1
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Umamaheswaran R, Dutta S. Preservation of proteins in the geosphere. Nat Ecol Evol 2024; 8:858-865. [PMID: 38472431 DOI: 10.1038/s41559-024-02366-z] [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: 06/26/2023] [Accepted: 02/13/2024] [Indexed: 03/14/2024]
Abstract
Deep-time protein preservation has attracted increasing interest and rapid research activity within the palaeobiological community in recent years, but there are several different viewpoints without a cohesive framework for the interpretation of these proteins. Therefore, despite this activity, crucial gaps exist in the understanding of how proteins are preserved in the geological record and we believe it is vital to arrive at a synthesis of the various taphonomic pathways in order to proceed forward with their elucidation. Here we take a critical look at the state of knowledge regarding deep-time protein preservation and argue for the necessity of a more nuanced approach to understanding the molecular taphonomy of proteins through the lens of diagenetic pathways. We also propound an initial framework with which to comprehend the chemical changes undergone by proteins via the concept of 'proteagen'.
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Affiliation(s)
- Raman Umamaheswaran
- Department of Earth Sciences, Indian Institute of Technology Bombay, Mumbai, India.
- Department of Earth and Planetary Sciences, Hokkaido University, Sapporo, Japan.
| | - Suryendu Dutta
- Department of Earth Sciences, Indian Institute of Technology Bombay, Mumbai, India.
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2
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Boualam MA, Heitzmann A, Mousset F, Aboudharam G, Drancourt M, Pradines B. Use of rapid diagnostic tests for the detection of ancient malaria infections in dental pulp from the sixth century in Versailles, France. Malar J 2023; 22:151. [PMID: 37161537 PMCID: PMC10169320 DOI: 10.1186/s12936-023-04582-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/03/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Paleomicrobiological data have clarified that Plasmodium spp. was circulating in the past in southern European populations, which are now devoid of malaria. The aim of this study was to evaluate the efficacy of immunodetection and, more particularly, rapid diagnostic tests (RDT), in order to further assess Plasmodium infections in ancient northern European populations. METHODS A commercially available RDT, PALUTOP® + 4 OPTIMA, which is routinely used to detect malaria, was used to detect Plasmodium antigens from proteins recovered from ancient specimens extracted from 39 dental pulp samples. These samples were collected from 39 individuals who were buried in the sixth century, near the site of the current Palace of Versailles in France. Positive and negative controls were also used. Antigens detected were quantified using chemiluminescence imaging system analysis. RESULTS Plasmodium antigens were detected in 14/39 (35.9%) individuals, including Plasmodium vivax antigens in 11 individuals and Plasmodium falciparum antigens co-detected in two individuals, while Pan-Plasmodium antigens were detected in three individuals. Controls all yielded expected results. CONCLUSIONS The data reported here showed that RDTs are a suitable tool for detecting Plasmodium spp. antigens in ancient dental pulp samples, and demonstrated the existence of malaria in Versailles, France, in the sixth century. Plasmodium vivax, which is regarded as being responsible for an attenuated form of malaria and less deadly forms, was the most prevalent species. This illustrates, for the first time in ancient populations, co-infection with P. falciparum, bringing into question the climate-driven ecosystems prevailing at that time in the Versailles area.
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Affiliation(s)
- Mahmoud A Boualam
- IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
- Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Annick Heitzmann
- Direction du Patrimoine et des Jardins, Château de Versailles, Place d'Armes, 78008, Versailles, France
| | - Florence Mousset
- Direction régionale des affaires culturelles d'Île-de-France, Service Régional de l'archéologie, 311 Rue Le Peletier, 75009, Paris, France
| | - Gérard Aboudharam
- IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
- Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Bd Jean Moulin, 13005, Marseille, France
- Ecole de Médecine Dentaire, Aix-Marseille Univ, Bd Jean Moulin, 13005, Marseille, France
| | - Michel Drancourt
- IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
- Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Bruno Pradines
- IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.
