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Charlier P, Augias A, Weil R, Bouchet F, Poupon J, Popescu MS, Decloquement P, Azza S, Angelakis E, Richardin P, Colson P, Dubourg G, Million M, Raoult D. Scurvy complicated with Capnocytophaga sputigena sepsis as a possible cause of death of king Saint-Louis of France (1270 AD). Microb Pathog 2023; 185:106399. [PMID: 37884212 DOI: 10.1016/j.micpath.2023.106399] [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: 09/03/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023]
Abstract
The cause of death of Saint-Louis is not known, but recent findings indicated that he presented scurvy and inflammatory jaw disease, which has been associated with infection by oral commensals. Here, we have the exceptional opportunity to analyze the relics of the viscera of King Saint-Louis. A 4.3 g sample from the viscera relics of King Saint-Louis conserved in Versailles' cathedral was subjected to radiocarbon dating, electronic and optic microscopy, and elementary, palynological, molecular, proteomics and microbiological analyses including specific PCR and v3v4 16 S rRNA gene amplification prior to large-scale sequencing using an Illumina MiSeq instrument. The measured radiocarbon age was Cal 1290 CE-1400, which was compatible with that of the viscera of St Louis viscera, considering the addition of lime, incense and vegetables within the human organs. Elemental and palynological analyses confirmed a medieval embalming process. Proteomics analysis identified mainly human muscle and blood proteins. Specific PCR for plague, amoebiasis, shigellosis and typhoid fever was negative. C. sputigena was identified as the main pathogenic species representing 10.8 % of all microbial sequences. In contrast, C. sputigena was found in only 0.001 % of samples sequenced in our center, and the 23 positive human samples showed a dramatically lower abundance (0.02-2.6 %). In the literature, human infections with C. sputigena included odontitis, dental abscess, sinusitis, thoracic infections and bacteremia, particularly in immunocompromised patients with oral and dental diseases consistent with recent analysis of King Saint-Louis' jaw. C. sputigena, a commensal of the mouth that is potentially pathogenic and responsible for fatal bacteremia, may have been the cause of the king's death.
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Affiliation(s)
- Philippe Charlier
- Laboratory Anthropology, Archaeology, Biology (LAAB), UFR of Health Sciences (UVSQ), Paris-Saclay University, 2 Avenue de La Source de La Bièvre, 78180, Montigny-Le-Bretonneux, France; Museum of 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.
| | - Anaïs Augias
- Laboratory Anthropology, Archaeology, Biology (LAAB), UFR of Health Sciences (UVSQ), Paris-Saclay University, 2 Avenue de La Source de La Bièvre, 78180, Montigny-Le-Bretonneux, France
| | - Raphaël Weil
- Laboratory Anthropology, Archaeology, Biology (LAAB), UFR of Health Sciences (UVSQ), Paris-Saclay University, 2 Avenue de La Source de La Bièvre, 78180, Montigny-Le-Bretonneux, France; Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris-Saclay, Orsay, Cedex, 91405, France
| | - Françoise Bouchet
- Académie Nationale de Pharmacie, Avenue de L'Observatoire, 75006, Paris, France
| | - Joël Poupon
- Laboratory Anthropology, Archaeology, Biology (LAAB), UFR of Health Sciences (UVSQ), Paris-Saclay University, 2 Avenue de La Source de La Bièvre, 78180, Montigny-Le-Bretonneux, France; Laboratoire de Toxicologie Biologique, CHU Lariboisière (AP-HP), 2 Rue Ambroise Paré, 75010, Paris, France
| | | | - Philippe Decloquement
- Aix Marseille University, IRD, APHM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Saïd Azza
- Aix Marseille University, IRD, APHM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Emmanouil Angelakis
- Laboratory of Medical Microbiology, Hellenic Pasteur Institute, Athens, Greece
| | - Pascale Richardin
- Centre de Recherche et de Restauration des Musées de France (C2RMF), Palais Du Louvre, Porte des Lions, 14 Quai François Mitterrand, 75001, Paris, France; UMR 7055, Préhistoire et Technologie (Pretech), Université Paris Nanterre / CNRS, 21 Allée de L'Université, 92023, Nanterre Cedex, France
| | - Philippe Colson
- Aix Marseille University, IRD, APHM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Gregory Dubourg
- Aix Marseille University, IRD, APHM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Matthieu Million
- Aix Marseille University, IRD, APHM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille University, IRD, APHM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France
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2
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Zhang Y, Wang Z, Wang W, Yu H, Jin M. Applications of polymerase chain reaction‑based methods for the diagnosis of plague (Review). Exp Ther Med 2022; 24:511. [DOI: 10.3892/etm.2022.11438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/22/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Yanan Zhang
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Zhanli Wang
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Wenrui Wang
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot, Inner Mongolia 010031, P.R. China
| | - Hui Yu
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Min Jin
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
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Genetic Evidence of the Black Death in the Abbey of San Leonardo (Apulia Region, Italy): Tracing the Cause of Death in Two Individuals Buried with Coins. Pathogens 2021; 10:pathogens10111354. [PMID: 34832510 PMCID: PMC8619915 DOI: 10.3390/pathogens10111354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 11/30/2022] Open
Abstract
The Abbey of San Leonardo in Siponto (Apulia, Southern Italy) was an important religious and medical center during the Middle Ages. It was a crossroads for pilgrims heading along the Via Francigena to the Sanctuary of Monte Sant’Angelo and for merchants passing through the harbor of Manfredonia. A recent excavation of Soprintendenza Archeologica della Puglia investigated a portion of the related cemetery, confirming its chronology to be between the end of the 13th and beginning of the 14th century. Two single graves preserved individuals accompanied by numerous coins dating back to the 14th century, hidden in clothes and in a bag tied to the waist. The human remains of the individuals were analyzed in the Laboratorio di Antropologia Fisica of Soprintendenza ABAP della città metropolitana di Bari. Three teeth from each individual were collected and sent to the Istituto Zooprofilattico Sperimentale di Puglia e Basilicata to study infectious diseases such as malaria, plague, tuberculosis, epidemic typhus and Maltese fever (Brucellosis), potentially related to the lack of inspection of the bodies during burial procedures. DNA extracted from six collected teeth and two additional unrelated human teeth (negative controls) were analyzed using PCR to verify the presence of human DNA (β-globulin) and of pathogens such as Plasmodium spp., Yersinia pestis, Mycobacterium spp., Rickettsia spp. and Brucella spp. The nucleotide sequence of the amplicon was determined to confirm the results. Human DNA was successfully amplified from all eight dental extracts and two different genes of Y. pestis were amplified and sequenced in 4 out of the 6 teeth. Molecular analyses ascertained that the individuals buried in San Leonardo were victims of the Black Death (1347–1353) and the data confirmed the lack of inspection of the corpses despite the presence of numerous coins. This study represents molecular evidence, for the first time, of Southern Italy’s involvement in the second wave of the plague pandemic.
