2025
Personalized inhaled bacteriophage therapy for treatment of multidrug-resistant Pseudomonas aeruginosa in cystic fibrosis
Chan B, Stanley G, Kortright K, Vill A, Modak M, Ott I, Sun Y, Würstle S, Grun C, Kazmierczak B, Rajagopalan G, Harris Z, Britto C, Stewart J, Talwalkar J, Appell C, Chaudary N, Jagpal S, Jain R, Kanu A, Quon B, Reynolds J, Teneback C, Mai Q, Shabanova V, Turner P, Koff J. Personalized inhaled bacteriophage therapy for treatment of multidrug-resistant Pseudomonas aeruginosa in cystic fibrosis. Nature Medicine 2025, 31: 1494-1501. PMID: 40301561, PMCID: PMC12092284, DOI: 10.1038/s41591-025-03678-8.Peer-Reviewed Original ResearchConceptsPhage therapyCystic fibrosisEvidence of trade-offsTreated with phagesEvolutionary trade-offClinical impact of antimicrobial resistanceMultidrug-resistant Pseudomonas aeruginosaBacterial virulenceAntimicrobial resistance crisisLytic virusesDecrease antibiotic resistanceSputum microbiomePhageBacteriophage therapyImpact of antimicrobial resistanceAntibiotic resistanceResistance crisisStandard antibioticsAntimicrobial resistanceSputum densityMultidrug resistancePulmonary infectionCompassionate basisClinical courseMedian ageSecondary Spontaneous Bacterial Peritonitis Prophylaxis Is Associated With a Higher Rate of Infections other than Spontaneous Bacterial Peritonitis in 2 US-Based National Cirrhosis Cohorts
Silvey S, Patel N, O'Leary J, Jakab S, Patton H, Rogal S, Markley J, Cheung R, Patel A, Morgan T, Bajaj J. Secondary Spontaneous Bacterial Peritonitis Prophylaxis Is Associated With a Higher Rate of Infections other than Spontaneous Bacterial Peritonitis in 2 US-Based National Cirrhosis Cohorts. Clinical And Translational Gastroenterology 2025, 16: e00837. PMID: 40062879, PMCID: PMC12101923, DOI: 10.14309/ctg.0000000000000837.Peer-Reviewed Original ResearchConceptsNon-SBP infectionsUrinary tract infectionSpontaneous bacterial peritonitis prophylaxisTract infectionsMultivariate regressionNational cohort of patientsSpontaneous bacterial peritonitisCohort of patientsBacterial peritonitisRate of infectionCirrhosis cohortAntibiotic overuseHigh riskAntibiotic resistanceC. difficileInfection outcomesPatientsCirrhosisInfectionBacteremiaSBPProphylaxisPneumoniaPeritonitisRecurrence
2024
Antibiotic resistance and serotype distribution of Shigella strains in Bangladesh over the period of 2014–2022: evidence from a nationwide hospital-based surveillance for cholera and other diarrheal diseases
Afrad M, Islam M, Begum Y, Saifullah M, Ahmmed F, Khan Z, Habib Z, Alam A, Shirin T, Bhuiyan T, Ryan E, Khan A, Qadri F. Antibiotic resistance and serotype distribution of Shigella strains in Bangladesh over the period of 2014–2022: evidence from a nationwide hospital-based surveillance for cholera and other diarrheal diseases. Microbiology Spectrum 2024, 12: e00739-24. PMID: 39540737, PMCID: PMC11619575, DOI: 10.1128/spectrum.00739-24.Peer-Reviewed Original ResearchAntimicrobial resistance patternsAntibiotic resistanceNalidixic acidResistance patternsAntibiotic susceptibility testingDisc diffusion methodStool specimensLevels of resistance to ciprofloxacinResistant to ciprofloxacinDiarrheal disease surveillanceQuinolone class of antibioticsClasses of antibioticsShigella strainsSerotype 2aShigella sonneiMonitoring of drug resistanceSusceptibility testingVaccine clinical trialsAcute watery diarrheaHospital-based surveillanceDiffusion methodIntermediate susceptibilityMultidrug resistanceSerotype distributionImproved hygieneAntibiotic resistance and draft genome profiles of 10 Streptococcus pneumoniae and 3 Streptococcus pseudopneumoniae strains isolated from the nasopharynx of people living with human immunodeficiency virus in Ghana
