1
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Gómez-Palacio A, Morinaga G, Turner PE, Micieli MV, Elnour MAB, Salim B, Surendran SN, Ramasamy R, Powell JR, Soghigian J, Gloria-Soria A. Robustness in population-structure and demographic-inference results derived from the Aedes aegypti SNP chip and whole-genome sequencing data. G3 (Bethesda) 2024:jkae082. [PMID: 38626295 DOI: 10.1093/g3journal/jkae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/04/2024] [Accepted: 04/04/2024] [Indexed: 04/18/2024]
Abstract
The mosquito Aedes aegypti is the primary vector of many human arboviruses such as dengue, yellow fever, chikungunya and Zika, which affect millions of people world-wide. Population genetics studies on this mosquito have been important in understanding its invasion pathways and success as a vector of human disease. The Axiom aegypti1 SNP chip was developed from a sample of geographically diverse Ae. aegypti populations to facilitate genomic studies on this species. We evaluate the utility of the Axiom aegypti1 SNP chip for population genetics and compare it with a low-depth shot-gun sequencing approach using mosquitoes from the native (Africa) and invasive range (outside Africa). These analyses indicate that results from the SNP chip are highly reproducible and have a higher sensitivity to capture alternative alleles than a low-coverage whole-genome sequencing approach. Although the SNP chip suffers from ascertainment bias, results from population structure, ancestry, demographic and phylogenetic analyses using the SNP chip were congruent with those derived from low coverage whole genome sequencing, and consistent with previous reports on Africa and outside Africa populations using microsatellites. More importantly, we identified a subset of SNPs that can be reliably used to generate merged databases, opening the door to combined analyses. We conclude that the Axiom aegypti1 SNP chip is a convenient, more accurate, low-cost alternative to low-depth whole genome sequencing for population genetic studies of Ae. aegypti that do not rely on full allelic frequency spectra. Whole genome sequencing and SNP chip data can be easily merged, extending the usefulness of both approaches.
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Affiliation(s)
- Andrés Gómez-Palacio
- Department of Entomology. Center for Vector Biology & Zoonotic Diseases. The Connecticut Agricultural Experiment Station. 123 Huntington St. New Haven, CT, USA 06511
- Laboratorio de Investigación en Genética Evolutiva. Universidad Pedagógica y Tecnológica de Colombia. Avenida Central del Norte 39-115. Boyacá, Colombia. 150003
| | - Gen Morinaga
- Faculty of Veterinary Medicine. University of Calgary. 2500 University Drive NW. Calgary, AB, CAN 2TN 1N4
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology. Yale University. 165 Prospect St. New Haven, CT, USA 06511
- Quantitative Biology Institute. Yale University. 260 Whitney Ave. New Haven, CT, USA. 06511
| | - Maria Victoria Micieli
- Centro de Estudios Parasitológicos y de Vectores (CEPAVE) CONICET Universidad de la Plata. Boulevard 120 s/n between Av. 60 and Calle 64. La Plata, Argentina. 1900
| | - Mohammed-Ahmed B Elnour
- Department of Parasitology and Medical Entomology. Tropical Medicine Research Institute. National Center for Research. JG5R+WXF, Khartoum, Sudan. 11111
| | - Bashir Salim
- Department of Parasitology. Faculty of Veterinary Medicine. University of Khartoum. Khartoum North, Sudan. 11111
- Camel Research Center, King Faisal University. P.O. Box. 400. Al-Ahsa 31982, Saudi Arabia
| | | | - Ranjan Ramasamy
- Department of Zoology. University of Jaffna. Jaffna, Sri Lanka. 40000
| | - Jeffrey R Powell
- Department of Ecology and Evolutionary Biology. Yale University. 165 Prospect St. New Haven, CT, USA 06511
| | - John Soghigian
- Faculty of Veterinary Medicine. University of Calgary. 2500 University Drive NW. Calgary, AB, CAN 2TN 1N4
| | - Andrea Gloria-Soria
- Department of Entomology. Center for Vector Biology & Zoonotic Diseases. The Connecticut Agricultural Experiment Station. 123 Huntington St. New Haven, CT, USA 06511
- Department of Ecology and Evolutionary Biology. Yale University. 165 Prospect St. New Haven, CT, USA 06511
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2
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Zamora PF, Reidy TG, Armbruster CR, Sun M, Van Tyne D, Turner PE, Koff JL, Bomberger JM. Lytic bacteriophages induce the secretion of antiviral and proinflammatory cytokines from human respiratory epithelial cells. PLoS Biol 2024; 22:e3002566. [PMID: 38652717 PMCID: PMC11037538 DOI: 10.1371/journal.pbio.3002566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/27/2024] [Indexed: 04/25/2024] Open
Abstract
Phage therapy is a therapeutic approach to treat multidrug-resistant (MDR) infections that employs lytic bacteriophages (phages) to eliminate bacteria. Despite the abundant evidence for its success as an antimicrobial in Eastern Europe, there is scarce data regarding its effects on the human host. Here, we aimed to understand how lytic phages interact with cells of the airway epithelium, the tissue site that is colonized by bacterial biofilms in numerous chronic respiratory disorders. Using a panel of Pseudomonas aeruginosa phages and human airway epithelial cells (AECs) derived from a person with cystic fibrosis (CF), we determined that interactions between phages and epithelial cells depend on specific phage properties as well as physiochemical features of the microenvironment. Although poor at internalizing phages, the airway epithelium responds to phage exposure by changing its transcriptional profile and secreting antiviral and proinflammatory cytokines that correlate with specific phage families. Overall, our findings indicate that mammalian responses to phages are heterogenous and could potentially alter the way that respiratory local defenses aid in bacterial clearance during phage therapy. Thus, besides phage receptor specificity in a particular bacterial isolate, the criteria to select lytic phages for therapy should be expanded to include mammalian cell responses.
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Affiliation(s)
- Paula F. Zamora
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, New Hampshire, United States of America
| | - Thomas G. Reidy
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Catherine R. Armbruster
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, New Hampshire, United States of America
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Ming Sun
- Center for Biological Imaging, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Daria Van Tyne
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Paul E. Turner
- Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Quantitative Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Jonathan L. Koff
- Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, United States of America
- Department of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Jennifer M. Bomberger
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, New Hampshire, United States of America
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3
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Zamora PF, Reidy TG, Armbruster CR, Sun M, Van Tyne D, Turner PE, Koff JL, Bomberger JM. Lytic bacteriophages interact with respiratory epithelial cells and induce the secretion of antiviral and proinflammatory cytokines. bioRxiv 2024:2024.02.06.579115. [PMID: 38370761 PMCID: PMC10871231 DOI: 10.1101/2024.02.06.579115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Phage therapy is a therapeutic approach to treat multidrug resistant infections that employs lytic bacteriophages (phages) to eliminate bacteria. Despite the abundant evidence for its success as an antimicrobial in Eastern Europe, there is scarce data regarding its effects on the human host. Here, we aimed to understand how lytic phages interact with cells of the airway epithelium, the tissue site that is colonized by bacterial biofilms in numerous chronic respiratory disorders. We determined that interactions between phages and epithelial cells depend on specific phage properties as well as physiochemical features of the microenvironment. Although poor at internalizing phages, the airway epithelium responds to phage exposure by changing its transcriptional profile and secreting antiviral and proinflammatory cytokines that correlate with specific phage families. Overall, our findings indicate that mammalian responses to phages are heterogenous and could potentially alter the way that respiratory local defenses aid in bacterial clearance during phage therapy. Thus, besides phage receptor specificity in a particular bacterial isolate, the criteria to select lytic phages for therapy should be expanded to include mammalian cell responses.
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Affiliation(s)
- Paula F Zamora
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH
| | - Thomas G Reidy
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Catherine R Armbruster
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA
| | - Ming Sun
- Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA
| | - Daria Van Tyne
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Paul E Turner
- Center for Phage Biology and Therapy, Yale University, New Haven, CT
| | - Jonathan L Koff
- Center for Phage Biology and Therapy, Yale University, New Haven, CT
| | - Jennifer M Bomberger
- Department of Microbiology and Immunology, Dartmouth Geisel School of Medicine, Hanover, NH
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4
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Würstle S, Lee A, Kortright KE, Winzig F, An W, Stanley GL, Rajagopalan G, Harris Z, Sun Y, Hu B, Blazanin M, Hajfathalian M, Bollyky PL, Turner PE, Koff JL, Chan BK. Optimized preparation pipeline for emergency phage therapy against Pseudomonas aeruginosa at Yale University. Sci Rep 2024; 14:2657. [PMID: 38302552 PMCID: PMC10834462 DOI: 10.1038/s41598-024-52192-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Bacteriophage therapy is one potential strategy to treat antimicrobial resistant or persistent bacterial infections, and the year 2021 marked the centennial of Felix d'Hérelle's first publication on the clinical applications of phages. At the Center for Phage Biology & Therapy at Yale University, a preparatory modular approach has been established to offer safe and potent phages for single-patient investigational new drug applications while recognizing the time constraints imposed by infection(s). This study provides a practical walkthrough of the pipeline with an Autographiviridae phage targeting Pseudomonas aeruginosa (phage vB_PaeA_SB, abbreviated to ΦSB). Notably, a thorough phage characterization and the evolutionary selection pressure exerted on bacteria by phages, analogous to antibiotics, are incorporated into the pipeline.
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Affiliation(s)
- Silvia Würstle
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Technical University of Munich, 81675, Munich, Germany
| | - Alina Lee
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Kaitlyn E Kortright
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Franziska Winzig
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Technical University of Munich, 81675, Munich, Germany
| | - William An
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Gail L Stanley
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Govindarajan Rajagopalan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Zach Harris
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Ying Sun
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Buqu Hu
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Michael Blazanin
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Maryam Hajfathalian
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul L Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Paul E Turner
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA
- Program in Microbiology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Jonathan L Koff
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06519, USA.
| | - Benjamin K Chan
- Yale Center for Phage Biology and Therapy, Yale University, 165 Prospect Street, New Haven, CT, 06520, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA.
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5
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Oromí-Bosch A, Antani JD, Turner PE. Developing Phage Therapy That Overcomes the Evolution of Bacterial Resistance. Annu Rev Virol 2023; 10:503-524. [PMID: 37268007 DOI: 10.1146/annurev-virology-012423-110530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The global rise of antibiotic resistance in bacterial pathogens and the waning efficacy of antibiotics urge consideration of alternative antimicrobial strategies. Phage therapy is a classic approach where bacteriophages (bacteria-specific viruses) are used against bacterial infections, with many recent successes in personalized medicine treatment of intractable infections. However, a perpetual challenge for developing generalized phage therapy is the expectation that viruses will exert selection for target bacteria to deploy defenses against virus attack, causing evolution of phage resistance during patient treatment. Here we review the two main complementary strategies for mitigating bacterial resistance in phage therapy: minimizing the ability for bacterial populations to evolve phage resistance and driving (steering) evolution of phage-resistant bacteria toward clinically favorable outcomes. We discuss future research directions that might further address the phage-resistance problem, to foster widespread development and deployment of therapeutic phage strategies that outsmart evolved bacterial resistance in clinical settings.
