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Chrispin Chaguza, PhD

Postdoctoral Associate

Contact Information

Chrispin Chaguza, PhD

Research Summary

My research focuses on the comparative genomics and epidemiology of microbial pathogens (bacteria and viruses) to understand pathogen evolution at population-level and within hosts, population structure, spatial and temporal distribution of strains, genetic determinants for antimicrobial resistance, virulence, and diseases. I undertake large-scale genomic analysis of high throughput next-generation sequencing data from microbial populations using bioinformatics and statistical approaches. My multidisciplinary research aims to bring together a wide range of skills, including but not limited to genomics, data science, epidemiology, and bioinformatics, working closely with epidemiologists, wet-lab and computational biologists, and clinicians. The overarching goal of my research is to understand how pathogens populations spread, evolve, and adapt to cause diseases in humans and animals to improve diagnosis and surveillance to inform disease prevention and control strategies.

Coauthors

Research Interests

Bacteria; Carrier State; Disease Outbreaks; Drug Resistance, Microbial; Opportunistic Infections; Phylogeny; Pneumococcal Infections; Pneumonia, Pneumococcal; Respiratory Tract Infections; Statistics as Topic; Streptococcal Infections; Virulence; Viruses; Meningitis, Bacterial; Molecular Epidemiology; Disease Transmission, Infectious; Sepsis; Evolution, Molecular; Computational Biology; Drug Resistance, Bacterial; Public Health Informatics; Host-Pathogen Interactions; Genome-Wide Association Study; Coinfection; Microbiota; Data Science; Vaccine-Preventable Diseases

Public Health Interests

Antibiotic Resistance; Disease Transmission; Global Health; Infectious Diseases; Respiratory Disease/Infections; Vaccines

