phaidra.vetmeduni.ac.at o:4911 DOI 10.1128/aem.00569-25 Genomic analysis reveals two dominant strains of Ornithobacterium rhinotracheale in Austria and Hungary with distinct multidrug resistance profiles 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. eng Ornithobacterium Rhinotracheale Multidrug Resistance Whole-genome Sequencing Phylogenetics Resistance Genes Mobile Genetic Elements GWAS 2026-02-10T16:43:00.797Z LOMv1.0 Author BEGIN:VCARD VERSION:3.0 N:Palmieri;Nicola; FN:Nicola Palmieri X-ORCID:https://orcid.org/0000-0002-6164-1843 END:VCARD BEGIN:VCARD VERSION:3.0 N:Hess;Claudia; FN:Claudia Hess X-ORCID:https://orcid.org/0000-0002-3535-5157 END:VCARD BEGIN:VCARD VERSION:3.0 N:Pollak;Boglarka; FN:Boglarka Pollak END:VCARD BEGIN:VCARD VERSION:3.0 N:Magyar;Tibor; FN:Tibor Magyar END:VCARD BEGIN:VCARD VERSION:3.0 N:Pinter;Krisztina; FN:Krisztina Pinter END:VCARD BEGIN:VCARD VERSION:3.0 N:Doman;Marianna; FN:Marianna Doman END:VCARD BEGIN:VCARD VERSION:3.0 N:Bilic;Ivana; FN:Ivana Bilic X-ORCID:https://orcid.org/0000-0003-3296-5117 END:VCARD BEGIN:VCARD VERSION:3.0 N:Hess;Michael; FN:Michael Hess X-ORCID:https://orcid.org/0000-0002-6991-0120 END:VCARD https://w3id.org/kim/hcrt/scheme https://w3id.org/kim/hcrt/text Textdokument Text LOMv1.0 yes https://creativecommons.org/licenses/by/4.0 application/pdf 2434700 https://phaidra.vetmeduni.ac.at/o:4911 https://phaidra.vetmeduni.ac.at/api/object/o:4911/thumbnail LOMv1.0 discipline