2024
Expansion of pneumococcal serotype 23F and 14 lineages with genotypic changes in capsule polysaccharide locus and virulence gene profiles post introduction of pneumococcal conjugate vaccine in Blantyre, Malawi.
Cave R, Kalizang'oma A, Chaguza C, Mwalukomo T, Kamng’ona A, Brown C, Msefula J, Bonomali F, Nyirenda R, Swarthout T, Kwambana-Adams B, French N, Heyderman R. Expansion of pneumococcal serotype 23F and 14 lineages with genotypic changes in capsule polysaccharide locus and virulence gene profiles post introduction of pneumococcal conjugate vaccine in Blantyre, Malawi. Microbial Genomics 2024, 10 PMID: 38896467, DOI: 10.1099/mgen.0.001264.Peer-Reviewed Original ResearchConceptsGenes associated with antibiotic resistanceAntibiotic resistancePneumococcal conjugate vaccineVirulence factor expressionDNA binding sitesVaccine serotypesB-type domainWzy proteinsPolysaccharide locusConjugate vaccineCarriage of vaccine serotypesIntroduction of pneumococcal conjugate vaccinesCapsule polysaccharideEmergent lineagesGenetic changesStreptococcus pneumoniae</i>Vaccination coverageLineagesPersistent carriageGenotypic changesBinding sitesSerotypesMultidrug resistanceT mutationVirulenceDengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus
Vogels C, Hill V, Breban M, Chaguza C, Paul L, Sodeinde A, Taylor-Salmon E, Ott I, Petrone M, Dijk D, Jonges M, Welkers M, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Herzog K, Fauver J, Morrison A, Michael S, Grubaugh N. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics 2024, 25: 433. PMID: 38693476, PMCID: PMC11062901, DOI: 10.1186/s12864-024-10350-x.Peer-Reviewed Original ResearchConceptsAmplicon sequencing protocolsPrimer schemeSequencing protocolGenomic surveillanceDengue virus serotypesAmplicon sequencing workflowClinical specimensHigh genome coverageWhole-genome sequencingDengue virusVirus serotypesGenome coverageVirus stocksGenetic diversitySequencing instrumentsSequencing workflowGenotype VIDiverse serotypesSequence of samplesGenotype IVPrimersSurveillance of dengue virusSerotypesVirus copiesSerotype-specificTravel 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
Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints
Senghore M, Chaguza C, Bojang E, Tientcheu P, Bancroft R, Lo S, Gladstone R, McGee L, Worwui A, Foster-Nyarko E, Ceesay F, Okoi C, Klugman K, Breiman R, Bentley S, Adegbola R, Antonio M, Hanage W, Kwambana-Adams B. Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints. Microbial Genomics 2022, 8: 000732. PMID: 35119356, PMCID: PMC8942022, DOI: 10.1099/mgen.0.000732.Peer-Reviewed Original ResearchConceptsTransmission dynamicsRural African settingLogistic regression modelsPCV7 serotypesLongitudinal cohortCarriage episodesUnique serotypesPneumococcal strainsInfantsPairwise SNP distanceMultiple timepointsAfrican settingSNP distanceSustained colonizationRegression modelsSaharan AfricaCarriageSerotypesRural AfricaIntra-strain diversityPneumococcal genomeNeighbouring villagesCohort
2021
Carriage Dynamics of Pneumococcal Serotypes in Naturally Colonized Infants in a Rural African Setting During the First Year of Life
Chaguza C, Senghore M, Bojang E, Lo SW, Ebruke C, Gladstone RA, Tientcheu PE, Bancroft RE, Worwui A, Foster-Nyarko E, Ceesay F, Okoi C, McGee L, Klugman KP, Breiman RF, Barer MR, Adegbola RA, Antonio M, Bentley SD, Kwambana-Adams BA. Carriage Dynamics of Pneumococcal Serotypes in Naturally Colonized Infants in a Rural African Setting During the First Year of Life. Frontiers In Pediatrics 2021, 8: 587730. PMID: 33489998, PMCID: PMC7820366, DOI: 10.3389/fped.2020.587730.Peer-Reviewed Original ResearchPneumococcal serotypesPneumococcal conjugate vaccineRural African settingFirst yearColonized infantsPneumococcal acquisitionConjugate vaccineCarriage prevalenceInvasive diseaseNewborn infantsWeek 35Week 1Carriage patternsDisease preventionLatex agglutinationInfantsClinical interventionsMultiple serotypesFirst weekCarriage durationAfrican settingCarriage dynamicsBaseline dataSerotypesLimited data
2019
Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data
Chaguza C, Heinsbroek E, Gladstone RA, Tafatatha T, Alaerts M, Peno C, Cornick JE, Musicha P, Bar-Zeev N, Kamng’ona A, Kadioglu A, McGee L, Hanage WP, Breiman RF, Heyderman RS, French N, Everett DB, Bentley SD. Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data. Clinical Infectious Diseases 2019, 70: 1294-1303. PMID: 31094423, PMCID: PMC7768739, DOI: 10.1093/cid/ciz404.Peer-Reviewed Original ResearchConceptsYears of ageVaccine serotypesWhole-genome sequencingHigh disease burdenAntibiotic resistanceLow-income settingsPCV introductionReplacement serotypesVT serotypesPneumococcal diseaseNonvaccine serotypesCarriage rateDisease burdenPneumococcal isolatesSerotype dynamicsContinued surveillancePCV effectsAge groupsSerotypesSerotype diversityAgeVaccineResistant lineagesPCVChildren
2017
Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States
Andam CP, Mitchell PK, Callendrello A, Chang Q, Corander J, Chaguza C, McGee L, Beall BW, Hanage WP. Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States. Journal Of Clinical Microbiology 2017, 55: 1104-1115. PMID: 28100596, PMCID: PMC5377837, DOI: 10.1128/jcm.02453-16.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAgedAged, 80 and overChildChild, PreschoolEpidemiological MonitoringEvolution, MolecularFemaleGenome, BacterialGenotypeHumansInfantInfant, NewbornMaleMiddle AgedMolecular EpidemiologyPenicillin ResistancePneumococcal InfectionsSequence Analysis, DNASerogroupStreptococcus pneumoniaeUnited StatesYoung AdultConceptsActive Bacterial Core surveillancePneumococcal Molecular Epidemiology NetworkNonvaccine typesVaccine typesPenicillin-nonsusceptible pneumococciAntibiotic-resistant strainsNVT pneumococciNonvaccine serotypesSerotype 35BPneumococcal serotypesInvasive diseaseSerogroups 23Core surveillanceEpidemiology NetworkDisease controlDisease prevalencePNSPGenomic epidemiologyFuture surveillanceVaccinationSerotypesResistant clonesSerotype switchingPneumococciDisease