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Hernandez CA, Delesalle VA, Krukonis GP, DeCurzio JM, Koskella B. Genomic and phenotypic signatures of bacteriophage coevolution with the phytopathogen Pseudomonas syringae. Mol Ecol 2024; 33:e16850. [PMID: 36651263 DOI: 10.1111/mec.16850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/21/2022] [Accepted: 12/06/2022] [Indexed: 01/19/2023]
Abstract
The rate and trajectory of evolution in an obligate parasite is critically dependent on those of its host(s). Adaptation to a genetically homogeneous host population should theoretically result in specialization, while adaptation to an evolving host population (i.e., coevolution) can result in various outcomes including diversification, range expansion, and/or local adaptation. For viruses of bacteria (bacteriophages, or phages), our understanding of how evolutionary history of the bacterial host(s) impacts viral genotypic and phenotypic evolution is currently limited. In this study, we used whole genome sequencing and two different metrics of phage impacts to compare the genotypes and phenotypes of lytic phages that had either coevolved with or were repeatedly passaged on an unchanging (ancestral) strain of the phytopathogen Pseudomonas syringae. Genomes of coevolved phages had more mutations than those of phages passaged on a constant host, and most mutations were in genes encoding phage tail-associated proteins. Phages from both passaging treatments shared some phenotypic outcomes, including range expansion and divergence across replicate populations, but coevolved phages were more efficient at reducing population growth (particularly of sympatric coevolved hosts). Genotypic similarity correlated with infectivity profile similarity in coevolved phages, but not in phages passaged on the ancestral host. Overall, while adaptation to either host type (coevolving or ancestral) led to divergence in phage tail proteins and infectivity patterns, coevolution led to more rapid molecular changes that increased bacterial killing efficiency and had more predictable effects on infectivity range. Together, these results underscore the important role of hosts in driving viral evolution and in shaping the genotype-phenotype relationship.
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Affiliation(s)
- Catherine A Hernandez
- Department of Integrative Biology, University of California, Berkeley, California, Berkeley, USA
| | | | - Greg P Krukonis
- Department of Biology, Angelo State University, San Angelo, Texas, USA
| | - Jenna M DeCurzio
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California, Berkeley, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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2
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Carvalho T, Belasen AM, Toledo LF, James TY. Coevolution of a generalist pathogen with many hosts: the case of the amphibian chytrid Batrachochytrium dendrobatidis. Curr Opin Microbiol 2024; 78:102435. [PMID: 38387210 DOI: 10.1016/j.mib.2024.102435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 12/22/2023] [Accepted: 01/21/2024] [Indexed: 02/24/2024]
Abstract
Generalist pathogens maintain infectivity in numerous hosts; how this broad ecological niche impacts host-pathogen coevolution remains to be widely explored. Batrachochytrium dendrobatidis (Bd) is a highly generalist pathogenic fungus that has caused devastating declines in hundreds of amphibian species worldwide. This review examines amphibian chytridiomycosis host-pathogen interactions and available evidence for coevolution between Bd and its numerous hosts. We summarize recent evidence showing that Bd genotypes vary in geographic distribution and virulence, and that amphibian species also vary in Bd susceptibility according to their geographic distribution. How much variation can be explained by phenotypic plasticity or genetic differences remains uncertain. Recent research suggests that Bd genotypes display preferences for specific hosts and that some hosts are undergoing evolution as populations rebound from Bd outbreaks. Taken together, these findings suggest the potential for coevolution to occur and illuminate a path for addressing open questions through integrating historical and contemporary genetic data.
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Affiliation(s)
- Tamilie Carvalho
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Anat M Belasen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, United States
| | - L Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Unicamp, Campinas, São Paulo, Brazil
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, United States.