Ativi L, Adusei-Poku M, Boateng W, Owusu-Nyantantakyi C, Danso J, Oclu A, Bortey A, Amuasi G, Tabi B, Paintsil E, Torpey K, Dayie N, Egyir B. Antibiotic resistance and draft genome profiles of 10 Streptococcus pneumoniae and 3 Streptococcus pseudopneumoniae strains isolated from the nasopharynx of people living with human immunodeficiency virus in Ghana. Microbiology Resource Announcements 2024, 13: e00505-24. PMID: 39365088, PMCID: PMC11556032, DOI: 10.1128/mra.00505-24.Peer-Reviewed Original ResearchAntimicrobial resistanceWhole-genome profilingGenomic dataAntibiotic resistanceBacteria speciesStreptococcus pneumoniae</i>Streptococcus speciesGenomic profilingHuman immunodeficiency virusSpeciesStreptococcus pneumoniaeAntimicrobial resistance surveillance effortsImmunodeficiency virusSurveillance effortsMiddle-income countriesStrainResistanceMechanistic Basis for the Translation Inhibition of Cutibacterium acnes by Clindamycin
Lomakin I, Devarkar S, Grada A, Bunick C. Mechanistic Basis for the Translation Inhibition of Cutibacterium acnes by Clindamycin. Journal Of Investigative Dermatology 2024, 144: 2553-2561.e3. PMID: 39122144, DOI: 10.1016/j.jid.2024.07.013.Peer-Reviewed Original ResearchNetwork of water-mediated interactionsCutibacterium acnesPeptide bond formationNascent peptideWater-mediated interactionsTranslational inhibitionAntibiotic resistanceCryogenic electron microscopyA-resolutionMechanistic basesAntibiotic-based therapiesRRNAAminoacyl groupRibosomeAcne pathogenesisAcne therapyAntibiotic stewardshipClindamycinIncreased resistanceAcne vulgarisClinical targetsAcneAntibioticsPeptideTRNAClindamycin: A Comprehensive Status Report with Emphasis on Use in Dermatology.
Del Rosso J, Armillei M, Lomakin I, Grada A, Bunick C. Clindamycin: A Comprehensive Status Report with Emphasis on Use in Dermatology. The Journal Of Clinical And Aesthetic Dermatology 2024, 17: 29-40. PMID: 39148960, PMCID: PMC11324192.Peer-Reviewed Original ResearchAcne vulgarisTreatment of acne vulgarisApplication of clindamycinCutaneous bacterial infectionsAntibiotic treatment efficacyTopical clindamycinTopical agentsOral treatmentClindamycinSystemic agentsMultiple disease statesPharmacokinetic profileTreatment efficacyAntibiotic resistanceBacterial infectionsAntibiotic mechanismsTherapeutic valueRelevance to cliniciansDisease statesDermatologyLincosamide antibioticsAnti-inflammatoryGram-positiveAnaerobic bacteriaAcneA nucleoid-associated protein is involved in the emergence of antibiotic resistance by promoting the frequent exchange of the replicative DNA polymerase in Mycobacterium smegmatis
Ng W, Rego E. A nucleoid-associated protein is involved in the emergence of antibiotic resistance by promoting the frequent exchange of the replicative DNA polymerase in Mycobacterium smegmatis. MSphere 2024, 9: e00122-24. PMID: 38591887, PMCID: PMC11237743, DOI: 10.1128/msphere.00122-24.Peer-Reviewed Original ResearchNucleoid-associated proteinsReplicative DNA polymerasesBypass DNA lesionsDNA replicationDNA polymeraseAntibiotic resistanceDamaged DNAExpression of error-prone DNA polymerasesReplicative polymerasesHigh-fidelity replicative polymerasesQuantitative fluorescence imaging techniqueError-prone DNA synthesisDNA lesionsError-prone DNA polymerasesHorizontal gene transferEmergence of antibiotic resistanceDNA-damaging agentsRepair damaged DNAResistance to rifampinRobust cell growthGrowth defectLsr2Replication forksBacterial speciesChromosomal mutationsScientific Rationale and Clinical Basis for Clindamycin Use in the Treatment of Dermatologic Disease
