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Bergström A. Improving data archiving practices in ancient genomics. Sci Data 2024; 11:754. [PMID: 38987254 PMCID: PMC11236975 DOI: 10.1038/s41597-024-03563-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/21/2024] [Indexed: 07/12/2024] Open
Abstract
Ancient DNA is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is appropriately archived, its long-term value will not be fully realised. I surveyed publicly archived data from 42 recent ancient genomics studies. Half of the studies archived incomplete datasets, preventing accurate replication and representing a loss of data of potential future use. No studies met all criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: (1) archive all sequencing reads, not just those that aligned to a reference genome, (2) archive read alignments too, but as secondary analysis files, (3) provide correct experiment metadata on samples, libraries and sequencing runs, (4) provide informative sample metadata, (5) archive data from low-coverage and negative experiments, and (6) document archiving choices in papers, and peer review these. Given the reliance on destructive sampling of finite material, ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.
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Affiliation(s)
- Anders Bergström
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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2
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Ganz JC. Renaissance-Europe-16th century. PROGRESS IN BRAIN RESEARCH 2024; 285:5-27. [PMID: 38705718 DOI: 10.1016/bs.pbr.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Realistic images became available for the first time. The first major figure was Berengario da Carpi (1460-1530). He made contributions to knowledge. He stated the dura was attached all over the interior of the cranium not just at the sutures. He also noted that deterioration following traumatic hematomas was speedier the deeper within the brain the bleed had occurred and he noticed that post-traumatic neurological deficits were contralateral. Moreover, he introduced new instruments of a practical design. Specifically, he launched trepanation using a brace and bit handle. This instrument required two hands and rotated the trepan in the same direction all the time. In addition, he illustrated a crown trepan in which the bits could be interchanged. He also developed an improved elevator. He also provided the first drawing of a lenticular. The next illustrations came from Vidus Vidius (1509-1569). The illustrations in his text were elegant and realistic but some of them were impractical or unusable. Ambroise Paré (1510-1590) was a major surgeon. He designed an improved brace and bit trepan with a collar to control penetration. He also introduced instruments for expanding a cranial opening by biting up the bone and for depressing the dura to enable material to escape more easily.
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Affiliation(s)
- Jeremy C Ganz
- Department of Neurosurgery, Haukeland University Hospital, Bergen, Norway.
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3
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Brack J, Biran M, Amitai R. Plague and the Mongol conquest of Baghdad (1258)? A reevaluation of the sources. MEDICAL HISTORY 2024:1-19. [PMID: 38586998 DOI: 10.1017/mdh.2023.38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
This paper reexamines the sources used by N. Fancy and M.H. Green in "Plague and the Fall of Baghdad (1258)" (Medical History, 65/2 (2021), 157-177). Fancy and Green argued that the Arabic and Persian descriptions of the Mongol sieges in Iran and Iraq, and in particular, in the conquest of Baghdad in 1258, indicate that the besieged fortresses and cities were struck by Plague after the Mongol sieges were lifted. This, they suggested, is part of a recurrent pattern of the outbreak of Plague transmitted by the Mongol expansion across Eurasia. Fancy and Green concluded that the primary sources substantiate the theory driven by recent paleogenetic studies indicating that the Mongol conquests of the thirteenth century set the stage for the massive pandemic of the mid-fourteenth century. The link between the Plague outbreak and the Mongol siege of Baghdad relies on three near-contemporaneous historical accounts. However, our re-examination of the sources shows that the main text (in Persian) has been significantly misunderstood, and that the two other texts (in Syriac and Arabic) have been mis-contextualized, and thus not understood properly. They do not support the authors' claim regarding Plague epidemic in Baghdad in 1258, nor do other contemporary and later Arabic texts from Syria and Egypt adduced by them, which we re-examine in detail here. We conclude that there is no evidence for the appearance of Plague during or immediately after the Mongol conquests in the Middle East, certainly not for its transmission by the Mongols.
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Affiliation(s)
- Jonathan Brack
- Dept. of History, Northwestern University, and Dept. of Middle East Studies, Ben-Gurion University of the Negev
| | - Michal Biran
- Institute of Asian and African Studies, Hebrew University of Jerusalem, and Ewha Womans University, Seoul
| | - Reuven Amitai
- Institute of Asian and African Studies, Hebrew University of Jerusalem
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4
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Bergfeldt N, Kırdök E, Oskolkov N, Mirabello C, Unneberg P, Malmström H, Fraser M, Sanchez-Quinto F, Jorgensen R, Skar B, Lidén K, Jakobsson M, Storå J, Götherström A. Identification of microbial pathogens in Neolithic Scandinavian humans. Sci Rep 2024; 14:5630. [PMID: 38453993 PMCID: PMC10920878 DOI: 10.1038/s41598-024-56096-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/01/2024] [Indexed: 03/09/2024] Open
Abstract
With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.
