2024
Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean
Taylor-Salmon E, Hill V, Paul L, Koch R, Breban M, Chaguza C, Sodeinde A, Warren J, Bunch S, Cano N, Cone M, Eysoldt S, Garcia A, Gilles N, Hagy A, Heberlein L, Jaber R, Kassens E, Colarusso P, Davis A, Baudin S, Rico E, Mejía-Echeverri Á, Scott B, Stanek D, Zimler R, Muñoz-Jordán J, Santiago G, Adams L, Paz-Bailey G, Spillane M, Katebi V, Paulino-Ramírez R, Mueses S, Peguero A, Sánchez N, Norman F, Galán J, Huits R, Hamer D, Vogels C, Morrison A, Michael S, Grubaugh N. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean. Nature Communications 2024, 15: 3508. PMID: 38664380, PMCID: PMC11045810, DOI: 10.1038/s41467-024-47774-8.Peer-Reviewed Original ResearchConceptsDengue virusDENV-3Rates of severe diseaseMosquito-borne viral diseasePublic health threatPattern of spreadSevere diseaseLocal surveillanceGenomic epidemiologyEpidemiological patternsVirus surveillanceSurveillanceHealth threatSerotypesDiseaseIncreased rateDengueViral diseasesVirusInfected travelersFrequent outbreaks
2022
Novel Multilocus Sequence Typing and Global Sequence Clustering Schemes for Characterizing the Population Diversity of Streptococcus mitis
Kalizang’oma A, Kwambana-Adams B, Chan J, Viswanath A, Gori A, Richard D, Jolley K, Lees J, Goldblatt D, Beleza S, Bentley S, Heyderman R, Chaguza C. Novel Multilocus Sequence Typing and Global Sequence Clustering Schemes for Characterizing the Population Diversity of Streptococcus mitis. Journal Of Clinical Microbiology 2022, 61: e00802-22. PMID: 36515506, PMCID: PMC9879099, DOI: 10.1128/jcm.00802-22.Peer-Reviewed Original ResearchMeSH KeywordsCluster AnalysisHumansMultilocus Sequence TypingPhylogenyStreptococcusStreptococcus mitisConceptsSequence clustersPathogenic streptococcal speciesMultilocus sequence typing (MLST) schemePopulation diversitySingle-nucleotide polymorphism distancesSequence typesSequence typing schemeUnique sequence typesGenetic diversityPopulation structureBacterial population diversityMolecular typing toolsS. mitisHousekeeping genesSequence fragmentsMLST schemeDiversityOpportunistic pathogenStreptococcus mitisStreptococcal speciesTyping toolSpeciesNew insightsTyping schemeMultilocus sequence typing
2021
Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis
Kalizang'oma A, Chaguza C, Gori A, Davison C, Beleza S, Antonio M, Beall B, Goldblatt D, Kwambana-Adams B, Bentley SD, Heyderman RS. Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis. Microbial Genomics 2021, 7: 000622. PMID: 34550067, PMCID: PMC8715442, DOI: 10.1099/mgen.0.000622.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsBeta-Lactam ResistanceDrug Resistance, BacterialGene Transfer, HorizontalGenes, BacterialHumansMicrobial Sensitivity TestsNasopharynxPenicillin-Binding ProteinsPenicillinsPhylogenyPneumococcal InfectionsPneumococcal VaccinesSerogroupStreptococcusStreptococcus mitisStreptococcus oralisStreptococcus pneumoniaeWhole Genome SequencingConceptsMinimum inhibitory concentrationPneumococcal vaccine programsFirst-line treatmentHigh minimum inhibitory concentrationsStreptococcus pneumoniae serotypesPneumococcal population structurePneumococcal serotypes 6ABeta-lactam antibioticsLonger carriage durationBeta-lactam resistanceImportant global pathogenPneumococcal diseaseBacterial pneumoniaPneumococcal serotypesVaccine programSerotypes 6APneumoniae serotypesΒ-lactam susceptibilityPenicillin-binding protein (PBP) genesHuman nasopharynxCarriage durationCommensal streptococciCommon recipientInhibitory concentrationStreptococciWhole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco
