Genomic characterization of Aliarcobacter spp. from livestock in commercial and smallholder farms and from children in Ghana and Tanzania

Background Aliarcobacter spp. are emerging foodborne pathogens posing public health risks through zoonotic transmission in agricultural settings. Characterizing their phylogenetic relatedness, antimicrobial resistance (AMR), and virulence factors is critical for assessing their impact on food safety and health in Ghana and Tanzania. Methods We collected 144 Aliarcobacter isolates (139 from farm animals and 5 from human clinical cases) and analyzed their genomes using molecular phylogenetics, antimicrobial resistance gene (ARG) profiling, and virulence gene identification. Results Phylogenetic analysis confirmed Aliarcobacter butzleri as the predominant species with two distinct subclades exhibiting multiple drug resistance. Notably, we identified a second clade of Aliarcobacter lanthieri that may represent a novel species. Additionally, a potential new subspecies within A. butzleri was detected, supported by genomic and digital DNA:DNA hybridization (dDDH) analyses. A multiple antibiotic-resistant Aliarcobacter cryaerophilus isolate was found to harbor a resistance plasmid encoding five AMR genes. The pangenome reflected an open genome structure with a vast accessory gene pool related to resistance and virulence. ARGs conferring tetracycline, macrolide, and aminoglycoside resistance were widespread, with commercial farm isolates showing higher resistance burdens than those from smallholder farms. Virulence genes varied, illustrating broad genetic diversity and adaptive potential. Conclusions This study highlights genomic plasticity and emerging resistance in Aliarcobacter spp. from human and animal sources in sub-Saharan Africa. The discovery of new clades and a resistant plasmid underscore the need for enhanced One Health surveillance to control the spread and impact of these pathogens on public health and food safety.