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Affiliation(s)
| | - Jyot D Antani
- Department of Ecology and Evolutionary Biology, Center for Phage Biology & Therapy, and Quantitative Biology Institute, Yale University, New Haven, Connecticut, USA;
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Center for Phage Biology & Therapy, and Quantitative Biology Institute, Yale University, New Haven, Connecticut, USA;
- Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, USA
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6
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Schwarz JC, An W, Theroux A, Vargas LD, Chan BK, Turner PE, Burmeister AR. Complete Genome Assembly and Annotation of Escherichia coli Bacteriophage 55 from Rivière la Quint in Gonaïves, Haiti. Microbiol Resour Announc 2023:e0010723. [PMID: 37272828 DOI: 10.1128/mra.00107-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
We present the structural and functional annotation of Escherichia coli bacteriophage 55, which has a genome length of 170,393 bp, with 219 predicted genes.
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Affiliation(s)
- Joshua C Schwarz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - William An
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Austen Theroux
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Luz D Vargas
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
- Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, USA
| | - Alita R Burmeister
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
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7
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Schwarz JC, Chan BK, Turner PE, Burmeister AR. Complete Genome Assembly and Annotation of Escherichia coli Bacteriophage 107. Microbiol Resour Announc 2023:e0010623. [PMID: 37191527 DOI: 10.1128/mra.00106-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
We present the annotated genome sequence of Escherichia coli bacteriophage 107, a T4-like bacteriophage. Phage 107 has a genome length of 167,509 bp and 287 predicted genes.
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Affiliation(s)
- Joshua C Schwarz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
- Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, USA
| | - Alita R Burmeister
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
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8
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Burmeister AR, Tzintzun-Tapia E, Roush C, Mangal I, Barahman R, Bjornson RD, Turner PE. Experimental Evolution of the TolC-Receptor Phage U136B Functionally Identifies a Tail Fiber Protein Involved in Adsorption through Strong Parallel Adaptation. Appl Environ Microbiol 2023:e0007923. [PMID: 37191555 DOI: 10.1128/aem.00079-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Bacteriophages have received recent attention for their therapeutic potential to treat antibiotic-resistant bacterial infections. One particular idea in phage therapy is to use phages that not only directly kill their bacterial hosts but also rely on particular bacterial receptors, such as proteins involved in virulence or antibiotic resistance. In such cases, the evolution of phage resistance would correspond to the loss of those receptors, an approach termed evolutionary steering. We previously found that during experimental evolution, phage U136B can exert selection pressure on Escherichia coli to lose or modify its receptor, the antibiotic efflux protein TolC, often resulting in reduced antibiotic resistance. However, for TolC-reliant phages like U136B to be used therapeutically, we also need to study their own evolutionary potential. Understanding phage evolution is critical for the development of improved phage therapies as well as the tracking of phage populations during infection. Here, we characterized phage U136B evolution in 10 replicate experimental populations. We quantified phage dynamics that resulted in five surviving phage populations at the end of the 10-day experiment. We found that phages from all five surviving populations had evolved higher rates of adsorption on either ancestral or coevolved E. coli hosts. Using whole-genome and whole-population sequencing, we established that these higher rates of adsorption were associated with parallel molecular evolution in phage tail protein genes. These findings will be useful in future studies to predict how key phage genotypes and phenotypes influence phage efficacy and survival despite the evolution of host resistance. IMPORTANCE Antibiotic resistance is a persistent problem in health care and a factor that may help maintain bacterial diversity in natural environments. Bacteriophages ("phages") are viruses that specifically infect bacteria. We previously discovered and characterized a phage called U136B, which infects bacteria through TolC. TolC is an antibiotic resistance protein that helps bacteria pump antibiotics out of the cell. Over short timescales, phage U136B can be used to evolutionarily "steer" bacterial populations to lose or modify the TolC protein, sometimes reducing antibiotic resistance. In this study, we investigate whether U136B itself evolves to better infect bacterial cells. We discovered that the phage can readily evolve specific mutations that increase its infection rate. This work will be useful for understanding how phages can be used to treat bacterial infections.
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Affiliation(s)
- Alita R Burmeister
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
- Department of Biological Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA
| | - Eddy Tzintzun-Tapia
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
| | - Carli Roush
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
| | - Ivan Mangal
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
| | - Roxanna Barahman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
| | | | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA
- Microbiology Program, Yale School of Medicine, New Haven, Connecticut, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, USA
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9
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Würstle S, Hapfelmeier A, Karapetyan S, Studen F, Isaakidou A, Schneider T, Schmid RM, von Delius S, Gundling F, Burgkart R, Obermeier A, Mayr U, Ringelhan M, Rasch S, Lahmer T, Geisler F, Turner PE, Chan BK, Spinner CD, Schneider J. Differentiation of Spontaneous Bacterial Peritonitis from Secondary Peritonitis in Patients with Liver Cirrhosis: Retrospective Multicentre Study. Diagnostics (Basel) 2023; 13:diagnostics13050994. [PMID: 36900138 PMCID: PMC10000989 DOI: 10.3390/diagnostics13050994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Ascitic fluid infection is a serious complication of liver cirrhosis. The distinction between the more common spontaneous bacterial peritonitis (SBP) and the less common secondary peritonitis in patients with liver cirrhosis is crucial due to the varying treatment approaches. This retrospective multicentre study was conducted in three German hospitals and analysed 532 SBP episodes and 37 secondary peritonitis episodes. Overall, >30 clinical, microbiological, and laboratory parameters were evaluated to identify key differentiation criteria. Microbiological characteristics in ascites followed by severity of illness and clinicopathological parameters in ascites were the most important predictors identified by a random forest model to distinguish between SBP and secondary peritonitis. To establish a point-score model, a least absolute shrinkage and selection operator (LASSO) regression model selected the ten most promising discriminatory features. By aiming at a sensitivity of 95% either to rule out or rule in SBP episodes, two cut-off scores were defined, dividing patients with infected ascites into a low-risk (score ≥ 45) and high-risk group (score < 25) for secondary peritonitis. Overall, the discrimination of secondary peritonitis from SBP remains challenging. Our univariable analyses, random forest model, and LASSO point score may help clinicians with the crucial differentiation between SBP and secondary peritonitis.
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Affiliation(s)
- Silvia Würstle
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
| | - Alexander Hapfelmeier
- Institute of General Practice and Health Services Research, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
- Institute of AI and Informatics in Medicine, School of Medicine, Technical University of Munich, Einsteinstr. 25, 81675 Munich, Germany
| | - Siranush Karapetyan
- Institute of AI and Informatics in Medicine, School of Medicine, Technical University of Munich, Einsteinstr. 25, 81675 Munich, Germany
| | - Fabian Studen
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
| | - Andriana Isaakidou
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
| | - Tillman Schneider
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
| | - Roland M. Schmid
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
| | - Stefan von Delius
- Department of Internal Medicine II, RoMed Hospital Rosenheim, Pettenkoferstr. 10, 83022 Rosenheim, Germany
| | - Felix Gundling
- Department of Gastroenterology, Hepatology, and Gastrointestinal Oncology, Bogenhausen Hospital of the Munich Municipal Hospital Group, Englschalkinger Straße 77, 81925 Munich, Germany
- Department of Internal Medicine II, Klinikum am Bruderwald, Sozialstiftung Bamberg, Buger Straße 80, 96049 Bamberg, Germany
| | - Rainer Burgkart
- Clinic of Orthopaedics and Sports Orthopaedics, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
| | - Andreas Obermeier
- Clinic of Orthopaedics and Sports Orthopaedics, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
| | - Ulrich Mayr
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
| | - Marc Ringelhan
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
| | - Sebastian Rasch
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
| | - Tobias Lahmer
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
| | - Fabian Geisler
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
- Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Benjamin K. Chan
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA
| | - Christoph D. Spinner
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Ismaninger Str. 22, 81675 Munich, Germany
| | - Jochen Schneider
- Department of Internal Medicine II, University Hospital Rechts der Isar, School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675 Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, Ismaninger Str. 22, 81675 Munich, Germany
- Correspondence:
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10
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Natterson-Horowitz B, Aktipis A, Fox M, Gluckman PD, Low FM, Mace R, Read A, Turner PE, Blumstein DT. The future of evolutionary medicine: sparking innovation in biomedicine and public health. Front Sci 2023; 1:997136. [PMID: 37869257 PMCID: PMC10590274 DOI: 10.3389/fsci.2023.997136] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Evolutionary medicine - i.e. the application of insights from evolution and ecology to biomedicine - has tremendous untapped potential to spark transformational innovation in biomedical research, clinical care and public health. Fundamentally, a systematic mapping across the full diversity of life is required to identify animal model systems for disease vulnerability, resistance, and counter-resistance that could lead to novel clinical treatments. Evolutionary dynamics should guide novel therapeutic approaches that target the development of treatment resistance in cancers (e.g., via adaptive or extinction therapy) and antimicrobial resistance (e.g., via innovations in chemistry, antimicrobial usage, and phage therapy). With respect to public health, the insight that many modern human pathologies (e.g., obesity) result from mismatches between the ecologies in which we evolved and our modern environments has important implications for disease prevention. Life-history evolution can also shed important light on patterns of disease burden, for example in reproductive health. Experience during the COVID-19 (SARS-CoV-2) pandemic has underlined the critical role of evolutionary dynamics (e.g., with respect to virulence and transmissibility) in predicting and managing this and future pandemics, and in using evolutionary principles to understand and address aspects of human behavior that impede biomedical innovation and public health (e.g., unhealthy behaviors and vaccine hesitancy). In conclusion, greater interdisciplinary collaboration is vital to systematically leverage the insight-generating power of evolutionary medicine to better understand, prevent, and treat existing and emerging threats to human, animal, and planetary health.