Armillei M, Lomakin I, Del Rosso J, Grada A, Bunick C. Scientific Rationale and Clinical Basis for Clindamycin Use in the Treatment of Dermatologic Disease. Antibiotics 2024, 13: 270. PMID: 38534705, PMCID: PMC10967556, DOI: 10.3390/antibiotics13030270.Peer-Reviewed Original ResearchSoft tissue infectionsTetracycline class antibioticsTreatment of dermatological diseasesMechanism of protein synthesis inhibitionClindamycin useStaphylococcal infectionsTissue infectionsClinical presentationAnti-inflammatory propertiesHidradenitis suppurativaEffective antibioticsTreatment optionsClindamycinClinical evidenceAcne vulgarisClinical basisProtein synthesis inhibitionDermatological indicationsAmeliorate inflammationAntibiotic resistanceDermatology practiceBacterial ribosomeDermatological diseasesClass antibioticsLesion formationNovel Approaches to Multidrug-Resistant Infections in Cystic Fibrosis
Murray T, Stanley G, Koff J. Novel Approaches to Multidrug-Resistant Infections in Cystic Fibrosis. Infectious Disease Clinics Of North America 2024, 38: 149-162. PMID: 38280761, DOI: 10.1016/j.idc.2023.12.002.Peer-Reviewed Original ResearchConceptsMultidrug-resistant organismsCystic fibrosis transmembrane conductance regulatorCystic fibrosisBeta-lactam/beta-lactamase combinationDevelopment of inhaled formulationsMethicillin-resistant Staphylococcus aureusTherapeutic approachesMultidrug-resistant organism infectionSystemic adverse eventsMultidrug-resistant infectionsTransmembrane conductance regulatorRespiratory tract infectionsCystic fibrosis patientsGram-negative organismsInnovative therapeutic approachesPulmonary infectionTract infectionsConductance regulatorBurkholderia sp.Multidrug resistanceAdverse eventsTreatment optionsAntibiotic resistanceFibrosis patientsOptimal doseAvoiding the Danger of Rising Resistance in Cutibacterium acnes: Criticality of Benzoyl Peroxide and Antibiotic Fixed Combinations
Ghannoum M, Gamal A, Kadry A, Del Rosso J, Bunick C, Stein Gold L, Kircik L, Harper J. Avoiding the Danger of Rising Resistance in Cutibacterium acnes: Criticality of Benzoyl Peroxide and Antibiotic Fixed Combinations. SKIN The Journal Of Cutaneous Medicine 2024, 8: s355. DOI: 10.25251/skin.8.supp.355.Peer-Reviewed Original ResearchCombination of clindamycinC. acnes strainsMinimum inhibitory concentrationCutibacterium acnesCombination of benzoyl peroxideExposure to antibioticsConcentrations of clindamycinEpsilometer testBacterial cultureDevelopment of resistanceFixed combinationMeasuring zones of inhibitionAntibiotic susceptibilityCheckerboard assayClinical strainsClindamycinAntibiotic formulationsC. acnesAntibiotic resistanceProlonged useAntibioticsZone of inhibitionAgar diffusion methodInhibitory concentrationCombination formulationAvoiding the Danger of Rising Resistance in Cutibacterium acnes: Criticality of Benzoyl Peroxide and Antibiotic Fixed Combinations
Ghannoum M, Gamal A, Kadry A, Del Rosso J, Bunick C, Stein Gold L, Kircik L, Harper J. Avoiding the Danger of Rising Resistance in Cutibacterium acnes: Criticality of Benzoyl Peroxide and Antibiotic Fixed Combinations. SKIN The Journal Of Cutaneous Medicine 2024, 8: s354. DOI: 10.25251/skin.8.supp.354.Peer-Reviewed Original ResearchCombination of clindamycinC. acnes strainsMinimum inhibitory concentrationCutibacterium acnesCombination of benzoyl peroxideExposure to antibioticsConcentrations of clindamycinEpsilometer testBacterial cultureDevelopment of resistanceFixed combinationMeasuring zones of inhibitionAntibiotic susceptibilityCheckerboard assayClinical strainsClindamycinAntibiotic formulationsC. acnesAntibiotic resistanceProlonged useAntibioticsZone of inhibitionAgar diffusion methodInhibitory concentrationCombination formulation
2023
Emergence of Extended-Spectrum Cephalosporin- and Colistin-Resistant Enterobacterales in Otherwise Healthy University Students