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Newfield TP. Syndemics and the history of disease: Towards a new engagement. Soc Sci Med 2021; 295:114454. [PMID: 34627635 DOI: 10.1016/j.socscimed.2021.114454] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 09/30/2021] [Indexed: 12/23/2022]
Abstract
Historians of medicine and disease have yet to think through a syndemic lens. This commentary aims to point out why they should. Although there are several hurdles to overcome, our histories of disease and our understanding of current syndemics both stand to gain should historians begin to explore episodes of cooccurring diseases that share root causes.
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Affiliation(s)
- Timothy P Newfield
- Department of History, Department of Biology, Georgetown University, 37th and O Streets NW, ICC 600, Washington, DC, 20057, USA.
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Barbieri R, Signoli M, Chevé D, Costedoat C, Tzortzis S, Aboudharam G, Raoult D, Drancourt M. Yersinia pestis: the Natural History of Plague. Clin Microbiol Rev 2020; 34:e00044-19. [PMID: 33298527 PMCID: PMC7920731 DOI: 10.1128/cmr.00044-19] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.
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Affiliation(s)
- R Barbieri
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
| | - M Signoli
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - D Chevé
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - C Costedoat
- Aix-Marseille University, CNRS, EFS, ADES, Marseille, France
| | - S Tzortzis
- Ministère de la Culture, Direction Régionale des Affaires Culturelles de Provence-Alpes-Côte d'Azur, Service Régional de l'Archéologie, Aix-en-Provence, France
| | - G Aboudharam
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille University, Faculty of Odontology, Marseille, France
| | - D Raoult
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
| | - M Drancourt
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Fondation Méditerranée Infection, Marseille, France
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Abstract
During the two World Wars, Bartonella quintana was responsible for trench fever and is now recognised as an agent of re-emerging infection. Many reports have indicated widespread B. quintana exposure since the 1990s. In order to evaluate its prevalence in ancient populations, we used real-time PCR to detect B. quintana DNA in 400 teeth collected from 145 individuals dating from the 1st to 19th centuries in nine archaeological sites, with the presence of negative controls. Fisher’s exact test was used to compare the prevalence of B. quintana in civil and military populations. B. quintana DNA was confirmed in a total of 28/145 (19.3%) individuals, comprising 78 citizens and 67 soldiers, 20.1% and 17.9% of which were positive for B. quintana bacteraemia, respectively. This study analysed previous studies on these ancient samples and showed that the presence of B. quintana infection followed the course of time in human history; a total of 14/15 sites from five European countries had a positive prevalence. The positive rate in soldiers was higher than those of civilians, with 20% and 18.8%, respectively, in the 18th and 19th centuries, but the difference in frequency was not significant. These results confirmed the role of dental pulp in diagnosing B. quintana bacteraemia in ancient populations and showed the incidence of B. quintana in both civilians and soldiers.
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Lazzari G, Colavizza G, Bortoluzzi F, Drago D, Erboso A, Zugno F, Kaplan F, Salathé M. A digital reconstruction of the 1630-1631 large plague outbreak in Venice. Sci Rep 2020; 10:17849. [PMID: 33082432 PMCID: PMC7576796 DOI: 10.1038/s41598-020-74775-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 10/05/2020] [Indexed: 11/23/2022] Open
Abstract
The plague, an infectious disease caused by the bacterium Yersinia pestis, is widely considered to be responsible for the most devastating and deadly pandemics in human history. Starting with the infamous Black Death, plague outbreaks are estimated to have killed around 100 million people over multiple centuries, with local mortality rates as high as 60%. However, detailed pictures of the disease dynamics of these outbreaks centuries ago remain scarce, mainly due to the lack of high-quality historical data in digital form. Here, we present an analysis of the 1630-1631 plague outbreak in the city of Venice, using newly collected daily death records. We identify the presence of a two-peak pattern, for which we present two possible explanations based on computational models of disease dynamics. Systematically digitized historical records like the ones presented here promise to enrich our understanding of historical phenomena of enduring importance. This work contributes to the recently renewed interdisciplinary foray into the epidemiological and societal impact of pre-modern epidemics.
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Affiliation(s)
- Gianrocco Lazzari
- Digital Epidemiology Laboratory, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Giovanni Colavizza
- Institute for Logic, Language and Computation (ILLC), University of Amsterdam, Amsterdam, The Netherlands.