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Affiliation(s)
- B. Natterson-Horowitz
- Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Athena Aktipis
- Department of Psychology, Arizona State University, Tempe, AZ, United States
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
| | - Molly Fox
- Department of Anthropology, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, United States
| | - Peter D. Gluckman
- Koi Tū: The Centre for Informed Futures, University of Auckland, Auckland, New Zealand
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Felicia M. Low
- Koi Tū: The Centre for Informed Futures, University of Auckland, Auckland, New Zealand
| | - Ruth Mace
- Department of Anthropology, University College London, London, United Kingdom
| | - Andrew Read
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, State College, PA, United States
- Department of Entomology, The Pennsylvania State University, State College, PA, United States
- Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA, United States
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
- Program in Microbiology, Yale School of Medicine, New Haven, CT, United States
| | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
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11
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Winzig F, Gandhi S, Lee A, Würstle S, Stanley GL, Capuano I, Neuringer I, Koff JL, Turner PE, Chan BK. Inhaled Bacteriophage Therapy for Multi-Drug Resistant Achromobacter. Yale J Biol Med 2022; 95:413-427. [PMID: 36568830 PMCID: PMC9765334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The rise of antimicrobial resistant (AMR) bacteria is a global public health threat. AMR Achromobacter bacteria pose a challenging clinical problem, particularly for those with cystic fibrosis (CF) who are predisposed to chronic bacterial lung infections. Lytic bacteriophages (phages) offer a potential alternative to treat AMR infections, with the possible benefit that phage selection for resistance in target bacteria might coincide with reduced pathogenicity. The result is a genetic "trade-off," such as increased sensitivity to chemical antibiotics, and/or decreased virulence of surviving bacteria that are phage resistant. Here, we show that two newly discovered lytic phages against Achromobacter were associated with stabilization of respiratory status when deployed to treat a chronic pulmonary infection in a CF patient using inhaled (nebulized) phage therapy. The two phages demonstrate traits that could be generally useful in their development as therapeutics, especially the possibility that the phages can select for clinically useful trade-offs if bacteria evolve phage resistance following therapy. We discuss the limitations of the current study and suggest further work that should explore whether the phages could be generally useful in targeting pulmonary or other Achromobacter infections in CF patients.
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Affiliation(s)
- Franziska Winzig
- Department of Ecology and Evolutionary Biology, Yale
University, New Haven, CT, USA
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- Technische Universität München, München, Germany
| | - Shiv Gandhi
- Department of Ecology and Evolutionary Biology, Yale
University, New Haven, CT, USA
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- Department of Internal Medicine, Section of Infectious
Disease, Yale School of Medicine, New Haven, CT, USA
| | - Alina Lee
- Department of Ecology and Evolutionary Biology, Yale
University, New Haven, CT, USA
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
| | - Silvia Würstle
- Department of Ecology and Evolutionary Biology, Yale
University, New Haven, CT, USA
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- Department of Internal Medicine II, University Hospital
rechts der Isar, School of Medicine, Technische Universität München, München,
Germany
| | - Gail L. Stanley
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- Department of Internal Medicine, Section of Pulmonary,
Critical Care, & Sleep Medicine, Yale School of Medicine, New Haven, CT,
USA
| | - Isabella Capuano
- Department of Internal Medicine, Section of Pulmonary,
Critical Care, & Sleep Medicine, Yale School of Medicine, New Haven, CT,
USA
- Cornell University, Ithaca, NY, USA
| | | | - Jonathan L. Koff
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- Department of Internal Medicine, Section of Pulmonary,
Critical Care, & Sleep Medicine, Yale School of Medicine, New Haven, CT,
USA
- To whom all correspondence should be addressed:
Paul E. Turner, ; ORCID:
https://www.orcid.org/0000-0003-3490-7498. Benjamin K. Chan,
. Jonathan L. Koff,
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale
University, New Haven, CT, USA
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- Program in Microbiology, Yale School of Medicine, New
Haven, CT, USA
- To whom all correspondence should be addressed:
Paul E. Turner, ; ORCID:
https://www.orcid.org/0000-0003-3490-7498. Benjamin K. Chan,
. Jonathan L. Koff,
| | - Benjamin K. Chan
- Department of Ecology and Evolutionary Biology, Yale
University, New Haven, CT, USA
- Center for Phage Biology & Therapy, Yale
University, New Haven, CT, USA
- To whom all correspondence should be addressed:
Paul E. Turner, ; ORCID:
https://www.orcid.org/0000-0003-3490-7498. Benjamin K. Chan,
. Jonathan L. Koff,
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12
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Würstle S, Hapfelmeier A, Karapetyan S, Studen F, Isaakidou A, Schneider T, Schmid RM, von Delius S, Gundling F, Triebelhorn J, Burgkart R, Obermeier A, Mayr U, Heller S, Rasch S, Lahmer T, Geisler F, Chan B, Turner PE, Rothe K, Spinner CD, Schneider J. A Novel Machine Learning-Based Point-Score Model as a Non-Invasive Decision-Making Tool for Identifying Infected Ascites in Patients with Hydropic Decompensated Liver Cirrhosis: A Retrospective Multicentre Study. Antibiotics (Basel) 2022; 11:antibiotics11111610. [PMID: 36421254 PMCID: PMC9686825 DOI: 10.3390/antibiotics11111610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/06/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
This study is aimed at assessing the distinctive features of patients with infected ascites and liver cirrhosis and developing a scoring system to allow for the accurate identification of patients not requiring abdominocentesis to rule out infected ascites. A total of 700 episodes of patients with decompensated liver cirrhosis undergoing abdominocentesis between 2006 and 2020 were included. Overall, 34 clinical, drug, and laboratory features were evaluated using machine learning to identify key differentiation criteria and integrate them into a point-score model. In total, 11 discriminatory features were selected using a Lasso regression model to establish a point-score model. Considering pre-test probabilities for infected ascites of 10%, 15%, and 25%, the negative and positive predictive values of the point-score model for infected ascites were 98.1%, 97.0%, 94.6% and 14.9%, 21.8%, and 34.5%, respectively. Besides the main model, a simplified model was generated, containing only features that are fast to collect, which revealed similar predictive values. Our point-score model appears to be a promising non-invasive approach to rule out infected ascites in clinical routine with high negative predictive values in patients with hydropic decompensated liver cirrhosis, but further external validation in a prospective study is needed.
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Affiliation(s)
- Silvia Würstle
- Department of Internal Medicine II, University Hospital rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Alexander Hapfelmeier
- Institute of General Practice and Health Services Research, School of Medicine, Technical University of Munich, 81667 Munich, Germany
- Institute of AI and Informatics in Medicine, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Siranush Karapetyan
- Institute of AI and Informatics in Medicine, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Fabian Studen
- Department of Internal Medicine II, University Hospital rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Andriana Isaakidou
- Department of Internal Medicine II, University Hospital rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Tillman Schneider
- Department of Internal Medicine II, University Hospital rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Roland M. Schmid
- Department of Internal Medicine II, University Hospital rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Stefan von Delius
- Department of Internal Medicine II, RoMed Hospital Rosenheim, 83022 Rosenheim, Germany
| | - Felix Gundling
- Department of Gastroenterology, Hepatology, and Gastrointestinal Oncology, Bogenhausen Hospital of the Munich Municipal Hospital Group, 81925 Munich, Germany
- Department of Internal Medicine II, Klinikum am Bruderwald, Sozialstiftung Bamberg, 96049 Bamberg, Germany
| | - Julian Triebelhorn
- Department of Internal Medicine II, University Hospital rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Rainer Burgkart
- Clinic of Orthopaedics and Sports Orthopaedics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Andreas Obermeier
- Clinic of Orthopaedics and Sports Orthopaedics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Ulrich Mayr
- Department of Internal Medicine II, University Hospital rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Stephan Heller
- Clinic of Orthopaedics and Sports Orthopaedics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Sebastian Rasch
- Department of Internal Medicine II, University Hospital rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Tobias Lahmer
- Department of Internal Medicine II, University Hospital rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Fabian Geisler
- Department of Internal Medicine II, University Hospital rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Benjamin Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kathrin Rothe
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Christoph D. Spinner
- Department of Internal Medicine II, University Hospital rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
| | - Jochen Schneider
- Department of Internal Medicine II, University Hospital rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- German Centre for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
- Correspondence:
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13
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Turner PE. Paul E. Turner. Curr Biol 2022; 32:R1203-R1206. [DOI: 10.1016/j.cub.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Kortright KE, Chan BK, Evans BR, Turner PE. Arms race and fluctuating selection dynamics in Pseudomonas aeruginosa bacteria coevolving with phage OMKO1. J Evol Biol 2022; 35:1475-1487. [PMID: 36168737 DOI: 10.1111/jeb.14095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/03/2022] [Accepted: 08/22/2022] [Indexed: 11/28/2022]
Abstract
Experimental evolution studies have examined coevolutionary dynamics between bacteria and lytic phages, where two models for antagonistic coevolution dominate: arms-race dynamics (ARD) and fluctuating-selection dynamics (FSD). Here, we tested the ability for Pseudomonas aeruginosa to coevolve with phage OMKO1 during 10 passages in the laboratory, whether ARD versus FSD coevolution occurred, and how coevolution affected a predicted phenotypic trade-off between phage resistance and antibiotic sensitivity. We used a unique "deep" sampling design, where 96 bacterial clones per passage were obtained from the three replicate coevolving communities. Next, we examined phenotypic changes in growth ability, susceptibility to phage infection and resistance to antibiotics. Results confirmed that the bacteria and phages coexisted throughout the study with one community undergoing ARD, whereas the other two showed evidence for FSD. Surprisingly, only the ARD bacteria demonstrated the anticipated trade-off. Whole genome sequencing revealed that treatment populations of bacteria accrued more de novo mutations, relative to a control bacterial population. Additionally, coevolved bacteria presented mutations in genes for biosynthesis of flagella, type-IV pilus and lipopolysaccharide, with three mutations fixing contemporaneously with the occurrence of the phenotypic trade-off in the ARD-coevolved bacteria. Our study demonstrates that both ARD and FSD coevolution outcomes are possible in a single interacting bacteria-phage system and that occurrence of predicted phage-driven evolutionary trade-offs may depend on the genetics underlying evolution of phage resistance in bacteria. These results are relevant for the ongoing development of lytic phages, such as OMKO1, in personalized treatment of human patients, as an alternative to antibiotics.
