Affiliation

Mary Njeri Chege

Fellowship

mchege@kipre.go.ke

Qualifications

PhD in Bioinformatics
University of Nairobi (doctoral research conducted in collaboration with the University of Notre Dame) · 2026 (Expected)
MSc in Bioinformatics and Molecular Biology
Jomo Kenyatta University of Agriculture and Technology · 2018
BSc in Biochemistry and Molecular Biology
Jomo Kenyatta University of Agriculture and Technology · 2013

Projects

Gut microbiome and antimicrobial resistance at the wildlife-livestock-human interface in the Amboseli ecosystem (2023-Present) - Doctoral research programme using shotgun metagenomics to characterize microbial communities, antimicrobial res…
Ongoing
Gut microbiome and antimicrobial resistance at the wildlife-livestock-human interface in the Amboseli ecosystem (2023-Present) - Doctoral research programme using shotgun metagenomics to characterize microbial communities, antimicrobial resistance genes, metagenome-assembled genomes, virulence factors, and potential ecological pathways of AMR exposure in wild baboons and livestock.
Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons (2023-2025) - First doctoral research study
Investigated variation in gut microbial eukaryotic communities across seasons and social groups using shotgun metagenomic data from the Amboseli Baboon Research Project. The study was published in Animal Microbiome in 2025.
Tick-borne pathogen surveillance in Northern Kenya (2023). Supported field collection, vector processing, and molecular screening of ticks for zoonotic pathogens across remote field sites.
Remote Emerging Disease Intelligence Network-REDI-NET (2022). Supported standardized field and laboratory workflows for detecting emerging pathogens at human-wildlife-livestock-environment interfaces in Laikipia County.
COVID-19 molecular detection and surveillance (2020-2022). Participated in high-throughput molecular diagnostics, clinical sample tracking, quality control, and management of testing data.
Bat-borne viral pathogen surveillance in Western Kenya (2020-2021). Contributed to wildlife sampling and molecular surveillance of coronaviruses and other viruses in cave-dwelling bats.
Diversity of cassava bacterial blight pathogens in Kenya (published in 2017). Characterized the phenotypic and genotypic diversity of Xanthomonas axonopodis pv. manihotis associated with cassava bacterial blight.

Publications

1.2026: Southworth CA, Winans JC, Gordon JB, Learn NH, Wilber WA, Andreadis C, Andreasen G, Arandjelovic M, Campbell CR, Chege MN, Creighton MJA, Cromer CM, Debray R, Dickson CC, Ferretti P, George EM, Gesquiere LR, He S, Hey L, Jefferson EE, Kulahci IG, Lerch BA, Nonnamaker L, Rivas-González I, Tuliozi B, Webb SE, Alberts SC, Archie EA, and Tung J. Demographic, behavioral, and ecological data from a long-term field study of wild baboons in Amboseli, Kenya. Scientific Data.
2.2025: Chege MN, Ferretti P, Webb S, Macharia RW, Obiero G, Kamau J, Alberts SC, Tung J, Akinyi M, and Archie EA. Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons. Animal Microbiome.
3.2024: Obanda V, Akinyi M, King’ori E, Nyakundi R, Ochola G, Oreng P, Mugambi K, Waiguchu GM, Chege MN, Rosenbaum W, Ylitalo EB, Bäck AT, Pettersson L, Mukunzi OS, Agwanda B, Stenberg-Lewerin S, and Lwande OW. Epidemiology and ecology of the sylvatic cycle of African swine fever virus in Kenya. Virus Research.
4.2022: Kamau J, Ergünay K, Webala PW, Justi SA, Bourke BP, Kamau MW, Hassell J, Chege MN, Mwaura DK, Simiyu C, Kibiwot S, Onyuok S, Caicedo-Quiroga L, Li T, Zimmerman DM, and Linton Y-M. A novel coronavirus and a broad range of viruses in Kenyan cave bats. Viruses.
5.2017: Chege MN, Wamunyokoli F, Kamau J, and Nyaboga EN. Phenotypic and genotypic diversity of Xanthomonas axonopodis pv. manihotis causing bacterial blight disease of cassava in Kenya. Journal of Applied Biology & Biotechnology.