Chrispin Chaguza, PhD
Associate Research Scientist in Epidemiology (Microbial Diseases)Cards
Additional Titles
Affiliated Faculty, Yale Institute for Global Health
Contact Info
About
Titles
Associate Research Scientist in Epidemiology (Microbial Diseases)
Affiliated Faculty, Yale Institute for Global Health
Biography
Dr. Chaguza is an Associate Research Scientist in the Department of Epidemiology of Microbial Diseases at the Yale School of Public Health, Yale University. His research uses large genomic and epidemiological datasets of microbial pathogens (bacteria and viruses) to understand pathogenesis, molecular evolution, the genetic basis of phenotypes, antimicrobial resistance, transmission, and epidemiology to inform public health – disease control and prevention.
His research at Yale primarily focuses on understanding the evolution and epidemiology of viral pathogens of public health importance, including but not limited to SARS-CoV-2, rotavirus, monkeypox, and dengue virus. Beyond viruses, his research focuses on comparative genomics of bacterial pathogens, including but not limited to Streptococcus pneumoniae, Streptococcus agalactiae (Group B Streptococcus), Staphylococcus aureus, and Enterococcus species. He is also keen to collaborate on microbial genomics projects within and outside Yale.
Appointments
Epidemiology of Microbial Diseases
Associate Research ScientistPrimary
Other Departments & Organizations
Education & Training
- PhD
- The University of Liverpool, Infection and Immunity (2018)
- MSc
- The University of Manchester, Bioinformatics and Systems Biology (2012)
- BSc
- The University of Malawi, Computer Science and Statistics (2010)
Research
Overview
Medical Subject Headings (MeSH)
ORCID
0000-0002-2108-1757
Research at a Glance
Yale Co-Authors
Publications Timeline
Research Interests
Chantal Vogels, PhD
Nathan Grubaugh, PhD
Bony De Kumar, PhD
Akiko Iwasaki, PhD
Wade Schulz, MD, PhD
David Ferguson
Pneumococcal Infections
Phylogeny
Virulence
Carrier State
Evolution, Molecular
Genome-Wide Association Study
Publications
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 ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsPopulation 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 diseaseRecombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule
Chaguza C, Andam CP, Harris SR, Cornick JE, Yang M, Bricio-Moreno L, Kamng’ona A, Parkhill J, French N, Heyderman RS, Kadioglu A, Everett DB, Bentley SD, Hanage WP. Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule. MBio 2016, 7: e01053-16. PMID: 27677790, PMCID: PMC5040112, DOI: 10.1128/mbio.01053-16.Peer-Reviewed Original ResearchCitationsAltmetricConceptsPneumococcal conjugate vaccineInvasive pneumococcal diseasePrevalence of carriageCarriage durationCarriage prevalenceComplex polysaccharide capsulePolysaccharide capsuleVaccine escape variantsSerotype-specific responsesDifferent pneumococcal serotypesResource-poor settingsLonger carriage durationPneumococcal diseaseConjugate vaccinePneumococcal serotypesEscape variantsUnivariate analysisHigh burdenMultivariate analysisStreptococcus pneumoniaeDrug resistanceClinical interventionsPneumococciPrevalenceVaccineWithin-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 ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsNatural colonisationHost microevolutionNucleotide substitution ratesWhole-genome sequencingGenomic evolutionNeutral evolutionGenetic diversityHomologous recombinationParallel evolutionGenomic changesAdhesion genesSubstitution ratesHuman-adapted pathogenMicroevolutionStrain variantsColonisationImmune evasionStreptococcus pneumoniaeAntibiotic resistanceGenesEvolutionSequencingDiversityNasopharyngeal carriageBacteria
2024
Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study
Thorpe H, Pesonen M, Corbella M, Pesonen H, Gaiarsa S, Boinett C, Tonkin-Hill G, Mäklin T, Pöntinen A, MacAlasdair N, Gladstone R, Arredondo-Alonso S, Kallonen T, Jamrozy D, Lo S, Chaguza C, Blackwell G, Honkela A, Schürch A, Willems R, Merla C, Petazzoni G, Feil E, Cambieri P, Thomson N, Bentley S, Sassera D, Corander J. Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study. The Lancet Microbe 2024, 100890. PMID: 39178869, DOI: 10.1016/s2666-5247(24)00113-7.Peer-Reviewed Original ResearchAltmetricConceptsIntensive care unitProspective cohort studyCohort studyHospital transmissionWhole-genome sequencingCare unitDeep sequencing approachSingle nucleotide polymorphism distancesNosocomial bacterial pathogensInfection control measuresAntimicrobial resistance genesPathogenic speciesBacterial pathogensDeep sequencingEffectiveness of infection control measuresAntimicrobial resistance genes prevalenceAcinetobacter baumanniiNosocomial infectionsStreptococcus pneumoniaeSan Matteo HospitalClinical surveillanceWithin-patientKlebsiella pneumoniaeCo-colonisationGene prevalenceGenomic insights into the 2022–2023Vibrio cholerae outbreak in Malawi