- Unité parasitologie et entomologie, Département microbiologie et maladies infectieuses, Institut de recherche biomédicale des armées, 19-21 Bd Jean Moulin, 13005, Marseille, France.
- Aix-Marseille Univ, IRD, SSA, AP-HM, VITROME, 19-21 Bd Jean Moulin, 13005, Marseille, France.
- Centre national de référence du paludisme, 19-21 Bd Jean Moulin, 13005, Marseille, France.
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Duchêne S, Ho SYW, Carmichael AG, Holmes EC, Poinar H. The Recovery, Interpretation and Use of Ancient Pathogen Genomes. Curr Biol 2020; 30:R1215-R1231. [PMID: 33022266 PMCID: PMC7534838 DOI: 10.1016/j.cub.2020.08.081] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biology and engaged considerable public interest. Although most studies of ancient genomes have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of microbial pathogens and microbiomes from ancient and historical human and non-human remains. This coming of age has been made possible by techniques that allow the preferential capture and amplification of discrete genomes from a background of predominantly host and environmental DNA. There are now near-complete ancient genome sequences for three pathogens of considerable historical interest - pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae) - and for three equally important endemic human disease agents - Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy) and Treponema pallidum pallidum (syphilis). Genomic data from these pathogens have extended earlier work by paleopathologists. There have been efforts to sequence the genomes of additional ancient pathogens, with the potential to broaden our understanding of the infectious disease burden common to past populations from the Bronze Age to the early 20th century. In this review we describe the state-of-the-art of this rapidly developing field, highlight the contributions of ancient pathogen genomics to multidisciplinary endeavors and describe some of the limitations in resolving questions about the emergence and long-term evolution of pathogens.
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Affiliation(s)
- Sebastián Duchêne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia.
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L9, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada.
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4
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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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5
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Borówka P, Pułaski Ł, Marciniak B, Borowska-Strugińska B, Dziadek J, Żądzińska E, Lorkiewicz W, Strapagiel D. Screening methods for detection of ancient Mycobacterium tuberculosis complex fingerprints in next-generation sequencing data derived from skeletal samples. Gigascience 2019; 8:5521156. [PMID: 31220249 PMCID: PMC6586198 DOI: 10.1093/gigascience/giz065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/07/2019] [Accepted: 05/10/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Recent advances in ancient DNA studies, especially in increasing isolated DNA yields and quality, have opened the possibility of analysis of ancient host microbiome. However, such pitfalls as spurious identification of pathogens based on fragmentary data or environmental contamination could lead to incorrect epidaemiological conclusions. Within the Mycobacterium genus, Mycobacterium tuberculosis complex members responsible for tuberculosis share up to ∼99% genomic sequence identity, while other more distantly related Mycobacteria other than M. tuberculosis can be causative agents for pulmonary diseases or soil dwellers. Therefore, reliable determination of species complex is crucial for interpretation of sequencing results. RESULTS Here we present a novel bioinformatical approach, used for screening of ancient tuberculosis in sequencing data, derived from 28 individuals (dated 4400-4000 and 3100-2900 BC) from central Poland. We demonstrate that cost-effective next-generation screening sequencing data (∼20M reads per sample) could yield enough information to provide statistically supported identification of probable ancient disease cases. CONCLUSIONS Application of appropriate bioinformatic tools, including an unbiased selection of genomic alignment targets for species specificity, makes it possible to extract valid data from full-sample sequencing results (without subjective targeted enrichment procedures). This approach broadens the potential scope of palaeoepidaemiology both to older, suboptimally preserved samples and to pathogens with difficult intrageneric taxonomy.
