Chrispin Chaguza, PhD
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Affiliated Faculty, Yale Institute for Global Health
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Associate Research Scientist in Epidemiology (Microbial Diseases)
Affiliated Faculty, Yale Institute for Global HealthBiography
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
- Epidemiology of Microbial Diseases
- Yale School of Public Health
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)
Bacteria; Carrier State; Computational Biology; Data Science; Disease Outbreaks; Disease Transmission, Infectious; Drug Resistance, Bacterial; Drug Resistance, Microbial; Evolution, Molecular; Genome-Wide Association Study; Microbiota; Molecular Epidemiology; Opportunistic Infections; Phylogeny; Pneumococcal Infections; Pneumonia, Pneumococcal; Public Health Informatics; Respiratory Tract Infections; Statistics as Topic; Streptococcal Infections; Vaccine-Preventable Diseases; Virulence; Viruses
ORCID
0000-0002-2108-1757
Research at a Glance
Yale Co-Authors
Frequent collaborators of Chrispin Chaguza's published research.
Publications Timeline
A big-picture view of Chrispin Chaguza's research output by year.
Research Interests
Research topics Chrispin Chaguza is interested in exploring.
Chantal Vogels, PhD
Nathan Grubaugh, PhD
Chikondi Peno
Bony De Kumar, PhD
Akiko Iwasaki, PhD
Wade Schulz, MD, PhD
61Publications
975Citations
Pneumococcal Infections
Phylogeny
Carrier State
Virulence
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
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 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-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 ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsDengue virusDENV-3Rates of severe diseaseMosquito-borne viral diseasePublic health threatPattern of spreadSevere diseaseLocal surveillanceGenomic epidemiologyEpidemiological patternsVirus surveillanceSurveillanceHealth threatSerotypesDiseaseIncreased rateDengueViral diseasesVirusInfected travelersFrequent outbreaksIntranasal neomycin evokes broad-spectrum antiviral immunity in the upper respiratory tract
Mao T, Kim J, Peña-Hernández M, Valle G, Moriyama M, Luyten S, Ott I, Gomez-Calvo M, Gehlhausen J, Baker E, Israelow B, Slade M, Sharma L, Liu W, Ryu C, Korde A, Lee C, Monteiro V, Lucas C, Dong H, Yang Y, Initiative Y, Gopinath S, Wilen C, Palm N, Dela Cruz C, Iwasaki A, Vogels C, Hahn A, Chen N, Breban M, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W, Grubaugh N. Intranasal neomycin evokes broad-spectrum antiviral immunity in the upper respiratory tract. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2319566121. PMID: 38648490, PMCID: PMC11067057, DOI: 10.1073/pnas.2319566121.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and ConceptsConceptsInterferon-stimulated genesRespiratory infectionsStrains of influenza A virusTreatment of respiratory viral infectionsRespiratory virus infectionsInfluenza A virusMouse model of COVID-19Respiratory viral infectionsNeomycin treatmentExpression of interferon-stimulated genesUpper respiratory infectionInterferon-stimulated gene expressionLower respiratory infectionsBroad spectrum of diseasesAdministration of neomycinRespiratory viral diseasesDisease to patientsUpper respiratory tractIntranasal deliveryCongenic miceIntranasal applicationNasal mucosaSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2A virusClonal 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 ResearchAltmetricConceptsClonal 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
Academic Achievements and 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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350 George Street, Fl 3
New Haven, CT 06511