Whole-genome sequencing and concordance between antimicrobial susceptibility genotypes and phenotypes of bacterial isolates associated with bovine respiratory disease

Joseph R. Owen, Noelle Noyes, Amy E. Young, Daniel J. Prince, Patricia C. Blanchard, Terry W. Lehenbauer, Sharif S. Aly, Jessica H. Davis, Sean M. O'Rourke, Zaid Abdo, Keith Belk, Michael R. Miller, Paul Morley, Alison L. Van Eenennaam

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


Extended laboratory culture and antimicrobial susceptibility testing timelines hinder rapid species identification and susceptibility profiling of bacterial pathogens associated with bovine respiratory disease, the most prevalent cause of cattle mortality in the United States. Whole-genome sequencing offers a cultureindependent alternative to current bacterial identification methods, but requires a library of bacterial reference genomes for comparison. To contribute new bacterial genome assemblies and evaluate genetic diversity and variation in antimicrobial resistance genotypes, whole-genome sequencing was performed on bovine respiratory disease-associated bacterial isolates (Histophilus somni, Mycoplasma bovis, Mannheimia haemolytica, and Pasteurella multocida) from dairy and beef cattle. One hundred genomically distinct assemblies were added to the NCBI database, doubling the available genomic sequences for these four species. Computerbased methods identified 11 predicted antimicrobial resistance genes in three species, with none being detected in M. bovis. While computer-based analysis can identify antibiotic resistance genes within whole-genome sequences (genotype), it may not predict the actual antimicrobial resistance observed in a living organism (phenotype). Antimicrobial susceptibility testing on 64 H. somni, M. haemolytica, and P. multocida isolates had an overall concordance rate between genotype and phenotypic resistance to the associated class of antimicrobials of 72.7% (P < 0.001), showing substantial discordance. Concordance rates varied greatly among different antimicrobial, antibiotic resistance gene, and bacterial species combinations. This suggests that antimicrobial susceptibility phenotypes are needed to complement genomically predicted antibiotic resistance gene genotypes to better understand how the presence of antibiotic resistance genes within a given bacterial species could potentially impact optimal bovine respiratory disease treatment and morbidity/mortality outcomes.

Original languageEnglish (US)
Pages (from-to)3059-3071
Number of pages13
JournalG3: Genes, Genomes, Genetics
Issue number9
StatePublished - Sep 1 2017
Externally publishedYes

Bibliographical note

Funding Information:
Library preparation was performed at the University of California Davis DNA Technologies Core Facility. The authors would like to thank the University of California Davis Bioinformatics Core Facility for assistance with data analysis. The authors would also like to thank Paul Rossitto, James Moller, Bryan Welly, Ellen Lai, and Nadia Torok for assistance with sample collection, and Julie Cleek, Toni Ortiz, and Muhammad Ilyas for bacterial work-up and biochemical identification. Dairy cattle samples were collected as part of the US Department of Agriculture, Agriculture and Food Research Initiative competitive grant no. 2011-68004-30367. The sequencing and antimicrobial resistance phenotyping was funded by a grant from the Russell L. Rustici Rangeland and Cattle Research Endowment.

Publisher Copyright:
© 2017 Owen et al.


  • Histophilus somni
  • Mannheimia haemolytica
  • Mycoplasma bovis
  • Pasteurella multocida


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