Cross-country comparative genomics of Campylobacter jejuni in East Africa: A harmonized One Health comparative genomic re-analysis

Motivation Campylobacter jejuni is a major foodborne zoonotic pathogen associated with antimicrobial resistance (AMR), particularly in low- and middle-income countries with limited genomic surveillance. We analysed 225 publicly available C.jejuni genomes from Ethiopia, Kenya, and Tanzania using a harmonized whole-genome sequencing workflow within a One Health framework. Analyses included genome assembly, annotation, AMR and virulence gene screening, plasmid replicon and mobile genetic element detection, multilocus sequence typing (MLST), phylogenetic reconstruction, principal component analysis (PCA), and minimum spanning tree (MST) analysis. Results Using thresholds of ≥ 90% nucleotide identity and ≥60% gene coverage, blaOXA-193 was detected in 66.67% (150/225) of genomes, tet(O) in 18.22% (41/225), tet(O/32/O) in 4.00% (9/225), and blaOXA-61 in 1.33% (3/225). The gyrA T86I substitution occurred in 24.9% (56/225) of isolates. The applied screening approach detected no acquired macrolide resistance determinants. Virulence-associated gene profiles were broadly conserved, with variation in selected genes. Three known plasmid replicon types and prophage-associated intA hits were identified. Phylogenomic analysis revealed 65 sequence types and substantial genetic overlap between poultry- and human-associated isolates, indicating relatedness but not proving direct transmission. These findings highlight the importance of integrated One Health genomic surveillance for monitoring AMR and genomic diversity of C. jejuni in East Africa. Availability and implementation data underlying this article will be shared on reasonable request to the corresponding author