Estimation of the Minimum Read Coverage Required for Detection of ARG

An estimate of the average genome coverage needed to reliably detect an ARG was determined by screening at increasing levels of read coverage. For each isolate, the raw reads were randomly sampled to genome coverage levels of 1, 2.5, 5, 10, 15, 20, 25, and 30X, using the reformat.sh script (version 37.61) provided with the BBMap suite (Bushnell, 2014). Each set of subsampled raw reads was then screened for ARGs using sipprverse (v 0.0.76) with the ResFinder database (2019-04-26), and SRST2 (v 0.2.0) (Inouye et al., 2014), and KMA (v 1.3.3) (Clausen et al., 2018) with the NCBI-AMR database (2019-04-29.1) (Table 1). For all three tools, default settings were used, with a minimum gene coverage was set to 90%. For each isolate, at each genome coverage level, the subsampling and ARG screening was repeated 100X. The expected ARG profile of each isolate was determined by running each of the tools against the raw reads without subsampling. A false positive result was defined as an ARG detected in the subsampled raw reads but not detected using all available raw reads.