Selected Publications

  • Complete Genome Sequence of Streptococcus pneumoniae Strain BVJ1JL, a Serotype 1 Carriage Isolate from Malawi.Betts M, Jarvis S, Jeffries A, Gori A, Chaguza C, Msefula J, Weight CM, Kwambana-Adams B, French N, Swarthout TD, Brown JS, Heyderman RS. Complete Genome Sequence of Streptococcus pneumoniae Strain BVJ1JL, a Serotype 1 Carriage Isolate from Malawi. Microbiology Resource Announcements 2021, 10: e0071521. PMID: 34591678, PMCID: PMC8483660, DOI: 10.1128/MRA.00715-21.
  • Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco.Nzoyikorera N, Diawara I, Fresia P, Maaloum F, Katfy K, Nayme K, Maaloum M, Cornick J, Chaguza C, Timinouni M, Belabess H, Zerouali K, Elmdaghri N. Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco. BMC Genomics 2021, 22: 39. PMID: 33413118, PMCID: PMC7792055, DOI: 10.1186/s12864-020-07316-0.
  • Pneumococcal Colonization and Virulence Factors Identified Via Experimental Evolution in Infection Models.Green AE, Howarth D, Chaguza C, Echlin H, Langendonk RF, Munro C, Barton TE, Hinton JCD, Bentley SD, Rosch JW, Neill DR. Pneumococcal Colonization and Virulence Factors Identified Via Experimental Evolution in Infection Models. Molecular Biology And Evolution 2021, 38: 2209-2226. PMID: 33502519, PMCID: PMC8136498, DOI: 10.1093/molbev/msab018.
  • Metagenomics for surveillance of respiratory pathogens.Carr VR, Chaguza C. Metagenomics for surveillance of respiratory pathogens. Nature Reviews. Microbiology 2021, 19: 285. PMID: 33707741, PMCID: PMC7950416, DOI: 10.1038/s41579-021-00541-8.
  • Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis.Kalizang'oma A, Chaguza C, Gori A, Davison C, Beleza S, Antonio M, Beall B, Goldblatt D, Kwambana-Adams B, Bentley SD, Heyderman RS. Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis. Microbial Genomics 2021, 7 PMID: 34550067, PMCID: PMC8715442, DOI: 10.1099/mgen.0.000622.
  • 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 AW, 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 PMID: 33033832, DOI: 10.1093/infdis/jiaa616.
  • 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 : An Official Publication Of The Infectious Diseases Society Of America 2020, 70: 1294-1303. PMID: 31094423, PMCID: PMC7768739, DOI: 10.1093/cid/ciz404.
  • Bacterial survival: evolve and adapt or perish.Chaguza C. Bacterial survival: evolve and adapt or perish. Nature Reviews. Microbiology 2020, 18: 5. PMID: 31748737, DOI: 10.1038/s41579-019-0303-5.
  • 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.
  • Bacterial 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.
  • Hypervirulent pneumococcal serotype 1 harbours two pneumolysin variants with differential haemolytic activity.Panagiotou S, Chaguza C, Yahya R, Audshasai T, Baltazar M, Ressel L, Khandaker S, Alsahag M, Mitchell TJ, Prudhomme M, Kadioglu A, Yang M. Hypervirulent pneumococcal serotype 1 harbours two pneumolysin variants with differential haemolytic activity. Scientific Reports 2020, 10: 17313. PMID: 33057054, PMCID: PMC7560715, DOI: 10.1038/s41598-020-73454-w.
  • Lower Density and Shorter Duration of Nasopharyngeal Carriage by Pneumococcal Serotype 1 (ST217) May Explain Its Increased Invasiveness over Other Serotypes.Bricio-Moreno L, Chaguza C, Yahya R, Shears RK, Cornick JE, Hokamp K, Yang M, Neill DR, French N, Hinton JCD, Everett DB, Kadioglu A. Lower Density and Shorter Duration of Nasopharyngeal Carriage by Pneumococcal Serotype 1 (ST217) May Explain Its Increased Invasiveness over Other Serotypes. MBio 2020, 11 PMID: 33293378, PMCID: PMC7733939, DOI: 10.1128/mBio.00814-20.
  • Using genomics to improve preparedness and response of future epidemics or pandemics in Africa.Chaguza C, Nyaga MM, Mwenda JM, Esona MD, Jere KC. Using genomics to improve preparedness and response of future epidemics or pandemics in Africa. The Lancet. Microbe 2020, 1: e275-e276. PMID: 33345202, PMCID: PMC7729821, DOI: 10.1016/S2666-5247(20)30169-5.
  • 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 2020, 8: 587730. PMID: 33489998, PMCID: PMC7820366, DOI: 10.3389/fped.2020.587730.
  • Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages.Musicha P, Msefula CL, Mather AE, Chaguza C, Cain AK, Peno C, Kallonen T, Khonga M, Denis B, Gray KJ, Heyderman RS, Thomson NR, Everett DB, Feasey NA. Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages. The Journal Of Antimicrobial Chemotherapy 2019, 74: 1223-1232. PMID: 30778540, PMCID: PMC6477993, DOI: 10.1093/jac/dkz032.
  • Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010-2018.Arana A, Jere KC, Chaguza C, Montes M, Alkorta M, Iturriza-Gomara M, Cilla G. Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010-2018. Infection, Genetics And Evolution : Journal Of Molecular Epidemiology And Evolutionary Genetics In Infectious Diseases 2019, 71: 67-75. PMID: 30905774, DOI: 10.1016/j.meegid.2019.03.016.
  • Emergence of Double- and Triple-Gene Reassortant G1P[8] Rotaviruses Possessing a DS-1-Like Backbone after Rotavirus Vaccine Introduction in Malawi.Jere KC, Chaguza C, Bar-Zeev N, Lowe J, Peno C, Kumwenda B, Nakagomi O, Tate JE, Parashar UD, Heyderman RS, French N, Cunliffe NA, Iturriza-Gomara M. Emergence of Double- and Triple-Gene Reassortant G1P[8] Rotaviruses Possessing a DS-1-Like Backbone after Rotavirus Vaccine Introduction in Malawi. Journal Of Virology 2018, 92 PMID: 29142125, PMCID: PMC5774894, DOI: 10.1128/JVI.01246-17.