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Affiliation(s)
- Kaitlyn E Kortright
- Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, USA
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, USA
| | - Benjamin R Evans
- Yale Center for Research Computing, Yale University, New Haven, Connecticut, USA
| | - Paul E Turner
- Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,Center for Phage Biology and Therapy, Yale University, New Haven, Connecticut, USA
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15
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Blazanin M, Lam WT, Vasen E, Chan BK, Turner PE. Decay and damage of therapeutic phage OMKO1 by environmental stressors. PLoS One 2022; 17:e0263887. [PMID: 35196336 PMCID: PMC8865689 DOI: 10.1371/journal.pone.0263887] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/25/2022] [Indexed: 01/21/2023] Open
Abstract
Antibiotic resistant bacterial pathogens are increasingly prevalent, driving the need for alternative approaches to chemical antibiotics when treating infections. One such approach is bacteriophage therapy: the use of bacteria-specific viruses that lyse (kill) their host cells. Just as the effect of environmental conditions (e.g. elevated temperature) on antibiotic efficacy is well-studied, the effect of environmental stressors on the potency of phage therapy candidates demands examination. Therapeutic phage OMKO1 infects and kills the opportunistic human pathogen Pseudomonas aeruginosa. Here, we used phage OMKO1 as a model to test how environmental stressors can lead to damage and decay of virus particles. We assessed the effects of elevated temperatures, saline concentrations, and urea concentrations. We observed that OMKO1 particles were highly tolerant to different saline concentrations, but decayed more rapidly at elevated temperatures and under high concentrations of urea. Additionally, we found that exposure to elevated temperature reduced the ability of surviving phage particles to suppress the growth of P. aeruginosa, suggesting a temperature-induced damage. Our findings demonstrate that OMKO1 is highly tolerant to a range of conditions that could be experienced inside and outside the human body, while also showing the need for careful characterization of therapeutic phages to ensure that environmental exposure does not compromise their expected potency, dosing, and pharmacokinetics.
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Affiliation(s)
- Michael Blazanin
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
- * E-mail:
| | - Wai Tin Lam
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Emma Vasen
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Benjamin K. Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
- Program in Microbiology, Yale School of Medicine, New Haven, CT, United States of America
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Hinton DM, Turner PE. Call for Special Issue Papers: Phage/Host Combat: Phage Strategies for Taking Over the Host and Host Strategies for Defense: Deadline for Manuscript Submission: July 1, 2022. Phage (New Rochelle) 2022; 3:1-2. [PMID: 36161192 PMCID: PMC9436253 DOI: 10.1089/phage.2022.29026.cfp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Deborah M. Hinton
- Chief, Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Paul E. Turner
- Rachel Carson Professor of Ecology & Evolutionary Biology, Director of Center for Phage Biology and Therapy, Director of Quantitative Biology Institute and Program in Physics, Engineering & Biology, Yale University Microbiology Faculty, Yale School of Medicine, New Haven, CT, USA
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17
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Alizon S, Turner PE. Can we eradicate viral pathogens? J Evol Biol 2021; 34:1851-1854. [PMID: 34907625 DOI: 10.1111/jeb.13958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/10/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Samuel Alizon
- MIVEGEC, CNRS, IRD, Université de Montpellier, Montpellier, France
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, USA
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18
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Blazanin M, Turner PE. Community context matters for bacteria-phage ecology and evolution. ISME J 2021; 15:3119-3128. [PMID: 34127803 PMCID: PMC8528888 DOI: 10.1038/s41396-021-01012-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/30/2021] [Accepted: 05/11/2021] [Indexed: 02/03/2023]
Abstract
Bacteria-phage symbioses are ubiquitous in nature and serve as valuable biological models. Historically, the ecology and evolution of bacteria-phage systems have been studied in either very simple or very complex communities. Although both approaches provide insight, their shortcomings limit our understanding of bacteria and phages in multispecies contexts. To address this gap, here we synthesize the emerging body of bacteria-phage experiments in medium-complexity communities, specifically those that manipulate bacterial community presence. Generally, community presence suppresses both focal bacterial (phage host) and phage densities, while sometimes altering bacteria-phage ecological interactions in diverse ways. Simultaneously, community presence can have an array of evolutionary effects. Sometimes community presence has no effect on the coevolutionary dynamics of bacteria and their associated phages, whereas other times the presence of additional bacterial species constrains bacteria-phage coevolution. At the same time, community context can alter mechanisms of adaptation and interact with the pleiotropic consequences of (co)evolution. Ultimately, these experiments show that community context can have important ecological and evolutionary effects on bacteria-phage systems, but many questions still remain unanswered and ripe for additional investigation.
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Affiliation(s)
- Michael Blazanin
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Program in Microbiology, Yale School of Medicine, New Haven, CT, USA
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Abstract
Phages are viruses that specifically infect bacteria, and their biodiversity contributes to historical and current development of phage therapy to treat myriad bacterial infections. Phage therapy holds promise as an alternative to failing chemical antibiotics, but there are benefits and costs of this technology. Here, we review the rich history of phage therapy, highlighting reasons (often political) why it was widely rejected by Western medicine until recently. One longstanding idea involves mixing different phages together in cocktails, to increase the probability of killing target pathogenic bacteria without pre-screening for phage susceptibility. By challenging 30 lytic phages to infect 14 strains of the bacteria Pseudomonas aeruginosa, we showed that some phages were "generalists" with broad host-ranges, emphasizing that extreme host-specificity of phages was not necessarily a liability. Using a "greedy algorithm" analysis, we identified the best cocktail mixture of phages to achieve broad bacteria killing. Additionally, we review how virus host-range can evolve and connect lessons learned from virus emergence-including contributions of elevated virus mutation rates in promoting emergence and virus evolutionary transitions from specialized to generalized host-use-as cautionary tales for avoiding risk of "off-target" phage emergence on commensal bacteria in microbiomes. Throughout, we highlight how fundamental understanding of virus ecology and evolution is vital for developing phage therapy; heeding these principles should help in designing therapeutic strategies that do not recapitulate consequences of virus selection to emerge on novel hosts.
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Affiliation(s)
- Lisa M Bono
- Department of Biology, Emory University, Atlanta, GA, United States.
| | - Stephanie Mao
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rachel E Done
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA, United States; Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Kenichi W Okamoto
- Department of Biology, University of St. Thomas, St. Paul, MN, United States
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States; Microbiology Program, Yale School of Medicine, New Haven, CT, United States
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Abstract
In 1979, Richard Law introduced the conceptual idea of the 'Darwinian Demon': an organism that simultaneously maximizes all fitness traits [1]. Such an organism would dominate an ecosystem, displacing any competitors and collapsing biodiversity to only a singular species. Surveying the tremendous species diversity of bacteria in the microbial world reveals that Darwinian Demons do not exist on Earth, and the popular notion is that fitness trade-offs generally constrain such possible evolution. However, the trade-offs faced by evolving bacterial populations presumably hinder their adaptation in ways that are not fully understood. In some cases, bacteria show evolved trade-ups, whereby selection causes multiple fitness components to improve simultaneously. Understanding these trade-offs and trade-ups, as well as their prevalence and roles in shaping microbial fitness, is key to elucidating how the incredible diversity of the Bacteria domain came to be, what maintains that diversity, and whether such diversity can be leveraged for technologies that improve human health and protect environments.
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Affiliation(s)
- Alita R Burmeister
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA; BEACON Center for the Study of Evolution in Action, East Lansing, MI, USA.
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA; BEACON Center for the Study of Evolution in Action, East Lansing, MI, USA; Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
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21
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Fenster CB, Soltis PS, Turner PE. Pandemic Policy in the Vaccine Era: The Long Haul Approach. Bioscience 2021. [DOI: 10.1093/biosci/biab061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Charles B Fenster
- Oak Lake Field Station, South Dakota State University, Brookings, South Dakota, United States
| | - Pamela S Soltis
- Florida Museum of Natural History and with the Biodiversity Institute, University of Florida, Gainesville, Florida, United States
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University and with the Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, United States
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22
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Kortright KE, Doss-Gollin S, Chan BK, Turner PE. Evolution of Bacterial Cross-Resistance to Lytic Phages and Albicidin Antibiotic. Front Microbiol 2021; 12:658374. [PMID: 34220747 PMCID: PMC8245764 DOI: 10.3389/fmicb.2021.658374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/10/2021] [Indexed: 11/21/2022] Open
Abstract
Due to concerns over the global increase of antibiotic-resistant bacteria, alternative antibacterial strategies, such as phage therapy, are increasingly being considered. However, evolution of bacterial resistance to new therapeutics is almost a certainty; indeed, it is possible that resistance to alternative treatments might result in an evolved trade-up such as enhanced antibiotic resistance. Here, we hypothesize that selection for Escherichia coli bacteria to resist phage T6, phage U115, or albicidin, a DNA gyrase inhibitor, should often result in a pleiotropic trade-up in the form of cross-resistance, because all three antibacterial agents interact with the Tsx porin. Selection imposed by any one of the antibacterials resulted in cross-resistance to all three of them, in each of the 29 spontaneous bacterial mutants examined in this study. Furthermore, cross-resistance did not cause measurable fitness (growth) deficiencies for any of the bacterial mutants, when competed against wild-type E. coli in both low-resource and high-resource environments. A combination of whole-genome and targeted sequencing confirmed that mutants differed from wild-type E. coli via change(s) in the tsx gene. Our results indicate that evolution of cross-resistance occurs frequently in E. coli subjected to independent selection by phage T6, phage U115 or albicidin. This study cautions that deployment of new antibacterial therapies such as phage therapy, should be preceded by a thorough investigation of evolutionary consequences of the treatment, to avoid the potential for evolved trade-ups.
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Affiliation(s)
- Kaitlyn E Kortright
- Program in Microbiology, Yale School of Medicine, New Haven, CT, United States
| | - Simon Doss-Gollin
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Paul E Turner
- Program in Microbiology, Yale School of Medicine, New Haven, CT, United States.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
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23
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Singhal S, Turner PE. Effects of historical co-infection on host shift abilities of exploitative and competitive viruses. Evolution 2021; 75:1878-1888. [PMID: 33969482 DOI: 10.1111/evo.14263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/03/2021] [Accepted: 04/16/2021] [Indexed: 12/29/2022]
Abstract
Rapid evolution contributes to frequent emergence of RNA viral pathogens on novel hosts. However, accurately predicting which viral genotypes will emerge has been elusive. Prior work with lytic RNA bacteriophage ɸ6 (family Cystoviridae) suggested that evolution under low multiplicity of infection (MOI; proportion of viruses to susceptible cells) selected for greater host exploitation, while evolution under high MOI selected for better intracellular competition against co-infecting viruses. We predicted that phage genotypes that had experienced 300 generations of low MOI ecological history would be relatively advantaged in initial growth on two novel hosts. We inferred viral growth through changes in host population density, specifically by analyzing five attributes of growth curves of infected bacteria. Despite equivalent growth of evolved viruses on the original host, low MOI evolved clones were generally advantaged relative to high MOI clones in exploiting novel hosts. However, the specific attributes of growth curves that supported their advantage differed by host, indicating interactions between both viral and host genotype. Although there will be host specificity in viral growth, we suggest based on infectivity differences of viruses from high versus low MOI histories that prior MOI selection can later affect emergence potential.