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Affiliation(s)
- Nora Bergfeldt
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
| | - Emrah Kırdök
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin, Turkey
| | - Nikolay Oskolkov
- Science for Life Laboratory, Department of Biology, National Bioinformatics Infrastructure Sweden, Lund University, Lund, Sweden
| | - Claudio Mirabello
- Science for Life Laboratory, Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Linköping University, Linköping, Sweden
| | - Per Unneberg
- Science for Life Laboratory, Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | - Magdalena Fraser
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | | | - Roger Jorgensen
- Tromsø University Museum, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Birgitte Skar
- Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
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5
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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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6
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Lebrasseur O, More KD, Orlando L. Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago. Virus Evol 2024; 10:vead087. [PMID: 38465241 PMCID: PMC10924538 DOI: 10.1093/ve/vead087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/27/2023] [Accepted: 01/11/2024] [Indexed: 03/12/2024] Open
Abstract
Equine viral outbreaks have disrupted the socio-economic life of past human societies up until the late 19th century and continue to be of major concern to the horse industry today. With a seroprevalence of 60-80 per cent, equine herpesvirus 4 (EHV-4) is the most common horse pathogen on the planet. Yet, its evolutionary history remains understudied. Here, we screen the sequenced data of 264 archaeological horse remains to detect the presence of EHV-4. We recover the first ancient EHV-4 genome with 4.2× average depth-of-coverage from a specimen excavated in the Southeastern Urals and dated to the Early Bronze Age period, approximately 3,900 years ago. The recovery of an EHV-4 virus outside the upper respiratory tract not only points to an animal particularly infected but also highlights the importance of post-cranial bones in pathogen characterisation. Bayesian phylogenetic reconstruction provides a minimal time estimate for EHV-4 diversification to around 4,000 years ago, a time when modern domestic horses spread across the Central Asian steppes together with spoke-wheeled Sintashta chariots, or earlier. The analyses also considerably revise the diversification time of the two EHV-4 subclades from the 16th century based solely on modern data to nearly a thousand years ago. Our study paves the way for a robust reconstruction of the history of non-human pathogens and their impact on animal health.
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Affiliation(s)
- Ophélie Lebrasseur
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS/Université Paul Sabatier, 37 Allées Jules Guesde, 31000, Toulouse, France
- Instituto Nacional de Antropología y Pensamiento Latinoamericano, 3 de Febrero 1370 (1426), Ciudad Autónoma de Buenos Aires, Argentina
| | - Kuldeep Dilip More
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS/Université Paul Sabatier, 37 Allées Jules Guesde, 31000, Toulouse, France
| | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse (CAGT), CNRS/Université Paul Sabatier, 37 Allées Jules Guesde, 31000, Toulouse, France
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7
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Bennasar-Figueras A. The Natural and Clinical History of Plague: From the Ancient Pandemics to Modern Insights. Microorganisms 2024; 12:146. [PMID: 38257973 PMCID: PMC10818976 DOI: 10.3390/microorganisms12010146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The human pathogen Yersinia pestis is responsible for bubonic, septicemic, and pneumonic plague. A deeply comprehensive overview of its historical context, bacteriological characteristics, genomic analysis based on ancient DNA (aDNA) and modern strains, and its impact on historical and actual human populations, is explored. The results from multiple studies have been synthesized to investigate the origins of plague, its transmission, and effects on different populations. Additionally, molecular interactions of Y. pestis, from its evolutionary origins to its adaptation to flea-born transmission, and its impact on human and wild populations are considered. The characteristic combinations of aDNA patterns, which plays a decisive role in the reconstruction and analysis of ancient genomes, are reviewed. Bioinformatics is fundamental in identifying specific Y. pestis lineages, and automated pipelines are among the valuable tools in implementing such studies. Plague, which remains among human history's most lethal infectious diseases, but also other zoonotic diseases, requires the continuous investigation of plague topics. This can be achieved by improving molecular and genetic screening of animal populations, identifying ecological and social determinants of outbreaks, increasing interdisciplinary collaborations among scientists and public healthcare providers, and continued research into the characterization, diagnosis, and treatment of these diseases.
