151
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Malek MA, Bitam I, Levasseur A, Terras J, Gaudart J, Azza S, Flaudrops C, Robert C, Raoult D, Drancourt M. Yersinia pestis halotolerance illuminates plague reservoirs. Sci Rep 2017; 7:40022. [PMID: 28054667 PMCID: PMC5214965 DOI: 10.1038/srep40022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 12/01/2016] [Indexed: 11/20/2022] Open
Abstract
The plague agent Yersinia pestis persists for years in the soil. Two millennia after swiping over Europe and North Africa, plague established permanent foci in North Africa but not in neighboring Europe. Mapping human plague foci reported in North Africa for 70 years indicated a significant location at <3 kilometers from the Mediterranean seashore or the edge of salted lakes named chotts. In Algeria, culturing 352 environmental specimens naturally containing 0.5 to 70 g/L NaCl yielded one Y. pestis Orientalis biotype isolate in a 40 g/L NaCl chott soil specimen. Core genome SNP analysis placed this isolate within the Y. pestis branch 1, Orientalis biovar. Culturing Y. pestis in broth steadily enriched in NaCl indicated survival up to 150 g/L NaCl as L-form variants exhibiting a distinctive matrix assisted laser desorption-ionization time-of-flight mass spectrometry peptide profile. Further transcriptomic analyses found the upregulation of several outer-membrane proteins including TolC efflux pump and OmpF porin implied in osmotic pressure regulation. Salt tolerance of Y. pestis L-form may play a role in the maintenance of natural plague foci in North Africa and beyond, as these geographical correlations could be extended to 31 plague foci in the northern hemisphere (from 15°N to 50°N).
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Affiliation(s)
- Maliya Alia Malek
- Aix Marseille Université, URMITE, UMR 63, CNRS 7278, IRD 198, Inserm 1095, Faculté de Médecine, 27 Bd Jean MOULIN, 13385 Marseille Cedex 5, France
- Laboratoire Biodiversité et Environnement: Interactions Génomes, Faculté des Sciences Biologiques Université des Sciences et de la Technologie Houari Boumediene, El Alia, Bab Ezzouar 16111, Algérie
| | - Idir Bitam
- Aix Marseille Université, URMITE, UMR 63, CNRS 7278, IRD 198, Inserm 1095, Faculté de Médecine, 27 Bd Jean MOULIN, 13385 Marseille Cedex 5, France
- Laboratoire Biodiversité et Environnement: Interactions Génomes, Faculté des Sciences Biologiques Université des Sciences et de la Technologie Houari Boumediene, El Alia, Bab Ezzouar 16111, Algérie
| | - Anthony Levasseur
- Aix Marseille Université, URMITE, UMR 63, CNRS 7278, IRD 198, Inserm 1095, Faculté de Médecine, 27 Bd Jean MOULIN, 13385 Marseille Cedex 5, France
| | - Jérôme Terras
- Aix Marseille Université, URMITE, UMR 63, CNRS 7278, IRD 198, Inserm 1095, Faculté de Médecine, 27 Bd Jean MOULIN, 13385 Marseille Cedex 5, France
| | - Jean Gaudart
- Aix Marseille Université, URMITE, UMR 63, CNRS 7278, IRD 198, Inserm 1095, Faculté de Médecine, 27 Bd Jean MOULIN, 13385 Marseille Cedex 5, France
- Aix-Marseille Université, UMR912 SESSTIM (INSERM/IRD/AMU), Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
| | - Said Azza
- Aix Marseille Université, URMITE, UMR 63, CNRS 7278, IRD 198, Inserm 1095, Faculté de Médecine, 27 Bd Jean MOULIN, 13385 Marseille Cedex 5, France
| | - Christophe Flaudrops
- Aix Marseille Université, URMITE, UMR 63, CNRS 7278, IRD 198, Inserm 1095, Faculté de Médecine, 27 Bd Jean MOULIN, 13385 Marseille Cedex 5, France
| | - Catherine Robert
- Aix Marseille Université, URMITE, UMR 63, CNRS 7278, IRD 198, Inserm 1095, Faculté de Médecine, 27 Bd Jean MOULIN, 13385 Marseille Cedex 5, France
| | - Didier Raoult
- Aix Marseille Université, URMITE, UMR 63, CNRS 7278, IRD 198, Inserm 1095, Faculté de Médecine, 27 Bd Jean MOULIN, 13385 Marseille Cedex 5, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR 63, CNRS 7278, IRD 198, Inserm 1095, Faculté de Médecine, 27 Bd Jean MOULIN, 13385 Marseille Cedex 5, France
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152
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Baltrus DA, McCann HC, Guttman DS. Evolution, genomics and epidemiology of Pseudomonas syringae: Challenges in Bacterial Molecular Plant Pathology. MOLECULAR PLANT PATHOLOGY 2017; 18:152-168. [PMID: 27798954 PMCID: PMC6638251 DOI: 10.1111/mpp.12506] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 05/12/2023]
Abstract
A remarkable shift in our understanding of plant-pathogenic bacteria is underway. Until recently, nearly all research on phytopathogenic bacteria was focused on a small number of model strains, which provided a deep, but narrow, perspective on plant-microbe interactions. Advances in genome sequencing technologies have changed this by enabling the incorporation of much greater diversity into comparative and functional research. We are now moving beyond a typological understanding of a select collection of strains to a more generalized appreciation of the breadth and scope of plant-microbe interactions. The study of natural populations and evolution has particularly benefited from the expansion of genomic data. We are beginning to have a much deeper understanding of the natural genetic diversity, niche breadth, ecological constraints and defining characteristics of phytopathogenic species. Given this expanding genomic and ecological knowledge, we believe the time is ripe to evaluate what we know about the evolutionary dynamics of plant pathogens.
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Affiliation(s)
| | - Honour C. McCann
- New Zealand Institute for Advanced StudyMassey UniversityAuckland 0632New Zealand
| | - David S. Guttman
- Department of Cell and Systems BiologyUniversity of TorontoTorontoON M5S 3B2Canada
- Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoON M5S 3B2Canada
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153
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Collins C, Didelot X. Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes. Methods Mol Biol 2017; 1535:109-137. [PMID: 27914076 DOI: 10.1007/978-1-4939-6673-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Following recent developments in DNA sequencing technology, it is now possible to sequence hundreds of whole genomes from bacterial isolates at relatively low cost. Analyzing this growing wealth of genomic data in terms of ancestral relationships can reveal many interesting aspects of the evolution, ecology, and epidemiology of bacterial pathogens. However, reconstructing the ancestry of a sample of bacteria remains challenging, especially for the majority of species where recombination is frequent. Here, we review and describe the computational techniques currently available to infer ancestral relationships, including phylogenetic methods that either ignore or account for the effect of recombination, as well as model-based and model-free phylogeny-independent approaches.
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Affiliation(s)
- Caitlin Collins
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.
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154
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Dwibedi C, Birdsell D, Lärkeryd A, Myrtennäs K, Öhrman C, Nilsson E, Karlsson E, Hochhalter C, Rivera A, Maltinsky S, Bayer B, Keim P, Scholz HC, Tomaso H, Wittwer M, Beuret C, Schuerch N, Pilo P, Hernández Pérez M, Rodriguez-Lazaro D, Escudero R, Anda P, Forsman M, Wagner DM, Larsson P, Johansson A. Long-range dispersal moved Francisella tularensis into Western Europe from the East. Microb Genom 2016; 2:e000100. [PMID: 28348839 PMCID: PMC5359409 DOI: 10.1099/mgen.0.000100] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/22/2016] [Indexed: 01/31/2023] Open
Abstract
For many infections transmitting to humans from reservoirs in nature, disease dispersal patterns over space and time are largely unknown. Here, a reversed genomics approach helped us understand disease dispersal and yielded insight into evolution and biological properties of Francisella tularensis, the bacterium causing tularemia. We whole-genome sequenced 67 strains and characterized by single-nucleotide polymorphism assays 138 strains, collected from individuals infected 1947-2012 across Western Europe. We used the data for phylogenetic, population genetic and geographical network analyses. All strains (n=205) belonged to a monophyletic population of recent ancestry not found outside Western Europe. Most strains (n=195) throughout the study area were assigned to a star-like phylogenetic pattern indicating that colonization of Western Europe occurred via clonal expansion. In the East of the study area, strains were more diverse, consistent with a founder population spreading from east to west. The relationship of genetic and geographic distance within the F. tularensis population was complex and indicated multiple long-distance dispersal events. Mutation rate estimates based on year of isolation indicated null rates; in outbreak hotspots only, there was a rate of 0.4 mutations/genome/year. Patterns of nucleotide substitution showed marked AT mutational bias suggestive of genetic drift. These results demonstrate that tularemia has moved from east to west in Europe and that F. tularensis has a biology characterized by long-range geographical dispersal events and mostly slow, but variable, replication rates. The results indicate that mutation-driven evolution, a resting survival phase, genetic drift and long-distance geographical dispersal events have interacted to generate genetic diversity within this species.