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Affiliation(s)
- Sonia Singhal
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, 06520, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, 48824, USA.,Current affiliation: Department of Biological Sciences, San José Sate University, San José, California, 95192, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, 06520, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, 48824, USA.,Graduate Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, 06520, USA
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24
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Chan BK, Stanley G, Modak M, Koff JL, Turner PE. Bacteriophage therapy for infections in CF. Pediatr Pulmonol 2021; 56 Suppl 1:S4-S9. [PMID: 33434411 DOI: 10.1002/ppul.25190] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 01/19/2023]
Abstract
Pseudomonas aeruginosa and Staphylococcus aureus are bacterial pathogens frequently associated with pulmonary complications and disease progression in cystic fibrosis (CF). However, these bacteria increasingly show resistance to antibiotics, necessitating novel management strategies. One possibility is bacteriophage (phages; bacteria-specific viruses) therapy, where lytic phages are administered to kill target bacterial pathogens. Recent publications of case reports of phage therapy to treat antibiotic-resistant lung infections in CF have garnered significant attention. These cases exemplify the renewed interest in phage therapy, an older concept that is being newly updated to include rigorous collection and analysis of patient data to assess clinical benefit, which will inform the development of clinical trials. As outcomes of these trials become public, the results will valuable gauge the potential usefulness of phage therapy to address the rise in antibiotic-resistant bacterial infections. In addition, we highlight the further need for basic research to accurately predict the different responses of target bacterial pathogens when phages are administered alone, sequentially, or as mixtures (cocktails), and whether within-cocktail interactions among phages hold consequences for the efficacy of phage therapy in patient treatment.
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Affiliation(s)
- Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Gail Stanley
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Mrinalini Modak
- Department of Internal Medicine, Yale New Haven Hospital, New Haven, Connecticut, USA
| | - Jon L Koff
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, USA
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25
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Burmeister AR, Hansen E, Cunningham JJ, Rego EH, Turner PE, Weitz JS, Hochberg ME. Fighting microbial pathogens by integrating host ecosystem interactions and evolution. Bioessays 2020; 43:e2000272. [PMID: 33377530 DOI: 10.1002/bies.202000272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/22/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022]
Abstract
Successful therapies to combat microbial diseases and cancers require incorporating ecological and evolutionary principles. Drawing upon the fields of ecology and evolutionary biology, we present a systems-based approach in which host and disease-causing factors are considered as part of a complex network of interactions, analogous to studies of "classical" ecosystems. Centering this approach around empirical examples of disease treatment, we present evidence that successful therapies invariably engage multiple interactions with other components of the host ecosystem. Many of these factors interact nonlinearly to yield synergistic benefits and curative outcomes. We argue that these synergies and nonlinear feedbacks must be leveraged to improve the study of pathogenesis in situ and to develop more effective therapies. An eco-evolutionary systems perspective has surprising and important consequences, and we use it to articulate areas of high research priority for improving treatment strategies.
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Affiliation(s)
- Alita R Burmeister
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
| | - Elsa Hansen
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jessica J Cunningham
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - E Hesper Rego
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA.,Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.,School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Michael E Hochberg
- Institute of Evolutionary Sciences, University of Montpellier, Montpellier, France.,Santa Fe Institute, Santa Fe, New Mexico, USA
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26
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Cohan FM, Zandi M, Turner PE. Broadscale phage therapy is unlikely to select for widespread evolution of bacterial resistance to virus infection. Virus Evol 2020; 6:veaa060. [PMID: 33365149 PMCID: PMC7744382 DOI: 10.1093/ve/veaa060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multi-drug resistant bacterial pathogens are alarmingly on the rise, signaling that the golden age of antibiotics may be over. Phage therapy is a classic approach that often employs strictly lytic bacteriophages (bacteria-specific viruses that kill cells) to combat infections. Recent success in using phages in patient treatment stimulates greater interest in phage therapy among Western physicians. But there is concern that widespread use of phage therapy would eventually lead to global spread of phage-resistant bacteria and widespread failure of the approach. Here, we argue that various mechanisms of horizontal genetic transfer (HGT) have largely contributed to broad acquisition of antibiotic resistance in bacterial populations and species, whereas similar evolution of broad resistance to therapeutic phages is unlikely. The tendency for phages to infect only particular bacterial genotypes limits their broad use in therapy, in turn reducing the likelihood that bacteria could acquire beneficial resistance genes from distant relatives via HGT. We additionally consider whether HGT of clustered regularly interspaced short palindromic repeats (CRISPR) immunity would thwart generalized use of phages in therapy, and argue that phage-specific CRISPR spacer regions from one taxon are unlikely to provide adaptive value if horizontally-transferred to other taxa. For these reasons, we conclude that broadscale phage therapy efforts are unlikely to produce widespread selection for evolution of bacterial resistance.
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Affiliation(s)
- Frederick M Cohan
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA
| | - Matthew Zandi
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.,Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
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27
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Abstract
As the most abundant microbes on Earth, novel bacteriophages (phages; bacteria-specific viruses) are readily isolated from environmental samples. However, it remains challenging to characterize phage-bacteria interactions, such as the host receptor(s) phages bind to initiate infection. Here, we tested whether transposon insertion sequencing (INSeq) could be used to identify bacterial genes involved in phage binding. As proof of concept, results showed that INSeq screens successfully identified genes encoding known receptors for previously characterized viruses of Escherichia coli (phages T6, T2, T4, and T7). INSeq screens were then used to identify genes involved during infection of six newly isolated coliphages. Results showed that candidate receptors could be successfully identified for the majority (five of six) of the phages; furthermore, genes encoding the phage receptor(s) were the top hit(s) in the analyses of the successful screens. INSeq screens provide a generally useful method for high-throughput discovery of phage receptors. We discuss limitations of our approach when examining uncharacterized phages, as well as usefulness of the method for exploring the evolution of broad versus narrow use of cellular receptors among phages in the biosphere.
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Affiliation(s)
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520
| | - Paul E Turner
- Program in Microbiology, Yale School of Medicine, New Haven, CT 06520;
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520
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28
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Gurney J, Pradier L, Griffin JS, Gougat-Barbera C, Chan BK, Turner PE, Kaltz O, Hochberg ME. Phage steering of antibiotic-resistance evolution in the bacterial pathogen, Pseudomonas aeruginosa. Evol Med Public Health 2020; 2020:148-157. [PMID: 34254028 DOI: 10.1093/emph/eoaa026] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022]
Abstract
Background and objectives Antimicrobial resistance is a growing global concern and has spurred increasing efforts to find alternative therapeutics. Bacteriophage therapy has seen near constant use in Eastern Europe since its discovery over a century ago. One promising approach is to use phages that not only reduce bacterial pathogen loads but also select for phage resistance mechanisms that trade-off with antibiotic resistance-so called 'phage steering'. Methodology Recent work has shown that the phage OMKO1 can interact with efflux pumps and in so doing select for both phage resistance and antibiotic sensitivity of the pathogenic bacterium Pseudomonas aeruginosa. We tested the robustness of this approach to three different antibiotics in vitro (tetracycline, erythromycin and ciprofloxacin) and one in vivo (erythromycin). Results We show that in vitro OMKO1 can reduce antibiotic resistance of P. aeruginosa (Washington PAO1) even in the presence of antibiotics, an effect still detectable after ca.70 bacterial generations in continuous culture with phage. Our in vivo experiment showed that phage both increased the survival times of wax moth larvae (Galleria mellonella) and increased bacterial sensitivity to erythromycin. This increased antibiotic sensitivity occurred both in lines with and without the antibiotic. Conclusions and implications Our study supports a trade-off between antibiotic resistance and phage sensitivity. This trade-off was maintained over co-evolutionary time scales even under combined phage and antibiotic pressure. Similarly, OMKO1 maintained this trade-off in vivo, again under dual phage/antibiotic pressure. Our findings have implications for the future clinical use of steering in phage therapies. Lay Summary: Given the rise of antibiotic-resistant bacterial infection, new approaches to treatment are urgently needed. Bacteriophages (phages) are bacterial viruses. The use of such viruses to treat infections has been in near-continuous use in several countries since the early 1900s. Recent developments have shown that these viruses are not only effective against routine infections but can also target antibiotic resistant bacteria in a novel, unexpected way. Similar to other lytic phages, these so-called 'steering phages' kill the majority of bacteria directly. However, steering phages also leave behind bacterial variants that resist the phages, but are now sensitive to antibiotics. Treatment combinations of these phages and antibiotics can now be used to greater effect than either one independently. We evaluated the impact of steering using phage OMKO1 and a panel of three antibiotics on Pseudomonas aeruginosa, an important pathogen in hospital settings and in people with cystic fibrosis. Our findings indicate that OMKO1, either alone or in combination with antibiotics, maintains antibiotic sensitivity both in vitro and in vivo, giving hope that phage steering will be an effective treatment option against antibiotic-resistant bacteria.
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Affiliation(s)
- James Gurney
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Léa Pradier
- CEFE/CNRS, Université de Montpellier Campus du CNRS, 1919, route de Mende, Montpellier 34293, France
| | - Joanne S Griffin
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Claire Gougat-Barbera
- Institute of Evolution Sciences of Montpellier, Université de Montpellier, CNRS, IRD EPHE, Montpellier, France
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA.,Department is Program in Microbiology, Program in Microbiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Oliver Kaltz
- Institute of Evolution Sciences of Montpellier, Université de Montpellier, CNRS, IRD EPHE, Montpellier, France
| | - Michael E Hochberg
- Institute of Evolution Sciences of Montpellier, Université de Montpellier, CNRS, IRD EPHE, Montpellier, France.,Santa Fe Institute, Santa Fe, NM 87501, USA
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29
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Gloria‐Soria A, Mendiola SY, Morley VJ, Alto BW, Turner PE. Prior evolution in stochastic versus constant temperatures affects RNA virus evolvability at a thermal extreme. Ecol Evol 2020; 10:5440-5450. [PMID: 32607165 PMCID: PMC7319105 DOI: 10.1002/ece3.6287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 02/06/2023] Open
Abstract
It is unclear how historical adaptation versus maladaptation in a prior environment affects population evolvability in a novel habitat. Prior work showed that vesicular stomatitis virus (VSV) populations evolved at constant 37°C improved in cellular infection at both 29°C and 37°C; in contrast, those evolved under random changing temperatures between 29°C and 37°C failed to improve. Here, we tested whether prior evolution affected the rate of adaptation at the thermal-niche edge: 40°C. After 40 virus generations in the new environment, we observed that populations historically evolved at random temperatures showed greater adaptability. Deep sequencing revealed that most of the newly evolved mutations were de novo. Also, two novel evolved mutations in the VSV glycoprotein and replicase genes tended to co-occur in the populations previously evolved at constant 37°C, whereas this parallelism was not seen in populations with prior random temperature evolution. These results suggest that prior adaptation under constant versus random temperatures constrained the mutation landscape that could improve fitness in the novel 40°C environment, perhaps owing to differing epistatic effects of new mutations entering genetic architectures that earlier diverged. We concluded that RNA viruses maladapted to their previous environment could "leapfrog" over counterparts of higher fitness, to achieve faster adaptability in a novel environment.
