Gepotidacin is a first-in-chemical-class triazaacenaphthylene antibiotic with a distinct mechanism of action, in adult females with uncomplicated urinary tract infections for gepotidacin (GSK2140944). This analyses follow the patients of the Phase 2a clinical trial for Gepotidacin (NCT03568942).
Female patients with recurrent uUTI were administered Gepotidacin for 5 days. Samples were collected with pharyngeal swabs, vaginal swabs and stool sampling at first day of dosing (Day 1), at the end of regimen (Day 5) and at a follow-up visit happening 28±3 days after Day 1.
Distribution of samples
| Body site | Day 1 | Day 5 | Follow-up | Total Collected | Total Pass QC | |||
|---|---|---|---|---|---|---|---|---|
| Collected | Passed QC | Collected | Passed QC | Collected | Passed QC | |||
| GI Tract (stool) | 13 | 11 | 13 | 12 | 10 | 6 | 36 | 29 |
| Pharyngeal (saliva) | 21 | 18 | 20 | 16 | 19 | 19 | 60 | 53 |
| Vaginal (swabs) | 21 | 21 | 20 | 19 | 19 | 19 | 60 | 59 |
| Total | 55 | 50 | 53 | 47 | 48 | 44 | 156 | 141 |
16S V4 rRNA reads of microbiome samples are publically available at Sequence Read Archive (SRA) under BioProject ID: PRJNA630295 and SRA submission: SUB7386163.
16S V4 rRNA were analysed using Qiime2 v 2018.8 and Phyloseq v1.28.0.
Analyses can be reproduced by running the scripts in the qiime2 folder to your local installation of qiime. These will produce the following files:
- qiime2/table_wo_chl_mit.biom
- qiime2/tree.nwk
These can be then imported into Phyloseq to reproduce the full 16S.Rmd file.