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Affiliation(s)
- Antoni Bennasar-Figueras
- Microbiologia—Departament de Biologia, Universitat de les Illes Balears (UIB), Campus UIB, Carretera de Valldemossa, Km 7.5, 07122 Palma de Mallorca, Spain; ; Tel.: +34-971172778
- Facultat de Medicina, Hospital Universitari Son Espases (HUSE), Universitat de les Illes Balears (UIB), Carretera de Valldemossa, 79, 07122 Palma de Mallorca, Spain
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8
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Espí Forcén F, Freudenreich O. Coping With Pandemics: A Historical Perspective About Society's Tools to Deal With Global Infectious Diseases. J Nerv Ment Dis 2023; 211:927-933. [PMID: 37166245 DOI: 10.1097/nmd.0000000000001668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
ABSTRACT Throughout history, society has dealt with several devastating pandemics. Our objective is to analyze society's coping mechanisms to deal with pandemic-related stress in history congruent with the values of the time. For that purpose, we have carefully selected some of the most significant pandemics based on their impact and the available psychosocial literature. After a brief introduction, society's coping tools are reviewed and analyzed for the Antonine Plague, the second bubonic plague, the third cholera pandemic, the Spanish flu, the HIV pandemic, and the COVID-19 pandemic. Despite occurring at different times in history, parallels can be established in the study of society's psychological reactions among different pandemics. Magical thinking, political skepticism, fake accusations, and discrimination of minorities are recurrent reactions in society among different pandemics in history.
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9
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Dittmar JM, Mitchell PD, Inskip SA, Cessford C, Robb JE. Tuberculosis before and after the Black Death (1346-1353 CE) in the Hospital of St John the Evangelist in Cambridge, England. Tuberculosis (Edinb) 2023; 143S:102401. [PMID: 38012925 DOI: 10.1016/j.tube.2023.102401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 07/30/2023] [Accepted: 09/01/2023] [Indexed: 11/29/2023]
Abstract
This research explores how the prevalence of tuberculosis (TB) in a medieval hospital was affected by the demographic and social changes that following the Black Death (1346-1353 CE), the initial years of the Second Plague Pandemic. To do this, skeletal remains of individuals buried at the Hospital of St John the Evangelist in Cambridge, England, that could be dated to living before (n = 77) or after (n = 55) the Black Death were assessed for evidence of TB (indicated by destructive lesions of the spine, ribs, large joints, and other recognised criteria). Overall, the odds of females having skeletal lesions caused by TB were over four times higher than males. No significant difference was detected in the prevalence rates in those who lived before and after the Black Death (7.8%, 6/77 before and 11.0%, 6/55 after). However, the odds of females having skeletal evidence of TB were over five times greater after the Black Death than they were before. These findings indicate that women may have been 1) more susceptible to TB, 2) surviving longer post-infection than men, and/or 3) that women with TB were more likely to be admitted to the Hospital especially following the Black Death. It is also possible that impairment due to TB infection may have been a contributing factor for entry into the Hospital for women but not men.
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Affiliation(s)
- Jenna M Dittmar
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK; Department of Archaeology, University of Aberdeen, St Mary's Building Elphinstone Road, Aberdeen, AB24 3UF, UK.
| | - Piers D Mitchell
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK.
| | - Sarah A Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK; School of Archaeology and Ancient History, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Craig Cessford
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, 34 A&B Storey's Way, Cambridge, CB3 0DT, UK.
| | - John E Robb
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge, CB2 3DZ, UK.
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10
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Chatterjee S, De R, Hens C, Dana SK, Kapitaniak T, Bhattacharyya S. Response of a three-species cyclic ecosystem to a short-lived elevation of death rate. Sci Rep 2023; 13:20740. [PMID: 38007582 PMCID: PMC10676407 DOI: 10.1038/s41598-023-48104-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/22/2023] [Indexed: 11/27/2023] Open
Abstract
A balanced ecosystem with coexisting constituent species is often perturbed by different natural events that persist only for a finite duration of time. What becomes important is whether, in the aftermath, the ecosystem recovers its balance or not. Here we study the fate of an ecosystem by monitoring the dynamics of a particular species that encounters a sudden increase in death rate. For exploration of the fate of the species, we use Monte-Carlo simulation on a three-species cyclic rock-paper-scissor model. The density of the affected (by perturbation) species is found to drop exponentially immediately after the pulse is applied. In spite of showing this exponential decay as a short-time behavior, there exists a region in parameter space where this species surprisingly remains as a single survivor, wiping out the other two which had not been directly affected by the perturbation. Numerical simulations using stochastic differential equations of the species give consistency to our results.