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3
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Bisesi AT, Möbius W, Nadell CD, Hansen EG, Bowden SD, Harcombe WR. Bacteriophage specificity is impacted by interactions between bacteria. mSystems 2024; 9:e0117723. [PMID: 38376179 PMCID: PMC11237722 DOI: 10.1128/msystems.01177-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/20/2024] [Indexed: 02/21/2024] Open
Abstract
Predators play a central role in shaping community structure, function, and stability. The degree to which bacteriophage predators (viruses that infect bacteria) evolve to be specialists with a single bacterial prey species versus generalists able to consume multiple types of prey has implications for their effect on microbial communities. The presence and abundance of multiple bacterial prey types can alter selection for phage generalists, but less is known about how interactions between prey shape predator specificity in microbial systems. Using a phenomenological mathematical model of phage and bacterial populations, we find that the dominant phage strategy depends on prey ecology. Given a fitness cost for generalism, generalist predators maintain an advantage when prey species compete, while specialists dominate when prey are obligately engaged in cross-feeding interactions. We test these predictions in a synthetic microbial community with interacting strains of Escherichia coli and Salmonella enterica by competing a generalist T5-like phage able to infect both prey against P22vir, an S. enterica-specific phage. Our experimental data conform to our modeling expectations when prey species are competing or obligately mutualistic, although our results suggest that the in vitro cost of generalism is caused by a combination of biological mechanisms not anticipated in our model. Our work demonstrates that interactions between bacteria play a role in shaping ecological selection on predator specificity in obligately lytic bacteriophages and emphasizes the diversity of ways in which fitness trade-offs can manifest. IMPORTANCE There is significant natural diversity in how many different types of bacteria a bacteriophage can infect, but the mechanisms driving this diversity are unclear. This study uses a combination of mathematical modeling and an in vitro system consisting of Escherichia coli, Salmonella enterica, a T5-like generalist phage, and the specialist phage P22vir to highlight the connection between bacteriophage specificity and interactions between their potential microbial prey. Mathematical modeling suggests that competing bacteria tend to favor generalist bacteriophage, while bacteria that benefit each other tend to favor specialist bacteriophage. Experimental results support this general finding. The experiments also show that the optimal phage strategy is impacted by phage degradation and bacterial physiology. These findings enhance our understanding of how complex microbial communities shape selection on bacteriophage specificity, which may improve our ability to use phage to manage antibiotic-resistant microbial infections.
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Affiliation(s)
- Ave T. Bisesi
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Wolfram Möbius
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, University of Exeter, Exeter, United Kingdom
| | - Carey D. Nadell
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
| | - Eleanore G. Hansen
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, Minnesota, USA
| | - Steven D. Bowden
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, Minnesota, USA
| | - William R. Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
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4
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Bruijning M, Metcalf CJE, Visser MD. Closing the gap in the Janzen-Connell hypothesis: What determines pathogen diversity? Ecol Lett 2024; 27:e14316. [PMID: 37787147 DOI: 10.1111/ele.14316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 09/11/2023] [Accepted: 09/17/2023] [Indexed: 10/04/2023]
Abstract
The high tree diversity in tropical forests has long been a puzzle to ecologists. In the 1970s, Janzen and Connell proposed that tree species (hosts) coexist due to the stabilizing actions of specialized enemies. This Janzen-Connell hypothesis was subsequently supported by theoretical studies. Yet, such studies have taken the presence of specialized pathogens for granted, overlooking that pathogen coexistence also requires an explanation. Moreover, stable ecological coexistence does not necessarily imply evolutionary stability. What are the conditions that allow Janzen-Connell effects to evolve? We link theory from community ecology, evolutionary biology and epidemiology to tackle this question, structuring our approach around five theoretical frameworks. Phenomenological Lotka-Volterra competition models provide the most basic framework, which can be restructured to include (single- or multi-)pathogen dynamics. This ecological foundation can be extended to include pathogen evolution. Hosts, of course, may also evolve, and we introduce a coevolutionary model, showing that host-pathogen coevolution can lead to highly diverse systems. Our work unpacks the assumptions underpinning Janzen-Connell and places theoretical bounds on pathogen and host ecology and evolution. The five theoretical frameworks taken together provide a stronger theoretical basis for Janzen-Connell, delivering a wider lens that can yield important insights into the maintenance of diversity in these increasingly threatened systems.