Chaguza C, Chibwe I, Chaima D, Musicha P, Ndeketa L, Kasambara W, Mhango C, Mseka U, Bitilinyu-Bangoh J, Mvula B, Kipandula W, Bonongwe P, Munthali R, Ngwira S, Mwendera C, Kalizang’oma A, Jambo K, Kambalame D, Kamng’ona A, Steele A, Chauma-Mwale A, Hungerford D, Kagoli M, Nyaga M, Dube Q, French N, Msefula C, Cunliffe N, Jere K. Genomic insights into the 2022–2023Vibrio cholerae outbreak in Malawi. Nature Communications 2024, 15: 6291. PMID: 39060226, PMCID: PMC11282309, DOI: 10.1038/s41467-024-50484-w.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsSerogroup O1 strainsIntegrative conjugative elementsPhylogenetic reconstructionPopulation genomicsGenomic insightsOutbreak isolatesVirulence elementsConjugative elementsO1 strainsVibrio choleraeOutbreak strainEl TorAntimicrobial resistanceCholera outbreaksO1 OgawaIsolatesCholeraStrainCtxB7 genotypesProphageGenomeVirulenceCtxB7SublineagesLineagesMolecular Epidemiology of Isoniazid-resistant M tuberculosis in Port-au-Prince, Haiti
Walsh K, Lee M, Chaguza C, Pamphile W, Royal G, Escuyer V, Pape J, Fitzgerald D, Cohen T, Ocheretina O. Molecular Epidemiology of Isoniazid-resistant M tuberculosis in Port-au-Prince, Haiti. Open Forum Infectious Diseases 2024, 11: ofae421. PMID: 39119477, PMCID: PMC11306977, DOI: 10.1093/ofid/ofae421.Peer-Reviewed Original ResearchAltmetricConceptsCulture-positive pulmonary tuberculosisIsoniazid-resistant isolatesHR-TBIsoniazid-resistant M. tuberculosisPulmonary tuberculosisIsoniazid resistanceMutations associated with INH resistanceTransmission clustersGenoType MTBDRplus assayINH-resistant isolatesIsoniazid-susceptible isolatesPhenotypic isoniazid resistanceRifampin-susceptible tuberculosisSingle nucleotide polymorphism distancesMolecular epidemiologyAssociated with poor treatment outcomesWhole-genome sequencingM. tuberculosisPutative transmission clustersPoor treatment outcomesMTBDRplus assayGenoType MTBDRplusCulture-based testsINH resistanceTuberculosis clinicGenetic 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 ResearchAltmetricConceptsGroup 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 groupsExpansion 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 ResearchAltmetricMeSH Keywords and ConceptsConceptsGenes 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 mutationVirulenceMetagenomics to improve infectious disease diagnostics in low- and middle-income countries
Jamiu A, Chaguza C. Metagenomics to improve infectious disease diagnostics in low- and middle-income countries. Nature Microbiology 2024, 9: 1150-1151. PMID: 38714760, DOI: 10.1038/s41564-024-01681-2.Peer-Reviewed Original ResearchAltmetricDengueSeq: 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 ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsAmplicon 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-specific
Academic Achievements & Community Involvement
honor International Symposium on the Pneumococcus and Pneumococcal Diseases Travel Award
International AwardInternational Symposium on the Pneumococcus and Pneumococcal Diseases (ISPPD)Details03/15/2024honor Robert Austrian Research Awards in Pneumococcal Vaccinology
International AwardInternational Symposium on the Pneumococcus and Pneumococcal Diseases (funded by Pfizer)Details04/14/2022United Kingdomhonor Malawi-Liverpool-Wellcome Clinical Research Programme Annual Conference Best Oral Poster Presentation
International AwardMalawi-Liverpool-Wellcome Clinical Research Programme (A Wellcome Trust Major Overseas Programme)Details09/01/2015Malawihonor Commonwealth Full PhD Scholarship
International AwardUK Foreign, Commonwealth & Development OfficeDetails12/03/2014United Kingdomhonor International Symposium on the Pneumococcus and Pneumococcal Diseases Travel Award
International AwardInternational Symposium on the Pneumococcus and Pneumococcal Diseases (ISPPD)Details12/20/2013Malawi
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