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Affiliation(s)
- Andrea Gloria‐Soria
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
- Present address:
Department of Environmental Sciences, Center for Vector Biology and Zoonotic DiseasesThe Connecticut Agricultural Experiment StationNew HavenCTUSA
| | - Sandra Y. Mendiola
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
- Present address:
Department of BiologyEmory UniversityAtlantaGA30322USA
| | - Valerie J. Morley
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
- Present address:
Department of BiologyPennsylvania State UniversityUniversity ParkPA16802USA
| | - Barry W. Alto
- Florida Medical Entomology LaboratoryUniversity of FloridaVero BeachFLUSA
| | - Paul E. Turner
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
- Program in MicrobiologyYale School of MedicineNew HavenCTUSA
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30
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Okamoto KW, Amarasekare P, Post DM, Vasseur DA, Turner PE. The interplay between host community structure and pathogen life‐history constraints in driving the evolution of host‐range shifts. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Kenichi W. Okamoto
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
- Department of Biology University of St. Thomas St. Paul MN USA
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | - Priyanga Amarasekare
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | - David M. Post
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | - David A. Vasseur
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
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31
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Abstract
What prevents generalists from displacing specialists, despite obvious competitive advantages of utilizing a broad niche? The classic genetic explanation is antagonistic pleiotropy: genes underlying the generalism produce 'jacks-of-all-trades' that are masters of none. However, experiments challenge this assumption that mutations enabling niche expansion must reduce fitness in other environments. Theory suggests an alternative cost of generalism: decreased evolvability, or the reduced capacity to adapt. Generalists using multiple environments experience relaxed selection in any one environment, producing greater relative lag load. Additionally, mutations fixed by generalist lineages early during their evolution that avoid or compensate for antagonistic pleiotropy may limit access to certain future evolutionary trajectories. Hypothesized evolvability costs of generalism warrant further exploration, and we suggest outstanding questions meriting attention.
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Affiliation(s)
- Lisa M Bono
- Department of Ecology, Evolution, and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Jeremy A Draghi
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; Department of Biology, Brooklyn College, City University of New York, Brooklyn, NY 11210, USA; Program in Ecology, Evolutionary Biology and Behavior, Graduate Center, City University of New York, New York, NY 10016, USA
| | - Paul E Turner
- Microbiology Program, Yale School of Medicine, New Haven, CT 06510, USA; Yale University, Department of Ecology and Evolutionary Biology, New Haven, CT 06511, USA.
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32
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Abstract
Phage therapy, long overshadowed by chemical antibiotics, is garnering renewed interest in Western medicine. This stems from the rise in frequency of multi-drug-resistant bacterial infections in humans. There also have been recent case reports of phage therapy demonstrating clinical utility in resolving these otherwise intractable infections. Nevertheless, bacteria can readily evolve phage resistance too, making it crucial for modern phage therapy to develop strategies to capitalize on this inevitability. Here, we review the history of phage therapy research. We compare and contrast phage therapy and chemical antibiotics, highlighting their potential synergies when used in combination. We also examine the use of animal models, case studies, and results from clinical trials. Throughout, we explore how the modern scientific community works to improve the reliability and success of phage therapy in the clinic and discuss how to properly evaluate the potential for phage therapy to combat antibiotic-resistant bacteria.
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Affiliation(s)
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Jonathan L Koff
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Paul E Turner
- Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.
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33
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Chan BK, Turner PE, Kim S, Mojibian HR, Elefteriades JA, Narayan D. Publisher's Note: Phage treatment of an aortic graft infected with Pseudomonas aeruginosa. Evol Med Public Health 2019; 2019:35. [PMID: 30847220 PMCID: PMC6398325 DOI: 10.1093/emph/eoz006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.,Program in Microbiology, Yale School of Medicine, New Haven, CT, USA
| | - Samuel Kim
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Hamid R Mojibian
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - John A Elefteriades
- Section of Cardiac Surgery, Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Deepak Narayan
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale School of Medicine, New Haven, CT, USA
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34
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Okamoto KW, Post DM, Vasseur DA, Turner PE. Managing the emergence of pathogen resistance via spatially targeted antimicrobial use. Evol Appl 2018; 11:1822-1841. [PMID: 30459832 PMCID: PMC6231480 DOI: 10.1111/eva.12683] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 06/26/2018] [Indexed: 12/26/2022] Open
Abstract
From agriculture to public health to civil engineering, managing antimicrobial resistance presents a considerable challenge. The dynamics underlying resistance evolution reflect inherently spatial processes. Resistant pathogen strains increase in frequency when a strain that emerges in one locale can spread and replace pathogen subpopulations formerly sensitive to the antimicrobial agent. Moreover, the strength of selection for antimicrobial resistance is in part governed by the extent of antimicrobial use. Thus, altering how antimicrobials are used across a landscape can potentially shift the spatial context governing the dynamics of antimicrobial resistance and provide a potent management tool. Here, we model how the efficacy of adjusting antimicrobial use over space to manage antimicrobial resistance is mediated by competition among pathogen strains and the topology of pathogen metapopulations. For several pathogen migration scenarios, we derive critical thresholds for the spatial extent of antimicrobial use below which resistance cannot emerge, and relate these thresholds to (a) the ability to eradicate antimicrobial-sensitive pathogens locally and (b) the strength of the trade-off between resistance ability and competitive performance where antimicrobial use is absent. We find that in metapopulations where patches differ in connectedness, constraining antimicrobial use across space to mitigate resistance evolution only works if the migration of the resistant pathogen is modest; yet, this situation is reversed if the resistant strain has a high colonization rate, with variably connected metapopulations exhibiting less sensitivity to reducing antimicrobial use across space. Furthermore, when pathogens are alternately exposed to sites with and without the antimicrobial, bottlenecking resistant strains through sites without an antimicrobial is only likely to be effective under a strong competition-resistance trade-off. We therefore identify life-history constraints that are likely to suggest which pathogens can most effectively be controlled by a spatially targeted antimicrobial regime. We discuss implications of our results for managing and thinking about antimicrobial resistance evolution in spatially heterogeneous contexts.
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Affiliation(s)
- Kenichi W. Okamoto
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
- Department of BiologyUniversity of St. ThomasSaint PaulMinnesota
| | - David M. Post
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - David A. Vasseur
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - Paul E. Turner
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
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35
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Morley VJ, Noval MG, Chen R, Weaver SC, Vignuzzi M, Stapleford KA, Turner PE. Chikungunya virus evolution following a large 3'UTR deletion results in host-specific molecular changes in protein-coding regions. Virus Evol 2018; 4:vey012. [PMID: 29942653 PMCID: PMC6007266 DOI: 10.1093/ve/vey012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The 3′untranslated region (UTR) in alphavirus genomes functions in virus replication and plays a role in determining virus host range. However, the molecular evolution of virus UTRs is understudied compared to the evolution of protein-coding regions. Chikungunya virus (CHIKV) has the longest 3′UTR among the alphaviruses (500–700 nt), and 3′UTR length and sequence structure vary substantially among different CHIKV lineages. Previous studies showed that genomic deletions and insertions are key drivers of CHIKV 3′UTR evolution. Inspired by hypothesized deletion events in the evolutionary history of CHIKV, we used experimental evolution to examine CHIKV adaptation in response to a large 3′UTR deletion. We engineered a CHIKV mutant with a 258 nt deletion in the 3′UTR (ΔDR1/2). This deletion reduced viral replication on mosquito cells, but did not reduce replication on mammalian cells. To examine how selective pressures from vertebrate and invertebrate hosts shape CHIKV evolution after a deletion in the 3′UTR, we passaged ΔDR1/2 virus populations strictly on primate cells, strictly on mosquito cells, or with alternating primate/mosquito cell passages. We found that virus populations passaged on a single host cell line increased in fitness relative to the ancestral deletion mutant on their selected host, and viruses that were alternately passaged improved on both hosts. Surprisingly, whole genome sequencing revealed few changes in the 3′UTR of passaged populations. Rather, virus populations evolved improved fitness through mutations in protein coding regions that were associated with specific hosts.
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Affiliation(s)
- Valerie J Morley
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511-8934, USA
| | | | - Rubing Chen
- Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C Weaver
- Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Paris, France
| | | | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511-8934, USA.,Program in Microbiology, Yale School of Medicine, New Haven, CT, USA
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36
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Gloria-Soria A, Armstrong PM, Powell JR, Turner PE. Infection rate of Aedes aegypti mosquitoes with dengue virus depends on the interaction between temperature and mosquito genotype. Proc Biol Sci 2018; 284:rspb.2017.1506. [PMID: 28978730 DOI: 10.1098/rspb.2017.1506] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/04/2017] [Indexed: 11/12/2022] Open
Abstract
Dengue fever is the most prevalent arthropod-transmitted viral disease worldwide, with endemic transmission restricted to tropical and subtropical regions of different temperature profiles. Temperature is epidemiologically relevant because it affects dengue infection rates in Aedes aegypti mosquitoes, the major vector of the dengue virus (DENV). Aedes aegypti populations are also known to vary in competence for different DENV genotypes. We assessed the effects of mosquito and virus genotype on DENV infection in the context of temperature by challenging Ae. aegypti from two locations in Vietnam, which differ in temperature regimes, with two isolates of DENV-2 collected from the same two localities, followed by incubation at 25, 27 or 32°C for 10 days. Genotyping of the mosquito populations and virus isolates confirmed that each group was genetically distinct. Extrinsic incubation temperature (EIT) and DENV-2 genotype had a direct effect on the infection rate, consistent with previous studies. However, our results show that the EIT impacts the infection rate differently in each mosquito population, indicating a genotype by environment interaction. These results suggest that the magnitude of DENV epidemics may not only depend on the virus and mosquito genotypes present, but also on how they interact with local temperature. This information should be considered when estimating vector competence of local and introduced mosquito populations during disease risk evaluation.
