Deep nasopharyngeal swabs are more sensitive than short nasal swabs for identifying antimicrobial resistance genes in bovine respiratory pathogens examined using long-read metagenomic sequencing.

Challenges in sample collection have contributed to the limited use of diagnostic testing in bovine respiratory disease (BRD) management. Short nasal swabs (SNS) offer a practical and cost-effective alternative to deep nasopharyngeal swabs (DNPS) for sampling the upper respiratory tract, but gaps remain in understanding the efficacy of SNS for detecting clinically relevant bacteria and associated antimicrobial resistance genes (ARGs) compared to DNPS. This study compared detection of BRD-associated bacteria and ARGs between SNS and DNPS samples collected from 207 fall-placed calves at a research feedlot, using a recently developed long-read metagenomic sequencing protocol. More total reads and base pairs were identified from DNPS than SNS for Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Bibersteinia trehalosi, while no difference was detected for Mycoplasmopsis bovis. Additional bacteria of potential interest were also identified. Bacterial reads and total base pairs identified as Mesomycoplasma dispar, Moraxella bovoculi, and Mannheimia bovis were higher in DNPS compared to SNS, while reads identified as Moraxella bovis were higher in SNS. The prevalence of samples in which ARGs were detected within reads identified as M. haemolytica, P. multocida, H. somni or B. trehalosi was greater in DNPS samples compared to SNS for tetracyclines (OR = 1.6, P = 0.02), macrolides (OR = 2.3, P < 0.001), sulfonamides (OR = 2.5, P < 0.001), and aminoglycosides (OR = 2.5, P < 0.001). Overall, for the sequencing protocol used in this study, DNPS performed better than SNS for the detection of BRD bacteria and associated ARGs.