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Bonczarowska JH, Susat J, Krause-Kyora B, Dangvard Pedersen D, Boldsen J, Larsen LA, Seeberg L, Nebel A, Unterweger D. Ancient Yersinia pestis genomes lack the virulence-associated Ypf Φ prophage present in modern pandemic strains. Proc Biol Sci 2023; 290:20230622. [PMID: 37464758 DOI: 10.1098/rspb.2023.0622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/19/2023] [Indexed: 07/20/2023] Open
Abstract
Yersinia pestis is the causative agent of at least three major plague pandemics (Justinianic, Medieval and Modern). Previous studies on ancient Y. pestis genomes revealed that several genomic alterations had occurred approximately 5000-3000 years ago and contributed to the remarkable virulence of this pathogen. How a subset of strains evolved to cause the Modern pandemic is less well-understood. Here, we examined the virulence-associated prophage (YpfΦ), which had been postulated to be exclusively present in the genomes of strains associated with the Modern pandemic. The analysis of two new Y. pestis genomes from medieval/early modern Denmark confirmed that the phage is absent from the genome of strains dating to this time period. An extended comparative genome analysis of over 300 strains spanning more than 5000 years showed that the prophage is found in the genomes of modern strains only and suggests an integration into the genome during recent Y. pestis evolution. The phage-encoded Zot protein showed structural homology to a virulence factor of Vibrio cholerae. Similar to modern Y. pestis, we observed phages with a common origin to YpfΦ in individual strains of other bacterial species. Our findings present an updated view on the prevalence of YpfΦ, which might contribute to our understanding of the host spectrum, geographical spread and virulence of Y. pestis responsible for the Modern pandemic.
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Affiliation(s)
- Joanna H Bonczarowska
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, Kiel 24105, Germany
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, Kiel 24105, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, Kiel 24105, Germany
| | - Dorthe Dangvard Pedersen
- Unit of Anthropology, Department of Forensic Medicine, University of Southern Denmark, Odense M, 5230, Denmark
| | - Jesper Boldsen
- Unit of Anthropology, Department of Forensic Medicine, University of Southern Denmark, Odense M, 5230, Denmark
| | | | - Lone Seeberg
- Museum Horsens Arkæologisk Afdeling, Fussingsvej 8, Horsens 8700, Denmark
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, Kiel 24105, Germany
| | - Daniel Unterweger
- Institute for Experimental Medicine, Kiel University, Michaelisstraße 5, Kiel 24105, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, Plön 24306, Germany
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Clavel P, Louis L, Sarkissian CD, Thèves C, Gillet C, Chauvey L, Tressières G, Schiavinato S, Calvière-Tonasso L, Telmon N, Clavel B, Jonvel R, Tzortzis S, Bouniol L, Fémolant JM, Klunk J, Poinar H, Signoli M, Costedoat C, Spyrou MA, Seguin-Orlando A, Orlando L. Improving the extraction of ancient Yersinia pestis genomes from the dental pulp. iScience 2023; 26:106787. [PMID: 37250315 PMCID: PMC10214834 DOI: 10.1016/j.isci.2023.106787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/11/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023] Open
Abstract
Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of ancient Yersinia pestis DNA release in solution during a pre-digestion of the dental pulp. We found that most of the ancient Y. pestis DNA is released within 60 min at 37°C in our experimental conditions. We recommend a simple pre-digestion as an economical procedure to obtain extracts enriched in ancient pathogen DNA, as longer digestion times release other types of templates, including host DNA. Combining this procedure with DNA capture, we characterized the genome sequences of 12 ancient Y. pestis bacteria from France dating to the second pandemic outbreaks of the 17th and 18th centuries Common Era.