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Affiliation(s)
- Paulina Borówka
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland
| | - Łukasz Pułaski
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland.,Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Street, 93-232 Łódź, Poland
| | - Błażej Marciniak
- Biobank Lab, Faculty of Biology and Environmental Protection, Department of Molecular Biophysics, University of Lodz, 14 Pilarskiego Street, 90-231 Łódź, Poland.,BBMRI.pl Consortium, 147 Stabłowicka Street, 54-066 Wrocław, Poland
| | - Beata Borowska-Strugińska
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa Street, 93-232 Łódź, Poland
| | - Elżbieta Żądzińska
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland
| | - Wiesław Lorkiewicz
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha Street, 90-237 Łódź, Poland
| | - Dominik Strapagiel
- Biobank Lab, Faculty of Biology and Environmental Protection, Department of Molecular Biophysics, University of Lodz, 14 Pilarskiego Street, 90-231 Łódź, Poland.,BBMRI.pl Consortium, 147 Stabłowicka Street, 54-066 Wrocław, Poland
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AL-Khafif GD, El-Banna R, Khattab N, Gad Rashed T, Dahesh S. The Immunodetection of Non-Falciparum Malaria in Ancient Egyptian Bones (Giza Necropolis). BIOMED RESEARCH INTERNATIONAL 2018; 2018:9058108. [PMID: 30151391 PMCID: PMC6091407 DOI: 10.1155/2018/9058108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/08/2018] [Indexed: 12/30/2022]
Abstract
The detection of falciparum malaria in ancient Egyptian remains had been performed by many authors using several methodologies including the use of rapid diagnostic tests. Through the immunochromatographic analysis of bony specimens from Giza skeletal collection dated to Old Kingdom, we provide first evidence of non-falciparum malaria in Ancient Egypt. The histidine-rich protein-2 (HRP2) specific to Plasmodium falciparum was absent in 100% of examined samples, while aldolase, common to the four types of plasmodial pathogens causing human malaria, was detected in 56% of individuals with no significant difference between the two tested social groups: high officials (HO) and workers (W). It is suggested that the main risk factor was the presence of residences near natural and artificial waterways, which allowed prolonged contact between the vector and human host.
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Affiliation(s)
- Ghada Darwish AL-Khafif
- Anthropology and Mummy Conservation Lab., Conservation and Research Centre, Ministry of Antiquities, 11521 Cairo, Egypt
| | - Rokia El-Banna
- Biological Anthropology Department, National Research Centre, 12311 Giza, Egypt
| | - Nancy Khattab
- Department of Anthropology, Institute of African Research and Studies, Cairo University, 12613 Giza, Egypt
| | - Tamer Gad Rashed
- Department of Anthropology, Institute of African Research and Studies, Cairo University, 12613 Giza, Egypt
| | - Salwa Dahesh
- Research Institute of Medical Entomology, Ministry of Health, 12619 Giza, Egypt
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7
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Positive Diagnosis of Ancient Leprosy and Tuberculosis Using Ancient DNA and Lipid Biomarkers. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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8
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Abstract
Epidemic typhus caused by Rickettsia prowazekii is one of the oldest pestilential diseases of humankind. The disease is transmitted to human beings by the body louse Pediculus humanus corporis and is still considered a major threat by public health authorities, despite the efficacy of antibiotics, because poor sanitary conditions are conducive to louse proliferation. Epidemic typhus has accompanied disasters that impact humanity and has arguably determined the outcome of more wars than have soldiers and generals. The detection, identification, and characterization of microorganisms in ancient remains by paleomicrobiology has permitted the diagnosis of past epidemic typhus outbreaks through the detection of R. prowazekii. Various techniques, including microscopy and immunodetection, can be used in paleomicrobiology, but most of the data have been obtained by using PCR-based molecular techniques on dental pulp samples. Paleomicrobiology enabled the identification of the first outbreak of epidemic typhus in the 18th century in the context of a pan-European great war in the city of Douai, France, and supported the hypothesis that typhus was imported into Europe by Spanish soldiers returning from America. R. prowazekii was also detected in the remains of soldiers of Napoleon's Grand Army in Vilnius, Lithuania, which indicates that Napoleon's soldiers had epidemic typhus. The purpose of this article is to underscore the modern comprehension of clinical epidemic typhus, focus on the historical relationships of the disease, and examine the use of paleomicrobiology in the detection of past epidemic typhus outbreaks.