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Affiliation(s)
- Chinmay Dwibedi
- Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Dawn Birdsell
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Adrian Lärkeryd
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Kerstin Myrtennäs
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Caroline Öhrman
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Elin Nilsson
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Edvin Karlsson
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Christian Hochhalter
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Andrew Rivera
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Sara Maltinsky
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Brittany Bayer
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
- Translational Genomics Research Institute North, Flagstaff AZ, USA
| | | | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses Friedrich-Loeffler, Institut Federal Research Institute for Animal Health, Jena, Germany
| | - Matthias Wittwer
- Biology Division, Spietz Laboratory, Federal Office for Civil Protection, Spietz, Switzerland
| | - Christian Beuret
- Biology Division, Spietz Laboratory, Federal Office for Civil Protection, Spietz, Switzerland
| | - Nadia Schuerch
- Biology Division, Spietz Laboratory, Federal Office for Civil Protection, Spietz, Switzerland
| | - Paola Pilo
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Marta Hernández Pérez
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnológico Agrario de Castilla y León, Valladolid, Spain
- Departamento de Ingeniería Agrícola y Forestal, Universidad de Valladolid, Palencia, Spain
| | | | - Raquel Escudero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Anda
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Mats Forsman
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Pär Larsson
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Anders Johansson
- Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Correspondence Anders Johansson ()
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155
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Two Isoforms of Yersinia pestis Plasminogen Activator Pla: Intraspecies Distribution, Intrinsic Disorder Propensity, and Contribution to Virulence. PLoS One 2016; 11:e0168089. [PMID: 27936190 PMCID: PMC5148098 DOI: 10.1371/journal.pone.0168089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/25/2016] [Indexed: 12/12/2022] Open
Abstract
It has been shown previously that several endemic Y. pestis isolates with limited virulence contained the I259 isoform of the outer membrane protease Pla, while the epidemic highly virulent strains possessed only the T259 Pla isoform. Our sequence analysis of the pla gene from 118 Y. pestis subsp. microtus strains revealed that the I259 isoform was present exclusively in the endemic strains providing a convictive evidence of more ancestral origin of this isoform. Analysis of the effects of the I259T polymorphism on the intrinsic disorder propensity of Pla revealed that the I259T mutation slightly increases the intrinsic disorder propensity of the C-terminal tail of Pla and makes this protein slightly more prone for disorder-based protein-protein interactions, suggesting that the T259 Pla could be functionally more active than the I259 Pla. This assumption was proven experimentally by assessing the coagulase and fibrinolytic activities of the two Pla isoforms in human plasma, as well as in a direct fluorometric assay with the Pla peptide substrate. The virulence testing of Pla-negative or expressing the I259 and T259 Pla isoforms Y. pestis subsp. microtus and subsp. pestis strains did not reveal any significant difference in LD50 values and dose-dependent survival assays between them by using a subcutaneous route of challenge of mice and guinea pigs or intradermal challenge of mice. However, a significant decrease in time-to-death was observed in animals infected with the epidemic T259 Pla-producing strains as compared to the parent Pla-negative variants. Survival curves of the endemic I259 Pla+ strains fit between them, but significant difference in mean time to death post infection between the Pla−strains and their I259 Pla+ variants could be seen only in the isogenic set of subsp. pestis strains. These findings suggest an essential role for the outer membrane protease Pla evolution in Y. pestis bubonic infection exacerbation that is necessary for intensification of epidemic process from endemic natural focality with sporadic cases in men to rapidly expanding epizootics followed by human epidemic outbreaks, local epidemics or even pandemics.
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156
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Insights into the evolution of pathogenicity of Escherichia coli from genomic analysis of intestinal E. coli of Marmota himalayana in Qinghai-Tibet plateau of China. Emerg Microbes Infect 2016; 5:e122. [PMID: 27924811 PMCID: PMC5180367 DOI: 10.1038/emi.2016.122] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/10/2016] [Accepted: 09/19/2016] [Indexed: 01/09/2023]
Abstract
Escherichia coli is both of a widespread harmless gut commensal and a versatile pathogen of humans. Domestic animals are a well-known reservoir for pathogenic E. coli. However, studies of E. coli populations from wild animals that have been separated from human activities had been very limited. Here we obtained 580 isolates from intestinal contents of 116 wild Marmot Marmota himalayana from Qinghai–Tibet plateau, China, with five isolates per animal. We selected 125 (hereinafter referred to as strains) from the 580 isolates for genome sequencing, based on unique pulse field gel electrophoresis patterns and at least one isolate per animal. Whole genome sequence analysis revealed that all 125 strains carried at least one and the majority (79.2%) carried multiple virulence genes based on the analysis of 22 selected virulence genes. In particular, the majority of the strains carried virulence genes from different pathovars as potential 'hybrid pathogens'. The alleles of eight virulence genes from the Marmot E. coli were found to have diverged earlier than all known alleles from human and other animal E. coli. Phylogenetic analysis of the 125 Marmot E. coli genomes and 355 genomes selected from 1622 human and other E. coli strains identified two new phylogroups, G and H, both of which diverged earlier than the other phylogroups. Eight of the 12 well-known pathogenic E. coli lineages were found to share a most recent common ancestor with one or more Marmot E. coli strains. Our results suggested that the intestinal E. coli of the Marmots contained a diverse virulence gene pool and is potentially pathogenic to humans. These findings provided a new understanding of the evolutionary origin of pathogenic E. coli.
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157
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Duchêne S, Holt KE, Weill FX, Le Hello S, Hawkey J, Edwards DJ, Fourment M, Holmes EC. Genome-scale rates of evolutionary change in bacteria. Microb Genom 2016; 2:e000094. [PMID: 28348834 PMCID: PMC5320706 DOI: 10.1099/mgen.0.000094] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 10/24/2016] [Indexed: 01/26/2023] Open
Abstract
Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host–pathogen associations and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with ‘ancient DNA’ data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from approximately 10−5 to 10−8 nucleotide substitutions per site year−1. This variation was negatively associated with sampling time, with this relationship best described by an exponential decay curve. To avoid potential estimation biases, such time-dependency should be considered when inferring evolutionary time-scales in bacteria.
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Affiliation(s)
- Sebastian Duchêne
- 1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.,2Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia.,3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kathryn E Holt
- 2Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia.,3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | | | - Simon Le Hello
- 4Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris 75015, France
| | - Jane Hawkey
- 2Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia.,3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - David J Edwards
- 2Centre for Systems Genomics, The University of Melbourne, Melbourne, VIC 3010, Australia.,3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mathieu Fourment
- 1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- 1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
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158
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Feldman M, Harbeck M, Keller M, Spyrou MA, Rott A, Trautmann B, Scholz HC, Päffgen B, Peters J, McCormick M, Bos K, Herbig A, Krause J. A High-Coverage Yersinia pestis Genome from a Sixth-Century Justinianic Plague Victim. Mol Biol Evol 2016; 33:2911-2923. [PMID: 27578768 PMCID: PMC5062324 DOI: 10.1093/molbev/msw170] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The Justinianic Plague, which started in the sixth century and lasted to the mid eighth century, is thought to be the first of three historically documented plague pandemics causing massive casualties. Historical accounts and molecular data suggest the bacterium Yersinia pestis as its etiological agent. Here we present a new high-coverage (17.9-fold) Y. pestis genome obtained from a sixth-century skeleton recovered from a southern German burial site close to Munich. The reconstructed genome enabled the detection of 30 unique substitutions as well as structural differences that have not been previously described. We report indels affecting a lacl family transcription regulator gene as well as nonsynonymous substitutions in the nrdE, fadJ, and pcp genes, that have been suggested as plague virulence determinants or have been shown to be upregulated in different models of plague infection. In addition, we identify 19 false positive substitutions in a previously published lower-coverage Y. pestis genome from another archaeological site of the same time period and geographical region that is otherwise genetically identical to the high-coverage genome sequence reported here, suggesting low-genetic diversity of the plague during the sixth century in rural southern Germany.
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Affiliation(s)
- Michal Feldman
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Michaela Harbeck
- SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany
| | - Marcel Keller
- Max Planck Institute for the Science of Human History, Jena, Germany
- SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany
| | - Maria A. Spyrou
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Andreas Rott
- SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany
| | - Bernd Trautmann
- SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany
| | - Holger C. Scholz
- Bundeswehr Institute of Microbiology, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Bernd Päffgen
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilian University Munich, Germany
| | - Joris Peters
- SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilian University of Munich, Germany
| | - Michael McCormick
- Department of History, Harvard University, Initiative for the Science of the Human Past
| | - Kirsten Bos
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
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159
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Vogler AJ, Nottingham R, Busch JD, Sahl JW, Shuey MM, Foster JT, Schupp JM, Smith SR, Rocke TE, Keim P, Wagner DM. VNTR diversity in Yersinia pestis isolates from an animal challenge study reveals the potential for in vitro mutations during laboratory cultivation. INFECTION GENETICS AND EVOLUTION 2016; 45:297-302. [PMID: 27664903 DOI: 10.1016/j.meegid.2016.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/30/2016] [Accepted: 09/20/2016] [Indexed: 10/21/2022]
Abstract
Underlying mutation rates and other evolutionary forces shape the population structure of bacteria in nature. Although easily overlooked, similar forces are at work in the laboratory and may influence observed mutations. Here, we investigated tissue samples and Yersinia pestis isolates from a rodent laboratory challenge with strain CO92 using whole genome sequencing and multi-locus variable-number tandem repeat (VNTR) analysis (MLVA). We identified six VNTR mutations that were found to have occurred in vitro during laboratory cultivation rather than in vivo during the rodent challenge. In contrast, no single nucleotide polymorphism (SNP) mutations were observed, either in vivo or in vitro. These results were consistent with previously published mutation rates and the calculated number of Y. pestis generations that occurred during the in vitro versus the in vivo portions of the experiment. When genotyping disease outbreaks, the potential for in vitro mutations should be considered, particularly when highly variable genetic markers such as VNTRs are used.
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Affiliation(s)
- Amy J Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States
| | - Roxanne Nottingham
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States
| | - Joseph D Busch
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States
| | - Jason W Sahl
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States
| | - Megan M Shuey
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States; Department of Medicine, Vanderbilt University, School of Medicine, Nashville, TN, United States
| | - Jeffrey T Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States; Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - James M Schupp
- Translational Genomics Research Institute North, Flagstaff, AZ, United States
| | - Susan R Smith
- US Geological Survey, National Wildlife Health Center, Madison, WI, United States
| | - Tonie E Rocke
- US Geological Survey, National Wildlife Health Center, Madison, WI, United States
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States; Translational Genomics Research Institute North, Flagstaff, AZ, United States
| | - David M Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, United States.
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160
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Afanas’ev MV, Balakhonov SV, Tokmakova EG, Polovinkina VS, Sidorova EA, Sinkov VV. Analysis of complete sequence of cryptic plasmid pTP33 from Yersinia pestis isolated in Tuva natural focus of plague. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416090027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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161
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Kopylov PK, Platonov ME, Ablamunits VG, Kombarova TI, Ivanov SA, Kadnikova LA, Somov AN, Dentovskaya SV, Uversky VN, Anisimov AP. Yersinia pestis Caf1 Protein: Effect of Sequence Polymorphism on Intrinsic Disorder Propensity, Serological Cross-Reactivity and Cross-Protectivity of Isoforms. PLoS One 2016; 11:e0162308. [PMID: 27606595 PMCID: PMC5015843 DOI: 10.1371/journal.pone.0162308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/19/2016] [Indexed: 12/11/2022] Open
Abstract
Yersinia pestis Caf1 is a multifunctional protein responsible for antiphagocytic activity and is a key protective antigen. It is generally conserved between globally distributed Y. pestis strains, but Y. pestis subsp. microtus biovar caucasica strains circulating within populations of common voles in Georgia and Armenia were reported to carry a single substitution of alanine to serine. We investigated polymorphism of the Caf1 sequences among other Y. pestis subsp. microtus strains, which have a limited virulence in guinea pigs and in humans. Sequencing of caf1 genes from 119 Y. pestis strains belonging to different biovars within subsp. microtus showed that the Caf1 proteins exist in three isoforms, the global type Caf1NT1 (Ala48 Phe117), type Caf1NT2 (Ser48 Phe117) found in Transcaucasian-highland and Pre-Araks natural plague foci #4-7, and a novel Caf1NT3 type (Ala48 Val117) endemic in Dagestan-highland natural plague focus #39. Both minor types are the progenies of the global isoform. In this report, Caf1 polymorphism was analyzed by comparing predicted intrinsic disorder propensities and potential protein-protein interactivities of the three Caf1 isoforms. The analysis revealed that these properties of Caf1 protein are minimally affected by its polymorphism. All protein isoforms could be equally detected by an immunochromatography test for plague at the lowest protein concentration tested (1.0 ng/mL), which is the detection limit. When compared to the classic Caf1NT1 isoform, the endemic Caf1NT2 or Caf1NT3 had lower immunoreactivity in ELISA and lower indices of self- and cross-protection. Despite a visible reduction in cross-protection between all Caf1 isoforms, our data suggest that polymorphism in the caf1 gene may not allow the carriers of Caf1NT2 or Caf1NT3 variants escaping from the Caf1NT1-mediated immunity to plague in the case of a low-dose flea-borne infection.
