Rapid detection of causative bacteria including multiple infections of bovine respiratory disease using 16S rRNA amplicon-based nanopore sequencing.

Bovine respiratory disease (BRD) is a multifaceted condition that poses a primary challenge in calf rearing. Viruses and bacteria are etiological agents of BRD. Viral BRD is typically managed symptomatically, whereas bacterial BRD is predominantly managed through the empirical administration of antimicrobials. However, this empirical administration has raised concerns regarding the emergence of antimicrobial-resistant bacteria. Thus, rapid identification of pathogenic bacteria and judicious selection of antimicrobials are required. This study evaluated the usefulness of 16S rRNA analysis through nanopore sequencing for the rapid identification of BRD-causing bacteria. A comparative evaluation of nanopore sequencing and traditional culture method was performed on 100 calf samples detected with BRD. Nanopore sequencing facilitated the identification of bacteria at the species level in bovine nasal swabs, ear swabs, and lung tissue samples within approximately 6 h. Of the 92 samples in which BRD-causing bacteria were identified via nanopore sequencing, 82 (89%) were concordant with the results of culture isolation. In addition, the occurrence of multiple infections exceeded that of singular infections. These results suggest that 16S rRNA sequencing via nanopore technology is effective in reducing analysis time and accurately identifying BRD-causing bacteria. This method is particularly advantageous for the initial detectable screening of BRD.