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9
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Donoghue HD. Insights gained from ancient biomolecules into past and present tuberculosis—a personal perspective. Int J Infect Dis 2017; 56:176-180. [DOI: 10.1016/j.ijid.2016.11.413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/17/2016] [Accepted: 11/20/2016] [Indexed: 01/24/2023] Open
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10
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Andam CP, Worby CJ, Chang Q, Campana MG. Microbial Genomics of Ancient Plagues and Outbreaks. Trends Microbiol 2016; 24:978-990. [PMID: 27618404 DOI: 10.1016/j.tim.2016.08.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 07/29/2016] [Accepted: 08/16/2016] [Indexed: 01/22/2023]
Abstract
The recent use of next-generation sequencing methods to investigate historical disease outbreaks has provided us with an unprecedented ability to address important and long-standing questions in epidemiology, pathogen evolution, and human history. In this review, we present major findings that illustrate how microbial genomics has provided new insights into the nature and etiology of infectious diseases of historical importance, such as plague, tuberculosis, and leprosy. Sequenced isolates collected from archaeological remains also provide evidence for the timing of historical evolutionary events as well as geographic spread of these pathogens. Elucidating the genomic basis of virulence in historical diseases can provide relevant information on how we can effectively understand the emergence and re-emergence of infectious diseases today and in the future.
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Affiliation(s)
- Cheryl P Andam
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA; University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Durham, NH 03824, USA.
| | - Colin J Worby
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA
| | - Qiuzhi Chang
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA
| | - Michael G Campana
- Smithsonian Conservation Biology Institute, Center for Conservation Genomics, 3001 Connecticut Avenue NW, Washington, DC 20008, USA.
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11
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Abstract
The paleomicrobiology of coprolites, which are fossilized fecal materials, has already yielded data about various organisms, including micro-eukaryotes, bacteria, and archaea, thus expanding our comprehension of ancient human dietary habits, gut microbiota, and intestinal and systemic infections. This mini-review briefly describes previous works and summarizes the main techniques used in handling coprolites and the findings obtained about ancient gut microbiota. Past intestinal and systemic infections are outlined.
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12
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Paleomicrobiology Data: Authentification and Interpretation. Microbiol Spectr 2016; 4. [PMID: 27337456 DOI: 10.1128/microbiolspec.poh-0017-2015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The authenticity of some of the very first works in the field of paleopathology has been questioned, and standards have been progressively established for the experiments and the interpretation of data. Whereas most problems initially arose from the contamination of ancient specimens with modern human DNA, the situation is different in the field of paleomicrobiology, in which the risk for contamination is well-known and adequately managed by any laboratory team with expertise in the routine diagnosis of modern-day infections. Indeed, the exploration of ancient microbiota and pathogens is best done by such laboratory teams, with research directed toward the discovery and implementation of new techniques and the interpretation of data.
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13
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Darling MI, Donoghue HD. Insights from paleomicrobiology into the indigenous peoples of pre-colonial America - a review. Mem Inst Oswaldo Cruz 2016; 109:131-9. [PMID: 24714964 PMCID: PMC4015261 DOI: 10.1590/0074-0276140589] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Indexed: 02/06/2023] Open
Abstract
This review investigates ancient infectious diseases in the Americas dated to the
pre-colonial period and considers what these findings can tell us about the history
of the indigenous peoples of the Americas. It gives an overview, but focuses on four
microbial pathogens from this period: Helicobacter pylori,
Mycobacterium tuberculosis, Trypanosoma cruzi
and Coccidioides immitis, which cause stomach ulceration and gastric
cancer, tuberculosis, Chagas disease and valley fever, respectively. These pathogens
were selected as H. pylori can give insight into ancient human
migrations into the Americas, M. tuberculosis is associated with
population density and urban development, T. cruzi can elucidate
human living conditions and C. immitis can indicate agricultural
development. A range of methods are used to diagnose infectious disease in ancient
human remains, with DNA analysis by polymerase chain reaction one of the most
reliable, provided strict precautions are taken against cross contamination. The
review concludes with a brief summary of the changes that took place after European
exploration and colonisation.