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Affiliation(s)
- Pierre Clavel
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Lexane Louis
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Clio Der Sarkissian
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Catherine Thèves
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Claudia Gillet
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Lorelei Chauvey
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Gaétan Tressières
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Stéphanie Schiavinato
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Laure Calvière-Tonasso
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Norbert Telmon
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Benoît Clavel
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), CNRS-UMR7209, Muséum national d’histoire naturelle, 55 Rue Buffon, 75005 Paris, France
| | - Richard Jonvel
- Amiens Métropole Service Archéologie Préventive, 2 rue Colbert, 80000 Amiens, France
| | - Stéfan Tzortzis
- Service Régional de l’Archéologie, 21 allée Claude Forbin, 13100 Aix-en-Provence, France
| | - Laetitia Bouniol
- Service archéologique de la ville de Beauvais, 1 rue Desgroux, 60021 Beauvais, France
| | - Jean-Marc Fémolant
- Service archéologique de la ville de Beauvais, 1 rue Desgroux, 60021 Beauvais, France
| | | | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, ON L8S 4L9, Canada
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S, 4L9, Canada
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - Michel Signoli
- Aix-Marseille Université, CNRS, EFS, ADES, 13005 Marseille, France
| | | | - Maria A. Spyrou
- Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Andaine Seguin-Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Ludovic Orlando
- Centre d’Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR5288, Université Paul Sabatier, 37 allées Jules Guesde, 31000 Toulouse, France
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Epidemiological Characteristics of Human and Animal Plague in Yunnan Province, China, 1950 to 2020. Microbiol Spectr 2022; 10:e0166222. [PMID: 36219109 PMCID: PMC9784778 DOI: 10.1128/spectrum.01662-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
This study analyzed the epidemiological characteristics of 3,464 human plague cases and the distribution pattern of 4,968 Yersinia pestis isolates from humans, hosts, and vector insects from 1950 to 2020 among two natural plague foci in Yunnan Province, China. These foci include the Rattus flavipectus plague focus of the Yunnan, Guangdong, and Fujian provinces and the Apodemus chevrieri-Eothenomys miletus plague focus of the highlands of northwestern Yunnan Province. The case fatality rate for plague in humans was 18.39% (637/3,464), and the total isolation rate of Y. pestis was 0.17% (4,968/2,975,288). Despite that the frequency of human cases declined rapidly, the animal plague fluctuated greatly, alternating between activity and inactivity in these foci. The tendency among human cases can be divided into 4 stages, 1950 to 1955, 1956 to 1989, 1990 to 2005, and 2006 to 2020. Bubonic plague accounted for the majority of cases in Yunnan, where pneumonic and septicemic plague rarely occurred. The natural plague foci have been in a relatively active state due to the stability of local ecology. Dense human population and frequent contact with host animals contribute to the high risk of human infection. This study systematically analyzed the epidemic pattern of human plague and the distribution characteristics of Y. pestis in the natural plague foci in Yunnan, providing a scientific basis for further development and adjustment of plague prevention and control strategies. IMPORTANCE Yunnan is the origin of the third plague pandemic. The analysis of human and animal plague characteristics of plague foci in Yunnan enlightens the prevention and control of the next plague pandemics. The plague characteristics of Yunnan show that human plague occurred when animal plague reached a certain scale, and strengthened surveillance of animal plague and reducing the density of host animals and transmission vectors contribute to the prevention and control of human plague outbreaks. The phenomenon of alternation between the resting period and active period of plague foci in Yunnan further proves the endogenous preservation mechanism of plague.
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A 16 th century Escherichia coli draft genome associated with an opportunistic bile infection. Commun Biol 2022; 5:599. [PMID: 35710940 PMCID: PMC9203756 DOI: 10.1038/s42003-022-03527-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/23/2022] [Indexed: 11/12/2022] Open
Abstract
Escherichia coli – one of the most characterized bacteria and a major public health concern – remains invisible across the temporal landscape. Here, we present the meticulous reconstruction of the first ancient E. coli genome from a 16th century gallstone from an Italian mummy with chronic cholecystitis. We isolated ancient DNA and reconstructed the ancient E. coli genome. It consisted of one chromosome of 4446 genes and two putative plasmids with 52 genes. The E. coli strain belonged to the phylogroup A and an exceptionally rare sequence type 4995. The type VI secretion system component genes appears to be horizontally acquired from Klebsiella aerogenes, however we could not identify any pathovar specific genes nor any acquired antibiotic resistances. A sepsis mouse assay showed that a closely related contemporary E. coli strain was avirulent. Our reconstruction of this ancient E. coli helps paint a more complete picture of the burden of opportunistic infections of the past. Ancient DNA from an Italian mummy’s gallstone provides insight into opportunistic E. coli infection.
