Characterization of the Chicken-Derived Riemerella anatipestifer Strains in Beijing and Fujian Provinces, China

Riemerella anatipestifer is an infectious pathogen that mainly affects waterfowl such as ducks and geese. Recently, it is becoming increasingly prevalent in chicken flocks in China. In this study, we isolated 12 strains of R. anatipestifer from chickens with clinical signs in Beijing and Fujian Provinces, China. Serotyping indicated five strains from Fujian Province belonged to serotype 1, two strains from Beijing belonged to serotype 10, and five strains from Fujian Province were not assigned to serotypes 1-13. All the 12 strains exhibited high rates of resistance to amikacin, gentamicin, kanamycin, norfloxacin, and polymyxin B and low virulence to healthy chicks and ducklings. Chicks and ducklings in experimental infection groups showed temporary depression and decreased appetite within 2 days after infection with any of the 12 strains. Furthermore, we selected RA-FJ-C1 (serotype 1), RA-FJ-C4 (untypable by serotypes 1-13 primers), and RA-BJ-C1 (serotype 10) strains for whole genome sequencing and predicted genes related to virulence, antimicrobial resistance, and pathogen-host interactions. Comparative genomic analysis demonstrated that RA-FJ-C1, RA-FJ-C4, and RA-BJ-C1 harbored 399, 151, and 149 strain-specific genes, as well as 10, 9, and 1 unique virulence genes, respectively. There were seven and eight strain-specific virulence genes in serotype 1 strains CH3 and RA-FJ-C1, respectively, whereas nine and 15 specific virulence genes were identified in serotype 10 strains HXb2 and RA-BJ-C1. Moreover, most of these virulence genes were associated with capsules, lipopolysaccharide (LPS), or lipooligosaccharide (LOS). Colinearity analysis revealed that the gene arrangements of the genomes RA-FJ-C1, RA-FJ-C4, and RA-BJ-C1 were more similar to those of the Yb2 and JN1 strains, while it differed significantly from that of S63 and HXb2 strains. These findings provide a supplement to the limited study of R. anatipestifer from chicken; enhance our understanding of its prevalent serotype, drug resistance, and pathogenicity; and provide scientific foundation for the treatment and control of the disease.