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Affiliation(s)
- Pavel Kh. Kopylov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Mikhail E. Platonov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | | | - Tat’yana I. Kombarova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Sergey A. Ivanov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Lidiya A. Kadnikova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Aleksey N. Somov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Svetlana V. Dentovskaya
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Andrey P. Anisimov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
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162
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Andam CP, Worby CJ, Chang Q, Campana MG. Microbial Genomics of Ancient Plagues and Outbreaks. Trends Microbiol 2016; 24:978-990. [PMID: 27618404 DOI: 10.1016/j.tim.2016.08.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 07/29/2016] [Accepted: 08/16/2016] [Indexed: 01/22/2023]
Abstract
The recent use of next-generation sequencing methods to investigate historical disease outbreaks has provided us with an unprecedented ability to address important and long-standing questions in epidemiology, pathogen evolution, and human history. In this review, we present major findings that illustrate how microbial genomics has provided new insights into the nature and etiology of infectious diseases of historical importance, such as plague, tuberculosis, and leprosy. Sequenced isolates collected from archaeological remains also provide evidence for the timing of historical evolutionary events as well as geographic spread of these pathogens. Elucidating the genomic basis of virulence in historical diseases can provide relevant information on how we can effectively understand the emergence and re-emergence of infectious diseases today and in the future.
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Affiliation(s)
- Cheryl P Andam
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA; University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Durham, NH 03824, USA.
| | - Colin J Worby
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA
| | - Qiuzhi Chang
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA
| | - Michael G Campana
- Smithsonian Conservation Biology Institute, Center for Conservation Genomics, 3001 Connecticut Avenue NW, Washington, DC 20008, USA.
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163
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Drancourt M, Raoult D. Molecular history of plague. Clin Microbiol Infect 2016; 22:911-915. [PMID: 27615720 DOI: 10.1016/j.cmi.2016.08.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/30/2016] [Accepted: 08/30/2016] [Indexed: 12/20/2022]
Abstract
Plague, a deadly zoonose caused by the bacterium Yersinia pestis, has been firmly documented in 39 historical burial sites in Eurasia that date from the Bronze Age to two historical pandemics spanning the 6th to 18th centuries. Palaeomicrobiologic data, including gene and spacer sequences, whole genome sequences and protein data, confirmed that two historical pandemics swept over Europe from probable Asian sources and possible two-way-ticket journeys back from Europe to Asia. These investigations made it possible to address questions regarding the potential sources and routes of transmission by completing the standard rodent and rodent-flea transmission scheme. This suggested that plague was transmissible by human ectoparasites such as lice, and that Y. pestis was able to persist for months in the soil, which is a source of reinfection for burrowing mammals. The analyses of seven complete genome sequences from the Bronze Age indicated that Y. pestis was probably not an ectoparasite-borne pathogen in these populations. Further analyses of 14 genomes indicated that the Justinian pandemic strains may have formed a clade distinct from the one responsible for the second pandemic, spanning in Y. pestis branch 1, which also comprises the third pandemic strains. Further palaeomicrobiologic studies must tightly connect with historical and anthropologic studies to resolve questions regarding the actual sources of plague in ancient populations, alternative routes of transmission and resistance traits. Answering these questions will broaden our understanding of plague epidemiology so we may better face the actuality of this deadly infection in countries where it remains epidemic.
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Affiliation(s)
- M Drancourt
- Aix Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - D Raoult
- Aix Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France.
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164
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Shaban H, Na I, Kislichkina AA, Dentovskaya SV, Anisimov AP, Uversky VN. Effect of natural polymorphism on structure and function of the Yersinia pestis outer membrane porin F (OmpF protein): a computational study. J Biomol Struct Dyn 2016; 35:2588-2603. [PMID: 27593697 DOI: 10.1080/07391102.2016.1224734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The Yersinia pestis outer membrane porin F (OmpF) is a transmembrane protein located in the outer membrane of this Gram-negative bacterium which is the causative agent of plague, where it plays a significant role in controlling the selective permeability of the membrane. The amino acid sequences of OmpF proteins from 48 Y. pestis strains representing all currently available phylogenetic groups of this Gram-negative bacterium were recently deduced. Comparison of these amino acid sequences revealed that the OmpF can be present in four isoforms, the pestis-pestis type, and the pestis-microtus types I, II, and III. OmpF of the most recent pestis-pestis type has an alanine residue at the position 148, where all the pestis-microtus types have threonine there (T148A polymorphism). The variability of different pestis-microtus types is caused by an additional polymorphism at the 193rd position, where the OmpFs of the pestis-microtus type II and type III have isoleucine-glycine (IG+193) or isoleucine-glycine-isoleucine-glycine (IGIG+193) insertions, respectively (IG+193 and IGIG+193 polymorphism). To investigate potential effects of these sequence polymorphisms on the structural properties of the OmpF protein, we conducted multi-level computational analysis of its isoforms. Analysis of the I-TASSER-generated 3D-models revealed that the Yersinia OmpF is very similar to other non-specific enterobacterial porins. The T148A polymorphism affected a loop located in the external vestibule of the OmpF channel, whereas IG+193 and IGIG+193 polymorphisms affected one of its β-strands. Our analysis also suggested that polymorphism has moderate effect on the predicted local intrinsic disorder predisposition of OmpF, but might have some functional implementations.
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Affiliation(s)
- Hiba Shaban
- a Department of Molecular Medicine, Morsani College of Medicine , University of South Florida , Tampa 33612 , FL , USA
| | - Insing Na
- a Department of Molecular Medicine, Morsani College of Medicine , University of South Florida , Tampa 33612 , FL , USA
| | - Angelina A Kislichkina
- b State Research Center for Applied Microbiology and Biotechnology , Obolensk 142279 , Moscow Region , Russia
| | - Svetlana V Dentovskaya
- b State Research Center for Applied Microbiology and Biotechnology , Obolensk 142279 , Moscow Region , Russia
| | - Andrey P Anisimov
- b State Research Center for Applied Microbiology and Biotechnology , Obolensk 142279 , Moscow Region , Russia
| | - Vladimir N Uversky
- a Department of Molecular Medicine, Morsani College of Medicine , University of South Florida , Tampa 33612 , FL , USA.,c USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine, University of South Florida , Tampa 33612 , FL , USA.,d Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , St. Petersburg 194064 , Russia
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165
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Sahl JW, Lemmer D, Travis J, Schupp JM, Gillece JD, Aziz M, Driebe EM, Drees KP, Hicks ND, Williamson CHD, Hepp CM, Smith DE, Roe C, Engelthaler DM, Wagner DM, Keim P. NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats. Microb Genom 2016; 2:e000074. [PMID: 28348869 DOI: 10.1099/mgen.0.000074] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/17/2016] [Indexed: 12/30/2022] Open
Abstract
Whole-genome sequencing (WGS) of bacterial isolates has become standard practice in many laboratories. Applications for WGS analysis include phylogeography and molecular epidemiology, using single nucleotide polymorphisms (SNPs) as the unit of evolution. NASP was developed as a reproducible method that scales well with the hundreds to thousands of WGS data typically used in comparative genomics applications. In this study, we demonstrate how NASP compares with other tools in the analysis of two real bacterial genomics datasets and one simulated dataset. Our results demonstrate that NASP produces similar, and often better, results in comparison with other pipelines, but is much more flexible in terms of data input types, job management systems, diversity of supported tools and output formats. We also demonstrate differences in results based on the choice of the reference genome and choice of inferring phylogenies from concatenated SNPs or alignments including monomorphic positions. NASP represents a source-available, version-controlled, unit-tested method and can be obtained from tgennorth.github.io/NASP.
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Affiliation(s)
- Jason W Sahl
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA.,2Northern Arizona University, S San Francisco St, Flagstaff, AZ 86011, USA
| | - Darrin Lemmer
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Jason Travis
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - James M Schupp
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - John D Gillece
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Maliha Aziz
- 3The George Washington University, 2121 I St NW, Washington, DC 20052, USA
| | | | - Kevin P Drees
- 4University of New Hampshire, 105 Main St, Durham, NH 03824, USA
| | | | | | - Crystal M Hepp
- 2Northern Arizona University, S San Francisco St, Flagstaff, AZ 86011, USA
| | - David Earl Smith
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Chandler Roe
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA
| | | | - David M Wagner
- 2Northern Arizona University, S San Francisco St, Flagstaff, AZ 86011, USA
| | - Paul Keim
- 2Northern Arizona University, S San Francisco St, Flagstaff, AZ 86011, USA
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166
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Jones L, Nevell R. Plagued by doubt and viral misinformation: the need for evidence-based use of historical disease images. THE LANCET. INFECTIOUS DISEASES 2016; 16:e235-e240. [PMID: 27522232 DOI: 10.1016/s1473-3099(16)30119-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/02/2016] [Accepted: 05/05/2016] [Indexed: 12/21/2022]
Abstract
The digitisation of historical disease images and their widespread availability on the internet have been a boon to education and research, but with unintended consequences, including the misrepresentation of infectious diseases in the past and the viral spread of misinformation. Many medieval images containing scenes of infectious disease come from non-medical sources and are not meant to convey any medical meaning. Erroneous modern captions have led to the publication of several historical images labelled as depictions of the plague, although artistic and textual evidence shows that they are not. Mislabelled images lose their intended historical narrative, and their use creates a distorted view of the past and of the disease in question. Scholars should give the same careful consideration to an image's evidentiary context that they would insist on giving to all other forms of evidence.