| | - Fabio Bortoluzzi
- Digital Humanities Laboratory, College of Humanities, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Davide Drago
- Digital Humanities Laboratory, College of Humanities, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Andrea Erboso
- Digital Humanities Laboratory, College of Humanities, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Francesca Zugno
- Digital Humanities Laboratory, College of Humanities, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Frédéric Kaplan
- Digital Humanities Laboratory, College of Humanities, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marcel Salathé
- Digital Epidemiology Laboratory, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Barbieri R, Drancourt M, Raoult D. The role of louse-transmitted diseases in historical plague pandemics. THE LANCET. INFECTIOUS DISEASES 2020; 21:e17-e25. [PMID: 33035476 DOI: 10.1016/s1473-3099(20)30487-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 11/25/2022]
Abstract
The rodent-murine ectoparasite-human model of plague transmission does not correspond with historical details around plague pandemics in Europe. New analysis of ancient genomes reveal that Yersinia pestis was unable to be transmitted by rat fleas until around 4000 Before Present, which challenges the rodent-murine ectoparasite-human model of plague transmission and historical details around plague pandemics in Europe. In this Review, we summarise data regarding Y pestis transmission by human lice in the context of genomic evolution and co-transmission of other major epidemic deadly pathogens throughout human history, with the aim of broadening our view of plague transmission. Experimental models support the efficiency of human lice as plague vectors through infected faeces, which suggest that Y pestis could be a louse-borne disease, similar to Borrelia recurrentis, Rickettsia prowazekii, and Bartonella quintana. Studies have shown that louse-borne outbreaks often involve multiple pathogens, and several cases of co-transmission of Y pestis and B quintana have been reported. Furthermore, an exclusive louse-borne bacterium, namely B recurrentis, was found to be circulating in northern Europe during the second plague pandemic (14th-18th century). Current data make it possible to attribute large historical pandemics to multiple bacteria, and suggests that human lice probably played a preponderant role in the interhuman transmission of plague and pathogen co-transmission during previous large epidemics, including plague pandemics.
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Affiliation(s)
- Rémi Barbieri
- Aix-Marseille Université, Institut de Recherche pour le Développement, Microbes, Evolution, Phylogénie et Infection, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix-Marseille Université, Centre National de la Recherche Scientifique, Établissement Français du Sang, Anthropologie Bio-culturelle, Droit, Éthique et Santé, Marseille, France; Fondation Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- Aix-Marseille Université, Institut de Recherche pour le Développement, Microbes, Evolution, Phylogénie et Infection, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement, Microbes, Evolution, Phylogénie et Infection, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Fondation Méditerranée Infection, Marseille, France.
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A 2,000-year-old specimen with intraerythrocytic Bartonella quintana. Sci Rep 2020; 10:10069. [PMID: 32572066 PMCID: PMC7308320 DOI: 10.1038/s41598-020-66917-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/20/2020] [Indexed: 11/08/2022] Open
Abstract
Photogrammetry and cascading microscopy investigations of dental pulp specimens collected from 2,000-year-old individuals buried in a Roman necropolis in Besançon, France, revealed unprecedented preserved tissular and cellular morphology. Photogrammetry yielded 3-D images of the smallest archaeological human remains ever recovered. Optical microscopy examinations after standard haematoxylin-phloxine-saffron staining and anti-glycophorin A immunohistochemistry exposed dental pulp cells, in addition erythrocytes were visualised by electron microscopy, which indicated the ancient dental pulp trapped a blood drop. Fluorescence in situ hybridisation applied on red blood cells revealed the louse-borne pathogen Bartonella quintana, a finding confirmed by polymerase chain reaction assays. Through paleohistology and paleocytology, we demonstrate that the ancient dental pulp preserved intact blood cells at the time of the individual's death, offering an unprecedented opportunity to engage in direct and indirect tests to diagnose pathogens in ancient buried individuals.
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Mai BHA, Drancourt M, Aboudharam G. Ancient dental pulp: Masterpiece tissue for paleomicrobiology. Mol Genet Genomic Med 2020; 8:e1202. [PMID: 32233019 PMCID: PMC7284042 DOI: 10.1002/mgg3.1202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/21/2020] [Indexed: 12/19/2022] Open
Abstract
Introduction Dental pulp with special structure has become a good reference sample in paleomicrobiology‐related blood‐borne diseases, many pathogens were detected by different methods based on the diagnosis of nucleic acids and proteins. Objectives This review aims to propose the preparation process from ancient teeth collection to organic molecule extraction of dental pulp and summary, analyze the methods that have been applied to detect septicemic pathogens through ancient dental pulps during the past 20 years following the first detection of an ancient microbe. Methods The papers used in this review with two main objectives were obtained from PubMed and Google scholar with combining keywords: “ancient,” “dental pulp,” “teeth,” “anatomy,” “structure,” “collection,” “preservation,” “selection,” “photography,” “radiography,” “contamination,” “decontamination,” “DNA,” “protein,” “extraction,” “bone,” “paleomicrobiology,” “bacteria,” “virus,” “pathogen,” “molecular biology,” “proteomics,” “PCR,” “MALDI‐TOF,” “LC/MS,” “ELISA,” “immunology,” “immunochromatography,” “genome,” “microbiome,” “metagenomics.” Results The analysis of ancient dental pulp should have a careful preparation process with many different steps to give highly accurate results, each step complies with the rules in archaeology and paleomicrobiology. After the collection of organic molecules from dental pulp, they were investigated for pathogen identification based on the analysis of DNA and protein. Actually, DNA approach takes a principal role in diagnosis while the protein approach is more and more used. A total of seven techniques was used and ten bacteria (Yersinia pestis, Bartonella quintana, Salmonella enterica serovar Typhi, Salmonella enterica serovar Paratyphi C, Mycobacterium leprae, Mycobacterium tuberculosis, Rickettsia prowazeki, Staphylococcus aureus, Borrelia recurrentis, Bartonella henselae) and one virus (Anelloviridae) were identified. Y. pestis had the most published in quantity and all methods were investigated for this pathogen, S. aureus and B. recurrentis were identified by three different methods and others only by one. The combining methods interestingly increase the positive rate with ELISA, PCR and iPCR in Yersinia pestis diagnosis. Twenty‐seven ancient genomes of Y. pestis and one ancient genome of B. recurrentis were reconstructed. Comparing to the ancient bone, ancient teeth showed more advantage in septicemic diagnosis. Beside pathogen identification, ancient pulp help to distinguish species. Conclusions Dental pulp with specific tissue is a suitable sample for detection of the blood infection in the past through DNA and protein identification with the correct preparation process, furthermore, it helps to more understand the pathogens of historic diseases and epidemics.