  • The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1.Cornick JE, Tastan Bishop Ö, Yalcin F, Kiran AM, Kumwenda B, Chaguza C, Govindpershad S, Ousmane S, Senghore M, du Plessis M, Pluschke G, Ebruke C, McGee L, Sigaùque B, Collard JM, Bentley SD, Kadioglu A, Antonio M, von Gottberg A, French N, Klugman KP, Heyderman RS, Alderson M, Everett DB. The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1. Vaccine 2017, 35: 972-980. PMID: 28081968, PMCID: PMC5287219, DOI: 10.1016/j.vaccine.2016.12.037.
  • 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.
  • Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting.Musicha P, Feasey NA, Cain AK, Kallonen T, Chaguza C, Peno C, Khonga M, Thompson S, Gray KJ, Mather AE, Heyderman RS, Everett DB, Thomson NR, Msefula CL. Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting. The Journal Of Antimicrobial Chemotherapy 2017, 72: 1602-1609. PMID: 28333330, PMCID: PMC5437524, DOI: 10.1093/jac/dkx058.
  • Adaptation... that's what you need?Chaguza C, Bentley SD. Adaptation... that's what you need? Nature Reviews. Microbiology 2017, 15: 452. PMID: 28690321, DOI: 10.1038/nrmicro.2017.78.
  • 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.
  • Comparative Genomic Analysis and In Vivo Modeling of Streptococcus pneumoniae ST3081 and ST618 Isolates Reveal Key Genetic and Phenotypic Differences Contributing to Clonal Replacement of Serotype 1 in The Gambia.Bricio-Moreno L, Ebruke C, Chaguza C, Cornick J, Kwambana-Adams B, Yang M, Mackenzie G, Wren BW, Everett D, Antonio M, Kadioglu A. Comparative Genomic Analysis and In Vivo Modeling of Streptococcus pneumoniae ST3081 and ST618 Isolates Reveal Key Genetic and Phenotypic Differences Contributing to Clonal Replacement of Serotype 1 in The Gambia. The Journal Of Infectious Diseases 2017, 216: 1318-1327. PMID: 28968897, PMCID: PMC5853340, DOI: 10.1093/infdis/jix472.
  • Understanding pneumococcal serotype 1 biology through population genomic analysis.Chaguza C, Cornick JE, Harris SR, Andam CP, Bricio-Moreno L, Yang M, Yalcin F, Ousmane S, Govindpersad S, Senghore M, Ebruke C, Du Plessis M, Kiran AM, Pluschke G, Sigauque B, McGee L, Klugman KP, Turner P, Corander J, Parkhill J, Collard JM, Antonio M, von Gottberg A, Heyderman RS, French N, Kadioglu A, Hanage WP, Everett DB, Bentley SD. Understanding pneumococcal serotype 1 biology through population genomic analysis. BMC Infectious Diseases 2016, 16: 649. PMID: 27821148, PMCID: PMC5100261, DOI: 10.1186/s12879-016-1987-z.
  • Recombination 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 AW, 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 PMID: 27677790, PMCID: PMC5040112, DOI: 10.1128/mBio.01053-16.
  • Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae.Chaguza C, Cornick JE, Everett DB. Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae. Computational And Structural Biotechnology Journal 2015, 13: 241-7. PMID: 25904996, PMCID: PMC4404416, DOI: 10.1016/j.csbj.2015.03.007.
  • High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children.Kamng'ona AW, 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.
  • 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: 4165-73. PMID: 26259813, PMCID: PMC4567637, DOI: 10.1128/IAI.00814-15.
  • Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae.Cornick JE, Chaguza C, Harris SR, Yalcin F, Senghore M, Kiran AM, Govindpershad S, Ousmane S, Plessis MD, Pluschke G, Ebruke C, McGee L, Sigaùque B, Collard JM, Antonio M, von Gottberg A, French N, Klugman KP, Heyderman RS, Bentley SD, Everett DB, For The PAGe Consortium. Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae. Microbial Genomics 2015, 1: e000027. PMID: 28348812, PMCID: PMC5320570, DOI: 10.1099/mgen.0.000027.
  • Erratum for Betts et al., "Complete Genome Sequence of Streptococcus pneumoniae Strain BVJ1JL, a Serotype 1 Carriage Isolate from Malawi".Betts M, Jarvis S, Jeffries A, Gori A, Chaguza C, Msefula J, Weight CM, Kwambana-Adams B, French N, Swarthout TD, Brown JS, Heyderman RS. Erratum for Betts et al., "Complete Genome Sequence of Streptococcus pneumoniae Strain BVJ1JL, a Serotype 1 Carriage Isolate from Malawi". Microbiology Resource Announcements 2021, 10: e0098521. PMID: 34672715, PMCID: PMC8530034, DOI: 10.1128/MRA.00985-21.
  • A new perspective on ancient Mitis group streptococcal genetics.Belman S, Chaguza C, Kumar N, Lo S, Bentley SD. A new perspective on ancient Mitis group streptococcal genetics. Microbial Genomics 2022, 8 PMID: 35225216, PMCID: PMC8942026, DOI: 10.1099/mgen.0.000753.
  • Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons.Chaguza C, Coppi A, Earnest R, Ferguson D, Kerantzas N, Warner F, Young HP, Breban MI, Billig K, Koch RT, Pham K, Kalinich CC, Ott IM, Fauver JR, Hahn AM, Tikhonova IR, Castaldi C, De Kumar B, Pettker CM, Warren JL, Weinberger DM, Landry ML, Peaper DR, Schulz W, Vogels CBF, Grubaugh ND. Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Med (New York, N.Y.) 2022, 3: 325-334.e4. PMID: 35399324, PMCID: PMC8983481, DOI: 10.1016/j.medj.2022.03.010.
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