Whole-genome analysis of Ornithobacterium rhinotracheale from turkeys in Poland: Insights into global diversity, virulence, and antimicrobial resistance

Ornithobacterium rhinotracheale (ORT) is an emerging avian respiratory pathogen of global concern, causing significant economic losses, particularly in turkeys. Although its distribution is worldwide, genomic data from different geographic regions remain scarce, limiting understanding of its genetic diversity, virulence-associated features, and antimicrobial resistance profiles. In this study, we performed whole-genome sequencing of 49 O. rhinotracheale isolates recovered from respiratory tract and joint lesions during outbreaks of ornithobacteriosis in turkeys in Poland to characterize sequence types and explore the genomic diversity and the distribution of virulence- and resistance-associated genes. Comparative multilocus sequence typing revealed high genetic heterogeneity, including three novel sequence types (ST46, ST50, ST51), highlighting ongoing local diversification within a globally distributed pathogen. Whole-genome core single nucleotide polymorphism (SNP)–based phylogenetic analysis further resolved genetic relationships among isolates and identified major genomic clusters. Genomic profiling identified several virulence-associated genes and insertion sequences, including IS4351 and ISMlu9. Distinct resistance gene patterns observed between major STs (ST3, ST46) were observed. These findings provide new insights into the genomic diversity of O. rhinotracheale populations and contribute to a broader understanding of its epidemiology and antimicrobial resistance in poultry worldwide. • Whole-genome sequencing provides the first comprehensive genome-scale characterization of Polish O. rhinotracheale isolates. • Comparative genomic analyses reveal sequence type–specific distributions of virulence- and resistance-associated genes. • Previously underreported mobile genetic element families are identified across O. rhinotracheale lineages. • Stable maintenance of multidrug resistance determinants is observed in dominant and minor sequence types. • The study expands current knowledge of O. rhinotracheale population structure and genomic diversity in Europe