Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study
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Langdon, A., Schwartz, D.J., Bulow, C. et al. Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study. Genome Med 13, 28 (2021). https://doi.org/10.1186/s13073-021-00843-9 This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
Langdon, Amy; Schwartz, Drew J; Bulow, Christopher; Sun, Xiaoqing; Hink, Tiffany; Reske, Kimberly A; Jones, Courtney; Burnham, Carey-Ann D; Dubberke, Erik R; Dantas, Gautam; and CDC Prevention Epicenter Program, "Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study." Genome Medicine. 13, 1. 28 (2021).
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)
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.