Fig. 4: Within-host dynamics of antimicrobial resistance and the impact of antibiotic treatment.

a, The fraction of carriage events consisting of a single lineage found to be resistant to each antibiotic class. Only those classes found to be less likely to occur in instances of multiple colonization than expected given the background prevalence in the population are shown. b, The number of resistance calls for each antibiotic class in 1,158 samples for which both single colony picks and PDS had been performed. c, The distribution of the change in frequency of the GPSC1 lineage in 182 pairs of consecutive samples that have and have not received antimicrobial treatment. The median and interquartile range are given by the horizontal lines, with the whiskers indicating the largest and smallest values excluding those outside 1.5 times the interquartile range. d, A dot plot indicating the significance and effect size of unitigs found to be associated with antimicrobial treatment using a linear mixed model in Pyseer. e, The number of within-host SNV in 1,192 samples taken from distinct carriage episodes involving only a single pneumococcal lineage split by recently received antimicrobial treatment. f, The normalized count of unitigs found in CpsE in pairs of samples where a subset had received treatment between sampling events.