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Affiliation(s)
- Lori Jones
- Department of History, University of Ottawa, Ottawa, ON, Canada.
| | - Richard Nevell
- Department of Archaeology, University of Exeter, Exeter, Devon, UK
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167
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McNally A, Thomson NR, Reuter S, Wren BW. 'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution. Nat Rev Microbiol 2016; 14:177-90. [PMID: 26876035 DOI: 10.1038/nrmicro.2015.29] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pathogenic species in the Yersinia genus have historically been targets for research aimed at understanding how bacteria evolve into mammalian pathogens. The advent of large-scale population genomic studies has greatly accelerated the progress in this field, and Yersinia pestis, Yersinia pseudotuberculosis and Yersinia enterocolitica have once again acted as model organisms to help shape our understanding of the evolutionary processes involved in pathogenesis. In this Review, we highlight the gene gain, gene loss and genome rearrangement events that have been identified by genomic studies in pathogenic Yersinia species, and we discuss how these findings are changing our understanding of pathogen evolution. Finally, as these traits are also found in the genomes of other species in the Enterobacteriaceae, we suggest that they provide a blueprint for the evolution of enteropathogenic bacteria.
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Affiliation(s)
- Alan McNally
- Pathogen Research Group, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Nicholas R Thomson
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Sandra Reuter
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Brendan W Wren
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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168
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Abstract
The plague bacillus Yersinia pestis is unique among the pathogenic Enterobacteriaceae in utilizing an arthropod-borne transmission route. Transmission by fleabite is a recent evolutionary adaptation that followed the divergence of Y. pestis from the closely related food- and waterborne enteric pathogen Yersinia pseudotuberculosis A combination of population genetics, comparative genomics, and investigations of Yersinia-flea interactions have disclosed the important steps in the evolution and emergence of Y. pestis as a flea-borne pathogen. Only a few genetic changes, representing both gene gain by lateral transfer and gene loss by loss-of-function mutation (pseudogenization), were fundamental to this process. The emergence of Y. pestis fits evolutionary theories that emphasize ecological opportunity in adaptive diversification and rapid emergence of new species.
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169
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Archaeogenetics in evolutionary medicine. J Mol Med (Berl) 2016; 94:971-7. [PMID: 27289479 DOI: 10.1007/s00109-016-1438-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 05/22/2016] [Accepted: 06/03/2016] [Indexed: 12/24/2022]
Abstract
Archaeogenetics is the study of exploration of ancient DNA (aDNA) of more than 70 years old. It is an important part of the wider studies of many different areas of our past, including animal, plant and pathogen evolution and domestication events. Hereby, we address specifically the impact of research in archaeogenetics in the broader field of evolutionary medicine. Studies on ancient hominid genomes help to understand even modern health patterns. Human genetic microevolution, e.g. related to abilities of post-weaning milk consumption, and specifically genetic adaptation in disease susceptibility, e.g. towards malaria and other infectious diseases, are of the upmost importance in contributions of archeogenetics on the evolutionary understanding of human health and disease. With the increase in both the understanding of modern medical genetics and the ability to deep sequence ancient genetic information, the field of archaeogenetic evolutionary medicine is blossoming.
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170
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Transcriptome Remodeling Contributes to Epidemic Disease Caused by the Human Pathogen Streptococcus pyogenes. mBio 2016; 7:mBio.00403-16. [PMID: 27247229 PMCID: PMC4895104 DOI: 10.1128/mbio.00403-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
For over a century, a fundamental objective in infection biology research has been to understand the molecular processes contributing to the origin and perpetuation of epidemics. Divergent hypotheses have emerged concerning the extent to which environmental events or pathogen evolution dominates in these processes. Remarkably few studies bear on this important issue. Based on population pathogenomic analysis of 1,200 Streptococcus pyogenes type emm89 infection isolates, we report that a series of horizontal gene transfer events produced a new pathogenic genotype with increased ability to cause infection, leading to an epidemic wave of disease on at least two continents. In the aggregate, these and other genetic changes substantially remodeled the transcriptomes of the evolved progeny, causing extensive differential expression of virulence genes and altered pathogen-host interaction, including enhanced immune evasion. Our findings delineate the precise molecular genetic changes that occurred and enhance our understanding of the evolutionary processes that contribute to the emergence and persistence of epidemically successful pathogen clones. The data have significant implications for understanding bacterial epidemics and for translational research efforts to blunt their detrimental effects. The confluence of studies of molecular events underlying pathogen strain emergence, evolutionary genetic processes mediating altered virulence, and epidemics is in its infancy. Although understanding these events is necessary to develop new or improved strategies to protect health, surprisingly few studies have addressed this issue, in particular, at the comprehensive population genomic level. Herein we establish that substantial remodeling of the transcriptome of the human-specific pathogen Streptococcus pyogenes by horizontal gene flow and other evolutionary genetic changes is a central factor in precipitating and perpetuating epidemic disease. The data unambiguously show that the key outcome of these molecular events is evolution of a new, more virulent pathogenic genotype. Our findings provide new understanding of epidemic disease.
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171
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Rieux A, Balloux F. Inferences from tip-calibrated phylogenies: a review and a practical guide. Mol Ecol 2016; 25:1911-24. [PMID: 26880113 PMCID: PMC4949988 DOI: 10.1111/mec.13586] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 02/01/2016] [Accepted: 02/04/2016] [Indexed: 12/25/2022]
Abstract
Molecular dating of phylogenetic trees is a growing discipline using sequence data to co‐estimate the timing of evolutionary events and rates of molecular evolution. All molecular‐dating methods require converting genetic divergence between sequences into absolute time. Historically, this could only be achieved by associating externally derived dates obtained from fossil or biogeographical evidence to internal nodes of the tree. In some cases, notably for fast‐evolving genomes such as viruses and some bacteria, the time span over which samples were collected may cover a significant proportion of the time since they last shared a common ancestor. This situation allows phylogenetic trees to be calibrated by associating sampling dates directly to the sequences representing the tips (terminal nodes) of the tree. The increasing availability of genomic data from ancient DNA extends the applicability of such tip‐based calibration to a variety of taxa including humans, extinct megafauna and various microorganisms which typically have a scarce fossil record. The development of statistical models accounting for heterogeneity in different aspects of the evolutionary process while accommodating very large data sets (e.g. whole genomes) has allowed using tip‐dating methods to reach inferences on divergence times, substitution rates, past demography or the age of specific mutations on a variety of spatiotemporal scales. In this review, we summarize the current state of the art of tip dating, discuss some recent applications, highlight common pitfalls and provide a ‘how to’ guide to thoroughly perform such analyses.
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Affiliation(s)
- Adrien Rieux
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
| | - François Balloux
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
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172
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Cobble KR, Califf KJ, Stone NE, Shuey MM, Birdsell DN, Colman RE, Schupp JM, Aziz M, Van Andel R, Rocke TE, Wagner DM, Busch JD. Genetic variation at the MHC DRB1 locus is similar across Gunnison's prairie dog (Cynomys gunnisoni) colonies regardless of plague history. Ecol Evol 2016; 6:2624-51. [PMID: 27066243 PMCID: PMC4798151 DOI: 10.1002/ece3.2077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 01/16/2023] Open
Abstract
Yersinia pestis was introduced to North America around 1900 and leads to nearly 100% mortality in prairie dog (Cynomys spp.) colonies during epizootic events, which suggests this pathogen may exert a strong selective force. We characterized genetic diversity at an MHC class II locus (DRB1) in Gunnison's prairie dog (C. gunnisoni) and quantified population genetic structure at the DRB1 versus 12 microsatellite loci in three large Arizona colonies. Two colonies, Seligman (SE) and Espee Ranch (ES), have experienced multiple plague‐related die‐offs in recent years, whereas plague has never been documented at Aubrey Valley (AV). We found fairly low allelic diversity at the DRB1 locus, with one allele (DRB1*01) at high frequency (0.67–0.87) in all colonies. Two other DRB1 alleles appear to be trans‐species polymorphisms shared with the black‐tailed prairie dog (C. ludovicianus), indicating that these alleles have been maintained across evolutionary time frames. Estimates of genetic differentiation were generally lower at the MHC locus (FST = 0.033) than at microsatellite markers (FST = 0.098). The reduced differentiation at DRB1 may indicate that selection has been important for shaping variation at MHC loci, regardless of the presence or absence of plague in recent decades. However, genetic drift has probably also influenced the DRB1 locus because its level of differentiation was not different from that of microsatellites in an FST outlier analysis. We then compared specific MHC alleles to plague survivorship in 60 C. gunnisoni that had been experimentally infected with Y. pestis. We found that survival was greater in individuals that carried at least one copy of the most common allele (DRB1*01) compared to those that did not (60% vs. 20%). Although the sample sizes of these two groups were unbalanced, this result suggests the possibility that this MHC class II locus, or a nearby linked gene, could play a role in plague survival.
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Affiliation(s)
- Kacy R Cobble
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Katy J Califf
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Nathan E Stone
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Megan M Shuey
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Dawn N Birdsell
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Rebecca E Colman
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - James M Schupp
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - Maliha Aziz
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - Roger Van Andel
- University of California Berkeley MC 7150 Berkeley California 94720 USA
| | - Tonie E Rocke
- United States Geological Survey National Wildlife Health Center 6006 Schroeder Road Madison Wisconsin 53711 USA
| | - David M Wagner
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Joseph D Busch
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
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173
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Perry RD, Bobrov AG, Fetherston JD. The role of transition metal transporters for iron, zinc, manganese, and copper in the pathogenesis of Yersinia pestis. Metallomics 2016; 7:965-78. [PMID: 25891079 DOI: 10.1039/c4mt00332b] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Yersinia pestis, the causative agent of bubonic, septicemic and pneumonic plague, encodes a multitude of Fe transport systems. Some of these are defective due to frameshift or IS element insertions, while others are functional in vitro but have no established role in causing infections. Indeed only 3 Fe transporters (Ybt, Yfe and Feo) have been shown to be important in at least one form of plague. The yersiniabactin (Ybt) system is essential in the early dermal/lymphatic stages of bubonic plague, irrelevant in the septicemic stage, and critical in pneumonic plague. Two Mn transporters have been characterized (Yfe and MntH). These two systems play a role in bubonic plague but the double yfe mntH mutant is fully virulent in a mouse model of pneumonic plague. The same in vivo phenotype occurs with a mutant lacking two (Yfe and Feo) of four ferrous transporters. A role for the Ybt siderophore in Zn acquisition has been revealed. Ybt-dependent Zn acquisition uses a transport system completely independent of the Fe-Ybt uptake system. Together Ybt components and ZnuABC play a critical role in Zn acquisition in vivo. Single mutants in either system retain high virulence in a mouse model of septicemic plague while the double mutant is completely avirulent.
