Data Sheet 4_Laboratory tests for bovine respiratory bacteria and antimicrobial resistance

760 nasopharyngeal swab samples from commercial feedlot calves in western Canada were analyzed using three diagnostic methods. This large-scale field evaluation, conducted as part of Canadian surveillance, provides the first performance estimates for long-read metagenomic sequencing in a commercial lab setting. The work by Simon J. G. Otto, published in 2026, compares culture, metagenomics, and recombinase polymerase amplification for detecting key pathogens and resistance genes.

Use Cases

• Compare the diagnostic performance of culture, metagenomic sequencing, and RPA based on sensitivity and specificity estimates provided in the description
• Analyze patterns of antimicrobial resistance (AMR) gene detection across different cattle age cohorts mentioned in the study
• Evaluate the potential of long-read metagenomic sequencing for large-scale AMR surveillance in feedlot cattle as discussed in the results
• Assess detection rates for BRD pathogens like Mannheimia haemolytica and Mycoplasmopsis bovis over the early feeding period described in the methods

Strengths

• Contains results from 760 respiratory samples, providing a substantial field evaluation.
• Directly compares three distinct laboratory testing approaches (culture/AST, metagenomics, RPA) with Bayesian latent class models.
• Provides specific performance metrics, such as sensitivity below 65% and specificity above 90% for pathogen detection.
• Represents the first large-scale implementation of a specific long-read metagenomic protocol in a commercial laboratory setting.

Limitations

• The dataset is described in a 577.8 KB PDF file; the underlying raw data tables are not directly accessible.
• Column-level documentation is absent; field semantics must be inferred from the PDF report.
• Row count for any underlying data tables is unknown, which may limit suitability assessment.

Provenance

Source

Simon J. G. Otto via figshare.

Collection Method

Nasopharyngeal swabs collected by private veterinarians from western Canadian beef feedlots as part of surveillance, analyzed with culture, qPCR, long-read metagenomic sequencing, and recombinase polymerase amplification.

Time Range

The study period is not specified, but the dataset was updated in 2026.

Freshness

Last updated 2026-05-20 05:23:53; freshness should be verified.

Geography

Western Canadian beef feedlots.