2023
Genomic analysis of Shigella isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance
Yassine I, Rafei R, de la Gandara M, Osman M, Fabre L, Dabboussi F, Hamze M, Weill F. Genomic analysis of Shigella isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance. Microbial Genomics 2023, 9: 001157. PMID: 38100171, PMCID: PMC10763507, DOI: 10.1099/mgen.0.001157.Peer-Reviewed Original ResearchConceptsExtended-spectrum beta-lactamase genesThird-generation cephalosporinsMultidrug resistance phenotypeBeta-lactamase genesAntimicrobial resistance determinantsPrevalent serogroupsClinical isolatesQuinolone resistanceDNA gyrase genesAntimicrobial resistanceResistance determinantsCTXResistance phenotypeAmino acid substitutionsGyrase genesIsolatesNorth LebanonFirst studyAcid substitutionsPoint mutationsGenomic analysisCephalosporinsEmergence 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 factorsIsolatesBedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis
Sonnenkalb L, Carter J, Spitaleri A, Iqbal Z, Hunt M, Malone K, Utpatel C, Cirillo D, Rodrigues C, Nilgiriwala K, Fowler P, Merker M, Niemann S, Consortium C, Barilar I, Battaglia S, Borroni E, Brandao A, Brankin A, Cabibbe A, Carter J, Cirillo D, Claxton P, Clifton D, Cohen T, Coronel J, Crook D, Dreyer V, Earle S, Escuyer V, Ferrazoli L, Fowler P, Gao G, Gardy J, Gharbia S, Ghisi K, Ghodousi A, Cruz A, Grandjean L, Grazian C, Groenheit R, Guthrie J, He W, Hoffmann H, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Jarrett L, Joseph L, Jou R, Kambli P, Khot R, Knaggs J, Koch A, Kohlerschmidt D, Kouchaki S, Lachapelle A, Lalvani A, Lapierre S, Laurenson I, Letcher B, Lin W, Liu C, Liu D, Malone K, Mandal A, Mansjö M, Matias D, Meintjes G, de Freitas Mendes F, Merker M, Mihalic M, Millard J, Miotto P, Mistry N, Moore D, Musser K, Ngcamu D, Hoang N, Niemann S, Nilgiriwala K, Nimmo C, Okozi N, Oliveira R, Omar S, Paton N, Peto T, Pinhata J, Plesnik S, Puyen Z, Rabodoarivelo M, Rakotosamimanana N, Rancoita P, Rathod P, Rodger G, Rodrigues C, Rodwell T, Roohi E, Santos-Lazaro D, Shah S, Kohl T, Smith G, Solano W, Spitaleri A, Supply P, Surve U, Tahseen S, Thuong N, Thwaites G, Todt K, Trovato A, Utpatel C, Van Rie A, Vijay S, Walker T, Walker S, Warren R, Werngren J, Wijkander M, Wilkinson R, Wilson D, Wintringer P, Yu X, Yang Y, Zhao Y, Yao S, Zhu B. Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis. The Lancet Microbe 2023, 4: e358-e368. PMID: 37003285, PMCID: PMC10156607, DOI: 10.1016/s2666-5247(23)00002-2.Peer-Reviewed Original ResearchConceptsMutation catalogueIn silico data analysisBedaquiline resistanceClofazimine resistanceResistance mechanismsProtein modelsClinical Mycobacterium tuberculosis complex isolatesImpaired DNA bindingClinically resistant strainsMinimum inhibitory concentrationVariants in vitroPacBio sequencingGenome sequenceGenomic rearrangementsGenomic variantsIn vitroExperimental evolutionGenotype dataTranscriptional repressorDrug resistance mechanismsClinical isolatesPhenotypic dataResistance determinantsDNA bindingProtein dimerisation
2021
Cl415, a carbapenem-resistant Acinetobacter baumannii isolate containing four AbaR4 and a new variant of AbGRI2, represents a novel global clone 2 strain
Liepa R, Mann R, Osman M, Hamze M, Gunawan C, Hamidian M. Cl415, a carbapenem-resistant Acinetobacter baumannii isolate containing four AbaR4 and a new variant of AbGRI2, represents a novel global clone 2 strain. Journal Of Antimicrobial Chemotherapy 2021, 77: 345-350. PMID: 34741594, PMCID: PMC8809195, DOI: 10.1093/jac/dkab399.Peer-Reviewed Original ResearchConceptsWhole genome sequencesWide geographical distributionGene complementNovel variantsPhylogenetic analysisGenomic analysisNew lineageComplete genomeOxford NanoporeIllumina MiSeqGenetic contextResistance genesGenesAntibiotic resistance determinantsResistance phenotypeGeographical distributionCopiesAntibiotic resistance phenotypesResistance islandsGlobal distributionResistance determinantsComM geneAntibiotic resistanceSubcladesVariants