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Affiliation(s)
- A Gloria-Soria
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St. PO Box 208106, New Haven, CT 06520-8106, USA
| | - P M Armstrong
- The Connecticut Agricultural Experiment Station, 123 Huntington St. PO Box 1106, New Haven, CT 06504, USA
| | - J R Powell
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St. PO Box 208106, New Haven, CT 06520-8106, USA
| | - P E Turner
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St. PO Box 208106, New Haven, CT 06520-8106, USA.,Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
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37
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Gloria-Soria A, Mendiola S, Morley VJ, Turner PE. A48 Evolutionary history constrains adaptation in vesicular stomatitis virus. Virus Evol 2018. [PMCID: PMC5905482 DOI: 10.1093/ve/vey010.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
| | - Sandra Mendiola
- College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Valerie J Morley
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Paul E Turner
- Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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38
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Shapiro JW, Turner PE. Evolution of mutualism from parasitism in experimental virus populations. Evolution 2018; 72:707-712. [DOI: 10.1111/evo.13440] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 01/12/2018] [Accepted: 01/16/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Jason W. Shapiro
- Department of Ecology and Evolutionary Biology Yale University New Haven Connecticut 06520
- Current Address: Department of Biology Loyola University Chicago 1032 W Sheridan Rd. Chicago Illinois 60660
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology Yale University New Haven Connecticut 06520
- Program in Microbiology Yale School of Medicine New Haven Connecticut 06510
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39
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Abstract
As global environmental conditions continue to change at an unprecedented rate, many species will experience increases in natural and anthropogenic stress. Generally speaking, selection is expected to favor adaptations that reduce the negative impact of environmental stress (i.e., stress tolerance). However, natural environmental variables typically fluctuate, exhibiting various degrees of temporal autocorrelation, known as environmental colors, which may complicate evolutionary responses to stress. Here we combine experiments and theory to show that temporal environmental autocorrelation can determine long-term evolutionary responses to stress without affecting the total amount of stress experienced over time. Experimental evolution of RNA virus lineages in differing environmental autocorrelation treatments agreed closely with predictions from our theoretical models that stress tolerance is favored in less autocorrelated (whiter) environments but disfavored in more autocorrelated (redder) environments. This is explained by an interaction between environmental autocorrelation and a phenotypic trade-off between stress tolerance and reproductive ability. The degree to which environmental autocorrelation influences evolutionary trajectories depends on the shape of this trade-off as well as the relative level of tolerance exhibited by novel mutants. These results suggest that long-term evolutionary dynamics depend not only on the overall strength of selection but also on the way that selection is distributed over time.
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40
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Chan BK, Turner PE, Kim S, Mojibian HR, Elefteriades JA, Narayan D. Phage treatment of an aortic graft infected with Pseudomonas aeruginosa. Evol Med Public Health 2018; 2018:60-66. [PMID: 29588855 PMCID: PMC5842392 DOI: 10.1093/emph/eoy005] [Citation(s) in RCA: 271] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/28/2018] [Indexed: 12/11/2022]
Abstract
Management of prosthetic vascular graft infections caused by Pseudomonas aeruginosa can be a significant challenge to clinicians. These infections often do not resolve with antibiotic therapy alone due to antibiotic resistance/tolerance by bacteria, poor ability of antibiotics to permeate/reduce biofilms and/or other factors. Bacteriophage OMKO1 binding to efflux pump proteins in P. aeruginosa was consistent with an evolutionary trade-off: wildtype bacteria were killed by phage whereas evolution of phage-resistance led to increased antibiotic sensitivity. However, phage clinical-use has not been demonstrated. Here, we present a case report detailing therapeutic application of phage OMKO1 to treat a chronic P. aeruginosa infection of an aortic Dacron graft with associated aorto-cutaneous fistula. Following a single application of phage OMKO1 and ceftazidime, the infection appeared to resolve with no signs of recurrence.
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Affiliation(s)
- Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.,Program in Microbiology, Yale School of Medicine, New Haven, CT, USA
| | - Samuel Kim
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Hamid R Mojibian
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - John A Elefteriades
- Section of Cardiac Surgery, Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Deepak Narayan
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale School of Medicine, New Haven, CT, USA
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41
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Diaz KE, Remold SK, Onyiri O, Bozeman M, Raymond PA, Turner PE. Generalized Growth of Estuarine, Household and Clinical Isolates of Pseudomonas aeruginosa. Front Microbiol 2018; 9:305. [PMID: 29599754 PMCID: PMC5863524 DOI: 10.3389/fmicb.2018.00305] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 02/09/2018] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen of particular concern to immune-compromised people, such as cystic fibrosis patients and burn victims. These bacteria grow in built environments including hospitals and households, and in natural environments such as rivers and estuaries. However, there is conflicting evidence whether recent environments like the human lung and open ocean affect P. aeruginosa growth performance in alternate environments. We hypothesized that bacteria recently isolated from dissimilar habitats should grow differently in media containing artificial versus natural resources. To test this idea, we examined growth of P. aeruginosa isolates from three environments (estuary, household, and clinic) in three media types: minimal-glucose lab medium, and media prepared from sugar maple leaves or big bluestem grass. We used automated spectrophotometry to measure high-resolution growth curves for all isolate by media combinations, and studied two fitness parameters: growth rate and maximum population density. Results showed high variability in growth rate among isolates, both overall and in its dependence on assay media, but this variability was not associated with habitat of isolation. In contrast, total growth (change in absorbance over the experiment) differed overall among habitats of isolation, and there were media-specific differences in mean total growth among habitats of isolation, and in among-habitat variability in the media-specific response. This was driven primarily by greater total growth of estuary isolates when compared with those from other habitats of origin, and greater media-specific variability among household isolates than those from other habitats of origin. Taken together, these results suggest that for growth rate P. aeruginosa bacteria appear to be broad generalists without regard to current or recent habitat, whereas for total growth a signature of recent ecological history can be detected.
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Affiliation(s)
- Kelly E Diaz
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Susanna K Remold
- Department of Biology, University of Louisville, Louisville, KY, United States
| | - Ogochukwu Onyiri
- Department of Biology, University of Louisville, Louisville, KY, United States
| | - Maura Bozeman
- Yale School of Forestry & Environmental Studies, Yale University, New Haven, CT, United States
| | - Peter A Raymond
- Yale School of Forestry & Environmental Studies, Yale University, New Haven, CT, United States
| | - Paul E Turner
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, United States.,Program in Microbiology, Yale School of Medicine, New Haven, CT, United States
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42
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Turner PE, Cooper VS, Lenski RE. TRADEOFF BETWEEN HORIZONTAL AND VERTICAL MODES OF TRANSMISSION IN BACTERIAL PLASMIDS. Evolution 2017; 52:315-329. [PMID: 28568337 DOI: 10.1111/j.1558-5646.1998.tb01634.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/1997] [Accepted: 01/09/1998] [Indexed: 11/26/2022]
Abstract
It has been hypothesized that there is a fundamental conflict between horizontal (infectious) and vertical (intergenerational) modes of parasite transmission. Activities of a parasite that increase its rate of infectious transmission are presumed to reduce its host's fitness. This reduction in host fitness impedes vertical transmission of the parasite and causes a tradeoff between horizontal and vertical transmission. Given this tradeoff, and assuming no multiple infections (no within-host competition among parasites), a simple model predicts that the density of uninfected hosts in the environment should determine the optimum balance between modes of parasite transmission. When susceptible hosts are abundant, selection should favor increased rates of horizontal transfer, even at the expense of reduced vertical transmission. Conversely, when hosts are rare, selection should favor increased vertical transmission even at the expense of lower horizontal transfer. We tested the tradeoff hypothesis and these evolutionary predictions using conjugative plasmids and the bacteria that they infect. Plasmids were allowed to evolve for 500 generations in environments with different densities of susceptible hosts. The plasmid's rate of horizontal transfer by conjugation increased at the expense of host fitness, indicating a tradeoff between horizontal and vertical transmission. Also, reductions in conjugation rate repeatedly coincided with the loss of a particular plasmid-encoded antibiotic resistance gene. However, susceptible host density had no significant effect on the evolution of horizontal versus vertical modes of plasmid transmission. We consider several possible explanations for the failure to observe such an effect.
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Affiliation(s)
- Paul E Turner
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, 48824
| | - Vaughn S Cooper
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, 48824
| | - Richard E Lenski
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, 48824
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43
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Morley VJ, Turner PE. Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change. Evolution 2017; 71:872-883. [PMID: 28121018 PMCID: PMC5382103 DOI: 10.1111/evo.13193] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/03/2017] [Accepted: 01/12/2017] [Indexed: 12/31/2022]
Abstract
Understanding the dynamics of molecular adaptation is a fundamental goal of evolutionary biology. While adaptation to constant environments has been well characterized, the effects of environmental complexity remain seldom studied. One simple but understudied factor is the rate of environmental change. Here we used experimental evolution with RNA viruses to investigate whether evolutionary dynamics varied based on the rate of environmental turnover. We used whole-genome next-generation sequencing to characterize evolutionary dynamics in virus populations adapting to a sudden versus gradual shift onto a novel host cell type. In support of theoretical models, we found that when populations evolved in response to a sudden environmental change, mutations of large beneficial effect tended to fix early, followed by mutations of smaller beneficial effect; as predicted, this pattern broke down in response to a gradual environmental change. Early mutational steps were highly parallel across replicate populations in both treatments. The fixation of single mutations was less common than sweeps of associated "cohorts" of mutations, and this pattern intensified when the environment changed gradually. Additionally, clonal interference appeared stronger in response to a gradual change. Our results suggest that the rate of environmental change is an important determinant of evolutionary dynamics in asexual populations.