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Affiliation(s)
- Millie I Darling
- Division of Biosciences, Centre for Clinical Microbiology, University College London, London, UK
| | - Helen D Donoghue
- Division of Biosciences, Centre for Clinical Microbiology, University College London, London, UK
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Yang R, Cui Y, Bi Y. Perspectives on Yersinia pestis: A Model for Studying Zoonotic Pathogens. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 918:377-391. [PMID: 27722871 DOI: 10.1007/978-94-024-0890-4_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Yersinia pestis is a typical zoonotic bacterial pathogen. The following reasons make this pathogen a model for studying zoonotic pathogens: (1) Its unique lifestyle makes Y. pestis an ideal model for studying host-vector-environment-pathogen interactions; (2) population diversity characters in Y. pestis render it a model species for studying monomorphic bacterial evolution; (3) the pathogenic features of bacteria provide us with good opportunities to study human immune responses; (4) typical animal and vector models of Y. pestis infection create opportunities for experimental studies on pathogenesis and evolution; and (5) repeated pandemics and local outbreaks provide us with clues about the infectious disease outbreaks that have occurred in human history.
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Affiliation(s)
- Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.
| | - Yujun Cui
- Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China
| | - Yujing Bi
- Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China
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15
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Fournier PE, Drancourt M, Aboudharam G, Raoult D. Paleomicrobiology of Bartonella infections. Microbes Infect 2015; 17:879-83. [PMID: 26369716 DOI: 10.1016/j.micinf.2015.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 11/16/2022]
Abstract
Studying ancient infectious diseases is a challenge, as written contemporary descriptions, when available, are often imprecise and do not allow for accurate discrimination among the pathogens endemic at that time. Paleomicrobiology offers a unique access to the history of these infections by identifying precisely the causative agents. Body louse-transmitted infections are amongst the most epidemic diseases in history, especially in war and famine periods. Of these, Bartonella quintana was detected by suicide PCR in 4000-year-old human remains, thus representing the oldest evidence to date of an arthropod-transmitted infection to human beings. This species has also been detected in human specimens from the 11th to 15th, 18th and 19th centuries. In addition, Bartonella henselae, a cat- and flea-associated pathogen, was detected in cat specimens from the 13th to 18th centuries, therefore demonstrating an association of the bacterium and its reservoir for over 800 years. Therefore, pathogenic Bartonella species have been involved in several outbreaks in the past millennia and should systematically be investigated in human remains from suspected epidemics.
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Affiliation(s)
- Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergents (URMITE), UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France.
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergents (URMITE), UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France
| | - Gérard Aboudharam
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergents (URMITE), UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergents (URMITE), UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France
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Abstract
This article critically reviews the literature on the history of biological warfare, bioterrorism, and biocrimes. The first serious effort to review this entire history, made in 1969, had numerous limitations. In recent decades, several authors have filled many of the gaps in our understanding of the past use of biological agents (including both pathogens and toxins), making it possible to reconstruct that history with greater fidelity than previously possible. Nevertheless, there are numerous remaining gaps, and closer inspection indicates that some supposed uses of biological weapons never took place or are poorly substantiated. Topics requiring additional research are identified.
