Chrispin Chaguza

Postdoctoral Associate




Dr. Chaguza is a Postdoctoral Associate in the Department of Epidemiology of Microbial Diseases at the Yale School of Public Health, Yale University. His research focuses on using large genomic and epidemiological datasets of microbial pathogens to understand pathogenesis, molecular evolution, the genetic basis of phenotypes, antimicrobial resistance, transmission, and epidemiology to inform public health – disease control and prevention. His current research primarily focuses on bacterial pathogens, including Streptococcus pneumoniae, Group B Streptococcus, Group A Streptococcus, and Enterococcus species and viral pathogens of public health importance, including but not limited to SARS-CoV-2, dengue, and West Nile viruses. He is keen to collaborate on microbial genomics projects.

Preferred Pronouns


Personal Academic Website

Research/Topics of Interest

Agent-based models
Antibiotic resistance
Apply models to public health
Between-host modeling
Compartmental models
Geospatial models
Intra-host modeling
Machine learning models
Network models
New methods development
Outbreak science
Phylogenetic models
Public health application of models
Social determinants of health
Social networks/contact patterns
Spatial transmission patterns
Statistical models
Time-series models
Molecular evolution
Within-host evolution
Population structures
Pathogen genomics
Comparative genomics
Genomic epidemiology
Antimicrobial resistance

Pathogens/Diseases of Main Interest/Expertise

Diarrheal diseases
Human Immunodeficiency Virus (HIV)
Pandemic influenza
Respiratory diseases
Season influenza
Tuberculosis (TB)
Vaccine-preventable diseases
Vector-borne diseases
Streptococcus pneumoniae

Countries of Work/Collaboration

United States
United Kingdom
South Africa



Chaguza C, Jamrozy D, Bijlsma MW, Kuijpers TW, van de Beek D, van der Ende A, Bentley SD. (2022). Population genomics of Group B Streptococcus reveals the genetics of neonatal disease onset and meningeal invasion. Nature communications, 13(1)

Chaguza C, Ebruke C, Senghore M, Lo SW, Tientcheu PE, Gladstone RA, Tonkin-Hill G, Cornick JE, Yang M, Worwui A, McGee L, Breiman RF, Klugman KP, Kadioglu A, Everett DB, Mackenzie G, Croucher NJ, Roca A, Kwambana-Adams BA, Antonio M, Bentley SD. (2022). Comparative genomics of disease and carriage serotype 1 pneumococci. Genome biology and evolution

Tonkin-Hill G, Ling C, Chaguza C, Salter SJ, Hinfonthong P, Nikolaou E, Tate N, Pastusiak A, Turner C, Chewapreecha C, Frost SDW, Corander J, Croucher NJ, Turner P, Bentley SD. (2022). Pneumococcal within-host diversity during colonization, transmission and treatment. Nature microbiology

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. (2022). Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Med (New York, N.Y.)

Kwambana-Adams BA, Clark SA, Tay N, Agbla S, Chaguza C, Kagucia EW, Borrow R, Heyderman RS. (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. International journal of molecular sciences, 23(19)

Senghore M, Chaguza C, Bojang E, Tientcheu PE, Bancroft RE, Lo SW, Gladstone RA, McGee L, Worwui A, Foster-Nyarko E, Ceesay F, Okoi CB, Klugman KP, Breiman RF, Bentley SD, Adegbola R, Antonio M, Hanage WP, Kwambana-Adams BA. (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. Microbial genomics, 8(2)

Belman S, Chaguza C, Kumar N, Lo S, Bentley SD. (2022). A new perspective on ancient Mitis group streptococcal genetics. Microbial genomics, 8(2)

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