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Affiliation(s)
- Robert D Perry
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY, USA.
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174
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Vergnaud G, Girault G, Thierry S, Pourcel C, Madani N, Blouin Y. Comparison of French and Worldwide Bacillus anthracis Strains Favors a Recent, Post-Columbian Origin of the Predominant North-American Clade. PLoS One 2016; 11:e0146216. [PMID: 26901621 PMCID: PMC4763433 DOI: 10.1371/journal.pone.0146216] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 12/15/2015] [Indexed: 01/28/2023] Open
Abstract
Background Bacillus anthracis, the highly dangerous zoonotic bacterial pathogen species is currently composed of three genetic groups, called A, B and C. Group A is represented worldwide whereas group B is present essentially in Western Europe and Southern Africa. Only three strains from group C have been reported. This knowledge is derived from the genotyping of more than 2000 strains collected worldwide. Strains from both group A and group B are present in France. Previous investigations showed that the majority of sporadic French strains belong to the so-called A.Br.011/009 group A clade and define a very remarkable polytomy with six branches. Here we explore the significance of this polytomy by comparing the French B. anthracis lineages to worldwide lineages. We take advantage of whole genome sequence data previously determined for 122 French strains and 45 strains of various origins. Results A total of 6690 SNPs was identified among the available dataset and used to draw the phylogeny. The phylogeny of the French B group strains which belongs to B.Br.CNEVA indicates an expansion from the south-east part of France (the Alps) towards the south-west (Massif-Central and Pyrenees). The relatively small group A strains belonging to A.Br.001/002 results from at least two independent introductions. Strikingly, the data clearly demonstrates that the currently predominant B. anthracis lineage in North America, called WNA for Western North American, is derived from one branch of the A.Br.011/009 polytomy predominant in France. Conclusions/Significance The present work extends the range of observed substitution rate heterogeneity within B. anthracis, in agreement with its ecology and in contrast with some other pathogens. The population structure of the six branches A.Br.011/009 polytomy identified in France, diversity of branch length, and comparison with the WNA lineage, suggests that WNA is of post-Columbian and west European origin, with France as a likely source. Furthermore, it is tempting to speculate that the polytomy’s most recent common ancestor -MRCA- dates back to the Hundred Years' war between France and England started in the mid-fourteenth century. These events were associated in France with deadly epidemics and major economic and social changes.
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Affiliation(s)
- Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
- * E-mail:
| | - Guillaume Girault
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Simon Thierry
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
| | - Nora Madani
- Bacterial Zoonoses Unit, Animal Health Laboratory, Anses, University Paris-Est, Maisons-Alfort, France
| | - Yann Blouin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette, France
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175
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Whole genome sequencing revealed host adaptation-focused genomic plasticity of pathogenic Leptospira. Sci Rep 2016; 6:20020. [PMID: 26833181 PMCID: PMC4735792 DOI: 10.1038/srep20020] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/09/2015] [Indexed: 12/31/2022] Open
Abstract
Leptospirosis, caused by pathogenic Leptospira spp., has recently been recognized as an emerging infectious disease worldwide. Despite its severity and global importance, knowledge about the molecular pathogenesis and virulence evolution of Leptospira spp. remains limited. Here we sequenced and analyzed 102 isolates representing global sources. A high genomic variability were observed among different Leptospira species, which was attributed to massive gene gain and loss events allowing for adaptation to specific niche conditions and changing host environments. Horizontal gene transfer and gene duplication allowed the stepwise acquisition of virulence factors in pathogenic Leptospira evolved from a recent common ancestor. More importantly, the abundant expansion of specific virulence-related protein families, such as metalloproteases-associated paralogs, were exclusively identified in pathogenic species, reflecting the importance of these protein families in the pathogenesis of leptospirosis. Our observations also indicated that positive selection played a crucial role on this bacteria adaptation to hosts. These novel findings may lead to greater understanding of the global diversity and virulence evolution of Leptospira spp.
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176
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Abstract
Microbial genome evolution is shaped by a variety of selective pressures. Understanding how these processes occur can help to address important problems in microbiology by explaining observed differences in phenotypes, including virulence and resistance to antibiotics. Greater access to whole-genome sequencing provides microbiologists with the opportunity to perform large-scale analyses of selection in novel settings, such as within individual hosts. This tutorial aims to guide researchers through the fundamentals underpinning popular methods for measuring selection in pathogens. These methods are transferable to a wide variety of organisms, and the exercises provided are designed for researchers with any level of programming experience.
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Affiliation(s)
- Jessica Hedge
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Daniel J. Wilson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
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177
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Bos KI, Herbig A, Sahl J, Waglechner N, Fourment M, Forrest SA, Klunk J, Schuenemann VJ, Poinar D, Kuch M, Golding GB, Dutour O, Keim P, Wagner DM, Holmes EC, Krause J, Poinar HN. Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus. eLife 2016; 5:e12994. [PMID: 26795402 PMCID: PMC4798955 DOI: 10.7554/elife.12994] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/19/2016] [Indexed: 12/30/2022] Open
Abstract
The 14th-18th century pandemic of Yersinia pestis caused devastating disease outbreaks in Europe for almost 400 years. The reasons for plague's persistence and abrupt disappearance in Europe are poorly understood, but could have been due to either the presence of now-extinct plague foci in Europe itself, or successive disease introductions from other locations. Here we present five Y. pestis genomes from one of the last European outbreaks of plague, from 1722 in Marseille, France. The lineage identified has not been found in any extant Y. pestis foci sampled to date, and has its ancestry in strains obtained from victims of the 14th century Black Death. These data suggest the existence of a previously uncharacterized historical plague focus that persisted for at least three centuries. We propose that this disease source may have been responsible for the many resurgences of plague in Europe following the Black Death.
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Affiliation(s)
- Kirsten I Bos
- Department of Archeological Sciences, University of Tübingen, Tübingen, Germany
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Herbig
- Department of Archeological Sciences, University of Tübingen, Tübingen, Germany
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jason Sahl
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States
| | - Nicholas Waglechner
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Mathieu Fourment
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Stephen A Forrest
- Department of Archeological Sciences, University of Tübingen, Tübingen, Germany
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
- Department of Biology, McMaster University, Hamilton, Canada
| | | | - Debi Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, Canada
| | - Olivier Dutour
- Laboratoire d'anthropologie biologique Paul Broca, Ecole Pratique des Hautes Etudes, PACEA, Université Bordeaux, Bordeaux, France
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States
| | - David M Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Johannes Krause
- Department of Archeological Sciences, University of Tübingen, Tübingen, Germany
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hendrik N Poinar
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
- Department of Biology, McMaster University, Hamilton, Canada
- Department of Biochemistry, McMaster University, Hamilton, Canada
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178
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Fan Y, Zhou Y, Feng N, Wang Q, Tian G, Wu X, Liu Z, Bi Y, Yang R, Wang X. Recombinant murine toxin from Yersinia pestis shows high toxicity and β-adrenergic blocking activity in mice. Microbes Infect 2016; 18:329-35. [PMID: 26774329 DOI: 10.1016/j.micinf.2016.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 12/31/2015] [Accepted: 01/06/2016] [Indexed: 11/26/2022]
Abstract
Yersinia pestis murine toxin (Ymt) encoded on pMT1 is a 61-kDa protein, a member of the phospholipase D superfamily, which is found in all the domains of life. It is considered to be an intracellular protein required for the survival of Y. pestis in the midgut of the flea, but the exact role of Ymt in the pathogenesis of Y. pestis has not been clarified. Purified Ymt is highly toxic to mice and rats, but the exact mechanism of the animals' death is unclear. Here, we prepared a recombinant Ymt in Escherichia coli BL21 cells, and determined its toxicity and activity. We demonstrated that recombinant Ymt was as toxic to mice as the native protein when administered via the intraperitoneal or intravenous route, and inhibited the elevation of blood sugar caused by adrenaline. We also demonstrated that recombinant Ymt was highly toxic to mice when administered via the muscular or subcutaneous route. We also show that the multiple organ congestion or hemorrhage caused by Ymt poisoning may explain the death of the mice.
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Affiliation(s)
- Yanxiao Fan
- Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, People's Republic of China; Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing 100071, People's Republic of China
| | - Yazhou Zhou
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing 100071, People's Republic of China
| | - Na Feng
- Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, People's Republic of China; Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing 100071, People's Republic of China
| | - Qiong Wang
- Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, People's Republic of China; Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing 100071, People's Republic of China
| | - Guang Tian
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing 100071, People's Republic of China
| | - Xiaohong Wu
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing 100071, People's Republic of China
| | - Zizhong Liu
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing 100071, People's Republic of China
| | - Yujing Bi
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing 100071, People's Republic of China
| | - Ruifu Yang
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing 100071, People's Republic of China
| | - Xiaoyi Wang
- Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, People's Republic of China; Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing 100071, People's Republic of China.
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179
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Seifert L, Wiechmann I, Harbeck M, Thomas A, Grupe G, Projahn M, Scholz HC, Riehm JM. Genotyping Yersinia pestis in Historical Plague: Evidence for Long-Term Persistence of Y. pestis in Europe from the 14th to the 17th Century. PLoS One 2016; 11:e0145194. [PMID: 26760973 PMCID: PMC4712009 DOI: 10.1371/journal.pone.0145194] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 12/01/2015] [Indexed: 12/19/2022] Open
Abstract
Ancient DNA (aDNA) recovered from plague victims of the second plague pandemic (14th to 17th century), excavated from two different burial sites in Germany, and spanning a time period of more than 300 years, was characterized using single nucleotide polymorphism (SNP) analysis. Of 30 tested skeletons 8 were positive for Yersinia pestis-specific nucleic acid, as determined by qPCR targeting the pla gene. In one individual (MP-19-II), the pla copy number in DNA extracted from tooth pulp was as high as 700 gene copies/μl, indicating severe generalized infection. All positive individuals were identical in all 16 SNP positions, separating phylogenetic branches within nodes N07_N10 (14 SNPs), N07_N08 (SNP s19) and N06_N07 (s545), and were highly similar to previously investigated plague victims from other European countries. Thus, beside the assumed continuous reintroduction of Y. pestis from central Asia in multiple waves during the second pandemic, long-term persistence of Y. pestis in Europe in a yet unknown reservoir host has also to be considered.
