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Dr Ebenn Foster-Nyarko

Research Fellow

United Kingdom

I am a Research Fellow in Professor Kathryn Holt's group at the London School of Hygiene and Tropical Medicine, UK. My research focuses on computational genomics to elucidate the genetic determinants of antimicrobial resistance (AMR) and virulence in Klebsiella pneumoniae and Escherichia coli, with particular emphasis on improving phenotype prediction from genotypic data to enhance genomic surveillance. I hold a PhD in microbial genomics from the Quadram Institute Bioscience and Norwich Medical School at the University of East Anglia, UK. My doctoral research focused on understanding the within-host diversity of Escherichia coli in the vertebrate gut.

Previously, I worked as a Scientific Officer at the Medical Research Council Unit The Gambia at LSHTM, where I was involved in invasive bacterial disease surveillance in the WHO Regional Co-ordinating Centre headed by Professor Martin Antonio.

Beyond my research, I am honoured to serve as the Regional Coordinator for PulseNET Africa, a regional hub of PulseNET International. I also chair the African Pathogen Initiative's Foodborne Diseases Technical Focus Group, helping to shape the future of foodborne disease genomic surveillance in Africa. At LSHTM, I serve as the academic co-chair of the faculty EDI Committee, promoting an inclusive working environment. I also co-chair the Staff Research Forum and serve as the Early Career Researcher (ECR) representative on the School's Research Committee.

Affiliations

Department of Infection Biology
Faculty of Infectious and Tropical Diseases

Teaching

I help coordinate and teach the Short Course on Antimicrobial Resistance (AMR): a Multidisciplinary Approach. I deliver lectures and workshops on AMR and bacterial genomics for MSc modules in Pathogen Genomics, Bacteriology, and Virology. I also supervise and assess students undertaking research projects within the MSc Medical Microbiology module and the Infectious Diseases distance learning programme.

Research

My research interests centre on the application of computational genomics to understand the molecular basis of antimicrobial resistance and virulence in clinically important bacterial pathogens. I am particularly interested in elucidating how genomic variation translates into phenotypic outcomes, with a focus on improving the predictive accuracy of genomic surveillance for antimicrobial resistance and virulence. Much of my work has concentrated on Klebsiella pneumoniae and Escherichia coli, with emphasis on healthcare-associated and foodborne disease contexts across African settings.

I am committed to building capacity for genomic surveillance in resource-limited settings and to ensuring that the benefits of pathogen genomics are equitably distributed across the African continent. Beyond pathogen-specific research, I am interested in the broader questions of how within-host microbial diversity shapes disease outcomes and transmission dynamics, and how genomic approaches can enhance our understanding of epidemiological processes in complex transmission environments.

Research Area
Bacteria
Drug resistance
Surveillance
Bacteriology
Genomics
Microbiology