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Affiliation(s)
- Marjolein Bruijning
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Marco D Visser
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
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5
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Zamfir AD, Babalola BM, Fraile A, McLeish MJ, García-Arenal F. Tobamoviruses Show Broad Host Ranges and Little Genetic Diversity Among Four Habitat Types of a Heterogeneous Ecosystem. PHYTOPATHOLOGY 2023; 113:1697-1707. [PMID: 36916761 DOI: 10.1094/phyto-11-22-0439-v] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Host ranges of plant viruses are poorly known, as studies have focused on pathogenic viruses in crops and adjacent wild plants. High-throughput sequencing (HTS) avoids the bias toward plant-virus interactions that result in disease. Here we study the host ranges of tobamoviruses, important pathogens of crops, using HTS analyses of an extensive sample of plant communities in four habitats of a heterogeneous ecosystem. Sequences of 17 virus operational taxonomic units (OTUs) matched references in the Tobamovirus genus, eight had narrow host ranges, and five had wide host ranges. Regardless of host range, the OTU hosts belonged to taxonomically distant families, suggesting no phylogenetic constraints in host use associated with virus adaptation, and that tobamoviruses may be host generalists. The OTUs identified as tobacco mild green mosaic virus (TMGMV), tobacco mosaic virus (TMV), pepper mild mottle virus, and Youcai mosaic virus had the largest realized host ranges that occurred across habitats and exhibited host use unrelated to the degree of human intervention. This result is at odds with assumptions that contact-transmitted viruses would be more abundant in crops than in wild plant communities and could be explained by effective seed-, contact-, or pollinator-mediated transmission or by survival in the soil. TMGMV and TMV had low genetic diversity that was not structured according to habitat or host plant taxonomy, which indicated that phenotypic plasticity allows virus genotypes to infect new hosts with no need for adaptive evolution. Our results underscore the relevance of ecological factors in host range evolution, in addition to the more often studied genetic factors. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Adrián D Zamfir
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Bisola M Babalola
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Michael J McLeish
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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6
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Skoracka A, Laska A, Radwan J, Konczal M, Lewandowski M, Puchalska E, Karpicka‐Ignatowska K, Przychodzka A, Raubic J, Kuczyński L. Effective specialist or jack of all trades? Experimental evolution of a crop pest in fluctuating and stable environments. Evol Appl 2022; 15:1639-1652. [PMID: 36330306 PMCID: PMC9624081 DOI: 10.1111/eva.13360] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/30/2022] [Accepted: 02/06/2022] [Indexed: 11/30/2022] Open
Abstract
Understanding pest evolution in agricultural systems is crucial for developing effective and innovative pest control strategies. Types of cultivation, such as crop monocultures versus polycultures or crop rotation, may act as a selective pressure on pests' capability to exploit the host's resources. In this study, we examined the herbivorous mite Aceria tosichella (commonly known as wheat curl mite), a widespread wheat pest, to understand how fluctuating versus stable environments influence its niche breadth and ability to utilize different host plant species. We subjected a wheat-bred mite population to replicated experimental evolution in a single-host environment (either wheat or barley), or in an alternation between these two plant species every three mite generations. Next, we tested the fitness of these evolving populations on wheat, barley, and on two other plant species not encountered during experimental evolution, namely rye and smooth brome. Our results revealed that the niche breadth of A. tosichella evolved in response to the level of environmental variability. The fluctuating environment expanded the niche breadth by increasing the mite's ability to utilize different plant species, including novel ones. Such an environment may thus promote flexible host-use generalist phenotypes. However, the niche expansion resulted in some costs expressed as reduced performances on both wheat and barley as compared to specialists. Stable host environments led to specialized phenotypes. The population that evolved in a constant environment consisting of barley increased its fitness on barley without the cost of utilizing wheat. However, the population evolving on wheat did not significantly increase its fitness on wheat, but decreased its performance on barley. Altogether, our results indicated that, depending on the degree of environmental heterogeneity, agricultural systems create different conditions that influence pests' niche breadth evolution, which may in turn affect the ability of pests to persist in such systems.