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Affiliation(s)
- Lisa Seifert
- Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Michaela Harbeck
- State Collection for Anthropology and Palaeoanatomy, Munich, Germany
| | - Astrid Thomas
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Gisela Grupe
- Ludwig Maximilian University of Munich, Munich, Germany
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180
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Genomic Analysis of Bacterial Outbreaks. Evol Biol 2016. [DOI: 10.1007/978-3-319-41324-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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181
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Qi Z, Cui Y, Zhang Q, Yang R. Taxonomy of Yersinia pestis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 918:35-78. [PMID: 27722860 DOI: 10.1007/978-94-024-0890-4_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This chapter summarized the taxonomy and typing works of Yersinia pestis since it's firstly identified in Hong Kong in 1894. Phenotyping methods that based on phenotypic characteristics, including biotyping, serotyping, antibiogram analysis, bacteriocin typing, phage typing, and plasmid typing, were firstly applied in classification of Y. pestis in subspecies level. And then, with the advancement of molecular biological technology, the methods based on outer membrane protein profiles, fatty acid composition, and bacterial mass fingerprinting were also used to identify the populations within Y. pestis. However, Y. pestis is a highly homogenous species; therefore, the above typing methods could only provide low resolution, e.g., only one serotype and one phage type were observed for the whole species. Since the 1990s, molecular typing based on DNA variations, including single-nucleotide polymorphism, gene gain/loss, variable-number tandem repeats, clustered regularly interspaced short palindromic repeat, etc., was introduced and improved the resolution and robust of typing result. Especially in recent years, genotyping-based whole-genome-wide variations were successfully employed in Y. pestis, which built the "gold standard" of typing scheme of the species and could distinguish the samples under the strain level. The taxonomy and typing works leaved us enormous polymorphism data; therefore, a comprehensive fingerprint database of Y. pestis was needed to collect and standardize these data, for facilitating future works on evolution, plague surveillance and control, anti-bioterrorism, and microbial forensic researches.
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Affiliation(s)
- Zhizhen Qi
- Qinghai Provincial Key Laboratory for Plague Control and Research, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai Province, 811602, China
| | - Yujun Cui
- Beijing Institute of Microbiology and Epidemiology, No. Dongdajie, Fengtai, Beijing, 100071, China
| | - Qingwen Zhang
- Qinghai Provincial Key Laboratory for Plague Control and Research, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai Province, 811602, China
| | - Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, No. Dongdajie, Fengtai, Beijing, 100071, China.
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182
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Abstract
This chapter summarizes researches on genome and evolution features of Yersinia pestis, the young pathogen that evolved from Y. pseudotuberculosis at least 5000 years ago. Y. pestis is a highly clonal bacterial species with closed pan-genome. Comparative genomic analysis revealed that genome of Y. pestis experienced highly frequent rearrangement and genome decay events during the evolution. The genealogy of Y. pestis includes five major branches, and four of them seemed raised from a "big bang" node that is associated with the Black Death. Although whole genome-wide variation of Y. pestis reflected a neutral evolutionary process, the branch length in the genealogical tree revealed over dispersion, which was supposedly caused by varied historical molecular clock that is associated with demographical effect by alternate cycles of enzootic disease and epizootic disease in sylvatic plague foci. In recent years, palaeomicrobiology researches on victims of the Black Death, and Justinian's plague verified that two historical pandemics were indeed caused by Y. pestis, but the etiological lineages might be extinct today.
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183
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Yang R, Cui Y, Bi Y. Perspectives on Yersinia pestis: A Model for Studying Zoonotic Pathogens. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 918:377-391. [PMID: 27722871 DOI: 10.1007/978-94-024-0890-4_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Yersinia pestis is a typical zoonotic bacterial pathogen. The following reasons make this pathogen a model for studying zoonotic pathogens: (1) Its unique lifestyle makes Y. pestis an ideal model for studying host-vector-environment-pathogen interactions; (2) population diversity characters in Y. pestis render it a model species for studying monomorphic bacterial evolution; (3) the pathogenic features of bacteria provide us with good opportunities to study human immune responses; (4) typical animal and vector models of Y. pestis infection create opportunities for experimental studies on pathogenesis and evolution; and (5) repeated pandemics and local outbreaks provide us with clues about the infectious disease outbreaks that have occurred in human history.
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Affiliation(s)
- Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.
| | - Yujun Cui
- Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China
| | - Yujing Bi
- Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China
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184
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Bramanti B, Stenseth NC, Walløe L, Lei X. Plague: A Disease Which Changed the Path of Human Civilization. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 918:1-26. [PMID: 27722858 DOI: 10.1007/978-94-024-0890-4_1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Plague caused by Yersinia pestis is a zoonotic infection, i.e., it is maintained in wildlife by animal reservoirs and on occasion spills over into human populations, causing outbreaks of different entities. Large epidemics of plague, which have had significant demographic, social, and economic consequences, have been recorded in Western European historical documents since the sixth century. Plague has remained in Europe for over 1400 years, intermittently disappearing, yet it is not clear if there were reservoirs for Y. pestis in Western Europe or if the pathogen was rather reimported on different occasions from Asian reservoirs by human agency. The latter hypothesis thus far seems to be the most plausible one, as it is sustained by both ecological and climatological evidence, helping to interpret the phylogeny of this bacterium.
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Affiliation(s)
- Barbara Bramanti
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lars Walløe
- Department of Physiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Xu Lei
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206, Changping, Beijing, People's Republic of China
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185
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Kislichkina AA, Bogun AG, Kadnikova LA, Maiskaya NV, Platonov ME, Anisimov NV, Galkina EV, Dentovskaya SV, Anisimov AP. Nineteen Whole-Genome Assemblies of Yersinia pestis subsp. microtus, Including Representatives of Biovars caucasica, talassica, hissarica, altaica, xilingolensis, and ulegeica. GENOME ANNOUNCEMENTS 2015; 3:e01342-15. [PMID: 26634751 PMCID: PMC4669392 DOI: 10.1128/genomea.01342-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 10/16/2015] [Indexed: 11/20/2022]
Abstract
The etiologic agent of plague, Yersinia pestis, includes two subspecies, of which Y. pestis subsp. microtus contains the strains that cause only occasional diseases in humans that are not accompanied by human-to-human transmission. Here, we report the draft genome sequences of 19 Y. pestis strains (across 6 biovars of Y. pestis subsp. microtus).
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Affiliation(s)
| | - Aleksandr G Bogun
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Lidiya A Kadnikova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Nadezhda V Maiskaya
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Mikhail E Platonov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Nikolai V Anisimov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Elena V Galkina
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | | | - Andrey P Anisimov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
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186
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Vogler AJ, Keim P, Wagner DM. A review of methods for subtyping Yersinia pestis: From phenotypes to whole genome sequencing. INFECTION GENETICS AND EVOLUTION 2015; 37:21-36. [PMID: 26518910 DOI: 10.1016/j.meegid.2015.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/23/2015] [Accepted: 10/24/2015] [Indexed: 12/28/2022]
Abstract
Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this important human pathogen. Methods are evaluated in terms of expense, difficulty, transferability among laboratories, discriminatory power, usefulness for different study questions, and current applicability in light of the advent of whole genome sequencing.
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Affiliation(s)
- Amy J Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA; Translational Genomics Research Institute North, Flagstaff, AZ 86001, USA.
| | - David M Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
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187
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Yu J, Sun Z, Liu W, Xi X, Song Y, Xu H, Lv Q, Bao Q, Menghe B, Sun T. Multilocus sequence typing of Streptococcus thermophilus from naturally fermented dairy foods in China and Mongolia. BMC Microbiol 2015; 15:236. [PMID: 26497818 PMCID: PMC4620635 DOI: 10.1186/s12866-015-0551-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 10/07/2015] [Indexed: 12/04/2022] Open
Abstract
Background Streptococcus thermophilus is a major dairy starter used for manufacturing of dairy products. In the present study, we developed a multilocus sequence typing (MLST) scheme for this important food bacterium. Sequences of 10 housekeeping genes (carB, clpX, dnaA, murC, murE, pepN, pepX, pyrG, recA, and rpoB) were obtained for 239 S. thermophilus strains, which were isolated from home-made fermented dairy foods in 18 different regions of Mongolia and China. Methods All 10 genes of S. thermophilus were sequenced, aligned, and defined sequence types (STs) using the BioNumerics Software. The nucleotide diversity was calculated by START v2.0. The population structure, phylogenetic relationships and the role of recombination were inferred using ClonalFrame v1.2, SplitsTree 4.0 and Structure v2.3. Results The 239 S. thermophilus isolates and 18 reference strains could be assigned into 119 different STs, which could be further separated into 16 clonal complexes (CCs) and 38 singletons. Among the 10 loci, a total of 132 polymorphic sites were detected. The standardized index of association (IAS = 0.0916), split-decomposition and ρ/θ (relative frequency of occurrence of recombination and mutation) and r/m value (relative impact of recombination and mutation in the diversification) confirms that recombination may have occurred, but it occurred at a low frequency in these 10 loci. Phylogenetic trees indicated that there were five lineages in the S. thermophilus isolates used in our study. MSTree and ClonalFrame tree analyses suggest that the evolution of S. thermophilus isolates have little relationship with geographic locality, but revealed no association with the types of fermented dairy product. Phylogenetic analysis of 36 whole genome strains (18 S. thermophilus, 2 S. vestibularis and 16 S. salivarius strains) indicated that our MLST scheme could clearly separate three closely related species within the salivarius group and is suitable for analyzing the population structure of the other two species in the salivarius group. Conclusions Our newly developed MLST scheme improved the understanding on the genetic diversity and population structure of the S. thermophilus, as well as provided useful information for further studies on the genotyping and evolutionary research for S. thermophilus strains with global diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0551-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Xiaoxia Xi
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Yuqin Song
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Haiyan Xu
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Qiang Lv
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Qiuhua Bao
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Bilige Menghe
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
| | - Tiansong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of P. R. China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, 010018, P. R. China.
