Featured Publications
Population genomics of Group B Streptococcus reveals the genetics of neonatal disease onset and meningeal invasion
Chaguza C, Jamrozy D, Bijlsma M, Kuijpers T, van de Beek D, van der Ende A, Bentley S. Population genomics of Group B Streptococcus reveals the genetics of neonatal disease onset and meningeal invasion. Nature Communications 2022, 13: 4215. PMID: 35864107, PMCID: PMC9304382, DOI: 10.1038/s41467-022-31858-4.Peer-Reviewed Original ResearchConceptsPopulation genomicsMicrobial population genomicsGroup B streptococciWide association studyPopulation structureGenetic variationGenetic signaturesCapsule biosynthesis locusDisease onset timeAssociation studiesB streptococciInvasive neonatal GBS diseaseNeonatal GBS diseaseGenomicsPathogen surveillanceAcute invasive diseaseGeneticsOnset timeDisease pathogenesisGBS diseasePreterm birthTissue infectionsDisease burdenDisease onsetInvasive disease
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 mutationVirulence
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
2020
Rotavirus Genotypes in Hospitalized Children With Acute Gastroenteritis Before and After Rotavirus Vaccine Introduction in Blantyre, Malawi, 1997–2019
Mhango C, Mandolo JJ, Chinyama E, Wachepa R, Kanjerwa O, Malamba-Banda C, Matambo PB, Barnes KG, Chaguza C, Shawa IT, Nyaga MM, Hungerford D, Parashar UD, Pitzer VE, Kamng'ona A, Iturriza-Gomara M, Cunliffe NA, Jere KC. Rotavirus Genotypes in Hospitalized Children With Acute Gastroenteritis Before and After Rotavirus Vaccine Introduction in Blantyre, Malawi, 1997–2019. The Journal Of Infectious Diseases 2020, 225: 2127-2136. PMID: 33033832, PMCID: PMC9200156, DOI: 10.1093/infdis/jiaa616.Peer-Reviewed Original ResearchConceptsRV1 introductionRotavirus genotypesRotavirus-positive stool specimensDiarrhea-associated hospitalizationsRotavirus vaccine introductionReverse transcription-polymerase chain reactionRotavirus strain diversityPostvaccine periodRotavirus vaccineVaccine introductionHospitalized childrenPolymerase chain reactionStool specimensAcute gastroenteritisP genotypesPrevalent genotypeRotavirus GVaccine pressurePredominant genotypeChain reactionBlantyreStrain diversityChildrenGenotypesYearsBacterial 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
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
Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi
Chaguza C, Cornick JE, Andam CP, Gladstone RA, Alaerts M, Musicha P, Peno C, Bar-Zeev N, Kamng'ona AW, Kiran AM, Msefula CL, McGee L, Breiman RF, Kadioglu A, French N, Heyderman RS, Hanage WP, Bentley SD, Everett DB. Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi. Vaccine 2017, 35: 4594-4602. PMID: 28711389, PMCID: PMC5571440, DOI: 10.1016/j.vaccine.2017.07.009.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultBacterial CapsulesChildChild, PreschoolDrug Resistance, Multiple, BacterialEvolution, MolecularFemaleGenome, BacterialHigh-Throughput Nucleotide SequencingHumansInfantInfant, NewbornMalawiMalePneumococcal InfectionsPneumococcal VaccinesPrevalenceRetrospective StudiesSerogroupSerotypingStreptococcus pneumoniaeVaccinationVaccines, ConjugateYoung AdultConceptsPneumococcal conjugate vaccineMDR ratePneumococcal isolatesHigher MDR rateImplementation of PCV13Prevalence of serotypesNon-vaccine serotypesInvasive pneumococcal isolatesGood infection preventionAntibiotic resistance ratesAntibiotic resistanceAbsence of vaccinesReplacement serotypesSerotype replacementInvasive pneumococciPneumococcal infectionConjugate vaccineSerotype 12FDisease burdenInfection preventionSerotype prevalenceHigh prevalenceInvasive isolatesContinued surveillanceResistance ratesGenomic 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
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