Occurrence, genomic diversity, antimicrobial resistance and virulence profile of Campylobacter spp. from children, an abattoir and butcher shops in central Ethiopia

Abstract Background Campylobacter spp. are significant contributors to global diarrheal disease and are associated with severe infection in children in low- and middle-income countries. In Ethiopia, campylobacteriosis may be underreported due to limited data, diagnostic capacity and coordinated surveillance. This study assessed the occurrence, genomic diversity, antimicrobial resistance (AMR) and virulence profiles of Campylobacter spp. from diarrheic children and abattoir sources. Methods A cross-sectional investigation was conducted from November 2023 to September 2024 in Addis Ababa, Ethiopia. In total, 660 samples were collected from a beef abattoir ( n = 192), beef butcher shops ( n = 84) and children at a health center ( n = 384) and analyzed according to ISO 10272-1:2017. Isolates were identified using MALDI-TOF MS, tested for AMR by disc diffusion and sequenced. Results Campylobacter spp. were detected in 9.9% (38/384) of pediatric stools and 6.3% (12/192) of abattoir samples, mainly in cattle feces (14.6%) and beef carcasses (8.3%). Campylobacter jejuni predominated, while C. coli and C. fetus were detected only in children. Whole-genome analysis of 20 isolates showed substantial genetic diversity, identifying eight sequence types (STs) belonging to seven clonal complexes (CCs), plus four isolates with novel alleles. The most common were ST460 and ST1365, and CC443 and CC460. The occurrence of C. jejuni in cattle feces, carcasses and humans with similar STs and small genetic differences is consistent with carcass contamination during slaughter and a possible link to human infection or exposure to the same sources, although transmission was not established. Two human isolates belonged to CC21 and two cattle feces and carcass isolates to CC206, both generalist lineages able to colonize many hosts. Resistance was high for tetracycline (95.7%), ciprofloxacin (70.2%) and erythromycin (61.7%), and 66.0% of isolates were multidrug resistant. Among 18 C. jejuni genomes, cme ABC (100%), OXA-family β-lactamase genes (78%), tet genes (56%), gyrA T86I (33%) and rplV A103V (56%) were detected. Virulence genes for motility, adhesion, invasion and toxin production were broadly conserved. Conclusion Genetically diverse and AMR Campylobacter circulates among children and abattoir sources in Addis Ababa, with possible carcass contamination and potential for human exposure. This highlights the importance of strengthened hygiene, careful antimicrobial use and integrated One Health genomic surveillance. Clinical trial number N/A.