Featured Publications
Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation
Chaguza C, Senghore M, Bojang E, Gladstone RA, Lo SW, 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. Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation. Nature Communications 2020, 11: 3442. PMID: 32651390, PMCID: PMC7351774, DOI: 10.1038/s41467-020-17327-w.Peer-Reviewed Original ResearchConceptsNatural colonisationHost microevolutionNucleotide substitution ratesWhole-genome sequencingGenomic evolutionNeutral evolutionGenetic diversityHomologous recombinationParallel evolutionGenomic changesAdhesion genesSubstitution ratesHuman-adapted pathogenMicroevolutionStrain variantsColonisationImmune evasionStreptococcus pneumoniaeAntibiotic resistanceGenesEvolutionSequencingDiversityNasopharyngeal carriageBacteria
2024
Genetic markers associated with host status and clonal expansion of Group B Streptococcus in the Netherlands
Khan U, Dyster V, Chaguza C, van Sorge N, van de Beek D, Man K, Bentley S, Bijlsma M, Jamrozy D. Genetic markers associated with host status and clonal expansion of Group B Streptococcus in the Netherlands. Frontiers In Microbiology 2024, 15: 1410651. DOI: 10.3389/fmicb.2024.1410651.Peer-Reviewed Original ResearchGroup B streptococciDisease isolatesCarriage isolatesCC17 isolatesClonal complexesDistribution of genetic markersPrevalence of antimicrobial resistance genesWhole-genome sequencingMobile genetic elementsAntimicrobial resistance genesAssociated with invasive diseaseGBS populationB streptococciInvasive diseaseClonal expansion eventsGenome sequenceExpansion eventsGenetic elementsGenomic analysisGenetic markersResistance genesSub-lineagesInvasive isolatesSerotype IIHost groupsDengueSeq: 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-specificClonal Expansion of a Streptococcus pneumoniae Serotype 3 Capsule Variant Sequence Type 700 With Enhanced Vaccine Escape Potential After 13-Valent Pneumococcal Conjugate Vaccine Introduction
Kalizang'oma A, Swarthout T, Mwalukomo T, Kamng'ona A, Brown C, Msefula J, Demetriou H, Chan J, Roalfe L, Obolski U, Lourenço J, Goldblatt D, Chaguza C, French N, Heyderman R. Clonal Expansion of a Streptococcus pneumoniae Serotype 3 Capsule Variant Sequence Type 700 With Enhanced Vaccine Escape Potential After 13-Valent Pneumococcal Conjugate Vaccine Introduction. The Journal Of Infectious Diseases 2024, jiae040. PMID: 38530917, DOI: 10.1093/infdis/jiae040.Peer-Reviewed Original ResearchClonal expansionSequence typingAntimicrobial resistanceSusceptibility to opsonophagocytic killingWhole-genome sequencingStreptococcus pneumoniae serotype 3Serotype 3Post-PCV13 introductionNext-generation pneumococcal vaccinesPneumococcal conjugate vaccine introductionVaccine escapeConjugate vaccine introductionPneumococcal conjugate vaccineIncreased antimicrobial resistancePolysaccharide biosynthesisPhylogenetic reconstructionSequencing projectsLocus sequencesCapsule locusSequence clustersGenomic surveillanceOpsonophagocytic killingPhenotypic characteristicsVaccine introductionConjugate vaccine
2023
Development of an amplicon-based sequencing approach in response to the global emergence of mpox
Chen N, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak C, Sevinsky J, Libuit K, Park D, Hemarajata P, Garrigues J, Green N, Sierra-Patev S, Carpenter-Azevedo K, Huard R, Pearson C, Incekara K, Nishimura C, Huang J, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes J, Aquino C, Savino I, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa H, McHugh M, Maloney D, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton K, Churchwell G, Lee P, Pedrosa M, McGruder B, Schmedes S, Plumb M, Wang X, Barcellos R, Godinho F, Salvato R, Ceniseros A, Breban M, Grubaugh N, Gallagher G, Vogels C. Development of an amplicon-based sequencing approach in response to the global emergence of mpox. PLOS Biology 2023, 21: e3002151. PMID: 37310918, PMCID: PMC10263305, DOI: 10.1371/journal.pbio.3002151.Peer-Reviewed Original ResearchConceptsPublic health laboratoriesHealth laboratoriesSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Monkeypox virusRespiratory syndrome coronavirus 2Ongoing coronavirus disease 2019 (COVID-19) pandemicAnatomical body sitesAtypical clinical presentationCoronavirus disease 2019 (COVID-19) pandemicSyndrome coronavirus 2Course of infectionDisease 2019 pandemicRapid outbreak responseWhole-genome sequencingHuman monkeypox virusCT valuesClinical presentationViral loadCoronavirus 2Viral DNA concentrationsPathogen whole-genome sequencingZika virusClinical specimensBody sites
2022
Evaluation of Dried Blood and Cerebrospinal Fluid Filter Paper Spots for Storing and Transporting Clinical Material for the Molecular Diagnosis of Invasive Meningococcal Disease
Kwambana-Adams B, Clark S, Tay N, Agbla S, Chaguza C, Kagucia E, Borrow R, Heyderman R. Evaluation of Dried Blood and Cerebrospinal Fluid Filter Paper Spots for Storing and Transporting Clinical Material for the Molecular Diagnosis of Invasive Meningococcal Disease. International Journal Of Molecular Sciences 2022, 23: 11879. PMID: 36233182, PMCID: PMC9569512, DOI: 10.3390/ijms231911879.Peer-Reviewed Original ResearchConceptsInvasive meningococcal diseaseMeningococcal diseaseNeisseria meningitidis infectionResource-limited settingsLow-resource settingsFilter paper spotsMeningococcal infectionReal-time PCRCerebrospinal fluidClinical specimensSubset of specimensBlood spotsSpot assayAntimicrobial resistanceBloodMolecular diagnosisClonal complexesClinical materialPaper spotsWhole-genome sequencingDBSInfectionSequence typesDiseaseDiagnosis
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
2015
Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome
Kulohoma BW, Cornick JE, Chaguza C, Yalcin F, Harris SR, Gray KJ, Kiran AM, Molyneux E, French N, Parkhill J, Faragher BE, Everett DB, Bentley SD, Heyderman RS. Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome. Infection And Immunity 2015, 83: 4165-4173. PMID: 26259813, PMCID: PMC4567637, DOI: 10.1128/iai.00814-15.Peer-Reviewed Original ResearchConceptsBloodstream infectionsSterile sitesPneumococcal population structureDisease manifestationsMeningitisVaccine candidatesS. pneumoniaeStreptococcus pneumoniaeNasopharyngeal commensalPneumococciVirulence factorsWhole-genome sequencingInfectionPneumoniaeVirulence behaviorPresence/absenceIsolatesMeninges