Figure 2

Multivariable-adjusted association between presumed proxies of antibiotic selection pressure and the log-odds of antibiotic resistance gene (ARG) carriage. The effect of (a) collection date; (b) isolation source; (c) host taxonomy on the log-odds of ARG carriage (y-axis), is shown across 10 ARG types. ARG types are ordered by the date plasmid-mediated resistance was first reported (see Table 2) from earliest (aminoglycoside, sulphonamide) to most recent (colistin). For categorical factors (isolation source, host taxonomy), log-odds ratios indicate the effect of a given factor level, relative to reference factor level, and error bars show 95% confidence intervals. For collection date, smooth curves indicate the predicted effect of sample collection date. An effective degrees of freedom (edf) value > 1 indicates a non-linear smooth. Shaded areas around smooths show 95% confidence intervals. No Firmicutes plasmids encoded known sulphonamide, ESBL, quinolone, or colistin resistance genes, and only 2 Firmicutes plasmids encoded known carbapenem resistance genes; therefore, corresponding odds ratios are not shown.