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Rudenko O, Engelstädter J, Barnes AC. Evolutionary epidemiology of Streptococcus iniae: Linking mutation rate dynamics with adaptation to novel immunological landscapes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104435. [PMID: 32569744 DOI: 10.1016/j.meegid.2020.104435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022]
Abstract
Pathogens continuously adapt to changing host environments where variation in their virulence and antigenicity is critical to their long-term evolutionary success. The emergence of novel variants is accelerated in microbial mutator strains (mutators) deficient in DNA repair genes, most often from mismatch repair and oxidized-guanine repair systems (MMR and OG respectively). Bacterial MMR/OG mutants are abundant in clinical samples and show increased adaptive potential in experimental infection models, yet the role of mutators in the epidemiology and evolution of infectious disease is not well understood. Here we investigated the role of mutation rate dynamics in the evolution of a broad host range pathogen, Streptococcus iniae, using a set of 80 strains isolated globally over 40 years. We have resolved phylogenetic relationships using non-recombinant core genome variants, measured in vivo mutation rates by fluctuation analysis, identified variation in major MMR/OG genes and their regulatory regions, and phenotyped the major traits determining virulence in streptococci. We found that both mutation rate and MMR/OG genotype are remarkably conserved within phylogenetic clades but significantly differ between major phylogenetic lineages. Further, variation in MMR/OG loci correlates with occurrence of atypical virulence-associated phenotypes, infection in atypical hosts (mammals), and atypical (osseous) tissue of a vaccinated primary host. These findings suggest that mutators are likely to facilitate adaptations preceding major diversification events and may promote emergence of variation permitting colonization of a novel host tissue, novel host taxa (host jumps), and immune-escape in the vaccinated host.
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Affiliation(s)
- Oleksandra Rudenko
- The University of Queensland, School of Biological Sciences, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Jan Engelstädter
- The University of Queensland, School of Biological Sciences, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Andrew C Barnes
- The University of Queensland, School of Biological Sciences, St Lucia Campus, Brisbane, Queensland 4072, Australia.
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Rascovan N, Sjögren KG, Kristiansen K, Nielsen R, Willerslev E, Desnues C, Rasmussen S. Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline. Cell 2018; 176:295-305.e10. [PMID: 30528431 DOI: 10.1016/j.cell.2018.11.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/10/2018] [Accepted: 11/01/2018] [Indexed: 12/30/2022]
Abstract
Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.
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Affiliation(s)
- Nicolás Rascovan
- Aix Marseille Université, UMR MEPHI, CNRS FRE2013, IRD 198, AP-HM, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France.
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Kristian Kristiansen
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Rasmus Nielsen
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Eske Willerslev
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Christelle Desnues
- Aix Marseille Université, UMR MEPHI, CNRS FRE2013, IRD 198, AP-HM, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet 208, 2800 Kongens Lyngby, Denmark.
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Swings T, Van den Bergh B, Wuyts S, Oeyen E, Voordeckers K, Verstrepen KJ, Fauvart M, Verstraeten N, Michiels J. Adaptive tuning of mutation rates allows fast response to lethal stress in Escherichia coli. eLife 2017; 6. [PMID: 28460660 PMCID: PMC5429094 DOI: 10.7554/elife.22939] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 04/18/2017] [Indexed: 12/17/2022] Open
Abstract
While specific mutations allow organisms to adapt to stressful environments, most changes in an organism's DNA negatively impact fitness. The mutation rate is therefore strictly regulated and often considered a slowly-evolving parameter. In contrast, we demonstrate an unexpected flexibility in cellular mutation rates as a response to changes in selective pressure. We show that hypermutation independently evolves when different Escherichia coli cultures adapt to high ethanol stress. Furthermore, hypermutator states are transitory and repeatedly alternate with decreases in mutation rate. Specifically, population mutation rates rise when cells experience higher stress and decline again once cells are adapted. Interestingly, we identified cellular mortality as the major force driving the quick evolution of mutation rates. Together, these findings show how organisms balance robustness and evolvability and help explain the prevalence of hypermutation in various settings, ranging from emergence of antibiotic resistance in microbes to cancer relapses upon chemotherapy.