Osman M, Yassine I, Hamze M, Al Mir H, Tajani A, Bisha B, Cummings K, Madec J, Haenni M, Kassem I. Emergence of Extended-Spectrum Cephalosporin- and Colistin-Resistant Enterobacterales in Otherwise Healthy University Students. Microbial Drug Resistance 2023, 30: 101-107. PMID: 38011748, DOI: 10.1089/mdr.2023.0213.Peer-Reviewed Original ResearchLast-resort antibioticsHealthy university studentsExtended-spectrum cephalosporin-resistant isolatesComprehensive antimicrobial stewardship programAntimicrobial stewardship programsColistin-resistant isolatesExtended-spectrum cephalosporinsCephalosporin-resistant isolatesColistin-resistant EnterobacteralesMultidrug-resistant bacteriaMiddle-income countriesEvidence-based practiceAntimicrobial stewardshipStewardship programsOccurrence of resistanceCommunity settingsAntimicrobial resistanceClinical samplesAntibiotic resistanceFecal samplesResistance determinantsAntibioticsPublic healthMultiple factorsIsolatesDeveloping Phage Therapy That Overcomes the Evolution of Bacterial Resistance
Oromí-Bosch A, Antani J, Turner P. Developing Phage Therapy That Overcomes the Evolution of Bacterial Resistance. Annual Review Of Virology 2023, 10: 503-524. PMID: 37268007, DOI: 10.1146/annurev-virology-012423-110530.Peer-Reviewed Original ResearchConceptsPhage therapyPhage resistanceBacterial resistanceEvolution of phage resistancePhage-resistant bacteriaEvolution of bacterial resistanceBacteria-specific virusesTreatment of intractable infectionsAlternative antimicrobial strategiesPersonalized medicine treatmentsPhage strategyClinically favorable outcomesBacterial pathogensBacterial populationsPhageTarget bacteriaAntibiotic resistanceAntimicrobial strategiesIntractable infectionsWaning efficacyFavorable outcomeBacterial infectionsBacteriaTherapyPatient treatmentExperimental 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 dynamicsEfficient evolution of human antibodies from general protein language models
Hie B, Shanker V, Xu D, Bruun T, Weidenbacher P, Tang S, Wu W, Pak J, Kim P. Efficient evolution of human antibodies from general protein language models. Nature Biotechnology 2023, 42: 275-283. PMID: 37095349, PMCID: PMC10869273, DOI: 10.1038/s41587-023-01763-2.Peer-Reviewed Original ResearchConceptsProtein language modelsDiverse protein familiesLaboratory evolutionProtein familyProtein structureBinding specificityRare mutationsSelection pressureAntibiotic resistanceNatural evolutionary strategyEnzyme activityHuman antibodiesMature antibodiesAffinity maturationProteinAntibody bindingBinding affinityMutationsBindingEvolutionary strategyAffinityAntibodiesSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2Vibrio cholerae biofilms use modular adhesins with glycan-targeting and nonspecific surface binding domains for colonization
Huang X, Nero T, Weerasekera R, Matej K, Hinbest A, Jiang Z, Lee R, Wu L, Chak C, Nijjer J, Gibaldi I, Yang H, Gamble N, Ng W, Malaker S, Sumigray K, Olson R, Yan J. Vibrio cholerae biofilms use modular adhesins with glycan-targeting and nonspecific surface binding domains for colonization. Nature Communications 2023, 14: 2104. PMID: 37055389, PMCID: PMC10102183, DOI: 10.1038/s41467-023-37660-0.Peer-Reviewed Original ResearchConceptsBiofilm matrix exopolysaccharideFacilitate host colonizationVibrio cholerae biofilmsΒ-propeller domainMatrix exopolysaccharideModular domainsHost colonizationRedundant rolesDistinct functionsAbiotic surfacesAdhesive proteinsHost surfaceHuman pathogensVibrio choleraeAdhesinsBacterial biofilmsHost tissuesColonization modelColonizationBAP1BiofilmsPathogensAntibiotic resistanceRBMCDomainTrends in Oral Antibiotic Use for Acne Treatment: A Retrospective, Population-Based Study in the United States, 2014 to 2016.
