Recent emergence of a multidrug-resistant Campylobacter coli lineage linked to poultry intensification in the Peruvian Amazon

Abstract Campylobacter is a leading cause of bacterial gastroenteritis worldwide, with the highest burden among children in low- and middle-income countries (LMICs). Despite global significance, Campylobacter coli remains comparatively under-studied. Here we combine population genomics and phylodynamic analysis of 460 C. coli genomes from the Peruvian Amazon to investigate the emergence of a locally dominant, multidrug-resistant lineage. Genomes were obtained from children with gastroenteritis (n = 136) and asymptomatic carriage (n = 163) in Iquitos, Peru, alongside isolates from poultry in backyard (n = 29) and industrial systems (n = 60), pigs (n = 36), cattle (n = 15), and a small reference collection (n = 21). These genomes represented 102 multilocus sequence types (STs) spanning five distinct clonal complexes (CCs). The globally distributed ST-828 clonal complex accounted for most isolates, whereas a distinct lineage, ST-1150 CC, was significantly over-represented in paediatric diarrhoeal cases yet rare elsewhere globally. Time-scaled phylogenies showed that ST-1150 CC emerged and expanded rapidly from the 1980s, coinciding with intensification of poultry production in the region. Genomic antimicrobial-resistance profiling identified extensive acquired resistance to fluoroquinolones, macrolides, and tetracyclines, underpinned by conserved cmeB efflux-pump variants. Collectively, these findings strongly suggest that agricultural intensification and antimicrobial exposure have driven the ecological emergence and clonal success of a highly adapted C. coli lineage. This work illustrates how regional farming practices can shape bacterial evolution and resistance trajectories, underscoring the need for integrated One Health genomic surveillance to mitigate the spread of zoonotic pathogens that are global in scope.