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Affiliation(s)
- Sourin Chatterjee
- Department of Mathematics and Statistics, Indian Institute of Science Education and Research, Kolkata, West Bengal, 741246, India
| | - Rina De
- Department of Physics, Raja Rammohun Roy Mahavidyalaya, Radhanagar, Hooghly, 712406, India
| | - Chittaranjan Hens
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Gachibowli, Hyderabad, 500 032, India
- Division of Dynamics, Faculty of Mechanical Engineering, Lodz University of Technology, 90-924, Lodz, Poland
| | - Syamal K Dana
- Division of Dynamics, Faculty of Mechanical Engineering, Lodz University of Technology, 90-924, Lodz, Poland
- Centre for Mathematical Biology and Ecology, Department of Mathematics, Jadavpur University, Kolkata, 700032, India
| | - Tomasz Kapitaniak
- Division of Dynamics, Faculty of Mechanical Engineering, Lodz University of Technology, 90-924, Lodz, Poland
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11
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Kröger C, Lerminiaux NA, Ershova AS, MacKenzie KD, Kirzinger MW, Märtlbauer E, Perry BJ, Cameron ADS, Schauer K. Plasmid-encoded lactose metabolism and mobilized colistin resistance ( mcr-9) genes in Salmonella enterica serovars isolated from dairy facilities in the 1980s. Microb Genom 2023; 9. [PMID: 38031909 DOI: 10.1099/mgen.0.001149] [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] [Indexed: 12/01/2023] Open
Abstract
Horizontal gene transfer by plasmids can confer metabolic capabilities that expand a host cell's niche. Yet, it is less understood whether the coalescence of specialized catabolic functions, antibiotic resistances and metal resistances on plasmids provides synergistic benefits. In this study, we report whole-genome assembly and phenotypic analysis of five Salmonella enterica strains isolated in the 1980s from milk powder in Munich, Germany. All strains exhibited the unusual phenotype of lactose-fermentation and encoded either of two variants of the lac operon. Surprisingly, all strains encoded the mobilized colistin resistance gene 9 (mcr-9), long before the first report of this gene in the literature. In two cases, the mcr-9 gene and the lac locus were linked within a large gene island that formed an IncHI2A-type plasmid in one strain but was chromosomally integrated in the other strain. In two other strains, the mcr-9 gene was found on a large IncHI1B/IncP-type plasmid, whereas the lac locus was encoded on a separate chromosomally integrated plasmidic island. The mcr-9 sequences were identical and genomic contexts could not explain the wide range of colistin resistances exhibited by the Salmonella strains. Nucleotide variants did explain phenotypic differences in motility and exopolysaccharide production. The observed linkage of mcr-9 to lactose metabolism, an array of heavy-metal detoxification systems, and other antibiotic resistance genes may reflect a coalescence of specialized phenotypes that improve the spread of colistin resistance in dairy facilities, much earlier than previously suspected.
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Affiliation(s)
- Carsten Kröger
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Nicole A Lerminiaux
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
| | - Anna S Ershova
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Keith D MacKenzie
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
| | - Morgan W Kirzinger
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Present address: National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Erwin Märtlbauer
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Oberschleißheim, 85764, Germany
| | - Benjamin J Perry
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Present address: AgResearch, 176 Puddle Alley, Mosgiel 9092, New Zealand
| | - Andrew D S Cameron
- Department of Biology, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, Saskatchewan, S4S 0A2, Canada
| | - Kristina Schauer
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Oberschleißheim, 85764, Germany
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12
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Rametov NM, Steiner M, Bizhanova NA, Abdel ZZ, Yessimseit DT, Abdeliyev BZ, Mussagalieva RS. Mapping Plague Risk Using Super Species Distribution Models and Forecasts for Rodents in the Zhambyl Region, Kazakhstan. GEOHEALTH 2023; 7:e2023GH000853. [PMID: 37965638 PMCID: PMC10641984 DOI: 10.1029/2023gh000853] [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: 05/10/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
One of the most extensive natural plague centers, or foci, is located in Central Asia, in particular, the Zhambyl region in Southern Kazakhstan. Here, we conducted plague surveillance from 2000 to 2020 in the Zhambyl region in Kazakhstan and confirmed 3,072 cases of infected wild animals. We used Species Distribution Modeling by employing MaxEnt, and identified that the natural plague foci are primarily located in the Moiynqum, Betpaqdala, and Tauqum Deserts. The Zhambyl region's central part, including the Moiynqum and Sarysu districts, has a high potential risk of plague outbreak for the rural towns and villages. Since the phenomenon of climate change has been identified as a determinant that affects the rodent populations, thereby elevating the likelihood of an outbreak of plague, we investigated the potential dissemination routes of the disease under the changing climate conditions, thus creating Species Distribution Forecasts for the rodent species in southern part of Kazakhstan for the year 2100. By 2100, in case of increasing temperatures, the range of host species is likely to expand, leading to a higher risk of plague outbreaks. The highest risk of disease transmission can be expected at the outer limits of the modeled total distribution range, where infection rates are high, but antibody presence is low, making many species susceptible to the pathogen. To mitigate the risk of a potential plague outbreak, it is necessary to implement appropriate sanitary-epidemiological measures and climate mitigation policies.