Selected Publications

(TO DELETE-DUPLICATE) Isolates and sequence data included in the study "Contribution of nosocomial transmission to Klebsiella pneumoniae neonatal sepsis in Africa and South Asia: An observational study of infection clusters inferred from pathogen genomics and temporal data"
Odih, EE; ABDULAHI, JA; Amulele, AV; Bates, M; Heinz, E; Hu, W; Jain, K; Magobo, R; Olwagen, CP; Tembo, JM; Sonda, T; Strysko, J; Tigoi, CC; Bittinger, K; Cornick, J; FOSTER-NYARKO, E; Gumbi, W; Jones, SM; Musyani, CL; McGann, CM; Moustafa, AM; Musicha, P; Mwansa, JC L; Ndumba, ML; Stanton, TD; ... HOLT, KE.
2026
PLOS Medicine
Contribution of nosocomial transmission to Klebsiella pneumoniae neonatal sepsis in Africa and South Asia: An observational study of infection clusters inferred from pathogen genomics and temporal data.
Odih, EE; ABDULAHI, JA; Amulele, AV; Bates, M; Heinz, E; Hu, W; Jain, K; Magobo, R; Olwagen, CP; Tembo, JM; Sonda, T; Strysko, J; Tigoi, CC; Bittinger, K; Cornick, J; FOSTER-NYARKO, E; Gumbi, W; Jones, SM; Musyani, CL; McGann, CM; Moustafa, AM; Musicha, P; Mwansa, JC L; Ndumba, ML; Stanton, TD; ... HOLT, KE.
2026
PLoS medicine
AMRgen: an R package for antimicrobial resistance genotype-phenotype analysis
HOLT, KE; Argimón, S; Chaput, DL; Couto, N; DYSON, ZA; FOSTER-NYARKO, E; Goodman, RN; Hawkey, J; KNIGHT, GM; Nagy, D; Prasad, AB; Sánchez-Busó, L; Tsang, KK; Berends, MS;
2026
bioRxiv
AMRverse/AMRgen
HOLT, KE; Berends, M; FOSTER-NYARKO, E; Hawkey, J; Karatsang,; Nagy, DA; DYSON, ZA; Prasad, A; Couto, N; Goodman, R; Claude,; Silargi,; Cuddihy, T;
2026
Zenodo
Molecular characterisation of a
<i>Klebsiella pneumoniae</i>
neonatal sepsis outbreak in a rural Gambian hospital: a retrospective genomic epidemiology investigation
FOSTER-NYARKO, E; Bah, A; Adefila, WO; OSEI, I; Barjo, O; Salaudeen, R; Able-Thomas, S; Jammeh, M; Nyassi, A; Odih, EE; HOLT, KE; Sesay, AK; MACKENZIE, G;
2026
openRxiv
Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing.
Sauerborn, E; White, RT; Kalteis, A-L; Gygax, D; FOSTER-NYARKO, E; Wantia, N; Gebhardt, F; Urban, L;
2026
Microbial genomics
Isolates and sequence data included in the study "Transmission dynamics of Klebsiella pneumoniae in a neonatal intensive care unit in Zambia before and after an infection control bundle"
PHILLIPS, LT; Bates, M; Coffin, SE; FOSTER-NYARKO, E; Kapasa, M; Machona, S; Mwananyanda, L; Mwansa, JC L; Musyani, CL; Tembo, JM; Egbe, FN; HOLT, KE; Hamer, DH;
2026
London School of Hygiene & Tropical Medicine
Transmission dynamics of Klebsiella pneumoniae in a neonatal intensive care unit in Zambia before and after an infection control bundle.
PHILLIPS, LT; Bates, M; Coffin, SE; FOSTER-NYARKO, E; Kapasa, M; Machona, S; Mwananyanda, L; Mwansa, JC L; Musyani, CL; Tembo, JM; Egbe, FN; HOLT, KE; Hamer, DH;
2026
PLOS global public health
Distribution of capsule and O types in Klebsiella pneumoniae causing neonatal sepsis in Africa and South Asia: A meta-analysis of genome-predicted serotype prevalence to inform potential vaccine coverage.
Stanton, TD; KEEGAN, SP; ABDULAHI, JA; Amulele, AV; Bates, M; Heinz, E; Hooda, Y; Hu, W; Jain, K; Kanwar, S; Magobo, R; Olwagen, CP; Tembo, JM; Sonda, T; Strysko, J; Tigoi, CC; Amin, SA; Bittinger, K; Cornick, J; FOSTER-NYARKO, E; Gumbi, W; Hotwani, A; Iqbal, N; Jones, SM; Kabir, F; ... HOLT, KE.
2026
PLoS medicine
Genomic diversity and antimicrobial resistance of Vibrio cholerae isolates from Africa: a PulseNet Africa initiative using nanopore sequencing to enhance genomic surveillance.
FOSTER-NYARKO, E; Able-Thomas, S; Adade, NE; Adade, R; Anne, JC B; Antwi, L; Bah, Y; Boateng, G; Carleton, H; Chaima, D; Chilengi, R; Coulibaly, KJ; Derra, FA; Didon, D; Dimuna, C; Dosso, M; Drammeh, MM; Ferjani, S; HOLT, KE; Jatta, R; Kalule, JB; Kanteh, A; Kette, HF; KHAN, D; Kouadio, NK N; ... Vubil, D.
2025
Microbial genomics
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