Extended Data Fig. 4: Impact of Doxy-PEP use on tetracycline ARGs by number of doxycycline doses received for DNA-seq samples (a, b) and RNA-seq samples (c, d).

(a, c) Tetracycline ARG richness and (b, d) proportion of tetracycline ARG mass within the resistome by number of doxycycline doses received was plotted and fitted to a linear regression line for the outcome of tetracycline ARG richness and an inflated beta-regression line for the outcome of proportional tetracycline mass (DNA-seq: n = 127 samples, RNA-seq: n = 86 samples). The regression model is shown as a line, and the gray shaded areas surrounding the regression lines show the 95% confidence intervals. P-values from the regression models are obtained by two-sided Wald tests. Significant p-values (<0.05) are bolded. Significant p-values (<0.05) are bolded. Abbreviations: ARG, antimicrobial resistance gene; p.adj, adjusted p-value.