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Affiliation(s)
- Toon Swings
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Bram Van den Bergh
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Sander Wuyts
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Eline Oeyen
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Karin Voordeckers
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium.,VIB Laboratory for Genetics and Genomics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Kevin J Verstrepen
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium.,VIB Laboratory for Genetics and Genomics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium.,Smart Systems and Emerging Technologies Unit, Imec (Interuniversity Micro-Electronics Centre), Leuven, Belgium
| | - Natalie Verstraeten
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
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Comparing mutation rates under the Luria–Delbrück protocol. Genetica 2016; 144:351-9. [DOI: 10.1007/s10709-016-9904-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/04/2016] [Indexed: 12/11/2022]
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Whole-Genome Sequencing in Microbial Forensic Analysis of Gamma-Irradiated Microbial Materials. Appl Environ Microbiol 2015; 82:596-607. [PMID: 26567301 DOI: 10.1128/aem.02231-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/26/2015] [Indexed: 11/20/2022] Open
Abstract
Effective microbial forensic analysis of materials used in a potential biological attack requires robust methods of morphological and genetic characterization of the attack materials in order to enable the attribution of the materials to potential sources and to exclude other potential sources. The genetic homogeneity and potential intersample variability of many of the category A to C bioterrorism agents offer a particular challenge to the generation of attributive signatures, potentially requiring whole-genome or proteomic approaches to be utilized. Currently, irradiation of mail is standard practice at several government facilities judged to be at particularly high risk. Thus, initial forensic signatures would need to be recovered from inactivated (nonviable) material. In the study described in this report, we determined the effects of high-dose gamma irradiation on forensic markers of bacterial biothreat agent surrogate organisms with a particular emphasis on the suitability of genomic DNA (gDNA) recovered from such sources as a template for whole-genome analysis. While irradiation of spores and vegetative cells affected the retention of Gram and spore stains and sheared gDNA into small fragments, we found that irradiated material could be utilized to generate accurate whole-genome sequence data on the Illumina and Roche 454 sequencing platforms.
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Nozadze M, Zhgenti E, Meparishvili M, Tsverava L, Kiguradze T, Chanturia G, Babuadze G, Kekelidze M, Bakanidze L, Shutkova T, Imnadze P, Francesconi SC, Obiso R, Solomonia R. Comparative Proteomic Studies of Yersinia pestis Strains Isolated from Natural Foci in the Republic of Georgia. Front Public Health 2015; 3:239. [PMID: 26528469 PMCID: PMC4607876 DOI: 10.3389/fpubh.2015.00239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/02/2015] [Indexed: 11/18/2022] Open
Abstract
Yersinia pestis, the causative agent of plague, is a highly virulent bacterium responsible for millions of human deaths throughout history. In the last decade, two natural plague foci have been described in the Republic of Georgia from which dozens of Y. pestis strains have been isolated. Analyses indicate that there are genetic differences between these strains, but it is not known if these differences are also reflected in protein expression. We chose four strains of Y. pestis (1390, 1853, 2944, and 8787) from the National Center for Disease Control and Public Health collection for proteomic studies based on neighbor-joining tree genetic analysis and geographical loci of strain origin. Proteomic expression was analyzed using two-dimensional gel electrophoresis and mass spectrometry. Select Y. pestis strains were grown under different physiological conditions and their proteomes were compared: (1) 28°C without calcium; (2) 28°C with calcium; (3) 37°C without calcium; and (4) 37°C with calcium. Candidate proteins were identified and the differences in expression of F1 antigen, tellurium-resistance protein, and outer membrane protein C, porin were validated by Western blotting. The in vitro cytotoxicity activity of these strains was also compared. The results indicate that protein expression and cytotoxic activities differ significantly among the studied strains; these differences could contribute to variations in essential physiological functions in these strains.
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Affiliation(s)
- Maia Nozadze
- Institute of Chemical Biology, Ilia State University , Tbilisi , Georgia ; I.Beritashvili Center for Experimental Biomedicine , Tbilisi , Georgia
| | - Ekaterine Zhgenti
- Institute of Chemical Biology, Ilia State University , Tbilisi , Georgia ; National Center for Disease Control , Tbilisi , Georgia
| | - Maia Meparishvili
- I.Beritashvili Center for Experimental Biomedicine , Tbilisi , Georgia
| | - Lia Tsverava
- I.Beritashvili Center for Experimental Biomedicine , Tbilisi , Georgia
| | - Tamar Kiguradze
- I.Beritashvili Center for Experimental Biomedicine , Tbilisi , Georgia
| | | | | | | | | | | | - Paata Imnadze
- National Center for Disease Control , Tbilisi , Georgia
| | | | - Richard Obiso
- Attimo Research and Development , Blacksburg, VA , USA
| | - Revaz Solomonia
- Institute of Chemical Biology, Ilia State University , Tbilisi , Georgia ; I.Beritashvili Center for Experimental Biomedicine , Tbilisi , Georgia
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Zheng Q. A new practical guide to the Luria-Delbrück protocol. Mutat Res 2015; 781:7-13. [PMID: 26366669 DOI: 10.1016/j.mrfmmm.2015.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/25/2015] [Accepted: 08/23/2015] [Indexed: 06/05/2023]
Abstract
Since 2000 several review papers have been published about the analysis of experimental data obtained using the Luria-Delbrück protocol. These timely papers cleared much of the confusion surrounding various methods for estimating or comparing mutation rates. As a result, today the fluctuation test is more widely applied with much improved accuracy. The present paper provides guidelines on a few remaining problems that continue to baffle mutation researchers. Among the issues addressed are incomplete plating, relative fitness, and comparison of experiments where average final cell population sizes differ. It also offers a fresh view on the estimation methods that are based on the sample median.
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Affiliation(s)
- Qi Zheng
- Department of Epidemiology and Biostatistics, Texas A&M School of Public Health, College Station, TX 77843, United States.
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