Genome-resolved metagenomics of Campylobacter at a wildlife–livestock–human interface in Uganda reveals novel species

Campylobacter species are leading causes of gastroenteritis globally, but their diversity and transmission dynamics at wildlife–livestock–human interfaces are poorly understood. We investigated Campylobacter diversity across sympatric mountain gorillas, livestock, and humans in Uganda. We analysed 553 faecal samples from humans (n=197), mountain gorillas (n=200), cattle (n=83), and goats (n=73). Human samples were collected from healthcare patients and community volunteers. We used metagenomic shotgun sequencing to reconstruct Campylobacter metagenome-assembled genomes (MAGs). We assembled 44 MAGs representing seven Campylobacter species, including three novel species from gorilla gut microbiomes. The others belonged to provisionally designated species C. sp017646085 (cattle) and C. sp900539255 (humans) and known C. vicugnae (goats) and Candidatus C. infans (humans). C. sp900539255 was significantly enriched in healthcare-based human samples (p=0·001), whereas C. infans was common and showed no abundance differences between healthcare and community-based human samples, suggesting limited clinical significance.