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Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjögren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CMO, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, Gnuni A, Kriiska A, Lasak I, Metspalu M, Moiseyev V, Gromov A, Pokutta D, Saag L, Varul L, Yepiskoposyan L, Sicheritz-Pontén T, Foley RA, Lahr MM, Nielsen R, Kristiansen K, Willerslev E. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell 2015; 163:571-82. [PMID: 26496604 PMCID: PMC4644222 DOI: 10.1016/j.cell.2015.10.009] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/30/2015] [Accepted: 10/02/2015] [Indexed: 11/25/2022]
Abstract
The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics. Yersinia pestis was common across Eurasia in the Bronze Age The most recent common ancestor of all Y. pestis was 5,783 years ago The ymt gene was acquired before 951 cal BC, giving rise to transmission via fleas Bronze Age Y. pestis was not capable of causing bubonic plague
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Affiliation(s)
- Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Morten Erik Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Kasper Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Anders Gorm Pedersen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Alex Van Dam
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Christian Moliin Outzen Kapel
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Henrik Bjørn Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Pavel Avetisyan
- Division of Armenology and Social Sciences, Institute of Archaeology and Ethnography, National Academy of Sciences, 0025 Yerevan, Republic of Armenia
| | - Andrey Epimakhov
- Institute of History and Archaeology RAS (South Ural Department), South Ural State University, 454080 Chelyabinsk, Russia
| | | | - Artak Gnuni
- Department of Archaeology and Ethnography, Yerevan State University, 0025 Yerevan, Republic of Armenia
| | - Aivar Kriiska
- Department of Archaeology, University of Tartu, 51003 Tartu, Estonia
| | - Irena Lasak
- Institute of Archaeology, University of Wrocław, 50-139 Wrocław, Poland
| | - Mait Metspalu
- Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, 51010 Tartu, Estonia
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Andrei Gromov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Dalia Pokutta
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Lehti Saag
- Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, 51010 Tartu, Estonia
| | - Liivi Varul
- Department of Archaeology, University of Tartu, 51003 Tartu, Estonia
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, 0014 Yerevan, Armenia
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark
| | - Robert A Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Rasmus Nielsen
- Center for Theoretical Evolutionary Genetics, University of California, Berkeley, California 94720-3140, USA
| | - Kristian Kristiansen
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
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189
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Achtman M, Zhou Z, Didelot X. Formal Comment to Pettengill: The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence. PLoS One 2015; 10:e0134435. [PMID: 26274924 PMCID: PMC4537112 DOI: 10.1371/journal.pone.0134435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 06/09/2015] [Indexed: 01/22/2023] Open
Abstract
In 2013 Zhou et al. concluded that Salmonella enterica serovar Agona represents a genetically monomorphic lineage of recent ancestry, whose most recent common ancestor existed in 1932, or earlier. The Abstract stated 'Agona consists of three lineages with minimal mutational diversity: only 846 single nucleotide polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since Agona evolved in 1932 and subsequently underwent a major population expansion in the 1960s.' These conclusions have now been criticized by Pettengill, who claims that the evolutionary models used to date Agona may not have been appropriate, the dating estimates were inaccurate, and the age of emergence of Agona should have been qualified by an upper limit reflecting the date of its divergence from an outgroup, serovar Soerenga. We dispute these claims. Firstly, Pettengill's analysis of Agona is not justifiable on technical grounds. Secondly, an upper limit for divergence from an outgroup would only be meaningful if the outgroup were closely related to Agona, but close relatives of Agona are yet to be identified. Thirdly, it is not possible to reliably date the time of divergence between Agona and Soerenga. We conclude that Pettengill's criticism is comparable to a tempest in a teapot.
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Affiliation(s)
- Mark Achtman
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom
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190
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Califf KJ, Keim PS, Wagner DM, Sahl JW. Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics. Microb Genom 2015; 1:e000028. [PMID: 28348813 PMCID: PMC5320571 DOI: 10.1099/mgen.0.000028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/06/2015] [Indexed: 12/13/2022] Open
Abstract
Yersinia pestis, the causative agent of plague, is best known for historical pandemics, but still actively causes disease in many parts of the world. Y. pestis is a recently derived clone of the pathogenic species Yersinia pseudotuberculosis, but is more associated with human infection. Numerous studies have documented genomic changes since the two species differentiated, although all of these studies used a relatively small sample set for defining these differences. In this study, we compared the complete genomic content between a diverse set of Y. pestis and Y. pseudotuberculosis genomes, and identified unique loci that could serve as diagnostic markers or for better understanding the evolution and pathogenesis of each group. Comparative genomics analyses also identified subtle variations in gene content between individual monophyletic clades within these species, based on a core genome single nucleotide polymorphism phylogeny that would have been undetected in a less comprehensive genome dataset. We also screened loci that were identified in other published studies as unique to either species and generally found a non-uniform distribution, suggesting that the assignment of these unique genes to either species should be re-evaluated in the context of current sequencing efforts. Overall, this study provides a high-resolution view into the genomic differences between Y. pestis and Y. pseudotuberculosis, demonstrating fine-scale differentiation and unique gene composition in both species.
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Affiliation(s)
- Katy J. Califf
- Microbial Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul S. Keim
- Microbial Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - David M. Wagner
- Microbial Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason W. Sahl
- Microbial Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
- Translational Genomics Research Institute, Flagstaff, AZ, USA
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191
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Zhang M, Gilbert M, Yuki N, Cao F, Li J, Liu H, Li Q, Meng F, Zhang J. Association of Anti-GT1a Antibodies with an Outbreak of Guillain-Barré Syndrome and Analysis of Ganglioside Mimicry in an Associated Campylobacter jejuni Strain. PLoS One 2015; 10:e0131730. [PMID: 26197476 PMCID: PMC4510130 DOI: 10.1371/journal.pone.0131730] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 06/04/2015] [Indexed: 12/19/2022] Open
Abstract
An outbreak of Guillain-Barré syndrome (GBS), subsequent to Campylobacter jejuni enteritis, occurred in China in 2007. Serum anti-ganglioside antibodies were measured in GBS patients and controls. Genome sequencing was used to determine the phylogenetic relationship among three C. jejuni strains from a patient with GBS (ICDCCJ07001), a patient with gastroenteritis (ICDCCJ07002) and a healthy carrier (ICDCCJ07004), which were all associated with the outbreak. The ganglioside-like structures of the lipo-oligosaccharides of these strains were determined by mass spectrometry. Seventeen (53%) of the GBS patients had anti-GT1a IgG antibodies. GT1a mimicry was found in the lipo-oligosaccharides of strain ICDCCJ07002 and ICDCCJ07004; but a combination of GM3/GD3 mimics was observed in ICDCCJ07001, although this patient had anti-GT1a IgG antibodies. A single-base deletion in a glycosyltransferase gene caused the absence of GT1a mimicry in ICDCCJ07001. The phylogenetic tree showed that ICDCCJ07002 and ICDCCJ07004 were genetically closer to each other than to ICDCCJ07001. C. jejuni, bearing a GT1a-like lipo-oligosaccharide, might have caused the GBS outbreak and the loss of GT1a mimicry may have helped ICDCCJ07001 to survive in the host.
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Affiliation(s)
- Maojun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, 102206
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China, 310003
| | - Michel Gilbert
- Human Health Therapeutics, National Research Council Canada, Ottawa, K1A 0R6, Canada
| | - Nobuhiro Yuki
- National Neuroscience Institute, Singapore, Singapore, 308433
| | - Fangfang Cao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, 102206
| | - Jianjun Li
- Human Health Therapeutics, National Research Council Canada, Ottawa, K1A 0R6, Canada
| | - Hongying Liu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, 102206
| | - Qun Li
- Office for Disease Control and Emergency Response, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Fanliang Meng
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, 102206
| | - Jianzhong Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China, 102206
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China, 310003
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192
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Zimbler DL, Schroeder JA, Eddy JL, Lathem WW. Early emergence of Yersinia pestis as a severe respiratory pathogen. Nat Commun 2015; 6:7487. [PMID: 26123398 PMCID: PMC4491175 DOI: 10.1038/ncomms8487] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/12/2015] [Indexed: 11/09/2022] Open
Abstract
Yersinia pestis causes the fatal respiratory disease pneumonic plague. Y. pestis recently evolved from the gastrointestinal pathogen Y. pseudotuberculosis; however, it is not known at what point Y. pestis gained the ability to induce a fulminant pneumonia. Here we show that the acquisition of a single gene encoding the protease Pla was sufficient for the most ancestral, deeply rooted strains of Y. pestis to cause pneumonic plague, indicating that Y. pestis was primed to infect the lungs at a very early stage in its evolution. As Y. pestis further evolved, modern strains acquired a single amino-acid modification within Pla that optimizes protease activity. While this modification is unnecessary to cause pneumonic plague, the substitution is instead needed to efficiently induce the invasive infection associated with bubonic plague. These findings indicate that Y. pestis was capable of causing pneumonic plague before it evolved to optimally cause invasive infections in mammals.
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Affiliation(s)
- Daniel L Zimbler
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Jay A Schroeder
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Justin L Eddy
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Wyndham W Lathem
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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193
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Rouli L, Merhej V, Fournier PE, Raoult D. The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes New Infect 2015; 7:72-85. [PMID: 26442149 PMCID: PMC4552756 DOI: 10.1016/j.nmni.2015.06.005] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/16/2015] [Indexed: 01/18/2023] Open
Abstract
The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. In this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. We have also shown that the pangenome may be used as a new tool for redefining the pathogenic species. We applied this to the Escherichia coli and Shigella species, which have been a subject of controversy regarding their taxonomic and pathogenic position. Pangenome is a new way of studying pathogenic bacteria. Pangenome can be used as a taxonomic tool. This review describes pangenome in the world of pathogenic bacteria.
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Affiliation(s)
- L Rouli
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - V Merhej
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - P-E Fournier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - D Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
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194
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Sahl JW, Schupp JM, Rasko DA, Colman RE, Foster JT, Keim P. Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data. Genome Med 2015; 7:52. [PMID: 26136847 PMCID: PMC4487561 DOI: 10.1186/s13073-015-0176-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/15/2015] [Indexed: 12/30/2022] Open
Abstract
We describe an approach for genotyping bacterial strains from low coverage genome datasets, including metagenomic data from complex samples. Sequence reads from unknown samples are aligned to a reference genome where the allele states of known SNPs are determined. The Whole Genome Focused Array SNP Typing (WG-FAST) pipeline can identify unknown strains with much less read data than is needed for genome assembly. To test WG-FAST, we resampled SNPs from real samples to understand the relationship between low coverage metagenomic data and accurate phylogenetic placement. WG-FAST can be downloaded from https://github.com/jasonsahl/wgfast.