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Affiliation(s)
- N. M. Rametov
- National Scientific Center for Particularly Dangerous Infections named after M. AikimbaevAlmatyKazakhstan
- Institute of IonosphereAlmatyKazakhstan
- Department of Geospatial EngineeringSatpaev Kazakh National Research Technical UniversityAlmatyKazakhstan
| | - M. Steiner
- Department of Animal ScienceWageningen University and ResearchWageningenThe Netherlands
| | - N. A. Bizhanova
- Laboratory of TheriologyInstitute of ZoologyAlmatyKazakhstan
- Department of Biodiversity and BioresourcesAl‐Farabi Kazakh National UniversityAlmatyKazakhstan
- Wildlife Without Borders Public FundAlmatyKazakhstan
| | - Z. Zh. Abdel
- National Scientific Center for Particularly Dangerous Infections named after M. AikimbaevAlmatyKazakhstan
| | - D. T. Yessimseit
- National Scientific Center for Particularly Dangerous Infections named after M. AikimbaevAlmatyKazakhstan
| | - B. Z. Abdeliyev
- National Scientific Center for Particularly Dangerous Infections named after M. AikimbaevAlmatyKazakhstan
| | - R. S. Mussagalieva
- National Scientific Center for Particularly Dangerous Infections named after M. AikimbaevAlmatyKazakhstan
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14
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Parker CE, Hiss AN, Spyrou MA, Neumann GU, Slavin P, Nelson EA, Nagel S, Dalidowski X, Friederich S, Krause J, Herbig A, Haak W, Bos KI. 14th century Yersinia pestis genomes support emergence of pestis secunda within Europe. PLoS Pathog 2023; 19:e1011404. [PMID: 37463152 PMCID: PMC10414589 DOI: 10.1371/journal.ppat.1011404] [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: 11/30/2022] [Revised: 08/10/2023] [Accepted: 05/04/2023] [Indexed: 07/20/2023] Open
Abstract
Pestis secunda (1356-1366 CE) is the first of a series of plague outbreaks in Europe that followed the Black Death (1346-1353 CE). Collectively this period is called the Second Pandemic. From a genomic perspective, the majority of post-Black Death strains of Yersinia pestis thus far identified in Europe display diversity accumulated over a period of centuries that form a terminal sub-branch of the Y. pestis phylogeny. It has been debated if these strains arose from local evolution of Y. pestis or if the disease was repeatedly reintroduced from an external source. Plague lineages descended from the pestis secunda, however, are thought to have persisted in non-human reservoirs outside Europe, where they eventually gave rise to the Third Pandemic (19th and 20th centuries). Resolution of competing hypotheses on the origins of the many post-Black Death outbreaks has been hindered in part by the low representation of Y. pestis genomes in archaeological specimens, especially for the pestis secunda. Here we report on five individuals from Germany that were infected with lineages of plague associated with the pestis secunda. For the two genomes of high coverage, one groups within the known diversity of genotypes associated with the pestis secunda, while the second carries an ancestral genotype that places it earlier. Through consideration of historical sources that explore first documentation of the pandemic in today's Central Germany, we argue that these data provide robust evidence to support a post-Black Death evolution of the pathogen within Europe rather than a re-introduction from outside. Additionally, we demonstrate retrievability of Y. pestis DNA in post-cranial remains and highlight the importance of hypothesis-free pathogen screening approaches in evaluations of archaeological samples.
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Affiliation(s)
- Cody E. Parker
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alina N. Hiss
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Maria A. Spyrou
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute for Achaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Gunnar U. Neumann
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philip Slavin
- Division of History, Heritage and Politics, University of Stirling, Stirling, Scotland, United Kingdom
| | | | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Xandra Dalidowski
- Landesamt für Denkmalpflege und Archäologie, Sachsen-Anhalt, Halle (Saale), Germany
| | - Susanne Friederich
- Landesamt für Denkmalpflege und Archäologie, Sachsen-Anhalt, Halle (Saale), Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kirsten I. Bos
- Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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15
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Brüssow H. Viral infections at the animal-human interface-Learning lessons from the SARS-CoV-2 pandemic. Microb Biotechnol 2023; 16:1397-1411. [PMID: 37338856 DOI: 10.1111/1751-7915.14269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 06/21/2023] Open
Abstract
This Lilliput explores the current epidemiological and virological arguments for a zoonotic origin of the COVID-19 pandemic. While the role of bats, pangolins and racoon dogs as viral reservoirs has not yet been proven, a spill-over of a coronavirus infection from animals into humans at the Huanan food market in Wuhan has a much greater plausibility than alternative hypotheses such as a laboratory virus escape, deliberate genetic engineering or introduction by cold chain food products. This Lilliput highlights the dynamic nature of the animal-human interface for viral cross-infections from humans into feral white tail deer or farmed minks (reverse zoonosis). Surveillance of viral infections at the animal-human interface is an urgent task since live animal markets are not the only risks for future viral spill-overs. Climate change will induce animal migration which leads to viral exchanges between animal species that have not met in the past. Environmental change and deforestation will also increase contact between animals and humans. Developing an early warning system for emerging viral infections becomes thus a societal necessity not only for human but also for animal and environmental health (One Health concept). Microbiologists have developed tools ranging from virome analysis in key suspects such as viral reservoirs (bats, wild game animals, bushmeat) and in humans exposed to wild animals, to wastewater analysis to detect known and unknown viruses circulating in the human population and sentinel studies in animal-exposed patients with fever. Criteria need to be developed to assess the virulence and transmissibility of zoonotic viruses. An early virus warning system is costly and will need political lobbying. The accelerating number of viral infections with pandemic potential over the last decades should provide the public pressure to extend pandemic preparedness for the inclusion of early viral alert systems.