Grada A, Armstrong A, Bunick C, Salem R, Feldman S. Trends in Oral Antibiotic Use for Acne Treatment: A Retrospective, Population-Based Study in the United States, 2014 to 2016. Journal Of Drugs In Dermatology 2023, 22: 265-270. PMID: 36877883, DOI: 10.36849/jdd.7345.Peer-Reviewed Original ResearchConceptsOral antibiotic useOral antibioticsAntibiotic useAntibiotic treatmentAcne treatmentHealth care claims dataOral antibiotic treatmentShort study durationIBM MarketScanPrimary outcomeGuideline recommendationsRetrospective studyAcne vulgarisRetrospective analysisClaims dataJ DrugsPatientsStudy durationAmerican AcademyTherapeutic classesSeparate occasionsDay gapMonthsAntibiotic resistanceAntibioticsBacteriophage Therapy for Pan-Drug-Resistant Pseudomonas aeruginosa in Two Persons With Cystic Fibrosis
Hahn A, Sami I, Chaney H, Koumbourlis A, Del Valle Mojica C, Cochrane C, Chan B, Koff J. Bacteriophage Therapy for Pan-Drug-Resistant Pseudomonas aeruginosa in Two Persons With Cystic Fibrosis. Journal Of Investigative Medicine High Impact Case Reports 2023, 11: 23247096231188243. PMID: 37515541, PMCID: PMC10387758, DOI: 10.1177/23247096231188243.Peer-Reviewed Original ResearchConceptsPulmonary exacerbationsCF transmembrane conductance regulator geneTransmembrane conductance regulator geneChronic bacterial colonizationRecurrent lung infectionsStructural lung damagePediatric clinical trialsLung function declineLung inflammationTreatment modalitiesLung infectionCystic fibrosisLung damageClinical trialsTherapeutic strategiesAntibiotic resistanceBacterial colonizationMonogenic diseasesBacteriophage therapyRegulated genesViscous secretionsReduced survivalFunctional declineExacerbationBacteriophage
2022
Novel Approaches to Multidrug-Resistant Infections in Cystic Fibrosis
Murray T, Stanley G, Koff J. Novel Approaches to Multidrug-Resistant Infections in Cystic Fibrosis. Clinics In Chest Medicine 2022, 43: 667-676. PMID: 36344073, DOI: 10.1016/j.ccm.2022.06.008.Peer-Reviewed Original ResearchConceptsMultidrug-resistant organismsCystic fibrosisTherapeutic approachesNontuberculous mycobacteriaCystic fibrosis transmembrane conductance regulator (CFTR) dysfunctionSystemic adverse eventsRespiratory tract infectionsMethicillin-resistant Staphylococcus aureusAdditional clinical trialsNew treatment optionsPharmacokinetics/pharmacodynamicsInnovative therapeutic approachesMultidrug-resistant infectionsMDRO infectionAdverse eventsPulmonary infectionTract infectionsOptimal dosingTreatment optionsClinical trialsNew therapiesNegative organismsInfectionAntibiotic resistancePatientsAnalysis of pCl107 a large plasmid carried by an ST25 Acinetobacter baumannii strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways
Rafei R, Koong J, Osman M, Al Atrouni A, Hamze M, Hamidian M. Analysis of pCl107 a large plasmid carried by an ST25 Acinetobacter baumannii strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways. FEMS Microbes 2022, 3: xtac027. PMID: 37332503, PMCID: PMC10117892, DOI: 10.1093/femsmc/xtac027.Peer-Reviewed Original ResearchComplex evolutionary historyEvolutionary historyMetabolic pathwaysHybrid assembly approachConjugative transfer systemOxford Nanopore sequencingLarge plasmidsMetabolic modulesComplete sequenceMetabolism modulesAntibiotic resistance genesAncestral structureIllumina MiSeqNanopore sequencingResistance genesPossible ancestorAntibiotic resistanceGlobal clone 2PlasmidMultiple antibiotic resistanceClone 2Important pathogenResistance islandsKb plasmidSequence types
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