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Affiliation(s)
- W Seth Carus
- W. Seth Carus, PhD, is Distinguished Research Fellow, Center for the Study of WMD, National Defense University , Ft. McNair, Washington, DC
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17
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Gaul JS, Winter E, Grossschmidt K. Ancient pathogens in museal dry bone specimens: analysis of paleocytology and aDNA. Wien Med Wochenschr 2015; 165:133-9. [PMID: 25994097 DOI: 10.1007/s10354-015-0357-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/16/2015] [Indexed: 11/29/2022]
Abstract
Bone samples investigated in this study derive from the pathologic-anatomical collection of the Natural History Museum of Vienna. In order to explore the survival of treponemes and treponemal ancient DNA in museal dry bone specimens, we analyzed three individuals known to have been infected with Treponema pallidum pallidum. No reproducible evidence of surviving pathogen's ancient DNA (aDNA) was obtained, despite the highly sensitive extraction and amplification techniques (TPP15 and arp). Additionally, decalcification fluid of bone sections was smear stained with May-Gruenwald-Giemsa. The slides were examined using direct light microscope and dark field illumination. Remnants of spirochetal structures were detectable in every smear. Our results demonstrate that aDNA is unlikely to survive, but spirochetal remains are stainable and thus detectable.
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Affiliation(s)
- Johanna Sophia Gaul
- Department of Anthropology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria,
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18
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Fernández-Rodríguez A, Cohen MC, Lucena J, Van de Voorde W, Angelini A, Ziyade N, Saegeman V. How to optimise the yield of forensic and clinical post-mortem microbiology with an adequate sampling: a proposal for standardisation. Eur J Clin Microbiol Infect Dis 2015; 34:1045-57. [PMID: 25680317 DOI: 10.1007/s10096-015-2317-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/07/2015] [Indexed: 11/25/2022]
Abstract
Post-mortem microbiology (PMM) is an important tool in forensic pathology, helping to determine the cause and manner of death, especially in difficult scenarios such as sudden unexpected death (SD). Currently, there is a lack of standardization of PMM sampling throughout Europe. We present recommendations elaborated by a panel of European experts aimed to standardize microbiological sampling in the most frequent forensic and clinical post-mortem situations. A network of forensic microbiologists, pathologists and physicians from Spain, England, Belgium, Italy and Turkey shaped a flexible protocol providing minimal requirements for PMM sampling at four practical scenarios: SD, bioterrorism, tissue and cell transplantation (TCT) and paleomicrobiology. Biosafety recommendations were also included. SD was categorized into four subgroups according to the age of the deceased and circumstances at autopsy: (1) included SD in infancy and childhood (0-16 years); (2) corresponded to SD in the young (17-35 years); (3) comprised SD at any age with clinical symptoms; and (4) included traumatic/iatrogenic SD. For each subgroup, a minimum set of samples and general recommendations for microbiological analyses were established. Sampling recommendations for main bioterrorism scenarios were provided. In the TCT setting, the Belgian sampling protocol was presented as an example. Finally, regarding paleomicrobiology, the sampling selection for different types of human remains was reviewed. This proposal for standardization in the sampling constitutes the first step towards a consensus in PMM procedures. In addition, the protocol flexibility to adapt the sampling to the clinical scenario and specific forensic findings adds a cost-benefit value.
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Affiliation(s)
- A Fernández-Rodríguez
- Forensic Microbiology Laboratory, Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain,
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Ancient pathogen genomics: insights into timing and adaptation. J Hum Evol 2014; 79:137-49. [PMID: 25532802 DOI: 10.1016/j.jhevol.2014.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 09/08/2014] [Accepted: 11/05/2014] [Indexed: 12/15/2022]
Abstract
Disease is a major cause of natural selection affecting human evolution, whether through a sudden pandemic or persistent morbidity and mortality. Recent contributions in the field of ancient pathogen genomics have advanced our understanding of the antiquity and nature of human-pathogen interactions through time. Technical advancements have facilitated the recovery, enrichment, and high-throughput sequencing of pathogen and parasite DNA from archived and archaeological remains. These time-stamped genomes are crucial for calibrating molecular clocks to infer the timing of evolutionary events, while providing finer-grain resolution to phylogenetic reconstructions and complex biogeographical patterns. Additionally, genome scale data allow better identification of substitutions linked to adaptations of the pathogen to their human hosts. As methodology continues to improve, ancient genomes of humans and their diverse microbiomes from a range of eras and archaeological contexts will enable population-level ancient analyses in the near future and a better understanding of their co-evolutionary history.