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Affiliation(s)
- Harald Brüssow
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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16
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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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17
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Klapper M, Hübner A, Ibrahim A, Wasmuth I, Borry M, Haensch VG, Zhang S, Al-Jammal WK, Suma H, Fellows Yates JA, Frangenberg J, Velsko IM, Chowdhury S, Herbst R, Bratovanov EV, Dahse HM, Horch T, Hertweck C, González Morales MR, Straus LG, Vilotijevic I, Warinner C, Stallforth P. Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic. Science 2023; 380:619-624. [PMID: 37141315 DOI: 10.1126/science.adf5300] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. Here, we investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans spanning 100 kya to the present and reconstructed 459 bacterial metagenome-assembled genomes (MAGs). We identified a biosynthetic gene cluster (BGC) shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites we name paleofurans. This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.
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Affiliation(s)
- Martin Klapper
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Anan Ibrahim
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Ina Wasmuth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Veit G Haensch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Shuaibing Zhang
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Walid K Al-Jammal
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Harikumar Suma
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - James A Fellows Yates
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Jasmin Frangenberg
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Somak Chowdhury
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Rosa Herbst
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Evgeni V Bratovanov
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Therese Horch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Manuel Ramon González Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, 39071 Santander, Spain
| | - Lawrence Guy Straus
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA
- Grupo I+D+i EvoAdapta, Departmento de Ciencias Históricas, Universidad de Cantabria, 39005 Santander, Spain
| | - Ivan Vilotijevic
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
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18
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Dalal V, Pasupuleti N, Chaubey G, Rai N, Shinde V. Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide. Genes (Basel) 2023; 14:479. [PMID: 36833406 PMCID: PMC9956214 DOI: 10.3390/genes14020479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.
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Affiliation(s)
- Vasundhra Dalal
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | | | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Niraj Rai
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, Lucknow 226007, Uttar Pradesh, India
| | - Vasant Shinde
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
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19
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International Integration and Cooperation at the Present stage in the Fight Against Plague and Other Dangerous Infections in the Kyrgyz Republic. PROBLEMS OF PARTICULARLY DANGEROUS INFECTIONS 2023. [DOI: 10.21055/0370-1069-2022-4-7-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The paper contains the data on international cooperation of the Republican Center of Quarantine and Particularly Dangerous Infections of the Ministry of Health of the Kyrgyz Republic and the Russian Research Anti-Plague Institute “Microbe” of the Rospotrebnadzor to combat plague and other dangerous infections over the period from 2016 to 2022. Areas of cooperation include conducting joint epidemiological monitoring of plague foci in the Kyrgyz Republic; exchange of up-to-date information on the state of natural foci of the two countries; equipping the anti-plague service of the Republic with modern equipment and mobile laboratories, diagnostic tools and technologies; conducting joint exercises to ensure biological safety and prompt response to emergencies; provision of advisory and methodological assistance; training and strengthening of professional personnel; conducting joint scientific researches, conferences; publication of scientific works. Data on the complex characterization of properties and phylogeographic analysis of Yersinia pestis strains isolated during field studies in the Kyrgyz Republic in 2012–2020 are summarized. The prospects for carrying out joint cartographic, molecular-genetic and paleomicrobiological work in the natural foci of the Kyrgyz Republic are outlined.
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20
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Historical and Modern Classifications of the Plague Agent. PROBLEMS OF PARTICULARLY DANGEROUS INFECTIONS 2023. [DOI: 10.21055/0370-1069-2022-4-14-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The review presents the data on domestic and foreign phenotypic classifications of Yersinia pestis strains developed in the XX century; genetic classifications of the XXI century; as well as on the genealogy of ancient strains of the plague microbe, reconstructed using paleogenomic technologies. Since the discovery of the plague agent in 1894, many classifications were created that corresponded to the level of development of microbiology at that time. The intraspecific classification schemes of the XX century were based on three principles: phenotypic differences between strains, features of the species composition of carriers, and geographical affiliation. With the development of molecular microbiology early on in the XXI century, a genetic nomenclature of the branches of the pathogen evolution was developed and a number of classifications based on the analysis of the population structure of Y. pestis were created. Through the prism of the genetic diversity of Y. pestis strains from natural plague foci in Russia, near and far abroad countries, an improved classification with a division into seven subspecies has been developed: pestis, tibetica, caucasica, qinghaica, angolica, central asiatica, ulegeica, which allocates the subspecies according to the phylogenetic principle and epidemic significance. With the advancements in paleomicrobiology, prehistoric lineages of evolution have been included in the genealogy of Y. pestis, which expand the data on the intraspecific diversity of the plague microbe.