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Affiliation(s)
- Anna Skoracka
- Population Ecology LabFaculty of BiologyInstitute of Environmental BiologyAdam Mickiewicz UniversityPoznańPoland
- Center for Advanced TechnologyAdam Mickiewicz UniversityPoznańPoland
| | - Alicja Laska
- Population Ecology LabFaculty of BiologyInstitute of Environmental BiologyAdam Mickiewicz UniversityPoznańPoland
| | - Jacek Radwan
- Evolutionary Biology GroupFaculty of BiologyInstitute of Environmental BiologyAdam Mickiewicz UniversityPoznańPoland
| | - Mateusz Konczal
- Evolutionary Biology GroupFaculty of BiologyInstitute of Environmental BiologyAdam Mickiewicz UniversityPoznańPoland
| | - Mariusz Lewandowski
- Section of Applied EntomologyDepartment of Plant ProtectionInstitute of Horticultural SciencesWarsaw University of Life Sciences – SGGWWarsawPoland
| | - Ewa Puchalska
- Section of Applied EntomologyDepartment of Plant ProtectionInstitute of Horticultural SciencesWarsaw University of Life Sciences – SGGWWarsawPoland
| | - Kamila Karpicka‐Ignatowska
- Population Ecology LabFaculty of BiologyInstitute of Environmental BiologyAdam Mickiewicz UniversityPoznańPoland
| | - Anna Przychodzka
- Population Ecology LabFaculty of BiologyInstitute of Environmental BiologyAdam Mickiewicz UniversityPoznańPoland
| | - Jarosław Raubic
- Population Ecology LabFaculty of BiologyInstitute of Environmental BiologyAdam Mickiewicz UniversityPoznańPoland
| | - Lechosław Kuczyński
- Population Ecology LabFaculty of BiologyInstitute of Environmental BiologyAdam Mickiewicz UniversityPoznańPoland
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7
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Visher E, Uricchio L, Bartlett L, DeNamur N, Yarcan A, Alhassani D, Boots M. The evolution of host specialization in an insect pathogen. Evolution 2022; 76:2375-2388. [PMID: 35946063 DOI: 10.1111/evo.14594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 05/21/2022] [Accepted: 06/06/2022] [Indexed: 01/22/2023]
Abstract
Niche breadth coevolution between biotic partners underpins theories of diversity and co-existence and influences patterns of disease emergence and transmission in host-parasite systems. Despite these broad implications, we still do not fully understand how the breadth of parasites' infectivity evolves, the nature of any associated costs, or the genetic basis of specialization. Here, we serially passage a granulosis virus on multiple inbred populations of its Plodia interpunctella host to explore the dynamics and outcomes of specialization. In particular, we collect time series of phenotypic and genetic data to explore the dynamics of host genotype specialization throughout the course of experimental evolution and examine two fitness components. We find that the Plodia interpunctella granulosis virus consistently evolves and increases in overall specialization, but that our two fitness components evolve independently such that lines can specialize in productivity or infectivity. Furthermore, we find that specialization in our experiment is a highly polygenic trait best explained by a combination of evolutionary mechanisms. These results are important for understanding the evolution of specialization in host-parasite interactions and its broader implications for co-existence, diversification, and infectious disease management.
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Affiliation(s)
- Elisa Visher
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | | | - Lewis Bartlett
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
| | | | - Aren Yarcan
- University of California, Berkeley, CA, 94720, USA
| | | | - Mike Boots
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.,Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter Penryn Campus, Penryn, TR10 9FE, UK
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8
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Lin YP, Tufts DM, Combs M, Dupuis AP, Marcinkiewicz AL, Hirsbrunner AD, Diaz AJ, Stout JL, Blom AM, Strle K, Davis AD, Kramer LD, Kolokotronis SO, Diuk-Wasser MA. Cellular and immunological mechanisms influence host-adapted phenotypes in a vector-borne microparasite. Proc Biol Sci 2022; 289:20212087. [PMID: 35193398 PMCID: PMC8864362 DOI: 10.1098/rspb.2021.2087] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/18/2022] [Indexed: 01/15/2023] Open
Abstract
Predicting pathogen emergence and spillover risk requires understanding the determinants of a pathogens' host range and the traits involved in host competence. While host competence is often considered a fixed species-specific trait, it may be variable if pathogens diversify across hosts. Balancing selection can lead to maintenance of pathogen polymorphisms (multiple-niche-polymorphism; MNP). The causative agent of Lyme disease, Borrelia burgdorferi (Bb), provides a model to study the evolution of host adaptation, as some Bb strains defined by their outer surface protein C (ospC) genotype, are widespread in white-footed mice and others are associated with non-rodent vertebrates (e.g. birds). To identify the mechanisms underlying potential strain × host adaptation, we infected American robins and white-footed mice, with three Bb strains of different ospC genotypes. Bb burdens varied by strain in a host-dependent fashion, and strain persistence in hosts largely corresponded to Bb survival at early infection stages and with transmission to larvae (i.e. fitness). Early survival phenotypes are associated with cell adhesion, complement evasion and/or inflammatory and antibody-mediated removal of Bb, suggesting directional selective pressure for host adaptation and the potential role of MNP in maintaining OspC diversity. Our findings will guide future investigations to inform eco-evolutionary models of host adaptation for microparasites.
