Sequencing depth required for antimicrobial resistance gene detection from metagenomic samples

Next-generation sequencing is a commonly used technology for the detection of antimicrobial resistance (AMR) genes. Currently, there are no sequencing depth standards for the detection of AMR genes in whole genomes and metagenomes. Our goal was to quantify the minimum sequencing depth requirements to detect AMR genes from a multi-drug resistant E. coli isolate when it represented varying abundances in a complex bacterial community.