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21
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Chen KW, Brodsky IE. Yersinia interactions with regulated cell death pathways. Curr Opin Microbiol 2023; 71:102256. [PMID: 36584489 DOI: 10.1016/j.mib.2022.102256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/18/2022] [Accepted: 11/30/2022] [Indexed: 12/29/2022]
Abstract
Cell death in response to infection is conserved across all kingdoms of life. In metazoans, cell death upon bacterial infection is primarily carried out by the cysteine and aspartate protease and receptor-interacting serine/threonine protein kinase families. The Gram-negative bacterial genus Yersinia includes pathogens that cause disease in humans and other animals ranging from plague to gastrointestinal infections. Pathogenic Yersiniae express a type-III secretion system (T3SS), which translocates effectors that disrupt phagocytosis and innate immune signaling to evade immune defenses and replicate extracellularly in infected tissues. Blockade of innate immune signaling, disruption of the actin cytoskeleton, and the membrane-disrupting activity of the T3SS translocon pore, are all sensed by innate immune cells. Here, we discuss recent advances in understanding the pathways that regulate Yersinia-induced cell death, and how manipulation of these cell death pathways over the course of infection promotes bacterial dissemination or host defense.
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Affiliation(s)
- Kaiwen W Chen
- Immunology Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Igor E Brodsky
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, United States; Department of Microbiology, University of Pennsylvania Perelman School of Medicine, United States.
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22
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Abstract
This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens.
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23
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Begou P, Kassomenos P. The ecosyndemic framework of the global environmental change and the COVID-19 pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159327. [PMID: 36220476 PMCID: PMC9547397 DOI: 10.1016/j.scitotenv.2022.159327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/03/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
The ecosyndemic theory combines the concept of 'synergy' with 'epidemic' and the term "eco" implies the role of the environmental changes. Each of the conditions enhances the negative impacts of the other in an additive way making our society more vulnerable and heightening individual risk factors. In this study, we analyze the mutually reinforcing links between the environment and health from the complexity angle of the ecosyndemic theory and propose the characterization of the COVID-19 pandemic as ecosyndemic. We use the term 'ecosyndemic' because the global environmental change contributes to local-scale, regional-scale and global-scale alterations of the Earth's systems. These changes have their root causes in the way that people interact with the physical, chemical, and biotic factors of the environment. These interactions disturb nature and the consequences have feedbacks in every living organism.
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Affiliation(s)
- Paraskevi Begou
- Laboratory of Meteorology and Climatology, Department of Physics, University of Ioannina, GR-45110 Ioannina, Greece.
| | - Pavlos Kassomenos
- Laboratory of Meteorology and Climatology, Department of Physics, University of Ioannina, GR-45110 Ioannina, Greece
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24
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Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis. Commun Biol 2023; 6:23. [PMID: 36658311 PMCID: PMC9852431 DOI: 10.1038/s42003-022-04394-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/21/2022] [Indexed: 01/21/2023] Open
Abstract
Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis, regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences sampled globally. Through a detailed Bayesian evaluation of temporal signal in subsets of these data we demonstrate that a Y. pestis-wide molecular clock is unstable. To resolve this, we developed a new approach in which each Y. pestis population was assessed independently, enabling us to recover substantial temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this methodological advancement, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics.
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Yang R, Atkinson S, Chen Z, Cui Y, Du Z, Han Y, Sebbane F, Slavin P, Song Y, Yan Y, Wu Y, Xu L, Zhang C, Zhang Y, Hinnebusch BJ, Stenseth NC, Motin VL. Yersinia pestis and Plague: some knowns and unknowns. ZOONOSES (BURLINGTON, MASS.) 2023; 3:5. [PMID: 37602146 PMCID: PMC10438918 DOI: 10.15212/zoonoses-2022-0040] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Since its first identification in 1894 during the third pandemic in Hong Kong, there has been significant progress of understanding the lifestyle of Yersinia pestis, the pathogen that is responsible for plague. Although we now have some understanding of the pathogen's physiology, genetics, genomics, evolution, gene regulation, pathogenesis and immunity, there are many unknown aspects of the pathogen and its disease development. Here, we focus on some of the knowns and unknowns relating to Y. pestis and plague. We notably focus on some key Y. pestis physiological and virulence traits that are important for its mammal-flea-mammal life cycle but also its emergence from the enteropathogen Yersinia pseudotuberculosis. Some aspects of the genetic diversity of Y. pestis, the distribution and ecology of plague as well as the medical countermeasures to protect our population are also provided. Lastly, we present some biosafety and biosecurity information related to Y. pestis and plague.
