2024
Experimental Evolution Studies in Φ6 Cystovirus
Singhal S, Balitactac A, Nayagam A, Bahrami P, Nayeem S, Turner P. Experimental Evolution Studies in Φ6 Cystovirus. Viruses 2024, 16: 977. PMID: 38932268, PMCID: PMC11209170, DOI: 10.3390/v16060977.Peer-Reviewed Original ResearchConceptsExperimental evolution studiesFitness effects of spontaneous mutationsSpontaneous mutationsEffects of spontaneous mutationsEvolution of RNA virusesEvolution studiesEvolution of host rangeFast generation timesResponse to selectionMultiple phagesNon-pathogenic modelRNA genomeConsequence of evolutionOuter membraneHost rangeRNA virusesNovel traitsMutation rateHost cellsFitness effectsPopulation sizeMutationsCystovirusesBacteriophageGeneration timeNeutralizing antibodies after nebulized phage therapy in cystic fibrosis patients
Bernabéu-Gimeno M, Pardo-Freire M, Chan B, Turner P, Gil-Brusola A, Pérez-Tarazona S, Carrasco-Hernández L, Quintana-Gallego E, Domingo-Calap P. Neutralizing antibodies after nebulized phage therapy in cystic fibrosis patients. Med 2024 PMID: 38917792, DOI: 10.1016/j.medj.2024.05.017.Peer-Reviewed Original ResearchMulti-drug resistanceCystic fibrosis patientsPhage therapyClinical outcomesLung infectionFibrosis patientsCystic fibrosisPseudomonas aeruginosa lung infectionAnti-phage antibodiesImmune responseStandard-of-care antibioticsInvasive routes of administrationPhage-neutralizing antibodiesBacterial loadBacterial lung infectionsCystic Fibrosis FoundationNo adverse eventsRoute of administrationPhage preparationsEmergence of antibodiesPhage detectionAntibiotic susceptibilityPhageStaphylococcus aureusBacterial eradicationCystic Fibrosis Bacteriophage Study at Yale (CYPHY)
Stanley G, Cochrane C, Chan B, Kortright K, Rahman B, Lee A, Vill A, Sun Y, Stewart J, Britto-Leon C, Harris Z, Talwalker J, Shabanova V, Turner P, Koff J. Cystic Fibrosis Bacteriophage Study at Yale (CYPHY). 2024, a6808-a6808. DOI: 10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a6808.Peer-Reviewed Original ResearchLytic bacteriophages induce the secretion of antiviral and proinflammatory cytokines from human respiratory epithelial cells
Zamora P, Reidy T, Armbruster C, Sun M, Van Tyne D, Turner P, Koff J, Bomberger J. Lytic bacteriophages induce the secretion of antiviral and proinflammatory cytokines from human respiratory epithelial cells. PLOS Biology 2024, 22: e3002566. PMID: 38652717, PMCID: PMC11037538, DOI: 10.1371/journal.pbio.3002566.Peer-Reviewed Original ResearchConceptsLytic phagesLytic bacteriophagesPhage therapyAirway epithelial cellsPseudomonas aeruginosa phagesEpithelial cellsMultidrug resistanceAirway epitheliumCystic fibrosisProinflammatory cytokinesHuman respiratory epithelial cellsPhage exposurePhage familiesMammalian cell responsesHuman airway epithelial cellsInternalized phageTreat multidrug-resistantPhageBacterial isolatesTranscriptional profilesRespiratory epithelial cellsHuman hostChronic respiratory disordersBacterial biofilmsBacteriophageAddressing the Research and Development Gaps in Modern Phage Therapy
Turner P, Azeredo J, Buurman E, Green S, Haaber J, Haggstrom D, de Figueiredo Carvalho K, Kirchhelle C, Moreno M, Pirnay J, Portillo M. Addressing the Research and Development Gaps in Modern Phage Therapy. PHAGE 2024, 5: 30-39. DOI: 10.1089/phage.2023.0045.Peer-Reviewed Original ResearchOptimized preparation pipeline for emergency phage therapy against Pseudomonas aeruginosa at Yale University
Würstle S, Lee A, Kortright K, Winzig F, An W, Stanley G, Rajagopalan G, Harris Z, Sun Y, Hu B, Blazanin M, Hajfathalian M, Bollyky P, Turner P, Koff J, Chan B. Optimized preparation pipeline for emergency phage therapy against Pseudomonas aeruginosa at Yale University. Scientific Reports 2024, 14: 2657. PMID: 38302552, PMCID: PMC10834462, DOI: 10.1038/s41598-024-52192-3.Peer-Reviewed Original ResearchConceptsEvolutionary selection pressurePhage characterizationPhage therapyPersistent bacterial infectionsBacteriophage therapyPhageSelection pressurePseudomonas aeruginosaInvestigational new drug applicationBacterial infectionsNew Drug ApplicationTherapyDrug applicationClinical applicationAutographiviridaeBacteriaPotential strategy
