A phylogenetic landscape of Ornithobacterium rhinotracheale isolates from poultry in Iran presented based on 16S rRNA gene analysis.

Abstract

Ornithobacterium rhinotracheale (ORT) is one of the most important bacterial agents of respiratory diseases causing significant economic losses to the poultry industry. The partial 16S rRNA gene sequences of ORT isolates originating from different geographical areas in Iran have been deposited in the GenBank database from 2011 to the present. The objectivepresent study was to evaluate the molecular evolution of ORT isolates. to this end, a dataset comprising 16S rRNA gene sequences of 48 field strains derived from outbreaks on poultry farms and one reference strain was subjected to phylogenetic and evolutionary analysis using a series of substitution pattern homogeneity, nucleotide diversity, and neutrality assays. The phylogenetic tree, based on the 16S rRNA gene, revealed the presence of a large clade, designated as A, and a distinct clade B, which included six sequences derived from the recent ORT isolates. The majority of the isolates exhibited homogeneityand clustered together,irrespective of their geographical origin. The evolutionary inference indicated that a molecular divergence influences the genetic diversity of ORT isolates. The Tajima's D statistic yielded a negative value of -1.46, while the R-value for transition/transversion bias was 1.399. Additionally, the dN/dS ratio was estimated to be higher for clade B. These findings suggest that recent ORT isolates in Iran are subjected to increasing selection pressure on the 16S rRNA gene of recent ORT isolates in Iran. The phylogeny analysis and evolutionary affiliations of the ORT 16S rRNA gene are expected to prove effective in the monitoring of the strains for antibiotic resistance and selection pressure. These phylogenetic relationships have the potential to be determinative in the selection of the best vaccine candidate strain.