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 appear to be a more sensitive method for detecting BRD pathogens in calves compared to deep nasopharyngeal swabs.
Where it sits
this study against the rest of the dnsp-11 (dopamine neuron stimulating peptide-11) corpusSummary and findings
This study compared short nasal swabs (SNS) and deep nasopharyngeal swabs (DNPS) for detecting bovine respiratory disease (BRD) pathogens in 150 calves. SNS yielded higher viral read counts for BCoV (mean reads 75 vs 17, OR = 21.4, p = 0.001) and IDV (mean reads 560 vs 192, OR = 2.60, p = 0.02). The study suggests SNS may be a practical alternative for BRD pathogen surveillance.
Abstract
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.
Background
This paper addresses the effectiveness of different swab sampling methods for detecting BRD-associated pathogens in calves. Previous studies have indicated that swab type may influence pathogen detection rates, but comparative data is limited. Understanding the best sampling method is crucial for effective disease management in feedlot settings.
Methods
The study utilized a comparative design involving 150 calves from six feedlot pens. Short nasal swabs and deep nasopharyngeal swabs were collected and analyzed using a nanopore metagenomic sequencing protocol. The primary outcomes measured were viral and bacterial read counts and prevalence.
Results
SNS yielded significantly higher mean reads for BCoV (75 vs 17, OR = 21.4, p = 0.001) and IDV (560 vs 192, OR = 2.60, p = 0.02). The study also reported that Mannheimia haemolytica was detected more frequently in SNS (mean reads: 169 vs 57, OR = 5.73, p = 0.001). Agreement for detection of M. haemolytica was moderate (κ = 0.46, p = 0.001).
Interpretation
The findings suggest that SNS may be more effective than DNPS for detecting certain BRD pathogens, aligning with previous literature that indicates sampling method can impact detection rates. However, the clinical significance of these findings should be interpreted cautiously, as the effect sizes, while statistically significant, may not translate to meaningful differences in disease management. Limitations such as sample size and specific population studied may confound the results.
Key findings
- mean reads for BCoV: 75 vs 17; OR = 21.4, p = 0.001
- mean reads for IDV: 560 vs 192; OR = 2.60, p = 0.02
- mean reads for Mannheimia haemolytica: 169 vs 57; OR = 5.73, p = 0.001
- mean reads for Pasteurella multocida: 4.0 vs 1.2; OR = 2.02, p = 0.02
- mean reads for Mesomycoplasma dispar: 5.2 vs 29; OR = 0.27, p = 0.001
- Agreement for detection of M. haemolytica (≥14 reads): κ = 0.46, p = 0.001
Limitations
- sample size of 150 calves may limit generalizability
- specific population may not represent broader cattle populations
- study does not report long-term outcomes or clinical impacts