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Affiliation(s)
- Ba Hoang Anh Mai
- Aix-Marseille Université, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Hue University of Medicine and Pharmacy, Thua Thien Hue, Vietnam
| | - Michel Drancourt
- Aix-Marseille Université, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Gérard Aboudharam
- Aix-Marseille Université, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France.,UFR Odontologie, Aix-Marseille Université, Marseille, France
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11
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Guellil M, Kersten O, Namouchi A, Bauer EL, Derrick M, Jensen AØ, Stenseth NC, Bramanti B. Genomic blueprint of a relapsing fever pathogen in 15th century Scandinavia. Proc Natl Acad Sci U S A 2018; 115:10422-10427. [PMID: 30249639 PMCID: PMC6187149 DOI: 10.1073/pnas.1807266115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Louse-borne relapsing fever (LBRF) is known to have killed millions of people over the course of European history and remains a major cause of mortality in parts of the world. Its pathogen, Borrelia recurrentis, shares a common vector with global killers such as typhus and plague and is known for its involvement in devastating historical epidemics such as the Irish potato famine. Here, we describe a European and historical genome of Brecurrentis, recovered from a 15th century skeleton from Oslo. Our distinct European lineage has a discrete genomic makeup, displaying an ancestral oppA-1 gene and gene loss in antigenic variation sites. Our results illustrate the potential of ancient DNA research to elucidate dynamics of reductive evolution in a specialized human pathogen and to uncover aspects of human health usually invisible to the archaeological record.
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Affiliation(s)
- Meriam Guellil
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;
| | - Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Amine Namouchi
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Egil L Bauer
- Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway
| | - Michael Derrick
- Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway
| | - Anne Ø Jensen
- Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway
| | - Nils C Stenseth
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;
| | - Barbara Bramanti
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;
- Department of Biomedical and Specialty Surgical Sciences, Faculty of Medicine, Pharmacy and Prevention, University of Ferrara, 35-441221 Ferrara, Italy
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12
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Barbieri R, Drancourt M. Two thousand years of epidemics in Marseille and the Mediterranean Basin. New Microbes New Infect 2018; 26:S4-S9. [PMID: 30402237 PMCID: PMC6205573 DOI: 10.1016/j.nmni.2018.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/12/2018] [Accepted: 08/01/2018] [Indexed: 11/24/2022] Open
Abstract
Marseille has been exposed to epidemics for two millennia, including plague, cholera and yellow fever. This long-standing exposure to epidemics has given the people of Marseilles a particular expertise in fighting epidemics. Lazarets and other quarantine measures were implemented as a response to preventing the further spread of the disease in the community. The Institut Hospitalier Universitaire Méditerranée Infection is paving the way today, with its responses built on the region's long history and knowledge of epidemics, infectious diseases and medical microbiology.
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Affiliation(s)
| | - M. Drancourt
- Corresponding author: M. Drancourt, IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.
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13
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DeWitte SN. Stress, sex, and plague: Patterns of developmental stress and survival in pre‐ and post‐Black Death London. Am J Hum Biol 2017; 30. [DOI: 10.1002/ajhb.23073] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/25/2017] [Accepted: 10/12/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
- Sharon N. DeWitte
- Department of AnthropologyUniversity of South CarolinaColumbia South Carolina 29208
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14
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A Personal View of How Paleomicrobiology Aids Our Understanding of the Role of Lice in Plague Pandemics. Microbiol Spectr 2017; 4. [PMID: 27726806 DOI: 10.1128/microbiolspec.poh-0001-2014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We have been involved in the field of paleomicrobiology since 1998, when we used dental pulp to identify Yersinia pestis as the causative agent of the great plague of Marseille (1720). We recently designed a specific technique, "suicide PCR," that can prevent contamination. A controversy arose between two teams, with one claiming that DNA must be altered to amplify it and the other group claiming that demographic data did not support the role of Y. pestis in the Black Death (i.e., the great plague of the Middle Ages). These controversies led us to evaluate other epidemiological models and to propose the body louse as the vector of this pandemic. This proposal was substantiated by experimental models, the recovery of Y. pestis from lice in the Congo, and the identification of epidemics involving both Y. pestis and Bartonella quintana (the agent of trench fever, transmitted by the body louse) in ancient corpses from mass graves. Paleomicrobiology has led to a re-evaluation of plague pandemics.
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15
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Abstract
ABSTRACT
The development of paleomicrobiology with new molecular techniques such as metagenomics is revolutionizing our knowledge of microbial evolution in human history. The study of microbial agents that are concomitantly active in the same biological environment makes it possible to obtain a picture of the complex interrelations among the different pathogens and gives us the perspective to understand the microecosystem of ancient times. This research acts as a bridge between disciplines such as archaeology, biology, and medicine, and the development of paleomicrobiology forces archaeology to broaden and update its methods. This chapter addresses the archaeological issues related to the identification of cemeteries from epidemic catastrophes (typology of burials, stratigraphy, topography, paleodemography) and the issues related to the sampling of human remains for biomolecular analysis. Developments in the field of paleomicrobiology are described with the example of the plague. Because of its powerful interdisciplinary features, the paleomicrobiological study of
Yersinia pestis
is an extremely interesting field, in which paleomicrobiology, historical research, and archeology are closely related, and it has important implications for the current dynamics of epidemiology.
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16
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Drancourt M, Raoult D. Molecular history of plague. Clin Microbiol Infect 2016; 22:911-915. [PMID: 27615720 DOI: 10.1016/j.cmi.2016.08.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/30/2016] [Accepted: 08/30/2016] [Indexed: 12/20/2022]
Abstract
Plague, a deadly zoonose caused by the bacterium Yersinia pestis, has been firmly documented in 39 historical burial sites in Eurasia that date from the Bronze Age to two historical pandemics spanning the 6th to 18th centuries. Palaeomicrobiologic data, including gene and spacer sequences, whole genome sequences and protein data, confirmed that two historical pandemics swept over Europe from probable Asian sources and possible two-way-ticket journeys back from Europe to Asia. These investigations made it possible to address questions regarding the potential sources and routes of transmission by completing the standard rodent and rodent-flea transmission scheme. This suggested that plague was transmissible by human ectoparasites such as lice, and that Y. pestis was able to persist for months in the soil, which is a source of reinfection for burrowing mammals. The analyses of seven complete genome sequences from the Bronze Age indicated that Y. pestis was probably not an ectoparasite-borne pathogen in these populations. Further analyses of 14 genomes indicated that the Justinian pandemic strains may have formed a clade distinct from the one responsible for the second pandemic, spanning in Y. pestis branch 1, which also comprises the third pandemic strains. Further palaeomicrobiologic studies must tightly connect with historical and anthropologic studies to resolve questions regarding the actual sources of plague in ancient populations, alternative routes of transmission and resistance traits. Answering these questions will broaden our understanding of plague epidemiology so we may better face the actuality of this deadly infection in countries where it remains epidemic.
