Comparison of short nasal swab and deep nasopharyngeal swab sampling methods to describe BRD-associated viruses and bacteria detected using a metagenomics approach optimized for virus recovery in fall-placed beef calves shortly after feedlot arrival

Short nasal swabs (SNS) have potential advantages of lower costs, collection time and training of personnel than deep nasopharyngeal swabs (DNPS) for detecting bovine respiratory disease (BRD) pathogens. This study examined differences between DNPS and SNS in BRD-associated pathogens detected using a nanopore metagenomic sequencing protocol, optimized for respiratory RNA viruses, collected from 150 calves in six feedlot pens. Short nasal swabs yielded higher viral read counts and prevalence than DNPS for BCoV (mean reads 75 versus 17; OR = 21.4, <i>P</i> = 0.001) and IDV (mean reads: 560 versus 192; OR = 2.60, <i>P</i> = 0.02). Agreement varied among viruses: IDV (κ=0.57), BRSV (κ=0.43), and BCoV at both ≥1 read (κ=0.35) and ≥30 reads (κ=0.10). No BoHV-1 and BAdV3 were detected. <i>Mannheimia haemolytica</i> was detected (≥14 reads) more frequently in SNS than DNPS (mean reads: 169 versus 57; OR = 5.73, <i>P</i> = 0.001), as was <i>Pasteurella multocida</i> (≥ 1 read) (mean reads: 4.0 versus 1.2; OR = 2.02, <i>P</i> = 0.02). <i>Mesomycoplasma dispar</i> was less prevalent in SNS (mean reads: 5.2 versus 29; OR = 0.27, <i>P</i> = 0.001). Detection of <i>Histophilus somni, Bibersteinia trehalosi</i>, and <i>Mycoplasmopsis bovis</i> did not differ between swab types. Agreement for detection of <i>M. haemolytica</i> (≥14 reads) was moderate (κ = 0.46, <i>P</i> = 0.001). For all other bacteria examined in this analysis, kappa values were very low. Short nasal swabs were a sensitive and practical alternative for BRD pathogen surveillance providing evidence of which viruses and bacteria are circulating, potentially informing vaccination and disease management.