https://phaidra.vetmeduni.ac.at/o:4911 Genomic analysis reveals two dominant strains of Ornithobacterium rhinotracheale in Austria and Hungary with distinct multidrug resistance profiles Palmieri, Nicola Nicola Palmieri 0000-0002-6164-1843 University of Veterinary Medicine Vienna Hess, Claudia Claudia Hess 0000-0002-3535-5157 University of Veterinary Medicine Vienna Pollak, Boglarka Boglarka Pollak Magyar, Tibor Tibor Magyar Pinter, Krisztina Krisztina Pinter Doman, Marianna Marianna Doman Bilic, Ivana Ivana Bilic 0000-0003-3296-5117 University of Veterinary Medicine Vienna Hess, Michael Michael Hess 0000-0002-6991-0120 University of Veterinary Medicine Vienna American Society for Microbiology journal article open access eng Ornithobacterium rhinotracheale (ORT) is an emerging pathogen that poses significant challenges to commercial poultry production due to respiratory and systemic infections, leading to economic losses. Increasing multidrug resistance further complicates effective treatment strategies. Here, we present the first large-scale genomic analysis of ORT isolates from Europe, focusing on 94 newly sequenced isolates from Austria and Hungary. Phylogenetic analysis revealed two dominant clades, O1 and O2, which included isolates from both regions, indicating a lack of geographic segregation. Both clades display high genetic similarity, indicating that each represents a single strain. Notably, Clade O1 appears to be specific to Europe and exhibits higher resistance to several antibiotics compared to Clade O2. Genome-wide association studies and database screening identified resistance genes linked to beta-lactam antibiotics (ccrA/orr) and tylosin (ermF/ermD). Despite the widespread presence of tetX and tetQ, these genes did not consistently predict tetracycline resistance. Furthermore, we identified the insertion sequences IS4351 and IS1380 as key mobile elements mediating the co-localization of tetX and ermF/ermD resistance genes within ORT isolates of Clade O1. These findings enhance our understanding of ORT’s genetic diversity, strain distribution, and resistance mechanisms, providing a basis for improved monitoring, vaccine development, and targeted interventions. The limited genetic variability observed in our data set underscores the challenges of identifying resistance genes and highlights the need for novel approaches to fully elucidate resistance mechanisms. Ornithobacterium Rhinotracheale Multidrug Resistance Whole-genome Sequencing Phylogenetics Resistance Genes Mobile Genetic Elements GWAS http://creativecommons.org/licenses/by/4.0/ https://phaidra.vetmeduni.ac.at/api/object/o:4911/download 10.1128/aem.00569-25 https://phaidra.vetmeduni.ac.at/o:605 application/pdf Applied and Environmental Microbiology issn:1098-5336 VoR Applied and Environmental Microbiology 91 8 2.32 MB 2025