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Affiliation(s)
- M Drancourt
- Aix Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - D Raoult
- Aix Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France.
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17
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Abstract
ABSTRACT
Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.
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18
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Archaeogenetics in evolutionary medicine. J Mol Med (Berl) 2016; 94:971-7. [PMID: 27289479 DOI: 10.1007/s00109-016-1438-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 05/22/2016] [Accepted: 06/03/2016] [Indexed: 12/24/2022]
Abstract
Archaeogenetics is the study of exploration of ancient DNA (aDNA) of more than 70 years old. It is an important part of the wider studies of many different areas of our past, including animal, plant and pathogen evolution and domestication events. Hereby, we address specifically the impact of research in archaeogenetics in the broader field of evolutionary medicine. Studies on ancient hominid genomes help to understand even modern health patterns. Human genetic microevolution, e.g. related to abilities of post-weaning milk consumption, and specifically genetic adaptation in disease susceptibility, e.g. towards malaria and other infectious diseases, are of the upmost importance in contributions of archeogenetics on the evolutionary understanding of human health and disease. With the increase in both the understanding of modern medical genetics and the ability to deep sequence ancient genetic information, the field of archaeogenetic evolutionary medicine is blossoming.
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19
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Abstract
This chapter summarizes researches on genome and evolution features of Yersinia pestis, the young pathogen that evolved from Y. pseudotuberculosis at least 5000 years ago. Y. pestis is a highly clonal bacterial species with closed pan-genome. Comparative genomic analysis revealed that genome of Y. pestis experienced highly frequent rearrangement and genome decay events during the evolution. The genealogy of Y. pestis includes five major branches, and four of them seemed raised from a "big bang" node that is associated with the Black Death. Although whole genome-wide variation of Y. pestis reflected a neutral evolutionary process, the branch length in the genealogical tree revealed over dispersion, which was supposedly caused by varied historical molecular clock that is associated with demographical effect by alternate cycles of enzootic disease and epizootic disease in sylvatic plague foci. In recent years, palaeomicrobiology researches on victims of the Black Death, and Justinian's plague verified that two historical pandemics were indeed caused by Y. pestis, but the etiological lineages might be extinct today.
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20
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Vogler AJ, Keim P, Wagner DM. A review of methods for subtyping Yersinia pestis: From phenotypes to whole genome sequencing. INFECTION GENETICS AND EVOLUTION 2015; 37:21-36. [PMID: 26518910 DOI: 10.1016/j.meegid.2015.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/23/2015] [Accepted: 10/24/2015] [Indexed: 12/28/2022]
Abstract
Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this important human pathogen. Methods are evaluated in terms of expense, difficulty, transferability among laboratories, discriminatory power, usefulness for different study questions, and current applicability in light of the advent of whole genome sequencing.
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Affiliation(s)
- Amy J Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA; Translational Genomics Research Institute North, Flagstaff, AZ 86001, USA.
| | - David M Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
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21
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Mitchell PD. Human Parasites in Medieval Europe: Lifestyle, Sanitation and Medical Treatment. ADVANCES IN PARASITOLOGY 2015; 90:389-420. [PMID: 26597073 DOI: 10.1016/bs.apar.2015.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Parasites have been infecting humans throughout our evolution. However, not all people suffered with the same species or to the same intensity throughout this time. Our changing way of life has altered the suitability of humans to infection by each type of parasite. This analysis focuses upon the evidence for parasites from archaeological excavations at medieval sites across Europe. Comparison between the patterns of infection in the medieval period allows us to see how changes in sanitation, herding animals, growing and fertilizing crops, the fishing industry, food preparation and migration all affected human susceptibility to different parasites. We go on to explore how ectoparasites may have spread infectious bacterial diseases, and also consider what medieval medical practitioners thought of parasites and how they tried to treat them. While modern research has shown the use of a toilet decreases the risk of contracting certain intestinal parasites, the evidence for past societies presented here suggests that the invention of latrines had no observable beneficial effects upon intestinal health. This may be because toilets were not sufficiently ubiquitous until the last century, or that the use of fresh human faeces for manuring crops still ensured those parasite species were easily able to reinfect the population.
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Affiliation(s)
- Piers D Mitchell
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom.
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22
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Malek MA, Hammani A, Beneldjouzi A, Bitam I. Enzootic plague foci, Algeria. New Microbes New Infect 2014; 4:13-6. [PMID: 25834736 PMCID: PMC4354914 DOI: 10.1016/j.nmni.2014.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 11/01/2014] [Accepted: 11/08/2014] [Indexed: 11/25/2022] Open
Abstract
In Algeria, PCR sequencing of pla, glpD and rpoB genes found Yersinia pestis in 18/237 (8%) rodents of five species, including Apodemus sylvaticus, previously undescribed as pestiferous; and disclosed three new plague foci. Multiple spacer typing confirmed a new Orientalis variant. Rodent survey should be reinforced in this country hosting reemerging plague.
