A health metadata-based management approach for comparative analysis of high-throughput genetic sequences for quantifying antimicrobial resistance reduction in Canadian hog barns. manure metagenome

In this method paper, we investigated antimicrobial resistance due to antibiotics that are still massively-used worldwide and mostly in livestock, using next-generation sequencing (NGS) as an alternative to phenotypic susceptibility testing for surveillance and clinical diagnoses. We described a methodology comparing the effect of raising animals without antibiotics (RWA) approach to non-RWA operations in hog production. We describe a comprehensive next-generation whole-genome sequencing workflow analysis wherein reads are mapped directly to reference sequences, determined over time, in order to obtain taxonomic and resistome profiles as well as pathogen prevalence in animals and their environment.