2023
41 CYstic Fibrosis bacterioPHage study at Yale (CYPHY)
Chan B, Kortright K, Stanley G, Cochrane C, Lee A, Vill A, Sun Y, Stewart J, Britto-Leon C, Harris Z, Talkwalkar J, Shabanova V, Turner P, Koff J. 41 CYstic Fibrosis bacterioPHage study at Yale (CYPHY). Journal Of Cystic Fibrosis 2023, 22: s22. DOI: 10.1016/s1569-1993(23)00976-1.Peer-Reviewed Original ResearchComplete Genome Assembly and Annotation of Escherichia coli Bacteriophage 55 from Rivière la Quint in Gonaïves, Haiti
Schwarz J, An W, Theroux A, Vargas L, Chan B, Turner P, Burmeister A. Complete Genome Assembly and Annotation of Escherichia coli Bacteriophage 55 from Rivière la Quint in Gonaïves, Haiti. Microbiology Resource Announcements 2023, 12: e00107-23. PMID: 37272828, PMCID: PMC10353447, DOI: 10.1128/mra.00107-23.Peer-Reviewed Original ResearchExperimental Evolution of the TolC-Receptor Phage U136B Functionally Identifies a Tail Fiber Protein Involved in Adsorption through Strong Parallel Adaptation
Burmeister A, Tzintzun-Tapia E, Roush C, Mangal I, Barahman R, Bjornson R, Turner P. Experimental Evolution of the TolC-Receptor Phage U136B Functionally Identifies a Tail Fiber Protein Involved in Adsorption through Strong Parallel Adaptation. Applied And Environmental Microbiology 2023, 89: e00079-23. PMID: 37191555, PMCID: PMC10304864, DOI: 10.1128/aem.00079-23.Peer-Reviewed Original ResearchConceptsExperimental evolutionPhage populationsParallel molecular evolutionWhole-population sequencingAntibiotic resistance proteinsTail fiber proteinE. coli hostPhage evolutionEvolutionary potentialMolecular evolutionPhage genotypesTolC proteinParallel adaptationProtein geneAntibiotic resistanceExperimental populationsBacterial diversitySelection pressureBacterial hostsColi hostFiber proteinBacterial populationsBacterial cellsPhage resistancePhage dynamicsComplete Genome Assembly and Annotation of Escherichia coli Bacteriophage 107
Schwarz J, Chan B, Turner P, Burmeister A. Complete Genome Assembly and Annotation of Escherichia coli Bacteriophage 107. Microbiology Resource Announcements 2023, 12: e00106-23. PMID: 37191527, PMCID: PMC10281100, DOI: 10.1128/mra.00106-23.Peer-Reviewed Original ResearchSingle Sequential Bacteriophage Therapy Decreases Pseudomonas Virulence More Than a Cocktail Approach
Stanley G, Chan B, Wuerstle S, Grun C, Kazmierczak B, Sun Y, Kortright K, Turner P, Koff J. Single Sequential Bacteriophage Therapy Decreases Pseudomonas Virulence More Than a Cocktail Approach. 2023, a1228-a1228. DOI: 10.1164/ajrccm-conference.2023.207.1_meetingabstracts.a1228.Peer-Reviewed Original ResearchCheating leads to the evolution of multipartite viruses
Leeks A, Young P, Turner P, Wild G, West S. Cheating leads to the evolution of multipartite viruses. PLOS Biology 2023, 21: e3002092. PMID: 37093882, PMCID: PMC10159356, DOI: 10.1371/journal.pbio.3002092.Peer-Reviewed Original ResearchDifferentiation of Spontaneous Bacterial Peritonitis from Secondary Peritonitis in Patients with Liver Cirrhosis: Retrospective Multicentre Study
Würstle S, Hapfelmeier A, Karapetyan S, Studen F, Isaakidou A, Schneider T, Schmid R, von Delius S, Gundling F, Burgkart R, Obermeier A, Mayr U, Ringelhan M, Rasch S, Lahmer T, Geisler F, Turner P, Chan B, Spinner C, Schneider J. Differentiation of Spontaneous Bacterial Peritonitis from Secondary Peritonitis in Patients with Liver Cirrhosis: Retrospective Multicentre Study. Diagnostics 2023, 13: 994. PMID: 36900138, PMCID: PMC10000989, DOI: 10.3390/diagnostics13050994.Peer-Reviewed Original ResearchSpontaneous bacterial peritonitisRetrospective multicentre studySecondary peritonitisLiver cirrhosisSBP episodesBacterial peritonitisMulticentre studySeverity of illnessHigh-risk groupAscitic fluid infectionSelection operator (LASSO) regression modelPeritonitis episodesLaboratory parametersFluid infectionSerious complicationsUnivariable analysisInfected ascitesClinicopathological parametersPeritonitisTreatment approachesCirrhosisAscitesPatientsGerman hospitalsPoint score
2022
Inhaled Bacteriophage Therapy for Multi-Drug Resistant Achromobacter.
