Effects of antibiotic treatment on normal intestinal flora (ARG-study)
This randomized trial evaluated the effect of the use of common antibiotics to treat unrinary tract infections over over a year of follow up. A total of 84 clinically healthy participants with no chronic medication use were enrolled. Participants were randomized to one of 6 treatment arms: untreated, nitrofurantoin, pivmecillinam, sulfamethoxazole/ trimethoprim, ceftibuten, or ciprofloxacin. All antibiotics were given for a five-day course according to standard clinical dosing. Samples were collected before treatment and 7, 14, 30, 90, 6 months, and 1 year post treatment. Samples for sequencing were collected in DNA/RNA shield and frozen at -80 until sequenced. Samples were extracted using bead beating with lysozyme and the Zymo Quick-DNA Magbead Plus kit using a Tecan Freedom EVO robotic system. Samples were sequenced using a 2x100 paired end approach on the DNBSEQ sequencing instruments (MGI, Shenzhen, China). Sequences were demultiplexed using an inhouse demultiplexing algorithm. Sequences were quality-filtered using fastp (v. 0.2.0)12 and human reads were removed using Kraken 2 (v. 2.0.8-beta) by aligning reads against the 38th release of the Human Genome Assembly GRCh38 and retaining only those that did not align with the genome. The study found differing effects on the taxonomic microbiome composition from different antibiotics; the mechanism of excretion was related to the impact.
This randomized trial evaluated the effect of the use of common antibiotics to treat unrinary tract infections over over a year of follow up. A total of 84 clinically healthy participants with no chronic medication use were enrolled. Participants were randomized to one of 6 treatment arms: untreated, nitrofurantoin, pivmecillinam, sulfamethoxazole/ trimethoprim, ceftibuten, or ciprofloxacin. All antibiotics were given for a five-day course according to standard clinical dosing. Samples were collected before treatment and 7, 14, 30, 90, 6 months, and 1 year post treatment. Samples for sequencing were collected in DNA/RNA shield and frozen at -80 until sequenced. Samples were extracted using bead beating with lysozyme and the Zymo Quick-DNA Magbead Plus kit using a Tecan Freedom EVO robotic system. Samples were sequenced using a 2x100 paired end approach on the DNBSEQ sequencing instruments (MGI, Shenzhen, China). Sequences were demultiplexed using an inhouse demultiplexing algorithm. Sequences were quality-filtered using fastp (v. 0.2.0)12 and human reads were removed using Kraken 2 (v. 2.0.8-beta) by aligning reads against the 38th release of the Human Genome Assembly GRCh38 and retaining only those that did not align with the genome. The study found differing effects on the taxonomic microbiome composition from different antibiotics; the mechanism of excretion was related to the impact.