2020
Distribution of emm types and macrolide resistance determinants among group A streptococci in the Middle East and North Africa region
Rafei R, Hawli M, Osman M, Dabboussi F, Hamze M. Distribution of emm types and macrolide resistance determinants among group A streptococci in the Middle East and North Africa region. Journal Of Global Antimicrobial Resistance 2020, 22: 334-348. PMID: 32084609, DOI: 10.1016/j.jgar.2020.02.005.Peer-Reviewed Original ResearchConceptsInvasive GAS infectionsGAS infectionVaccine candidatesProtein-based vaccine candidatesEpidemiology of groupMacrolide resistance determinantsMacrolide resistance profilesGAS prevalencePharyngitis patientsDisease burdenEmm typesGAS isolatesHealthy carriersSystematic surveillanceResistance profilesErythromycin resistancePotential coverageBurdenResistance determinantsInfectionStreptococciCoverage rateEmm28Emm4Emm89Emerging Microbiology Diagnostics for Transplant Infections: On the Cusp of a Paradigm Shift.
Azar MM, Gaston DC, Kotton CN, Malinis MF. Emerging Microbiology Diagnostics for Transplant Infections: On the Cusp of a Paradigm Shift. Transplantation 2020, 104: 1358-1384. PMID: 31972701, DOI: 10.1097/tp.0000000000003123.BooksConceptsHematopoietic stem cell transplantationInfected transplant recipientsInfectious disease specialistsStem cell transplantationBlood culture specimensArray of pathogensTransplant recipientsTransplant cliniciansClinical outcomesDisease specialistsCell transplantationTransplant infectionsMagnetic resonance-based methodsMicrobiology diagnosticsSolid organsCulture specimensMolecular testingMolecular panelResistance determinantsInfectionOutcomesDiagnostic microbiologyResonance-based methodsPatientsTransplantation
2019
Bloodstream infections caused by multidrug-resistant gram-negative bacteria: epidemiological, clinical and microbiological features
Leal H, Azevedo J, Silva G, Amorim A, de Roma L, Arraes A, Gouveia E, Reis M, Mendes A, de Oliveira Silva M, Barberino M, Martins I, Reis J. Bloodstream infections caused by multidrug-resistant gram-negative bacteria: epidemiological, clinical and microbiological features. BMC Infectious Diseases 2019, 19: 609. PMID: 31296179, PMCID: PMC6624930, DOI: 10.1186/s12879-019-4265-z.Peer-Reviewed Original ResearchConceptsK. pneumoniaePrevious antimicrobial useLaboratory-based surveillanceAntimicrobial susceptibility testingMDR bacteremiaMDR-GNBDrug-resistant pathogensNegative bacteremiaLiver diseaseBloodstream infectionsHigh morbidityMale sexRisk factorsEpidemiological aspectsNegative bacilliHealthcare professionalsMicrobiological featuresSusceptibility testingBacteremiaInfectionAntimicrobial useCausative agentAntibiotic resistanceIntervention measuresResistance determinants
2018
β‑Lactam Biotransformations Activate Innate Immunity
Oh J, Patel J, Park HB, Crawford JM. β‑Lactam Biotransformations Activate Innate Immunity. The Journal Of Organic Chemistry 2018, 83: 7173-7179. PMID: 29616809, DOI: 10.1021/acs.joc.8b00241.Peer-Reviewed Original ResearchConceptsHuman microbiota compositionImmune responseImmune functionMicrobiota compositionInnate immunityBroad immunomodulatory mechanismPatient's immune responseClinical trial studyCommon resistance determinantsMicrobiome-dependent mannerImmunomodulatory mechanismsNF-κBTrial studyBacterial infectionsImmunomodulatory interactionsMinimal long-term impactAntibioticsΒ-lactamaseAmoxicillinHuman leukemic monocytesLeukemic monocytesResistance determinantsBiotransformation productsImmunityMolecular mechanisms
2015
Characterization of resistance genes to macrolides, lincosamides and streptogramins (MLS) among clinical isolates of Staphylococcus aureus in North Lebanon