Winzig F, Gandhi S, Lee A, Würstle S, Stanley G, Capuano I, Neuringer I, Koff J, Turner P, Chan B. Inhaled Bacteriophage Therapy for Multi-Drug Resistant Achromobacter. The Yale Journal Of Biology And Medicine 2022, 95: 413-427. PMID: 36568830, PMCID: PMC9765334.Peer-Reviewed Original ResearchConceptsCF patientsCystic fibrosisChronic pulmonary infectionGlobal public health threatBacterial lung infectionsChallenging clinical problemPublic health threatChronic bacterial lung infectionsPulmonary infectionRespiratory statusLung infectionClinical problemBacteriophage therapyInfectionAntimicrobial-resistant bacteriaTherapyHealth threatPhage therapyPatientsAMR infectionsResistant bacteriaLytic bacteriophagesPossible benefitsChemical antibioticsCurrent studyA 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
Würstle S, Hapfelmeier A, Karapetyan S, Studen F, Isaakidou A, Schneider T, Schmid R, von Delius S, Gundling F, Triebelhorn J, Burgkart R, Obermeier A, Mayr U, Heller S, Rasch S, Lahmer T, Geisler F, Chan B, Turner P, Rothe K, Spinner C, 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 2022, 11: 1610. PMID: 36421254, PMCID: PMC9686825, DOI: 10.3390/antibiotics11111610.Peer-Reviewed Original ResearchDecompensated liver cirrhosisInfected ascitesLiver cirrhosisPredictive valueHigh negative predictive valueRetrospective multicentre studySimilar predictive valuePre-test probabilityEpisodes of patientsFurther external validationNegative predictive valuePositive predictive valuePromising non-invasive approachLaboratory featuresMulticentre studyProspective studyAscitesCirrhosisPatientsNon-invasive approachClinical routineLASSO regression modelExternal validationAbdominocentesisRegression modelsAssembly and Annotation of Escherichia coli Bacteriophage U115
An W, Emsbo C, Frey E, Hu V, Jones A, Latif N, Perrilli M, Reillo K, Schwarz J, Strasner S, Theroux A, Vargas L, Turner P, Burmeister A. Assembly and Annotation of Escherichia coli Bacteriophage U115. Microbiology Resource Announcements 2022, 11: e00949-21. PMID: 35175109, PMCID: PMC8852279, DOI: 10.1128/mra.00949-21.Peer-Reviewed Original Research
2021
Assembly and Annotation of the Complete Genome Sequence of T4-Like Bacteriophage 132
Roush C, Chan B, Turner P, Burmeister A. Assembly and Annotation of the Complete Genome Sequence of T4-Like Bacteriophage 132. Microbiology Resource Announcements 2021, 10: 10.1128/mra.00649-21. PMID: 34591682, PMCID: PMC8483715, DOI: 10.1128/mra.00649-21.Peer-Reviewed Original ResearchCommunity context matters for bacteria-phage ecology and evolution
Blazanin M, Turner P. Community context matters for bacteria-phage ecology and evolution. The ISME Journal: Multidisciplinary Journal Of Microbial Ecology 2021, 15: 3119-3128. PMID: 34127803, PMCID: PMC8528888, DOI: 10.1038/s41396-021-01012-x.Peer-Reviewed Original ResearchConceptsBacteria-phage systemsEvolutionary effectsBacteria-phage coevolutionValuable biological modelUnderstanding of bacteriaAdditional bacterial speciesMechanisms of adaptationEcological interactionsPleiotropic consequencesComplex communitiesCoevolutionary dynamicsBacterial speciesEcologyPhagesBacteriaBiological modelsSymbiosesCoevolutionCommunity contextSpeciesEvolutionMultispeciesCommunityAdaptationCommunity presenceEffects of historical co‐infection on host shift abilities of exploitative and competitive viruses
Singhal S, Turner P. 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.Peer-Reviewed Original ResearchConceptsNovel hostRNA viral pathogensHost population densityViral growthPhage genotypesCo-infecting virusesHost specificityIntracellular competitionHost exploitationHost genotypeEcological historyOriginal hostInfected bacteriaRNA bacteriophagesRapid evolutionEmergence potentialHostGrowth curvesPopulation densityEquivalent growthViral pathogensClonesInfectivity differencesGenotypesCompetitive viruses
2020
Experimental Evolution of Human Rhinovirus Strains Adapting to Mouse Cells
Wasik B, Wasik B, Foxman E, Iwasaki A, Turner P. Experimental Evolution of Human Rhinovirus Strains Adapting to Mouse Cells. Genetic And Evolutionary Computation 2020, 145-157. DOI: 10.1007/978-3-030-39831-6_12.Peer-Reviewed Original ResearchMouse cellsIdentical selection pressuresExperimental evolution studiesLaboratory tissue cultureCommon cold illnessesViral capsid geneMolecular divergenceExperimental evolutionReplication genesSelection pressureRelated populationsGenetic changesRNA virusesHuman rhinovirus strainsCapsid geneEvolution studiesRV-1BInnate immunityGenesTissue cultureDifferent strainsCellsLA-4 cellsHostMouse host