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Mycolic Acids as Markers of Osseous Tuberculosis in the Neolithic Skeleton from Kujawy Region (Central Poland). ANTHROPOLOGICAL REVIEW 2014. [DOI: 10.2478/anre-2014-0012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
The subject of analysis is the male skeleton from a double burial of the Globular Amphora Culture, derived from the Neolithic site at Brześć Kujawski in Kujawy region (central Poland). Within the spine of the individual advanced lesions are observed (destruction of the vertebral bodies, symptoms of the periostitis in the thoracic region) which are characteristic of skeletal tuberculosis. To check whether the observed morphological changes resulted from infection with Mycobacterium tuberculosis (M.tb), the bone material was tested positively for the presence of mycolic acids, the specific components of the cell wall of pathogenic M.tb bacilli, by mass spectrometry.
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Mehta PK, Raj A, Singh NP, Khuller GK. Detection of potential microbial antigens by immuno-PCR (PCR-amplified immunoassay). J Med Microbiol 2014; 63:627-641. [PMID: 24568881 DOI: 10.1099/jmm.0.070318-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Immuno-PCR (PCR-amplified immunoassay; I-PCR) is a novel ultrasensitive method combining the versatility of ELISA with the sensitivity of nucleic acid amplification of PCR. The enormous exponential amplification power of PCR in an I-PCR assay leads to at least a 10(2)-10(4)-fold increase in sensitivity compared with an analogous ELISA. I-PCR has been used to detect many biological molecules such as proto-oncogenes, toxins, cytokines, hormones, and biomarkers for autoimmune and Alzheimer's diseases, as well as microbial antigens and antibodies, and it can be adapted as a novel diagnostic tool for various infectious and non-infectious diseases. Quantitative real-time I-PCR has the potential to become the most analytically sensitive method for the detection of proteins. The sensitivity and specificity of a real-time I-PCR assay can be enhanced further with the use of magnetic beads and nanoparticles. This review is primarily focused on the detection of potential viral, bacterial and parasitic antigens by I-PCR assay, thus enabling their application for immunological research and for early diagnosis of infectious diseases.
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Affiliation(s)
- Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001 (Haryana), India
| | - Ankush Raj
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001 (Haryana), India
| | - Netra Pal Singh
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001 (Haryana), India
| | - Gopal K Khuller
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh-160014, India
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Raoult D, Mouffok N, Bitam I, Piarroux R, Drancourt M. Plague: history and contemporary analysis. J Infect 2012; 66:18-26. [PMID: 23041039 DOI: 10.1016/j.jinf.2012.09.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 09/26/2012] [Accepted: 09/26/2012] [Indexed: 01/15/2023]
Abstract
Plague has caused ravaging outbreaks, including the Justinian plague and the "black death" in the Middle Ages. The causative agents of these outbreaks have been confirmed using modern molecular tests. The vector of plague during pandemics remains the subject of controversy. Nowadays, plague must be suspected in all areas where plague is endemic in rodents when patients present with adenitis or with pneumonia with a bloody expectorate. Diagnosis is more difficult in the situation of the reemergence of plague, as in Algeria for example, told by the first physician involved in that outbreak (NM). When in doubt, it is preferable to prescribe treatment with doxycycline while waiting for the test results because of the risk of fatality in individuals with plague. The typical bubo is a type of adenitis that is painful, red and nonfluctuating. The diagnosis is simple when microbiological analysis is conducted. Plague is a likely diagnosis when one sees gram-negative bacilli in lymph node aspirate or biopsy samples. Yersinia pestis grows very easily in blood cultures and is easy to identify by biochemical tests and MALDI-TOF mass spectrometry. Pneumonic plague and septicemic plague without adenitis are difficult to diagnose, and these diagnoses are often made by chance or retrospectively when cases are not part of an epidemic or related to another specific epidemiologic context. The treatment of plague must be based on gentamicin or doxycycline. Treatment with one of these antibiotics must be started as soon as plague is suspected. Analysis of past plague epidemics by using modern laboratory tools illustrated the value of epidemic buboes for the clinical diagnosis of plague; and brought new concepts regarding its transmission by human ectoparasites.