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Affiliation(s)
- M A Malek
- Aix Marseille Université, URMITE, UM 63, UMR_S 1095 UMR 7278, 13385 Marseille, France ; Laboratoire VALCORE, Faculté des Sciences, Université M'Hamed Bougara Boumerdès (UMBB), Boumerdès, Algeria
| | - A Hammani
- Faculté des Sciences Biologiques et Agronomiques, Université Mouloud Mammeri, Tizi Ouzou, Algeria
| | | | - I Bitam
- Laboratoire VALCORE, Faculté des Sciences, Université M'Hamed Bougara Boumerdès (UMBB), Boumerdès, Algeria
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23
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Seifert L, Harbeck M, Thomas A, Hoke N, Zöller L, Wiechmann I, Grupe G, Scholz HC, Riehm JM. Strategy for sensitive and specific detection of Yersinia pestis in skeletons of the black death pandemic. PLoS One 2013; 8:e75742. [PMID: 24069445 PMCID: PMC3775804 DOI: 10.1371/journal.pone.0075742] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 08/19/2013] [Indexed: 12/05/2022] Open
Abstract
Yersinia pestis has been identified as the causative agent of the Black Death pandemic in the 14(th) century. However, retrospective diagnostics in human skeletons after more than 600 years are critical. We describe a strategy following a modern diagnostic algorithm and working under strict ancient DNA regime for the identification of medieval human plague victims. An initial screening and DNA quantification assay detected the Y. pestis specific pla gene of the high copy number plasmid pPCP1. Results were confirmed by conventional PCR and sequence analysis targeting both Y. pestis specific virulence plasmids pPCP1 and pMT1. All assays were meticulously validated according to human clinical diagnostics requirements (ISO 15189) regarding efficiency, sensitivity, specificity, and limit of detection (LOD). Assay specificity was 100% tested on 41 clinically relevant bacteria and 29 Y. pseudotuberculosis strains as well as for DNA of 22 Y. pestis strains and 30 previously confirmed clinical human plague samples. The optimized LOD was down to 4 gene copies. 29 individuals from three different multiple inhumations were initially assessed as possible victims of the Black Death pandemic. 7 samples (24%) were positive in the pPCP1 specific screening assay. Confirmation through second target pMT1 specific PCR was successful for 4 of the positive individuals (14%). A maximum of 700 and 560 copies per µl aDNA were quantified in two of the samples. Those were positive in all assays including all repetitions, and are candidates for future continuative investigations such as whole genome sequencing. We discuss that all precautions taken here for the work with aDNA are sufficient to prevent external sample contamination and fulfill the criteria of authenticity. With regard to retrospective diagnostics of a human pathogen and the uniqueness of ancient material we strongly recommend using a careful strategy and validated assays as presented in our study.
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Affiliation(s)
- Lisa Seifert
- Ludwig Maximilian University of Munich, Department Biology I, Biodiversity research/Anthropology, Martinsried, Germany
| | - Michaela Harbeck
- State Collection for Anthropology and Palaeoanatomy, Munich, Germany
| | - Astrid Thomas
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Nadja Hoke
- Ludwig Maximilian University of Munich, Department Biology I, Biodiversity research/Anthropology, Martinsried, Germany
| | - Lothar Zöller
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Ingrid Wiechmann
- Ludwig Maximilian University of Munich, Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Munich, Germany
| | - Gisela Grupe
- Ludwig Maximilian University of Munich, Department Biology I, Biodiversity research/Anthropology, Martinsried, Germany
- State Collection for Anthropology and Palaeoanatomy, Munich, Germany
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24
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Raoult D, Foti B, Aboudharam G. Historical and geographical parallelism between the incidence of dental caries, Streptococcus mutans and sugar intake. Eur J Epidemiol 2013; 28:709-10. [PMID: 23880892 PMCID: PMC3778904 DOI: 10.1007/s10654-013-9826-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/02/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine, CNRS UMR 7278, IRD 198, Aix-Marseille Université, 13385, Marseille Cedex 5, France,
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25
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A decade of plague in Mahajanga, Madagascar: insights into the global maritime spread of pandemic plague. mBio 2013; 4:e00623-12. [PMID: 23404402 PMCID: PMC3573667 DOI: 10.1128/mbio.00623-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A cluster of human plague cases occurred in the seaport city of Mahajanga, Madagascar, from 1991 to 1999 following 62 years with no evidence of plague, which offered insights into plague pathogen dynamics in an urban environment. We analyzed a set of 44 Mahajanga isolates from this 9-year outbreak, as well as an additional 218 Malagasy isolates from the highland foci. We sequenced the genomes of four Mahajanga strains, performed whole-genome sequence single-nucleotide polymorphism (SNP) discovery on those strains, screened the discovered SNPs, and performed a high-resolution 43-locus multilocus variable-number tandem-repeat analysis of the isolate panel. Twenty-two new SNPs were identified and defined a new phylogenetic lineage among the Malagasy isolates. Phylogeographic analysis suggests that the Mahajanga lineage likely originated in the Ambositra district in the highlands, spread throughout the northern central highlands, and was then introduced into and became transiently established in Mahajanga. Although multiple transfers between the central highlands and Mahajanga occurred, there was a locally differentiating and dominant subpopulation that was primarily responsible for the 1991-to-1999 Mahajanga outbreaks. Phylotemporal analysis of this Mahajanga subpopulation revealed a cycling pattern of diversity generation and loss that occurred during and after each outbreak. This pattern is consistent with severe interseasonal genetic bottlenecks along with large seasonal population expansions. The ultimate extinction of plague pathogens in Mahajanga suggests that, in this environment, the plague pathogen niche is tenuous at best. However, the temporary large pathogen population expansion provides the means for plague pathogens to disperse and become ecologically established in more suitable nonurban environments. Maritime spread of plague led to the global dissemination of this disease and affected the course of human history. Multiple historical plague waves resulted in massive human mortalities in three classical plague pandemics: Justinian (6th and 7th centuries), Middle Ages (14th to 17th centuries), and third (mid-1800s to the present). Key to these events was the pathogen’s entry into new lands by “plague ships” via seaport cities. Although initial disease outbreaks in ports were common, they were almost never sustained for long and plague pathogens survived only if they could become established in ecologically suitable habitats. Although plague pathogens’ ability to invade port cities has been essential for intercontinental spread, these regions have not proven to be a suitable long-term niche. The disease dynamics in port cities such as Mahajanga are thus critical to plague pathogen amplification and dispersal into new suitable ecological niches for the observed global long-term maintenance of plague pathogens.
