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Background   Ornithobacterium  ( O. )  rhinotracheale  is an emerging bacterial pathogen in poultry and not fully understood to date. Because of its importance particularly for the global turkey meat industry, reliable diagnostic and characterization methods are needed for early treatment and in future for better vaccine production. The host range of birds infected by  O. rhinotracheale  or carrying the bacterium in their respiratory tract has constantly increased raising important epidemiological and taxonomic questions for a better understanding of its diversity, ecology and transmission cycles. The purpose of this study was to introduce partial  rpoB  gene sequencing for  O. rhinotracheale  into routine diagnostics to differentiate strains isolated from poultry and more diverse avian hosts (i.e., birds of prey, corvids and pigeons) and to compare phylogenetic relationships with results from 16S rRNA gene analysis and multilocus sequence typing (MLST).    Results  Partial 16S rRNA gene analysis revealed a high level of homogeneity among the 65 investigated  O. rhinotracheale  sequences with similarity values ranging from 98.6 to 100% between sequences from non-galliform and poultry species. The corresponding  rpoB  gene sequences were heterogeneous and ranged in their similarity values from 85.1 to 100%. The structure of the  rpoB  tree was in strong correlation with previous MLST results revealing three main clusters A (poultry and birds of prey), B (poultry, birds of prey and corvids) and C (pigeons), which were clearly separated from each other.    Conclusions  By using partial sequences from a single gene, the  rpoB  gene analysis is in good agreement with MLST results with a slight decrease in resolution to distinguish more similar strains. The present results provide strong evidence that traditional phenotypic and genetic methods may not properly represent the heterogeneous group of bacteria classified as  O. rhinotracheale . From housekeeping gene analyses, it is very likely that the genus  Ornithobacterium  includes additional species and partial  rpoB  gene sequencing can be recommended as fast, cost-effective and readily available method to identify strains and differentiate between  O. rhinotracheale  and  Ornithobacterium -like bacteria.

Phylogenetic relationship of Ornithobacterium rhinotracheale isolated from poultry and diverse avian hosts based on 16S rRNA and rpoB gene analyses