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Affiliation(s)
- Jason W. Sahl
- />Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ USA
- />Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - James M. Schupp
- />Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ USA
| | - David A. Rasko
- />Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Rebecca E. Colman
- />Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ USA
| | - Jeffrey T. Foster
- />Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 USA
- />Current address: Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH USA
| | - Paul Keim
- />Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ USA
- />Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 USA
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195
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Mitchell PD. Human Parasites in Medieval Europe: Lifestyle, Sanitation and Medical Treatment. ADVANCES IN PARASITOLOGY 2015; 90:389-420. [PMID: 26597073 DOI: 10.1016/bs.apar.2015.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Parasites have been infecting humans throughout our evolution. However, not all people suffered with the same species or to the same intensity throughout this time. Our changing way of life has altered the suitability of humans to infection by each type of parasite. This analysis focuses upon the evidence for parasites from archaeological excavations at medieval sites across Europe. Comparison between the patterns of infection in the medieval period allows us to see how changes in sanitation, herding animals, growing and fertilizing crops, the fishing industry, food preparation and migration all affected human susceptibility to different parasites. We go on to explore how ectoparasites may have spread infectious bacterial diseases, and also consider what medieval medical practitioners thought of parasites and how they tried to treat them. While modern research has shown the use of a toilet decreases the risk of contracting certain intestinal parasites, the evidence for past societies presented here suggests that the invention of latrines had no observable beneficial effects upon intestinal health. This may be because toilets were not sufficiently ubiquitous until the last century, or that the use of fresh human faeces for manuring crops still ensured those parasite species were easily able to reinfect the population.
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Affiliation(s)
- Piers D Mitchell
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom.
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196
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Lowell JL, Antolin MF, Andersen GL, Hu P, Stokowski RP, Gage KL. Single-Nucleotide Polymorphisms Reveal Spatial Diversity Among Clones of Yersinia pestis During Plague Outbreaks in Colorado and the Western United States. Vector Borne Zoonotic Dis 2015; 15:291-302. [PMID: 25988438 PMCID: PMC4449629 DOI: 10.1089/vbz.2014.1714] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND In western North America, plague epizootics caused by Yersinia pestis appear to sweep across landscapes, primarily infecting and killing rodents, especially ground squirrels and prairie dogs. During these epizootics, the risk of Y. pestis transmission to humans is highest. While empirical models that include climatic conditions and densities of rodent hosts and fleas can predict when epizootics are triggered, bacterial transmission patterns across landscapes, and the scale at which Y. pestis is maintained in nature during inter-epizootic periods, are poorly defined. Elucidating the spatial extent of Y. pestis clones during epizootics can determine whether bacteria are propagated across landscapes or arise independently from local inter-epizootic maintenance reservoirs. MATERIAL AND METHODS We used DNA microarray technology to identify single-nucleotide polymorphisms (SNPs) in 34 Y. pestis isolates collected in the western United States from 1980 to 2006, 21 of which were collected during plague epizootics in Colorado. Phylogenetic comparisons were used to elucidate the hypothesized spread of Y. pestis between the mountainous Front Range and the eastern plains of northern Colorado during epizootics. Isolates collected from across the western United States were included for regional comparisons. RESULTS By identifying SNPs that mark individual clones, our results strongly suggest that Y. pestis is maintained locally and that widespread epizootic activity is caused by multiple clones arising independently at small geographic scales. This is in contrast to propagation of individual clones being transported widely across landscapes. Regionally, our data are consistent with the notion that Y. pestis diversifies at relatively local scales following long-range translocation events. We recommend that surveillance and prediction by public health and wildlife management professionals focus more on models of local or regional weather patterns and ecological factors that may increase risk of widespread epizootics, rather than predicting or attempting to explain epizootics on the basis of movement of host species that may transport plague.
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Affiliation(s)
- Jennifer L. Lowell
- Department of Health Sciences, Carroll College, Helena, Montana
- Department of Biology, Colorado State University, Fort Collins, Colorado
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado
| | - Michael F. Antolin
- Department of Biology, Colorado State University, Fort Collins, Colorado
| | - Gary L. Andersen
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Ping Hu
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | | | - Kenneth L. Gage
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado
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Clarke CR, Studholme DJ, Hayes B, Runde B, Weisberg A, Cai R, Wroblewski T, Daunay MC, Wicker E, Castillo JA, Vinatzer BA. Genome-Enabled Phylogeographic Investigation of the Quarantine Pathogen Ralstonia solanacearum Race 3 Biovar 2 and Screening for Sources of Resistance Against Its Core Effectors. PHYTOPATHOLOGY 2015; 105:597-607. [PMID: 25710204 DOI: 10.1094/phyto-12-14-0373-r] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Phylogeographic studies inform about routes of pathogen dissemination and are instrumental for improving import/export controls. Genomes of 17 isolates of the bacterial wilt and potato brown rot pathogen Ralstonia solanacearum race 3 biovar 2 (R3bv2), a Select Agent in the United States, were thus analyzed to get insight into the phylogeography of this pathogen. Thirteen of fourteen isolates from Europe, Africa, and Asia were found to belong to a single clonal lineage while isolates from South America were genetically diverse and tended to carry ancestral alleles at the analyzed genomic loci consistent with a South American origin of R3bv2. The R3bv2 isolates share a core repertoire of 31 type III-secreted effector genes representing excellent candidates to be targeted with resistance genes in breeding programs to develop durable disease resistance. Toward this goal, 27 R3bv2 effectors were tested in eggplant, tomato, pepper, tobacco, and lettuce for induction of a hypersensitive-like response indicative of recognition by cognate resistance receptors. Fifteen effectors, eight of them core effectors, triggered a response in one or more plant species. These genotypes may harbor resistance genes that could be identified and mapped, cloned, and expressed in tomato or potato, for which sources of genetic resistance to R3bv2 are extremely limited.
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Affiliation(s)
- Christopher R Clarke
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - David J Studholme
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Byron Hayes
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Brendan Runde
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Alexandra Weisberg
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Rongman Cai
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Tadeusz Wroblewski
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Marie-Christine Daunay
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Emmanuel Wicker
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Jose A Castillo
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
| | - Boris A Vinatzer
- First, third, fourth, fifth, sixth, and eleventh authors: Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Latham Hall, Ag Quad Lane, Blacksburg, VA; second author: Biosciences, University of Exeter, Exeter, Devon, UK; seventh author: Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616; eighth author: Unité de Genetique et Amelioration des Fruits et Legumes, INRA, Centre d'Avignon, Montfavet, France; ninth author: CIRAD, UMR Peuplements Vegetaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Reunion, France; and tenth author: PROINPA Foundation, Cochabamba, Bolivia
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198
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Inter-individual differences in the gene content of human gut bacterial species. Genome Biol 2015; 16:82. [PMID: 25896518 PMCID: PMC4428241 DOI: 10.1186/s13059-015-0646-9] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/01/2015] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Gene content differences in human gut microbes can lead to inter-individual phenotypic variations such as digestive capacity. It is unclear whether gene content variation is caused by differences in microbial species composition or by the presence of different strains of the same species; the extent of gene content variation in the latter is unknown. Unlike pan-genome studies of cultivable strains, the use of metagenomic data can provide an unbiased view of structural variation of gut bacterial strains by measuring them in their natural habitats, the gut of each individual in this case, representing native boundaries between gut bacterial populations. We analyzed publicly available metagenomic data from fecal samples to characterize inter-individual variation in gut bacterial species. RESULTS A comparison of 11 abundant gut bacterial species showed that the gene content of strains from the same species differed, on average, by 13% between individuals. This number is based on gene deletions only and represents a lower limit, yet the variation is already in a similar range as observed between completely sequenced strains of cultivable species. We show that accessory genes that differ considerably between individuals can encode important functions, such as polysaccharide utilization and capsular polysaccharide synthesis loci. CONCLUSION Metagenomics can yield insights into gene content variation of strains in complex communities, which cannot be predicted by phylogenetic marker genes alone. The large degree of inter-individual variability in gene content implies that strain resolution must be considered in order to fully assess the functional potential of an individual's human gut microbiome.
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Biek R, Pybus OG, Lloyd-Smith JO, Didelot X. Measurably evolving pathogens in the genomic era. Trends Ecol Evol 2015; 30:306-13. [PMID: 25887947 DOI: 10.1016/j.tree.2015.03.009] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/06/2015] [Accepted: 03/11/2015] [Indexed: 01/26/2023]
Abstract
Current sequencing technologies have created unprecedented opportunities for studying microbial populations. For pathogens with comparatively low per-site mutation rates, such as DNA viruses and bacteria, whole-genome sequencing can reveal the accumulation of novel genetic variation between population samples taken at different times. The concept of 'measurably evolving populations' and related analytical approaches have provided powerful insights for fast-evolving RNA viruses, but their application to other pathogens is still in its infancy. We argue that previous distinctions between slow- and fast-evolving pathogens become blurred once evolution is assessed at a genome-wide scale, and we highlight important analytical challenges to be overcome to infer pathogen population dynamics from genomic data.
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Affiliation(s)
- Roman Biek
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, UK; Fogarty International Center, National Institutes of Health, Bethesda MD, USA.
| | | | - James O Lloyd-Smith
- Fogarty International Center, National Institutes of Health, Bethesda MD, USA; Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College, London, UK
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Koskela KA, Mattinen L, Kalin-Mänttäri L, Vergnaud G, Gorgé O, Nikkari S, Skurnik M. Generation of a CRISPR database forYersinia pseudotuberculosiscomplex and role of CRISPR-based immunity in conjugation. Environ Microbiol 2015; 17:4306-21. [DOI: 10.1111/1462-2920.12816] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 02/11/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Katja A. Koskela
- Research and Development Department; Centre for Military Medicine; Helsinki Finland
| | - Laura Mattinen
- Department of Bacteriology and Immunology; Haartman Institute and Research Programs Unit; Immunobiology; University of Helsinki; PO Box 21, 00014 Helsinki Finland
| | - Laura Kalin-Mänttäri
- Research and Development Department; Centre for Military Medicine; Helsinki Finland
- Department of Bacteriology and Immunology; Haartman Institute and Research Programs Unit; Immunobiology; University of Helsinki; PO Box 21, 00014 Helsinki Finland
| | - Gilles Vergnaud
- Univ Paris-Sud; Institut de Génétique et Microbiologie; UMR8621; Orsay France
- CNRS; Orsay France
- ENSTA ParisTech; Palaiseau France
| | - Olivier Gorgé
- Univ Paris-Sud; Institut de Génétique et Microbiologie; UMR8621; Orsay France
- CNRS; Orsay France
- DGA/MNRBC; Vert le Petit France
| | - Simo Nikkari
- Research and Development Department; Centre for Military Medicine; Helsinki Finland
| | - Mikael Skurnik
- Department of Bacteriology and Immunology; Haartman Institute and Research Programs Unit; Immunobiology; University of Helsinki; PO Box 21, 00014 Helsinki Finland
- Helsinki University Central Hospital Laboratory Diagnostics; Helsinki Finland
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