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Affiliation(s)
- Yi-Pin Lin
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
- Department of Biomedical Sciences, SUNY Albany, Albany, NY, USA
| | - Danielle M. Tufts
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
- Infectious Diseases and Microbiology Department, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew Combs
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
| | - Alan P. Dupuis
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
| | | | | | - Alexander J. Diaz
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
| | - Jessica L. Stout
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
| | - Anna M. Blom
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, Malmo, Sweden
| | - Klemen Strle
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
- Department of Biomedical Sciences, SUNY Albany, Albany, NY, USA
| | - April D. Davis
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
| | - Laura D. Kramer
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
- Department of Biomedical Sciences, SUNY Albany, Albany, NY, USA
| | - Sergios-Orestis Kolokotronis
- Department of Epidemiology and Biostatistics, School of Public Health, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
- Institute for Genomic Health, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
- Division of Infectious Diseases, Department of Medicine, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Maria A. Diuk-Wasser
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
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9
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Ardell SM, Kryazhimskiy S. The population genetics of collateral resistance and sensitivity. eLife 2021; 10:73250. [PMID: 34889185 PMCID: PMC8765753 DOI: 10.7554/elife.73250] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 12/06/2021] [Indexed: 12/05/2022] Open
Abstract
Resistance mutations against one drug can elicit collateral sensitivity against other drugs. Multi-drug treatments exploiting such trade-offs can help slow down the evolution of resistance. However, if mutations with diverse collateral effects are available, a treated population may evolve either collateral sensitivity or collateral resistance. How to design treatments robust to such uncertainty is unclear. We show that many resistance mutations in Escherichia coli against various antibiotics indeed have diverse collateral effects. We propose to characterize such diversity with a joint distribution of fitness effects (JDFE) and develop a theory for describing and predicting collateral evolution based on simple statistics of the JDFE. We show how to robustly rank drug pairs to minimize the risk of collateral resistance and how to estimate JDFEs. In addition to practical applications, these results have implications for our understanding of evolution in variable environments. Drugs known as antibiotics are the main treatment for most serious infections caused by bacteria. However, many bacteria are acquiring genetic mutations that make them resistant to the effects of one or more types of antibiotics, making them harder to eliminate. One way to tackle drug-resistant bacteria is to develop new types of antibiotics; however, in recent years, the rate at which new antibiotics have become available has been dwindling. Using two or more existing drugs, one after another, can also be an effective way to eliminate resistant bacteria. The success of any such ‘multi-drug’ treatment lies in being able to predict whether mutations that make the bacteria resistant to one drug simultaneously make it sensitive to another, a phenomenon known as collateral sensitivity. Different resistance mutations may have different collateral effects: some may increase the bacteria’s sensitivity to the second drug, while others might make the bacteria more resistant. However, it is currently unclear how to design robust multi-drug treatments that take this diversity of collateral effects into account. Here, Ardell and Kryazhimskiy used a concept called JDFE (short for the joint distribution of fitness effects) to describe the diversity of collateral effects in a population of bacteria exposed to a single drug. This information was then used to mathematically model how collateral effects evolved in the population over time. Ardell and Kryazhimskiy showed that this approach can predict how likely a population is to become collaterally sensitive or collaterally resistant to a second antibiotic. Drug pairs can then be ranked according to the risk of collateral resistance emerging, so long as information on the variety of resistance mutations available to the bacteria are included in the model. Each year, more than 700,000 people die from infections caused by bacteria that are resistant to one or more antibiotics. The findings of Ardell and Kryazhimskiy may eventually help clinicians design multi-drug treatments that effectively eliminate bacterial infections and help to prevent more bacteria from evolving resistance to antibiotics. However, to achieve this goal, more research is needed to fully understand the range collateral effects caused by resistance mutations.
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Affiliation(s)
- Sarah M Ardell
- Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Sergey Kryazhimskiy
- Division of Biological Sciences, University of California, San Diego, La Jolla, United States
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10
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Visher E, Evensen C, Guth S, Lai E, Norfolk M, Rozins C, Sokolov NA, Sui M, Boots M. The three Ts of virulence evolution during zoonotic emergence. Proc Biol Sci 2021; 288:20210900. [PMID: 34375554 PMCID: PMC8354747 DOI: 10.1098/rspb.2021.0900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/16/2021] [Indexed: 12/21/2022] Open
Abstract
There is increasing interest in the role that evolution may play in current and future pandemics, but there is often also considerable confusion about the actual evolutionary predictions. This may be, in part, due to a historical separation of evolutionary and medical fields, but there is a large, somewhat nuanced body of evidence-supported theory on the evolution of infectious disease. In this review, we synthesize this evolutionary theory in order to provide a framework for clearer understanding of the key principles. Specifically, we discuss the selection acting on zoonotic pathogens' transmission rates and virulence at spillover and during emergence. We explain how the direction and strength of selection during epidemics of emerging zoonotic disease can be understood by a three Ts framework: trade-offs, transmission, and time scales. Virulence and transmission rate may trade-off, but transmission rate is likely to be favoured by selection early in emergence, particularly if maladapted zoonotic pathogens have 'no-cost' transmission rate improving mutations available to them. Additionally, the optimal virulence and transmission rates can shift with the time scale of the epidemic. Predicting pathogen evolution, therefore, depends on understanding both the trade-offs of transmission-improving mutations and the time scales of selection.