Nzoyikorera N, Diawara I, Fresia P, Maaloum F, Katfy K, Nayme K, Maaloum M, Cornick J, Chaguza C, Timinouni M, Belabess H, Zerouali K, Elmdaghri N. Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco. BMC Genomics 2021, 22: 39. PMID: 33413118, PMCID: PMC7792055, DOI: 10.1186/s12864-020-07316-0.Peer-Reviewed Original Research
2020
Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism
Chaguza C, Yang M, Cornick JE, du Plessis M, Gladstone RA, Kwambana-Adams BA, Lo SW, Ebruke C, Tonkin-Hill G, Peno C, Senghore M, Obaro SK, Ousmane S, Pluschke G, Collard JM, Sigaùque B, French N, Klugman KP, Heyderman RS, McGee L, Antonio M, Breiman RF, von Gottberg A, Everett DB, Kadioglu A, Bentley SD. Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism. Communications Biology 2020, 3: 559. PMID: 33033372, PMCID: PMC7545184, DOI: 10.1038/s42003-020-01290-9.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesPneumococcal serotype 1Genetic variationBacterial genome-wide association studiesAssociation studiesSerotype 1Central nervous system infectionSignificant genotype-phenotype associationsNervous system infectionGenotype-phenotype associationsHelicase proteinPopulation structureCNS infectionsSystem infectionNegligible heritabilityMeningitis outbreakCNS tissueCerebrospinal fluidImmune evasionSerotype 1 strainPneumococcal survivalPolygenic etiologySmall effect sizesMeningitisTropism
2019
Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010–2018
Arana A, Jere KC, Chaguza C, Montes M, Alkorta M, Iturriza-Gomara M, Cilla G. Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010–2018. Infection Genetics And Evolution 2019, 71: 67-75. PMID: 30905774, DOI: 10.1016/j.meegid.2019.03.016.Peer-Reviewed Original ResearchGenomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages
Musicha P, Msefula CL, Mather AE, Chaguza C, Cain AK, Peno C, Kallonen T, Khonga M, Denis B, Gray KJ, Heyderman RS, Thomson NR, Everett DB, Feasey NA. Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages. Journal Of Antimicrobial Chemotherapy 2019, 74: 1223-1232. PMID: 30778540, PMCID: PMC6477993, DOI: 10.1093/jac/dkz032.Peer-Reviewed Original Research
2018
Emergence of Double- and Triple-Gene Reassortant G1P[8] Rotaviruses Possessing a DS-1-Like Backbone after Rotavirus Vaccine Introduction in Malawi
Jere KC, Chaguza C, Bar-Zeev N, Lowe J, Peno C, Kumwenda B, Nakagomi O, Tate JE, Parashar UD, Heyderman RS, French N, Cunliffe NA, Iturriza-Gomara M. Emergence of Double- and Triple-Gene Reassortant G1P[8] Rotaviruses Possessing a DS-1-Like Backbone after Rotavirus Vaccine Introduction in Malawi. Journal Of Virology 2018, 92: e01246-17. PMID: 29142125, PMCID: PMC5774894, DOI: 10.1128/jvi.01246-17.Peer-Reviewed Original ResearchConceptsRotavirus vaccineVaccine introductionVaccine effectivenessVaccine-induced neutralizing antibodiesMultiple African countriesRotavirus gastroenteritis casesRotavirus vaccine introductionChildhood immunization programsCareful evaluationVaccine escape mutantsDS-1-like backboneSuch atypical strainsRotavirus gastroenteritisImmunization scheduleNeutralizing antibodiesAmino acid substitutionsImmunization programsPostvaccine eraHigh burdenGastroenteritis casesImmune evasionEscape mutantsHuman WaDS-1-like rotavirusesRotavirus
