Fig. 5

Antibiotic-resistant organisms cultured from patient and donor stools and the corresponding ASVs from species were tracked over time. a–e Antibiotic susceptibility profiles for each cultured organism from any sample from donor and patient with the corresponding phylogenetic tree. All breakpoints in antibiotic concentration were determined by CLSI 2016 criteria. Taxonomic labels are derived from DADA2 ASV assignments, with Enterobacter being further specified from family level based on metaphlan2 and MALDI-TOF taxonomy assignments. The designation A indicates recipient and D indicates donor. The following number indicates the study ID number followed by timepoint of isolation. A and E connote single colonies on separate plates. f–j Each of the ASVs corresponding to the species in a–e are shown in relative abundance over time in 131 fecal samples from 28 patients and 4 donors after the first study treatment. *p < 0.05, **p < 0.01 for relative abundance differences 7 days after therapy between SI and RI groups using Mann-Whitney U test. TMP-SMX, trimethoprim-sulfamethoxazole