Genome Medicine

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13073_2021_843_MOESM1_ESM.pdf (7049 kB)
Figures S1-S7

13073_2021_843_MOESM2_ESM.xlsx (18 kB)
This table shows cultured isolates, their associated ASVs, their taxonomy assignments according to DADA2 and MALDI-TOF, and antibiotic sensitivity results in terms of their clearance zone sizes and the interpretations of sensitive, intermediate, or resistant. Final taxonomy assignments were confirmed by genomic alignments with type strains.

13073_2021_843_MOESM3_ESM.csv (41 kB)
All genomic resistance gene annotations from Resfinder for all MDRO isolates are listed here, with their specific genomic location, predicted phenotype, and % identity to reference genes.

13073_2021_843_MOESM4_ESM.csv (2 kB)
The eradication status of ARO found in each patient is summarized here. If the first sample (notated as Patient ID – Dose number – Days from previous dose) was positive according to the ASV quantified by DADA2 and the last sample from the same patient was negative, the status for that ASV is shown as negative. Acquired means it was first negative (in both patient and donor) and later positive, absent means all samples were negative, masked means the donor was positive, and insufficient samples means the first and last sample were the same.

13073_2021_843_MOESM5_ESM.pdf (1295 kB)
Figures S8-S10

13073_2021_843_MOESM6_ESM.xlsx (14 kB)
The two tables show the total ARG hits in RPKM for donors and patients at each sample collection timepoint, as well as the standard deviation and variance over time.