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Affiliation(s)
- Didier Raoult
- Aix Marseille Université, Unité des Rickettsies, UMR CNRS, IRD, INSERM, IHU Méditerranée Infection, France.
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Lee OYC, Wu HHT, Donoghue HD, Spigelman M, Greenblatt CL, Bull ID, Rothschild BM, Martin LD, Minnikin DE, Besra GS. Mycobacterium tuberculosis complex lipid virulence factors preserved in the 17,000-year-old skeleton of an extinct bison, Bison antiquus. PLoS One 2012; 7:e41923. [PMID: 22860031 PMCID: PMC3408397 DOI: 10.1371/journal.pone.0041923] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/29/2012] [Indexed: 12/22/2022] Open
Abstract
Tracing the evolution of ancient diseases depends on the availability and accessibility of suitable biomarkers in archaeological specimens. DNA is potentially information-rich but it depends on a favourable environment for preservation. In the case of the major mycobacterial pathogens, Mycobacterium tuberculosis and Mycobacterium leprae, robust lipid biomarkers are established as alternatives or complements to DNA analyses. A DNA report, a decade ago, suggested that a 17,000-year-old skeleton of extinct Bison antiquus, from Natural Trap Cave, Wyoming, was the oldest known case of tuberculosis. In the current study, key mycobacterial lipid virulence factor biomarkers were detected in the same two samples from this bison. Fluorescence high-performance liquid chromatography (HPLC) indicated the presence of mycolic acids of the mycobacterial type, but they were degraded and could not be precisely correlated with tuberculosis. However, pristine profiles of C29, C30 and C32 mycocerosates and C27 mycolipenates, typical of the Mycobacterium tuberculosis complex, were recorded by negative ion chemical ionization gas chromatography mass spectrometry of pentafluorobenzyl ester derivatives. These findings were supported by the detection of C34 and C36 phthiocerols, which are usually esterified to the mycocerosates. The existence of Pleistocene tuberculosis in the Americas is confirmed and there are many even older animal bones with well-characterised tuberculous lesions similar to those on the analysed sample. In the absence of any evidence of tuberculosis in human skeletons older than 9,000 years BP, the hypothesis that this disease evolved as a zoonosis, before transfer to humans, is given detailed consideration and discussion.
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Affiliation(s)
- Oona Y-C. Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Houdini H. T. Wu
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Helen D. Donoghue
- Centre for Clinical Microbiology (M9), Royal Free Campus, University College London, London, United Kingdom
- Centre for the History of Medicine, University College London, London, United Kingdom
| | - Mark Spigelman
- Centre for Clinical Microbiology (M9), Royal Free Campus, University College London, London, United Kingdom
- Kuvin Center for the Study of Infectious and Tropical Diseases and Ancient DNA, Hadassah Medical School, Hebrew University, Jerusalem, Israel
| | - Charles L. Greenblatt
- Kuvin Center for the Study of Infectious and Tropical Diseases and Ancient DNA, Hadassah Medical School, Hebrew University, Jerusalem, Israel
| | - Ian D. Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Bruce M. Rothschild
- Department of Medicine, Northeast Ohio Medical University, Rootstown, Ohio, United States of America
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Larry D. Martin
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - David E. Minnikin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- * E-mail:
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Nerlich AG, Bianucci R, Trisciuoglio A, Schönian G, Ball M, Giuffra V, Bachmeier B, Pusch CM, Ferroglio E, Fornaciari G. Visceral Leishmaniasis during Italian Renaissance, 1522-1562. Emerg Infect Dis 2012; 18:184-6. [PMID: 22257739 PMCID: PMC3310084 DOI: 10.3201/eid1801.102001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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