Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review

Abstract

Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.

Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle

“…There were no previous reports of ARG detection within identified pathogen reads using long-read metagenomic sequencing in human or veterinary upper respiratory tract samples (Chen and Xu, 2023;Adewusi et al, 2024) with the exception of the limited success in earlier study published by our group (Freeman et al, 2022). Resistance genes were not recovered in a veterinary study of skin infections in dogs due to the high percentage of host DNA (Ring et al, 2023).…”

“…A shotgun metagenomic sequencing approach combines the rapidness of using DNA extracted directly from clinical samples with a broad, untargeted view of all genetic information in a sample. Metagenomics has the potential to find multiple pathogens and ARGs in a single sequencing run without the need for pathogen isolation or specifying a known genetic target ( Adewusi et al, 2024 ).…”