Fig. 5

Accurate ARG detection is dependent on isolate coverage in metagenome. Synthetic metagenomes containing A) lettuce soil metagenome and B) beef fecal metagenome mixed with synthetic-community mixed reads at 0.1-, 1-, 2-, 5-, and 10-X genome coverage (n = 10 at each coverage level) were evaluated for presence of ARGs using both KMA (□) and SRST2 (✕) in silico tools. Only results for CTX-M-15, CMY-2, and mcr-1 are displayed (see colour legend). Lettuce, soil and beef fecal metagenomes without added synthetic-community reads were analysed as a control (0X panel, n = 1). Percent ARG detection (y-axis) of 10 replicates, with upper and lower 95% confidence intervals (dashed lines), are plotted as a function of detected ARG template gene coverage (x-axis). Target gene panel (right y-axis label, top row), refers to the gene-allele detected in the original isolate assembly; Target clade (middle row), refers to detection of alleles within the same phylogenetic clade as the target gene (e.g. a CMY-allele closely related to CMY-2); Non-target (bottom row), refers to alleles of the target gene family that are not as closely related to the target gene (e.g. ≤ 90% nucleotide identity to CMY-2). Darker point-color intensity is a result of multiple points (different gene-alleles) overlapping. Where multiple points of the same shape/colour are present (e.g. B: Bottom right: 10X – Non-target Alleles—≥ 80% coverage there are five CMY-2 ✕s), each point represents a different allele (e.g. blaCMY-81, blaCMY-83, blaCMY-90, blaCMY-97, and blaCMY-114, were all detected by SRST2 and are each denoted by separate ✕ points)