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Turner WC, Kamath PL, van Heerden H, Huang YH, Barandongo ZR, Bruce SA, Kausrud K. The roles of environmental variation and parasite survival in virulence-transmission relationships. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210088. [PMID: 34109041 PMCID: PMC8170194 DOI: 10.1098/rsos.210088] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Disease outbreaks are a consequence of interactions among the three components of a host-parasite system: the infectious agent, the host and the environment. While virulence and transmission are widely investigated, most studies of parasite life-history trade-offs are conducted with theoretical models or tractable experimental systems where transmission is standardized and the environment controlled. Yet, biotic and abiotic environmental factors can strongly affect disease dynamics, and ultimately, host-parasite coevolution. Here, we review research on how environmental context alters virulence-transmission relationships, focusing on the off-host portion of the parasite life cycle, and how variation in parasite survival affects the evolution of virulence and transmission. We review three inter-related 'approaches' that have dominated the study of the evolution of virulence and transmission for different host-parasite systems: (i) evolutionary trade-off theory, (ii) parasite local adaptation and (iii) parasite phylodynamics. These approaches consider the role of the environment in virulence and transmission evolution from different angles, which entail different advantages and potential biases. We suggest improvements to how to investigate virulence-transmission relationships, through conceptual and methodological developments and taking environmental context into consideration. By combining developments in life-history evolution, phylogenetics, adaptive dynamics and comparative genomics, we can improve our understanding of virulence-transmission relationships across a diversity of host-parasite systems that have eluded experimental study of parasite life history.
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Affiliation(s)
- Wendy C. Turner
- US Geological Survey, Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Pauline L. Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Henriette van Heerden
- Faculty of Veterinary Science, Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, South Africa
| | - Yen-Hua Huang
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zoe R. Barandongo
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Spencer A. Bruce
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Kyrre Kausrud
- Section for Epidemiology, Norwegian Veterinary Institute, Ullevålsveien 68, 0454 Oslo, Norway
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Arning N, Wilson DJ. The past, present and future of ancient bacterial DNA. Microb Genom 2020; 6:mgen000384. [PMID: 32598277 PMCID: PMC7478633 DOI: 10.1099/mgen.0.000384] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.
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Affiliation(s)
- Nicolas Arning
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
| | - Daniel J. Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
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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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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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