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26
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Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc Natl Acad Sci U S A 2012; 110:577-82. [PMID: 23271803 DOI: 10.1073/pnas.1205750110] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The genetic diversity of Yersinia pestis, the etiologic agent of plague, is extremely limited because of its recent origin coupled with a slow clock rate. Here we identified 2,326 SNPs from 133 genomes of Y. pestis strains that were isolated in China and elsewhere. These SNPs define the genealogy of Y. pestis since its most recent common ancestor. All but 28 of these SNPs represented mutations that happened only once within the genealogy, and they were distributed essentially at random among individual genes. Only seven genes contained a significant excess of nonsynonymous SNP, suggesting that the fixation of SNPs mainly arises via neutral processes, such as genetic drift, rather than Darwinian selection. However, the rate of fixation varies dramatically over the genealogy: the number of SNPs accumulated by different lineages was highly variable and the genealogy contains multiple polytomies, one of which resulted in four branches near the time of the Black Death. We suggest that demographic changes can affect the speed of evolution in epidemic pathogens even in the absence of natural selection, and hypothesize that neutral SNPs are fixed rapidly during intermittent epidemics and outbreaks.
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27
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Chen S, Lu C, Gu H, Mehta A, Li J, Romano PB, Horn D, Hooper DC, Bazemore-Walker CR, Block T. Aleuria Aurantia Lectin (AAL)-reactive immunoglobulin G rapidly appears in sera of animals following antigen exposure. PLoS One 2012; 7:e44422. [PMID: 23024749 PMCID: PMC3443102 DOI: 10.1371/journal.pone.0044422] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 08/06/2012] [Indexed: 02/04/2023] Open
Abstract
We have discovered an Aleuria Aurantia Lectin (AAL)-reactive immunoglobulin G (IgG) that naturally occurs in the circulation of rabbits and mice, following immune responses induced by various foreign antigens. AAL can specifically bind to fucose moieties on glycoproteins. However, most serum IgGs are poorly bound by AAL unless they are denatured or treated with glycosidase. In this study, using an immunogen-independent AAL-antibody microarray assay that we developed, we detected AAL-reactive IgG in the sera of all animals that had been immunized 1–2 weeks previously with various immunogens with and without adjuvants and developed immunogen-specific responses. All of these animals subsequently developed immunogen-specific immune responses. The kinetics of the production of AAL-reactive IgG in mice and rabbits were distinct from those of the immunogen-specific IgGs elicited in the same animals: they rose and fell within one to two weeks, and peaked between four to seven days after exposure, while immunogen-specific IgGs continued to rise during the same period. Mass spectrometric profiling of the Fc glycoforms of purified AAL-reactive IgGs indicates that these are mainly comprised of IgGs with core-fucosylated and either mono-or non-galactosylated Fc N-glycan structures. Our results suggest that AAL-reactive IgG could be a previously unrecognized IgG subset that is selectively produced at the onset of a humoral response.
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Affiliation(s)
- Songming Chen
- Institute for Hepatitis and Virus Research, Doylestown, Pennsylvania, United States of America
- * E-mail: (SC); (TB)
| | - Chen Lu
- Institute for Hepatitis and Virus Research, Doylestown, Pennsylvania, United States of America
| | - Hongbo Gu
- Department of Chemistry, Brown University, Providence, Rhode Island, United States of America
| | - Anand Mehta
- Drexel University College of Medicine, Doylestown, Pennsylvania, United States of America
| | - Jianwei Li
- Departments of Cancer Biology and Neurological Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Patrick B. Romano
- Drexel University College of Medicine, Doylestown, Pennsylvania, United States of America
| | - David Horn
- Institute for Hepatitis and Virus Research, Doylestown, Pennsylvania, United States of America
| | - D. Craig Hooper
- Departments of Cancer Biology and Neurological Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | | | - Timothy Block
- Institute for Hepatitis and Virus Research, Doylestown, Pennsylvania, United States of America
- Drexel University College of Medicine, Doylestown, Pennsylvania, United States of America
- * E-mail: (SC); (TB)
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28
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Achtman M. Insights from genomic comparisons of genetically monomorphic bacterial pathogens. Philos Trans R Soc Lond B Biol Sci 2012; 367:860-7. [PMID: 22312053 DOI: 10.1098/rstb.2011.0303] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Some of the most deadly bacterial diseases, including leprosy, anthrax and plague, are caused by bacterial lineages with extremely low levels of genetic diversity, the so-called 'genetically monomorphic bacteria'. It has only become possible to analyse the population genetics of such bacteria since the recent advent of high-throughput comparative genomics. The genomes of genetically monomorphic lineages contain very few polymorphic sites, which often reflect unambiguous clonal genealogies. Some genetically monomorphic lineages have evolved in the last decades, e.g. antibiotic-resistant Staphylococcus aureus, whereas others have evolved over several millennia, e.g. the cause of plague, Yersinia pestis. Based on recent results, it is now possible to reconstruct the sources and the history of pandemic waves of plague by a combined analysis of phylogeographic signals in Y. pestis plus polymorphisms found in ancient DNA. Different from historical accounts based exclusively on human disease, Y. pestis evolved in China, or the vicinity, and has spread globally on multiple occasions. These routes of transmission can be reconstructed from the genealogy, most precisely for the most recent pandemic that was spread from Hong Kong in multiple independent waves in 1894.
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Affiliation(s)
- Mark Achtman
- Environmental Research Institute and Department of Microbiology, University College Cork, Cork, Ireland.
