Serotyping, molecular typing, and vaccine protein screening for Riemerella anatipestifer: overcoming challenges in prevention and treatment

Abstract

Abstract Background Riemerella anatipestifer affects the duck farming industry worldwide, causing substantial economic losses. Disease prevention and treatment mainly rely on vaccines and antibiotics; however, the large number of serotypes and increasing resistance of R. anatipestifer have caused great difficulties in preventing and treating the infection. Results Serotyping and molecular typing of 51 strains of R. anatipestifer was performed. We predicted vaccine proteins based on pan-genome analysis and via cross-immune protection potential. Rabbits were immunized with antigens, and nine serotyped sera were prepared, which were submitted to peer experts for serotype identification; six serotypes with two unformed strains were identified. The results for the self-made serotypes were consistent with those obtained from the externally submitted strains. Pan-genome analysis was carried out on 51 strains of R. anatipestifer, and an open pan-genome set of 5,094 genes was constructed. COG annotation classification revealed that the core and non-core genomes had apparent differences in gene function. Of the 51 strains of R. anatipestifer isolates, 18 belonged to the 3 previously known serotypes, and the 33 represented newly identified serotypes, totaling 13 species. The clustering analysis demonstrated a significant genetic variation at the gene level among the housekeeping genes of R. anatipestifer. The pan-genome phylogenetic tree demonstrated that the 51 strains of R. anatipestifer could be roughly divided into 8 branches, each with a similar unique gene distribution and biological characteristics. The core gene tree showed that the 51 strains of R. anatipestifer could be divided into 6 major branches and that the strains from the same region had a clustered distribution in the evolutionary tree, forming multiple geographic subpopulations. This information served as a guide for dividing the strains into smaller geographic subgroups. Five genes of interest were screened from 1,116 core genomes that have the potential to serve as better cross-protective vaccine proteins. Conclusions Fills the gaps in the existing typing systems for Riemerella anatipestifer by utilizing a combination of serotyping, MLST typing, and pan-genome analysis, it provided valuable insights into the epidemiology, evolution, and pathogenesis of this bacterium. Our research not only enhances our understanding of Riemerella anatipestifer but also paves the way for the development of effective cross-protective vaccines.