Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease.

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  • Additional Information
    • Source:
      Publisher: Oxford University Press Country of Publication: England NLM ID: 101566598 Publication Model: Electronic Cited Medium: Internet ISSN: 2160-1836 (Electronic) Linking ISSN: 21601836 NLM ISO Abbreviation: G3 (Bethesda) Subsets: MEDLINE
    • Publication Information:
      Publication: 2021- : [Oxford] : Oxford University Press
      Original Publication: Bethesda, MD : Genetics Society of America, 2011-
    • Subject Terms:
      Genome, Bacterial* ; Genotype* ; Phenotype*; Anti-Infective Agents/*pharmacology ; Bacteria/*drug effects ; Bacteria/*genetics ; Bacterial Infections/*veterinary; Animals ; Bacteria/classification ; Bacteria/isolation & purification ; Cattle ; Cattle Diseases/microbiology ; Chromosome Mapping ; Drug Resistance, Bacterial ; Genetic Association Studies ; Genetic Variation ; Genomics/methods ; Microbial Sensitivity Tests ; Phylogeny ; Respiratory Tract Infections/veterinary ; Sequence Analysis, DNA
    • Abstract:
      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 culture-independent 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. Computer-based 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.
      (Copyright © 2017 Owen et al.)
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    • Grant Information:
      T32 OD012201 United States OD NIH HHS
    • Contributed Indexing:
      Keywords: Histophilus somni; Mannheimia haemolytica; Mycoplasma bovis; Pasteurella multocida
    • Accession Number:
      0 (Anti-Infective Agents)
    • Publication Date:
      Date Created: 20170726 Date Completed: 20180503 Latest Revision: 20211022
    • Publication Date:
      20240829
    • Accession Number:
      PMC5592931
    • Accession Number:
      10.1534/g3.117.1137
    • Accession Number:
      28739600