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Affiliation(s)
- Elisa Visher
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Claire Evensen
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK
| | - Sarah Guth
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Edith Lai
- College of Natural Resources, University of California, Berkeley, CA 94720, USA
| | - Marina Norfolk
- College of Letters and Sciences, University of California, Berkeley, CA 94720, USA
| | - Carly Rozins
- Department of Science and Technology Studies, Division of Natural Science, York University, Toronto, Ontario, Canada M3J 1P3
| | - Nina A. Sokolov
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Melissa Sui
- College of Letters and Sciences, University of California, Berkeley, CA 94720, USA
| | - Michael Boots
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
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Common LK, Sumasgutner P, Dudaniec RY, Colombelli-Négrel D, Kleindorfer S. Avian vampire fly (Philornis downsi) mortality differs across Darwin's finch host species. Sci Rep 2021; 11:15832. [PMID: 34349147 PMCID: PMC8338931 DOI: 10.1038/s41598-021-94996-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 07/19/2021] [Indexed: 12/03/2022] Open
Abstract
In invasive parasites, generalism is considered advantageous during the initial phase of introduction. Thereafter, fitness costs to parasites, such as host-specific mortality, can drive parasites towards specialism to avoid costly hosts. It is important to determine changes in host specificity of invasive populations to understand host-parasite dynamics and their effects on vulnerable host populations. We examined changes in mortality in the introduced avian vampire fly (Philornis downsi) (Diptera: Muscidae), a generalist myasis-causing ectoparasite, between 2004 and 2020 on Floreana Island (Galápagos). Mortality was measured as the proportion of immature larvae found upon host nest termination. Over the time period, the avian vampire fly was most abundant and had low mortality in nests of the critically endangered medium tree finch (Camarhynchus pauper) and had the highest mortality in nests of hybrid tree finches (Camarhynchus spp.). Low larval mortality was also found in small tree (Camarhynchus parvulus) and small ground finch (Geospiza fuliginosa) nests. Selection could favour avian vampire flies that select medium tree finch nests and/or avoid hybrid nests. Overall, the finding of differences in avian vampire fly survival across host species is parsimonious with the idea that the introduced fly may be evolving towards host specialisation.
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Affiliation(s)
- Lauren K Common
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5001, Australia
| | - Petra Sumasgutner
- Department of Behavioral and Cognitive Biology, Konrad Lorenz Research Center, Core Facility for Behavior and Cognition, University of Vienna, Vienna, Austria
| | - Rachael Y Dudaniec
- Department of Biological Sciences, Macquarie University, Sydney, NSW , 2109, Australia
| | | | - Sonia Kleindorfer
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5001, Australia. .,Department of Behavioral and Cognitive Biology, Konrad Lorenz Research Center, Core Facility for Behavior and Cognition, University of Vienna, Vienna, Austria.
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Fisher AM. The evolutionary impact of population size, mutation rate and virulence on pathogen niche width. J Evol Biol 2021; 34:1256-1265. [PMID: 34101932 DOI: 10.1111/jeb.13882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 11/26/2022]
Abstract
Understanding the evolution of pathogen niche width is important for predicting disease spread and the probability that pathogens can emerge in novel hosts. Findings from previous theoretical studies often suggest that pathogens will evolve to be specialists in specific host environments. However, several of these studies make unrealistic assumptions regarding demographic stochasticity and the ability of pathogens to select their hosts. Here, an individual-based model was used to predict how population size, virulence and pathogen mutation rate affects the evolution niche specialism in pathogens. Pathogen specialism evolved regardless of virulence or populations size; thus, the findings of this study are somewhat consistent with those of previous work. However, because specialist pathogens had only a weak selective advantage over generalist pathogens, high mutation rates caused random trait variation to accumulate, preventing the evolution of specialism. Mutation rate varies greatly across different species and strains of pathogen. By showing that high mutation rates may prevent pathogen specialism evolving, this study highlights an intrinsic pathogen trait that may influence the evolution of pathogen niche width.
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Affiliation(s)
- Adam M Fisher
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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