Mwakalapa, E. B. | Search bioRxiv

bioRxiv2026

Host breadth, genomic exchange and antimicrobial-resistance evolution in East African Campylobacter

Campylobacter jejuni and Campylobacter coli occupy diverse animal reservoirs, yet the genomic processes associated with variation in host breadth remain poorly resolved in East Africa. Publicly available isolate-level whole-genome sequencing data from Ethiopia, Kenya, Tanzania and Uganda were analysed using a standardized population-genomic workflow. After genome reconstruction, species confirmation and quality filtering, 722 genomes were retained, comprising 586 C. jejuni and 136 C. coli. Animal-host breadth among sufficiently represented Ethiopian C. jejuni lineages was standardized by exact rarefaction across chicken, cattle, goat and sheep hosts. Fifteen lineages were eligible for discovery analyses. Host breadth showed no detectable association with homologous recombination, accessory-genome fluidity, human representation, antimicrobial-resistance class burden, recurrent AMR evolution or regional recurrence. Six discovery lineages recurred outside Ethiopia, but only one occurred in at least two validation countries, and validation animal sampling was insufficient for inferential replication of host-breadth or AMR associations. Recurrent within-lineage AMR evolution was restricted to a small number of determinants, lineage combinations involving tet(O) and gyrA T86I. Analysis of complete single-copy loci identified a restricted set of strongly supported cross-species placements, providing evidence consistent with localized interspecies introgression without implying whole-genome admixture or transfer direction. These findings indicate that animal-host breadth in regional C. jejuni populations is not explained by simple lineage-wide measures of genome exchange, human occurrence or AMR burden, but instead reflects lineage-specific combinations of ecological opportunity, selected genomic variation and population history.

evolutionary biology↗

bioRxiv2026

African Campylobacter jejuni genomes reveal globally connected population structure and regionally variable resistance, virulence and mobilome profiles

Campylobacter jejuni is a leading foodborne cause of gastroenteritis, but genomic surveillance remains uneven across Africa. A recent East Africa study combined whole-genome sequencing and antimicrobial susceptibility testing for Campylobacter isolates from humans with diarrhea in Kenya and poultry in Tanzania, showing high sequence-type diversity and substantially higher multidrug resistance in poultry. We extended this regional evidence by analyzing 1,013 publicly available C. jejuni genomes, including 718 African and 295 non-African comparator genomes, with standardized assembly, genotyping, phylogenomics, pangenome reconstruction, antimicrobial resistance, virulence, and mobile-element profiling. African genomes were geographically concentrated but genetically diverse, included globally distributed and regionally enriched lineages, and showed an open pangenome dominated by low-frequency gene families. Resistance and virulence determinants were unevenly distributed by region and lineage. These findings place African C. jejuni diversity within a global evolutionary framework and support expanded, integrated One Health genomic surveillance. Data summaryAll genome sequence data analysed in this study were retrieved from publicly accessible repositories, including the National Center for Biotechnology Information Sequence Read Archive and Assembly resources and corresponding records available through the International Nucleotide Sequence Database Collaboration where applicable. Accession identifiers, BioSample records, run accessions, country metadata and host/source information for all analysed genomes are provided in the combined Supplementary Data workbook. No new sequence data were generated. The analysis used publicly available data generated by other investigators, and the original data-generating studies are cited where appropriate. Derived analytical outputs supporting the findings are included in the manuscript and Supplementary Information. Impact statementGenomic surveillance of Campylobacter jejuni remains uneven globally, and African data are still underrepresented in many comparative analyses. This study brings together publicly available African and non-African C. jejuni genomes in a single standardized comparative framework, linking population structure, pangenome composition, antimicrobial-resistance determinants, virulence-associated loci and mobile-element profiles. The work shows that African C. jejuni diversity is not peripheral to the global population: African genomes include globally distributed sequence types, regionally enriched lineages and a large accessory-gene repertoire. By separating genomic surveillance signals from population-representative prevalence claims, the study provides a cautious framework for interpreting public genome collections from settings with unequal sampling. The findings support broader One Health genomic surveillance, improved metadata completeness and geographically balanced sequencing to better understand foodborne transmission, resistance evolution and lineage diversification in this important zoonotic pathogen.

microbiology↗