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29
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Scasciamacchia S, Serrecchia L, Giangrossi L, Garofolo G, Balestrucci A, Sammartino G, Fasanella A. Plague epidemic in the Kingdom of Naples, 1656-1658. Emerg Infect Dis 2012; 18:186-8. [PMID: 22260781 PMCID: PMC3310102 DOI: 10.3201/eid1801.110597] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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30
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Gibbons HS, Krepps MD, Ouellette G, Karavis M, Onischuk L, Leonard P, Broomall S, Sickler T, Betters JL, McGregor P, Donarum G, Liem A, Fochler E, McNew L, Rosenzweig CN, Skowronski E. Comparative genomics of 2009 seasonal plague (Yersinia pestis) in New Mexico. PLoS One 2012; 7:e31604. [PMID: 22359605 PMCID: PMC3281092 DOI: 10.1371/journal.pone.0031604] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/10/2012] [Indexed: 02/07/2023] Open
Abstract
Plague disease caused by the Gram-negative bacterium Yersinia pestis routinely affects animals and occasionally humans, in the western United States. The strains native to the North American continent are thought to be derived from a single introduction in the late 19th century. The degree to which these isolates have diverged genetically since their introduction is not clear, and new genomic markers to assay the diversity of North American plague are highly desired. To assay genetic diversity of plague isolates within confined geographic areas, draft genome sequences were generated by 454 pyrosequencing from nine environmental and clinical plague isolates. In silico assemblies of Variable Number Tandem Repeat (VNTR) loci were compared to laboratory-generated profiles for seven markers. High-confidence SNPs and small Insertion/Deletions (Indels) were compared to previously sequenced Y. pestis isolates. The resulting panel of mutations allowed clustering of the strains and tracing of the most likely evolutionary trajectory of the plague strains. The sequences also allowed the identification of new putative SNPs that differentiate the 2009 isolates from previously sequenced plague strains and from each other. In addition, new insertion points for the abundant insertion sequences (IS) of Y. pestis are present that allow additional discrimination of strains; several of these new insertions potentially inactivate genes implicated in virulence. These sequences enable whole-genome phylogenetic analysis and allow the unbiased comparison of closely related isolates of a genetically monomorphic pathogen.
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Affiliation(s)
- Henry S Gibbons
- United States Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, United States of America.
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31
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Malou N, Tran TNN, Nappez C, Signoli M, Le Forestier C, Castex D, Drancourt M, Raoult D. Immuno-PCR--a new tool for paleomicrobiology: the plague paradigm. PLoS One 2012; 7:e31744. [PMID: 22347507 PMCID: PMC3276503 DOI: 10.1371/journal.pone.0031744] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 01/12/2012] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The cause of past plague pandemics was controversial but several research teams used PCR techniques and dental pulp as the primary material to reveal that they were caused by Yersinia pestis. However, the degradation of DNA limits the ability to detect ancient infections. METHODS We used for the first time immuno-PCR to detect Yersinia pestis antigens; it can detect protein concentrations 70 times lower than the standard ELISA. After determining the cut-off value, we tested 34 teeth that were obtained from mass graves of plague, and compared previous PCR results with ELISA and immuno-PCR results. RESULTS The immuno-PCR technique was the most sensitive (14 out of 34) followed by the PCR technique (10 out of 34) and ELISA (3 out of 34). The combination of these three methods identified 18 out of 34 (53%) teeth as presumably being from people with the plague. CONCLUSION Immuno-PCR is specific (no false-positive samples were found) and more sensitive than the currently used method to detect antigens of ancient infections in dental pulp. The combination of three methods, ELISA, PCR and immuno-PCR, increased the capacity to identify ancient pathogens in dental pulp.
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Affiliation(s)
- Nada Malou
- Aix-Marseille Université, URMITE, UMR CNRS 6236- IRD 198, Faculté de Médecine, Marseille, France
| | - Thi-Nguyen-Ny Tran
- Aix-Marseille Université, URMITE, UMR CNRS 6236- IRD 198, Faculté de Médecine, Marseille, France
| | - Claude Nappez
- Aix-Marseille Université, URMITE, UMR CNRS 6236- IRD 198, Faculté de Médecine, Marseille, France
| | - Michel Signoli
- Aix-Marseille Université, Anthropologie Bioculturelle, UMR 6578 CNRS, EFS, Marseille, France
| | - Cyrille Le Forestier
- Institut National de Recherches Archéologiques Préventives UMR 6130, Centre d'Etudes Préhistoire, Antiquité, Moyen Age, Direction Interrégionale Centre, Ile de France, France
| | - Dominique Castex
- De la Préhistoire à l'Actuel: Culture Environnement et Anthropologie - Laboratoire d'Anthropologie des Populations du Passé, UMR 5199, Université de Bordeaux, Bordeaux, France
| | - Michel Drancourt
- Aix-Marseille Université, URMITE, UMR CNRS 6236- IRD 198, Faculté de Médecine, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, URMITE, UMR CNRS 6236- IRD 198, Faculté de Médecine, Marseille, France,* E-mail:
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Drancourt M, Raoult D. Genotyping Yersinia pestis in historical plague. THE LANCET. INFECTIOUS DISEASES 2011; 11:894-5. [DOI: 10.1016/s1473-3099(11)70292-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Grumbkow PV, Zipp A, Seidenberg V, Fehren-Schmitz L, Kempf VAJ, Gross U, Hummel S. Brief communication: Evidence of Bartonella quintana infections in skeletons of a historical mass grave in Kassel, Germany. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:134-7. [PMID: 21710687 DOI: 10.1002/ajpa.21551] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Philipp V Grumbkow
- Institute of Zoology and Anthropology, Department of Historical Anthropology and Human Ecology, Georg-August-University Goettingen, Buergerstraße 50, 37073 Goettingen, Germany.
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Tsangaras K, Greenwood AD. Museums and disease: using tissue archive and museum samples to study pathogens. Ann Anat 2011; 194:58-73. [PMID: 21641784 DOI: 10.1016/j.aanat.2011.04.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 04/06/2011] [Accepted: 04/06/2011] [Indexed: 11/28/2022]
Abstract
Molecular studies of archival and fossil samples have traditionally focused on the nucleic acids derived from the host species. However, there has recently been an increase in ancient DNA research on the identification and characterization of infectious agents within the hosts. The study of pathogens from the past provides great opportunities for discovering the causes of historical infection events, characterizing host-microorganism co-evolution and directly investigating the evolution of specific pathogens. Several research teams have been able to isolate and characterize a variety of different bacterial, parasite and viral microorganisms. However, this emerging field is not without obstacles. The diagenetic processes that make ancient DNA research generally difficult are also impediments to ancient pathogen research and perhaps more so given that their DNA may represent an even rarer proportion of the remaining nucleic acids in a fossil sample than host DNA. However, studies performed under controlled conditions and following stringent ancient DNA protocols can and have yielded reliable and often surprising results. This article reviews the advantages, problems, and failures of ancient microbiological research.
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