2017
Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting
Musicha P, Feasey NA, Cain AK, Kallonen T, Chaguza C, Peno C, Khonga M, Thompson S, Gray KJ, Mather AE, Heyderman RS, Everett DB, Thomson NR, Msefula CL. Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting. Journal Of Antimicrobial Chemotherapy 2017, 72: 1602-1609. PMID: 28333330, PMCID: PMC5437524, DOI: 10.1093/jac/dkx058.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultBeta-Lactam ResistanceBeta-LactamasesChildChild, PreschoolChloramphenicolDrug Resistance, Multiple, BacterialEscherichia coliEscherichia coli InfectionsFemaleGenes, BacterialGenetic VariationGenomicsHumansMalawiMaleMicrobial Sensitivity TestsMultilocus Sequence TypingPhylogenyUrban PopulationYoung AdultConceptsAntimicrobial resistanceExtended spectrum β-lactamase resistanceEscherichia coli infectionResource-rich settingsUrban African settingCommon ESBL geneLow-income settingsPhenotypic resistance profilesΒ-lactamase resistanceColi infectionESBL resistanceGlobal epidemiologyFluoroquinolone resistanceQueen's HospitalBla CTXESBL genesMolecular epidemiologyResistance profilesMolecular patternsAfrican settingClinical sourcesHospitalE. coliEpidemiologyST131
2016
Understanding pneumococcal serotype 1 biology through population genomic analysis
Chaguza C, Cornick JE, Harris SR, Andam CP, Bricio-Moreno L, Yang M, Yalcin F, Ousmane S, Govindpersad S, Senghore M, Ebruke C, Du Plessis M, Kiran AM, Pluschke G, Sigauque B, McGee L, Klugman KP, Turner P, Corander J, Parkhill J, Collard JM, Antonio M, von Gottberg A, Heyderman RS, French N, Kadioglu A, Hanage WP, Everett DB, Bentley SD, for the PAGe Consortium. Understanding pneumococcal serotype 1 biology through population genomic analysis. BMC Infectious Diseases 2016, 16: 649. PMID: 27821148, PMCID: PMC5100261, DOI: 10.1186/s12879-016-1987-z.Peer-Reviewed Original ResearchConceptsDisease burdenPneumococcal disease burdenSerotype 1 pneumococciSub-Saharan AfricaHigh prevalenceHuman nasopharynxAfrican isolatesLow-income countriesSerotype 1Longer durationFurther studiesTetracycline resistanceBiological mechanismsST217West African isolatesDifferent geographical regionsSuccessful clones
2015
High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children
Kamng’ona A, Hinds J, Bar-Zeev N, Gould KA, Chaguza C, Msefula C, Cornick JE, Kulohoma BW, Gray K, Bentley SD, French N, Heyderman RS, Everett DB. High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children. BMC Infectious Diseases 2015, 15: 234. PMID: 26088623, PMCID: PMC4474563, DOI: 10.1186/s12879-015-0980-2.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentBacterial CapsulesBacteriological TechniquesChildChild, PreschoolCross ProtectionDNA, BacterialFemaleGenetic VariationHIV InfectionsHumansInfantInfant, NewbornMalawiMaleNasopharynxOligonucleotide Array Sequence AnalysisPhylogenyPneumococcal InfectionsPneumococcal VaccinesSequence Analysis, DNASerogroupStreptococcus pneumoniaeConceptsPneumococcal carriageVaccine typesPneumococcal serotypesMalawian childrenMultiple carriageMultiple serotypesVaccine serotypes 6BInvasive pneumococcal diseaseMultiple pneumococcal serotypesCent of childrenYoung childrenVT serotypesPCV13 introductionPneumococcal diseaseNasopharyngeal samplesPossible genetic alterationsSerotypes 6BMethodsThe studyPneumococcal strainsVaccine escapeKaronga DistrictOlder childrenSterile swabsDistinct serotypesGenetic alterations