Osman M, Al Nasbeh A, Rafei R, Mallat H, Achkar M, Dabboussi F, Hamze M. Characterization of resistance genes to macrolides, lincosamides and streptogramins (MLS) among clinical isolates of Staphylococcus aureus in North Lebanon. The International Arabic Journal Of Antimicrobial Agents 2015, 5 DOI: 10.3823/780.Peer-Reviewed Original ResearchClinical isolatesStaphylococcus aureusStaphylococcus aureus infectionS. aureusPrevalence of genesMLS resistance genesMSB phenotypeNini HospitalSignificant morbidityAureus infectionDisc diffusion methodHigh prevalenceLow prevalenceMefA geneNorth LebanonPrevalenceSignificant pathogenL phenotypeResistance determinantsMLS resistanceInducible resistanceAureusErmC genePhenotypeResistance genes
2014
Plasmid-Mediated Sulfamethoxazole Resistance Encoded by the sul2 Gene in the Multidrug-Resistant Shigella flexneri 2a Isolated from Patients with Acute Diarrhea in Dhaka, Bangladesh
Iqbal MS, Rahman M, Islam R, Banik A, Amin MB, Akter F, Talukder KA. Plasmid-Mediated Sulfamethoxazole Resistance Encoded by the sul2 Gene in the Multidrug-Resistant Shigella flexneri 2a Isolated from Patients with Acute Diarrhea in Dhaka, Bangladesh. PLOS ONE 2014, 9: e85338. PMID: 24416393, PMCID: PMC3887042, DOI: 10.1371/journal.pone.0085338.Peer-Reviewed Original ResearchMeSH KeywordsAcute DiseaseAnti-Bacterial AgentsBacterial ProteinsBacterial Typing TechniquesBangladeshCarrier ProteinsDiarrheaDrug Resistance, Multiple, BacterialDysentery, BacillaryElectrophoresis, Gel, Pulsed-FieldGene ExpressionHumansPlasmidsShigella flexneriSulfamethoxazoleTrimethoprim, Sulfamethoxazole Drug CombinationConceptsShigella flexneri 2aFlexneri 2aMDa plasmidSulfamethoxazole resistanceEffective clinical managementS. flexneri 2aAcute diarrheaClinical managementPulsed-field gel electrophoresis analysisSul2 geneClinical isolatesAntimicrobial susceptibilityDrug resistanceEnteric pathogensClinical strainsPlasmid-cured derivativeMicrobiology laboratoryPlasmid profilingResistance determinantsFood microbiology laboratoriesPCR analysisHeterogeneous patternInvolvementDiarrheaPatients
2011
Retrospective evidence for a biological cost of vancomycin resistance determinants in the absence of glycopeptide selective pressures
Johnsen P, Townsend J, Bøhn T, Simonsen G, Sundsfjord A, Nielsen K. Retrospective evidence for a biological cost of vancomycin resistance determinants in the absence of glycopeptide selective pressures. Journal Of Antimicrobial Chemotherapy 2011, 66: 608-610. PMID: 21217128, PMCID: PMC3037156, DOI: 10.1093/jac/dkq512.Peer-Reviewed Original ResearchConceptsPopulation genetic modelsRelative fitness differencesStrong selectionBacterial fitnessFitness differencesFitness costsSelection coefficientsSelective pressureGlycopeptide-resistant Enterococcus faeciumResistance determinantsBiological fitness costBiological costGenetic modelsFarm environmentGlycopeptide resistance
2005
Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica
Zwir I, Shin D, Kato A, Nishino K, Latifi T, Solomon F, Hare JM, Huang H, Groisman EA. Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica. Proceedings Of The National Academy Of Sciences Of The United States Of America 2005, 102: 2862-2867. PMID: 15703297, PMCID: PMC548500, DOI: 10.1073/pnas.0408238102.Peer-Reviewed Original ResearchConceptsRegulatory networksEnteric bacteria Escherichia coliDistinct regulatory networksEscherichia coliPhoP/PhoQTwo-component systemSalmonella entericaCoregulated promotersPhoP proteinGenomic approachesPhoP regulonPromoter featuresRegulatory featuresGene transcriptionGene expressionBacteria Escherichia coliRegulatory systemGenesMultiple mechanismsColiResistance determinantsEntericaRegulonPhoQTranscription
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