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Affiliation(s)
- Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Steve Atkinson
- School of Life Sciences, Centre for Biomolecular Science, University of Nottingham, Nottingham, United Kingdom
| | - Ziqi Chen
- Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - Yujun Cui
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Zongmin Du
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Yanping Han
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Florent Sebbane
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Philip Slavin
- Division of History and Politics, University of Stirling, Stirling FK9 4LJ, UK
| | - Yajun Song
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Yanfeng Yan
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Yarong Wu
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Lei Xu
- Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - Chutian Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Yun Zhang
- Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - B. Joseph Hinnebusch
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, Montana, USA
| | - Nils Chr. Stenseth
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Vladimir L. Motin
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
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Juhas M. Emerging and Zoonotic Diseases. BRIEF LESSONS IN MICROBIOLOGY 2023:111-122. [DOI: 10.1007/978-3-031-29544-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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No evidence for persistent natural plague reservoirs in historical and modern Europe. Proc Natl Acad Sci U S A 2022; 119:e2209816119. [PMID: 36508668 PMCID: PMC9907128 DOI: 10.1073/pnas.2209816119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Caused by Yersinia pestis, plague ravaged the world through three known pandemics: the First or the Justinianic (6th-8th century); the Second (beginning with the Black Death during c.1338-1353 and lasting until the 19th century); and the Third (which became global in 1894). It is debatable whether Y. pestis persisted in European wildlife reservoirs or was repeatedly introduced from outside Europe (as covered by European Union and the British Isles). Here, we analyze environmental data (soil characteristics and climate) from active Chinese plague reservoirs to assess whether such environmental conditions in Europe had ever supported "natural plague reservoirs". We have used new statistical methods which are validated through predicting the presence of modern plague reservoirs in the western United States. We find no support for persistent natural plague reservoirs in either historical or modern Europe. Two factors make Europe unfavorable for long-term plague reservoirs: 1) Soil texture and biochemistry and 2) low rodent diversity. By comparing rodent communities in Europe with those in China and the United States, we conclude that a lack of suitable host species might be the main reason for the absence of plague reservoirs in Europe today. These findings support the hypothesis that long-term plague reservoirs did not exist in Europe and therefore question the importance of wildlife rodent species as the primary plague hosts in Europe.
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Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
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Launer J. Learning from the black death. Postgrad Med J 2022; 98:887-888. [PMID: 36270654 DOI: 10.1136/pmj-2022-142202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- John Launer
- Associate Editor, Postgraduate Medical Journal, London, UK
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van der Kuyl AC. Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens. EPIDEMIOLOGIA (BASEL, SWITZERLAND) 2022; 3:443-464. [PMID: 36547255 PMCID: PMC9778136 DOI: 10.3390/epidemiologia3040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022]
Abstract
Since life on earth developed, parasitic microbes have thrived. Increases in host numbers, or the conquest of a new species, provide an opportunity for such a pathogen to enjoy, before host defense systems kick in, a similar upsurge in reproduction. Outbreaks, caused by "endemic" pathogens, and epidemics, caused by "novel" pathogens, have thus been creating chaos and destruction since prehistorical times. To study such (pre)historic epidemics, recent advances in the ancient DNA field, applied to both archeological and historical remains, have helped tremendously to elucidate the evolutionary trajectory of pathogens. These studies have offered new and unexpected insights into the evolution of, for instance, smallpox virus, hepatitis B virus, and the plague-causing bacterium Yersinia pestis. Furthermore, burial patterns and historical publications can help in tracking down ancient pathogens. Another source of information is our genome, where selective sweeps in immune-related genes relate to past pathogen attacks, while multiple viruses have left their genomes behind for us to study. This review will discuss the sources available to investigate (pre)historic diseases, as molecular knowledge of historic and prehistoric pathogens may help us understand the past and the present, and prepare us for future epidemics.
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Affiliation(s)
- Antoinette C. van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; ; Tel.: +31-205-666-778
- Amsterdam Institute for Infection and Immunity, 1100 DD Amsterdam, The Netherlands
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Kreier F. Ancient tooth DNA reveals how 'cold sore' herpes virus has evolved. Nature 2022; 609:21-22. [PMID: 35999365 DOI: 10.1038/d41586-022-02246-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Gonzalez Lopez A. Black Death unravelled. Nat Rev Microbiol 2022; 20:509. [PMID: 35778565 DOI: 10.1038/s41579-022-00769-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Callaway E. Ancient DNA traces origin of Black Death. Nature 2022; 606:635-636. [PMID: 35705867 DOI: 10.1038/d41586-022-01673-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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