Pyle
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, USA; Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Fred D Quinn
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Murugesan V S Rajaram
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Oscar Rosas Mejia
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | | | - Saydie A Sago
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Liliana C M Salvador
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Andrew W Simonson
- Department of Microbiology and Molecular Genetics and the Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John S Spencer
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA
| | - Srinand Sreevatsan
- Pathobiology & Diagnostic Investigation Department, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Selvakumar Subbian
- Public Health Research Institute (PHRI), New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | | | - David M Tobin
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, USA; Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - K K Vidya Vijayan
- Department of Microbiology and Immunology, Center for AIDS Research, and Children's Research Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caelan T O Wright
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Richard T Robinson
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA.
| |
Collapse
|
16
|
Abstract
This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens.
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Charlier P, Bourdin V. Evidence of Cushing's syndrome in a pre-Columbian Mexican statue? ANNALES D'ENDOCRINOLOGIE 2022; 83:475-478. [PMID: 36183806 DOI: 10.1016/j.ando.2022.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/22/2022] [Accepted: 09/05/2022] [Indexed: 01/03/2023]
Abstract
INTRODUCTION In the absence of skeletons or written narrations, information about diseases in past societies may be acquired from icono-diagnosis. From the observation of a masterpiece presenting pathological features, we tried to make retrospective diagnosis. MATERIAL AND METHOD A pre-Columbian Mexican statuette originating from the Chupicuaro culture and dated 600 BC to 200 AD - conserved in the Louvre Museum in Paris (Section of the quai Branly - Jacques Chirac museum) was examined; it was found to display a huge spinal curvature with excessive dorsal kyphosis and obesity. RESULTS The appearance of the figurine with large head, shortened stature and limbs, may suggest a form of dwarfism; however, many statuettes in the Chupicuaro culture were found displaying large head and relatively short limbs, suggesting that these pictorial features are more of an artistic style. On the contrary, uncommon kyphosis and obesity led us to diagnose a case of either Pott disease associated with neuro-endocrine complications, or of Cushing's disease. CONCLUSION Although icono-diagnosis could have allowed us to contribute to the health mapping of ancient Americas and propose the presence of complicated tuberculosis in central Mexico between 600 BC and 200 AD, we believe "Choupi" portrays here an individual having suffered from hypercortisolism (Cushing's disease). Even though considerations related to cultural and artistic context may constitute limitations to interpretation, iconotopsy/iconodiagnosis are important for a better description of the natural history of diseases, as a complement to morphological analyses of human remains (paleopathology) and laboratory exams (DNA or immunology testing).
Collapse
Affiliation(s)
- Philippe Charlier
- Laboratoire anthropologie, archéologie, biologie (LAAB), université Paris-Saclay (UVSQ), UFR des sciences de la santé, 2, avenue de la source de la Bièvre, 78180 Montigny-le-Bretonneux, France; Direction département de la recherche et de l'enseignement, musée du quai Branly - Jacques Chirac, 222, rue de l'Université, 75007 Paris, France; Fondation Anthropologie, Archéologie, Biologie (FAAB) - Institut de France, Palais de l'Institut, 23 quai de Conti, 75006 Paris, France.
| | - Virginie Bourdin
- Laboratoire anthropologie, archéologie, biologie (LAAB), université Paris-Saclay (UVSQ), UFR des sciences de la santé, 2, avenue de la source de la Bièvre, 78180 Montigny-le-Bretonneux, France; Direction département de la recherche et de l'enseignement, musée du quai Branly - Jacques Chirac, 222, rue de l'Université, 75007 Paris, France.
| |
Collapse
|