Genomic Epidemiology of Cholera Outbreaks in Nigeria: Transmission Dynamics and Implications for Public Health Control Strategies

Recurrent cholera outbreaks in Nigeria remain a critical public health emergency, yet the genomic epidemiology of Vibrio cholerae transmission dynamics across the country's ecologically and demographically diverse zones is incompletely characterised. This study applies whole-genome sequencing and phylogenomic analysis to reconstruct the transmission dynamics of cholera outbreaks across twelve Nigerian states between 2020 and 2024, examining importation events, inter-state spread, and molecular determinants of antimicrobial resistance. A retrospective genomic epidemiological study design is used, with 280 V. cholerae O1 El Tor biotype isolates collected from confirmed cholera cases in outbreak facilities across all six geopolitical zones. Whole-genome sequencing is performed using Illumina NovaSeq 6000, and bioinformatic pipelines including BEAST2 and Gubbins are applied for phylogenetic tree construction, Bayesian evolutionary analysis, and recombination detection. Antibiogram testing determines resistance profiles, with resistance gene identification through CARD analysis. Spatial-temporal mapping in ArcGIS traces transmission corridors. The Evolutionary Epidemiology Theory and One Health framework guide the integrative analytical approach. The study produces an original genomic database of Nigerian V. cholerae isolates and generates a validated Bayesian transmission model with direct public health control applications. Findings will inform the Nigeria Centre for Disease Control's National Cholera Multi-Year Plan by identifying high-risk transmission corridors and resistance hotspots requiring prioritised oral cholera vaccination and water system investment. Keywords: cholera, genomic epidemiology, Vibrio cholerae, transmission dynamics, Nigeria.