Enhanced metagenomic surveillance for bovine respiratory disease pathogens and antimicrobial resistance by hybridization capture sequencing

Shotgun metagenomic sequencing for infectious disease diagnostics and surveillance benefits from simultaneous detection of multiple pathogens in a sample. Adding a hybridization probe capture step to the metagenomics workflow enriches targeted loci to improve the sensitivity of pathogen detection without compromising the ability to detect pathogen variants. Our custom probe panel enables multi-locus sequence typing of bovine respiratory disease agents as well as capture of antibiotic resistance genes, which improves the sensitivity of metagenomic testing and provides genotyping data compatible with traditional assays. This study demonstrates the utility of new design principles for probe panels; it also demonstrates how targeted metagenomics provides important new insights into co-infections and is equally useful for surveillance of environmental reservoirs of disease agents.