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Affiliation(s)
- Valerie J Morley
- Department of Ecology and Evolutionary Biology, Yale University, P. O. Box 208106, New Haven, Connecticut, 06520
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, P. O. Box 208106, New Haven, Connecticut, 06520.,Graduate Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, 06520
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44
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Affiliation(s)
- Benjamin K Chan
- Department of Ecology & Evolutionary Biology, Yale University, 165 Prospect St, PO Box 208106, New Haven, CT 06520, USA
| | - Kevin Brown
- Department of Ecology & Evolutionary Biology, Yale University, 165 Prospect St, PO Box 208106, New Haven, CT 06520, USA
| | - Kaitlyn E Kortright
- Department of Ecology & Evolutionary Biology, Yale University, 165 Prospect St, PO Box 208106, New Haven, CT 06520, USA
| | - Stephanie Mao
- Department of Ecology & Evolutionary Biology, Yale University, 165 Prospect St, PO Box 208106, New Haven, CT 06520, USA
| | - Paul E Turner
- Department of Ecology & Evolutionary Biology, Yale University, 165 Prospect St, PO Box 208106, New Haven, CT 06520, USA
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45
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Chan BK, Sistrom M, Wertz JE, Kortright KE, Narayan D, Turner PE. Phage selection restores antibiotic sensitivity in MDR Pseudomonas aeruginosa. Sci Rep 2016; 6:26717. [PMID: 27225966 PMCID: PMC4880932 DOI: 10.1038/srep26717] [Citation(s) in RCA: 360] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/05/2016] [Indexed: 02/08/2023] Open
Abstract
Increasing prevalence and severity of multi-drug-resistant (MDR) bacterial infections has necessitated novel antibacterial strategies. Ideally, new approaches would target bacterial pathogens while exerting selection for reduced pathogenesis when these bacteria inevitably evolve resistance to therapeutic intervention. As an example of such a management strategy, we isolated a lytic bacteriophage, OMKO1, (family Myoviridae) of Pseudomonas aeruginosa that utilizes the outer membrane porin M (OprM) of the multidrug efflux systems MexAB and MexXY as a receptor-binding site. Results show that phage selection produces an evolutionary trade-off in MDR P. aeruginosa, whereby the evolution of bacterial resistance to phage attack changes the efflux pump mechanism, causing increased sensitivity to drugs from several antibiotic classes. Although modern phage therapy is still in its infancy, we conclude that phages, such as OMKO1, represent a new approach to phage therapy where bacteriophages exert selection for MDR bacteria to become increasingly sensitive to traditional antibiotics. This approach, using phages as targeted antibacterials, could extend the lifetime of our current antibiotics and potentially reduce the incidence of antibiotic resistant infections.
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Affiliation(s)
- Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Mark Sistrom
- School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - John E Wertz
- E. coli Genetic Stock Center, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Kaitlyn E Kortright
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06520, USA
| | - Deepak Narayan
- Department of Surgery, Yale School of Medicine, New Haven, CT 06520, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.,Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
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46
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Shapiro JW, Williams ES, Turner PE. Evolution of parasitism and mutualism between filamentous phage M13 and Escherichia coli. PeerJ 2016; 4:e2060. [PMID: 27257543 PMCID: PMC4888304 DOI: 10.7717/peerj.2060] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/01/2016] [Indexed: 01/14/2023] Open
Abstract
Background. How host-symbiont interactions coevolve between mutualism and parasitism depends on the ecology of the system and on the genetic and physiological constraints of the organisms involved. Theory often predicts that greater reliance on horizontal transmission favors increased costs of infection and may result in more virulent parasites or less beneficial mutualists. We set out to understand transitions between parasitism and mutualism by evolving the filamentous bacteriophage M13 and its host Escherichia coli. Results. The effect of phage M13 on bacterial fitness depends on the growth environment, and initial assays revealed that infected bacteria reproduce faster and to higher density than uninfected bacteria in 96-well microplates. These data suggested that M13 is, in fact, a facultative mutualist of E. coli. We then allowed E. coli and M13 to evolve in replicated environments, which varied in the relative opportunity for horizontal and vertical transmission of phage in order to assess the evolutionary stability of this mutualism. After 20 experimental passages, infected bacteria from treatments with both vertical and horizontal transmission of phage had evolved the fastest growth rates. At the same time, phage from these treatments no longer benefited the ancestral bacteria. Conclusions. These data suggest a positive correlation between the positive effects of M13 on E. coli hosts from the same culture and the negative effects of the same phage toward the ancestral bacterial genotype. The results also expose flaws in applying concepts from the virulence-transmission tradeoff hypothesis to mutualism evolution. We discuss the data in the context of more recent theory on how horizontal transmission affects mutualisms and explore how these effects influence phages encoding virulence factors in pathogenic bacteria.
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Affiliation(s)
- Jason W. Shapiro
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | | | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
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47
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Abstract
Although differing rates of environmental turnover should be consequential for the dynamics of adaptive change, this idea has been rarely examined outside of theory. In particular, the importance of RNA viruses in disease emergence warrants experiments testing how differing rates of novel host invasion may impact the ability of viruses to adaptively shift onto a novel host. To test whether the rate of environmental turnover influences adaptation, we experimentally evolved 144 Sindbis virus lineages in replicated tissue-culture environments, which transitioned from being dominated by a permissive host cell type to a novel host cell type. The rate at which the novel host 'invaded' the environment varied by treatment. The fitness (growth rate) of evolved virus populations was measured on each host type, and molecular substitutions were mapped via whole genome consensus sequencing. Results showed that virus populations more consistently reached high fitness levels on the novel host when the novel host 'invaded' the environment more gradually, and gradual invasion resulted in less variable genomic outcomes. Moreover, virus populations that experienced a rapid shift onto the novel host converged upon different genotypes than populations that experienced a gradual shift onto the novel host, suggesting a strong effect of historical contingency.
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Affiliation(s)
- Valerie J Morley
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, 165 Prospect Street, New Haven, CT 06520-8106, USA
| | - Sandra Y Mendiola
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, 165 Prospect Street, New Haven, CT 06520-8106, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, 165 Prospect Street, New Haven, CT 06520-8106, USA
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48
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Williams ESCP, Morales NM, Wasik BR, Brusic V, Whelan SPJ, Turner PE. Repeatable Population Dynamics among Vesicular Stomatitis Virus Lineages Evolved under High Co-infection. Front Microbiol 2016; 7:370. [PMID: 27065953 PMCID: PMC4815288 DOI: 10.3389/fmicb.2016.00370] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 03/07/2016] [Indexed: 12/03/2022] Open
Abstract
Parasites and hosts can experience oscillatory cycles, where the densities of these interacting species dynamically fluctuate through time. Viruses with different replication strategies can also interact to produce cyclical dynamics. Frequent cellular co-infection can select for defective-interfering particles (DIPs): “cheater” viruses with shortened genomes that interfere with intracellular replication of full-length (ordinary) viruses. DIPs are positively selected when rare because they out-replicate ordinary viruses during co-infection, but DIPs are negatively selected when common because ordinary viruses become unavailable for intracellular exploitation via cheating. Here, we tested whether oscillatory dynamics of ordinary viruses were similar across independently evolved populations of vesicular stomatitis virus (VSV). Results showed identical cyclical dynamics across populations in the first 10 experimental passages, which transitioned to repeatable dampened oscillations by passage 20. Genomic analyses revealed parallel molecular substitutions across populations, particularly novel mutations that became dominant by passage 10. Our study showed that oscillatory dynamics and molecular evolution of interacting viruses were highly repeatable in VSV populations passaged under frequent co-infection. Furthermore, our data suggested that frequent co-infection with DIPs caused lowered performance of full-length viruses, by reducing their population densities by orders of magnitude compared to reproduction of ordinary viruses during strictly clonal infections.
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Affiliation(s)
| | - Nadya M Morales
- Department of Ecology and Evolutionary Biology, Yale University, New Haven CT, USA
| | - Brian R Wasik
- Department of Ecology and Evolutionary Biology, Yale University, New Haven CT, USA
| | - Vesna Brusic
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA, USA
| | - Sean P J Whelan
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven CT, USA
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49
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Morley VJ, Sistrom M, Usme-Ciro JA, Remold SK, Turner PE. Evolution in spatially mixed host environments increases divergence for evolved fitness and intrapopulation genetic diversity in RNA viruses. Virus Evol 2016; 2:vev022. [PMID: 27774292 PMCID: PMC4989875 DOI: 10.1093/ve/vev022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Virus populations may be challenged to evolve in spatially heterogeneous environments, such as mixtures of host cells that pose differing selection pressures. Spatial heterogeneity may select for evolved polymorphisms, where multiple virus subpopulations coexist by specializing on a narrow subset of the available hosts. Alternatively, spatial heterogeneity may select for evolved generalism, where a single genotype dominates the virus population by occupying a relatively broader host niche. In addition, the extent of spatial heterogeneity should influence the degree of divergence among virus populations encountering identical environmental challenges. Spatial heterogeneity creates environmental complexity that should increase the probability of differing adaptive phenotypic solutions, thus producing greater divergence among replicate virus populations, relative to counterparts evolving in strictly homogeneous host environments. Here, we tested these ideas using experimental evolution of RNA virus populations grown in laboratory tissue culture. We allowed vesicular stomatitis virus (VSV) lineages to evolve in replicated environments containing BHK-21 (baby hamster kidney) cells, HeLa (human epithelial) cells, or spatially heterogeneous host cell mixtures. Results showed that generalist phenotypes dominated in evolved virus populations across all treatments. Also, we observed greater variance in host-use performance (fitness) among VSV lineages evolved under spatial heterogeneity, relative to lineages evolved in homogeneous environments. Despite measurable differences in fitness, consensus Sanger sequencing revealed no fixed genetic differences separating the evolved lineages from their common ancestor. In contrast, deep sequencing of evolved VSV populations confirmed that the degree of divergence among replicate lineages was correlated with a larger number of minority variants. This correlation between divergence and the number of minority variants was significant only when we considered variants with a frequency of at least 10 per cent in the population. The number of lower-frequency minority variants per population did not significantly correlate with divergence.
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Affiliation(s)
- Valerie J Morley
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT, USA 06511
| | - Mark Sistrom
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT, USA 06511,; School of Natural Sciences, University of California Merced, 5200 N. Lake Road, Merced, CA, USA 95343
| | - Jose A Usme-Ciro
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT, USA 06511,; Department of Basic Sciences, Universidad de La Salle, Cra. 2 No. 10-70, Bogotá, Colombia and
| | - Susanna K Remold
- Department of Biology, Life Sciences Building, University of Louisville, Louisville, KY, USA 40292
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT, USA 06511
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50
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Wasik BR, Muñoz-Rojas AR, Okamoto KW, Miller-Jensen K, Turner PE. Generalized selection to overcome innate immunity selects for host breadth in an RNA virus. Evolution 2016; 70:270-81. [DOI: 10.1111/evo.12845] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 12/06/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Brian R. Wasik
- Department of Ecology and Evolutionary Biology; Yale University; New Haven Connecticut 06520
- Current Address: Baker Institute for Animal Health, College of Veterinary Medicine; Cornell University; Ithaca New York 14583
| | | | - Kenichi W. Okamoto
- Department of Ecology and Evolutionary Biology; Yale University; New Haven Connecticut 06520
- Yale Institute for Biospheric Studies; Yale University; New Haven Connecticut 06511
| | - Kathryn Miller-Jensen
- Department of Biomedical Engineering; Yale University; New Haven Connecticut 06520
- Department of Molecular, Cellular, and Developmental Biology; Yale University; New Haven Connecticut 06511
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology; Yale University; New Haven Connecticut 06520
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