Whole-genome sequencing and genomic characterization of Riemerella anatipestifer strain RA-NM from China

Riemerella anatipestifer infection is a major disease in waterfowl. Here, we characterized a virulent serotype 2 strain, RA-NM. It was resistant to kanamycin, amikacin, gentamicin, streptomycin, lomefloxacin, and polymyxin B, consistent with six detected resistance genes (tet (X4), erm(F), aadS, bla_OXA-209, ranA, ranB). The median lethal dose was 10³ colony forming units. Whole-genome sequencing revealed a 2.12 Mb circular chromosome with 1953 genes, 9 rRNA operons, 40 tRNAs, 14 CRISPRs, and 4 genomic islands. Phylogenomic analysis based on single-copy orthologs showed RA-NM clusters closely with RA-CH-1 and RA-GD. Virulence profiling identified 77 virulence genes, and heatmap comparison across nine strains revealed 12 variably distributed genes, with RA-NM lacking six, indicating strain-specific virulence traits. Pangenome analysis of nine R. anatipestifer genomes identified 3023 genes, of which 43% were core genes and the remainder formed a large accessory gene pool. No soft-core genes were detected, highlighting clear separation between conserved and variable genes and extensive genomic plasticity. Overall, this study provides a comprehensive phenotypic and genomic characterization of RA-NM, offering insights into its antimicrobial resistance, virulence, pangenome structure, and evolutionary background, serving as a foundation for future studies on R. anatipestifer pathogenicity.