Genomic landscape of Ornithobacterium rhinotracheale in commercial Turkey Production in the United States

Emily A. Smith, Elizabeth A. Miller, Bonnie P. Weber, Jeannette Munoz Aguayo, Cristian Flores Figueroa, Jared Huisinga, Jill Nezworski, Michelle Kromm, Ben Wileman, Timothy J. Johnson

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Ornithobacterium rhinotracheale is a causative agent of respiratory tract infections in avian hosts worldwide but is a particular problem for commercial turkey production. Little is known about the ecologic and evolutionary dynamics of O. rhinotracheale, which makes prevention and control of this pathogen a challenge. The purpose of this study was to gain insight into the genetic relationships between O. rhinotracheale populations through comparative genomics of clinical isolates from different U.S. turkey producers. O. rhinotracheale clinical isolates were collected from four major U.S. turkey producers and several independent turkey growers from the upper Midwest and Southeast, and whole-genome sequencing was performed. Genomes were compared phylogenetically using single nucleotide polymorphism (SNP)-based analysis, and then assembly and annotations were performed to identify genes encoding putative virulence factors and antimicrobial resistance determinants. A pangenome approach was also used to establish a core set of genes consistently present in O. rhinotracheale and to highlight differences in gene content between phylogenetic clades. A total of 1,457 nonrecombinant SNPs were identified from 157 O. rhinotracheale genomes, and four distinct phylogenetic clades were identified. Isolates clustered by company on the phylogenetic tree, however, and each company had isolates in multiple clades with similar collection dates, indicating that there are multiple O. rhinotracheale strains circulating within each of the companies examined. Additionally, several antimicrobial resistance proteins, putative virulence factors, and the pOR1 plasmid were associated with particular clades and multilocus sequence types, which may explain why the same strains seem to have persisted in the same turkey operations for decades. IMPORTANCE The whole-genome approach enhances our understanding of evolutionary relationships between clinical Ornithobacterium rhinotracheale isolates from different commercial turkey producers and allows for identification of genes associated with virulence, antimicrobial resistance, or mobile genetic elements that are often excluded using traditional typing methods. Additionally, differentiating O. rhinotracheale isolates at the whole-genome level may provide insight into selection of the most appropriate autogenous vaccine strain, or groups of strains, for a given population of clinical isolates.

Original languageEnglish (US)
Article number7419
JournalApplied and environmental microbiology
Issue number11
StatePublished - Jun 1 2020

Bibliographical note

Funding Information:
This study was funded through grants from the Minnesota Turkey Research and Promotion Council and the University of Minnesota MnDRIVE initiative and through USDA-NIFA Agriculture and Food Research Initiative competitive grant no. 2018-68003-27464. Bioinformatics were supported using tools available from the Minnesota Supercomputing Institute.

Publisher Copyright:
© 2020 American Society for Microbiology.


  • Bacteria
  • Genomics
  • Molecular epidemiology
  • Pangenome
  • Phylogenetics
  • Poultry
  • Turkey
  • Veterinary
  • Genome, Bacterial
  • Cross-Sectional Studies
  • Midwestern United States
  • Turkeys/microbiology
  • Animals
  • Ornithobacterium/genetics
  • Poultry Diseases/microbiology
  • Animal Husbandry
  • Flavobacteriaceae Infections/microbiology
  • Southeastern United States
  • Retrospective Studies

PubMed: MeSH publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Journal Article


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