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Barbieri R, Nodari R, Signoli M, Epis S, Raoult D, Drancourt M. Differential word expression analyses highlight plague dynamics during the second pandemic. ROYAL SOCIETY OPEN SCIENCE 2022; 9:210039. [PMID: 35070338 PMCID: PMC8728171 DOI: 10.1098/rsos.210039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Research on the second plague pandemic that swept over Europe from the fourteenth to nineteenth centuries mainly relies on the exegesis of contemporary texts and is prone to interpretive bias. By leveraging certain bioinformatic tools routinely used in biology, we developed a quantitative lexicography of 32 texts describing two major plague outbreaks, using contemporary plague-unrelated texts as negative controls. Nested, network and category analyses of a 207-word pan-lexicome, comprising overrepresented terms in plague-related texts, indicated that 'buboes' and 'carbuncles' are words that were significantly associated with the plague and signalled an ectoparasite-borne plague. Moreover, plague-related words were associated with the terms 'merchandise', 'movable', 'tatters', 'bed' and 'clothes'. Analysing ancient texts using the method reported in this paper can certify plague-related historical records and indicate the particularities of each plague outbreak, which can inform on the potential sources for the causative Yersinia pestis.
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Affiliation(s)
- Rémi Barbieri
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille 13005, France
- UMR 7268, Anthropologie bioculturelle, Droit, Ethique et Santé, Aix Marseille Univ, 11 CNRS, EFS, ADES, Marseille 13344, France
- IHU Méditerranée Infection, Marseille 13005, France
| | - Riccardo Nodari
- Department of Biosciences and Pediatric Clinical Research Center ‘Romeo and Enrica Invernizzi’, University of Milan, Milan 20133, Italy
| | - Michel Signoli
- UMR 7268, Anthropologie bioculturelle, Droit, Ethique et Santé, Aix Marseille Univ, 11 CNRS, EFS, ADES, Marseille 13344, France
| | - Sara Epis
- Department of Biosciences and Pediatric Clinical Research Center ‘Romeo and Enrica Invernizzi’, University of Milan, Milan 20133, Italy
| | - Didier Raoult
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille 13005, France
- IHU Méditerranée Infection, Marseille 13005, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille 13005, France
- IHU Méditerranée Infection, Marseille 13005, France
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Origin, transmission, and evolution of plague over 400 y in Europe. Proc Natl Acad Sci U S A 2021; 118:2114241118. [PMID: 34551981 DOI: 10.1073/pnas.2114241118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 11/18/2022] Open
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Bramanti B, Wu Y, Yang R, Cui Y, Stenseth NC. Assessing the origins of the European Plagues following the Black Death: A synthesis of genomic, historical, and ecological information. Proc Natl Acad Sci U S A 2021; 118:e2101940118. [PMID: 34465619 PMCID: PMC8433512 DOI: 10.1073/pnas.2101940118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The second plague pandemic started in Europe with the Black Death in 1346 and lasted until the 19th century. Based on ancient DNA studies, there is a scientific disagreement over whether the bacterium, Yersinia pestis, came into Europe once (Hypothesis 1) or repeatedly over the following four centuries (Hypothesis 2). Here, we synthesize the most updated phylogeny together with historical, archeological, evolutionary, and ecological information. On the basis of this holistic view, we conclude that Hypothesis 2 is the most plausible. We also suggest that Y. pestis lineages might have developed attenuated virulence during transmission, which can explain the convergent evolutionary signals, including pla decay, that appeared at the end of the pandemics.
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Affiliation(s)
- Barbara Bramanti
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;
- Department of Neuroscience and Rehabilitation, Faculty of Medicine, Pharmacy and Prevention, University of Ferrara, 44121 Ferrara, Italy
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China;
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China
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