Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Stewardson AJ, Gaïa N, François P, Malhotra-Kumar S, Delémont C, Martinez de Tejada B, Schrenzel J, Harbarth S, Lazarevic V
Journal
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
Year
2015
Keywords:
Antibiotics, ecologic damage, microbiomics, microbiota, urinary tract infection
Recent treatment guidelines for uncomplicated urinary tract infections (UTIs) discourage fluoroquinolone prescription because of collateral damage to commensal microbiota, but the ecologic impact of alternative agents has not been evaluated by culture-free techniques. We prospectively collected faecal samples at three time points from ambulatory patients with UTIs treated with ciprofloxacin or nitrofurantoin, patients not requiring antibiotics and household contacts of ciprofloxacin-treated patients. We described changes in gut microbiota using a culture-independent approach based on pyrosequencing of the V3-V4 region of the bacterial 16S rRNA gene. All groups were similar at baseline. Ciprofloxacin had a significant global impact on the gut microbiota whereas nitrofurantoin did not. The end of ciprofloxacin treatment correlated with a reduced proportion of Bifidobacterium (Actinobacteria), Alistipes (Bacteroidetes) and four genera from the phylum Firmicutes (Faecalibacterium, Oscillospira, Ruminococcus and Dialister) and an increased relative abundance of Bacteroides (Bacteroidetes) and the Firmicutes genera Blautia, Eubacterium and Roseburia. Substantial recovery had occurred 4 weeks later. Nitrofurantoin treatment correlated with a reduced relative proportion of the genus Clostridium and an increased proportion of the genus Faecalibacterium. This study supports use of nitrofurantoin over fluoroquinolones for treatment of uncomplicated UTIs to minimize perturbation of intestinal microbiota.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/09/17
Curator: Mmarin
Revision editor(s): WikiWorks, LGeistlinger, Mmarin, Victoria
Subjects
- Location of subjects
- Switzerland
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- baseline of the ciprofloxacin treated
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ciprofloxacin treated
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- UTI patients treated with ciprofloxacin 500mg twice daily
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Source: Figure 3
Description: Differential microbial abundance between baseline (timepoint 1) and timepoint 2 in ciprofloxacin treated patients
Abundance in Group 1: decreased abundance in ciprofloxacin treated
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Faecalibacterium | ||
| Oscillospira | ||
| Oscillospiraceae | ||
| Ruminococcus |
Revision editor(s): Mmarin, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Source: Figure 3
Description: Differential microbial abundance between baseline (timepoint 1) and timepoint 2 in ciprofloxacin treated patients
Abundance in Group 1: increased abundance in ciprofloxacin treated
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Blautia | ||
| Clostridium | ||
| Eubacterium | ||
| Lachnospiraceae | ||
| Roseburia |
Revision editor(s): Mmarin, Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Curated date: 2021/09/23
Curator: Mmarin
Revision editor(s): WikiWorks, LGeistlinger, Mmarin, Victoria
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Baseline of the Nitrofurantoin treated
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Nitrofurantoin treated
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- UTI patients treated with nitrofurantoin macrocrystals 100mg twice daily
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Source: Figure 3
Description: Differential microbial abundance between baseline and post-treatment timepoints in nitrofurantoin treated group
Abundance in Group 1: decreased abundance in Nitrofurantoin treated
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae |
Revision editor(s): Mmarin, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/31
Source: Figure 3
Description: Differential microbial abundance between baseline and post-treatment timepoints in nitrofurantoin treated group
Abundance in Group 1: increased abundance in Nitrofurantoin treated
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium |
Revision editor(s): Mmarin, Claregrieve1
Experiment 6
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/3
Curated date: 2021/10/15
Curator: Mmarin
Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Mmarin, Victoria
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Antimicrobial agent , Urinary tract infection antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent,INFECTION, URINARY TRACT,TRACT, INFECTION OF URINARY,urinary tract infection,urinary tract infection (disease),Urinary tract infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control group (timepoint 2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ciprofloxacin treated group (timepoint 2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ciprofloxacin group at end of antibiotic treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/3
Source: Table S2
Description: Differential microbial abundance between the control group and ciprofloxacin-treated group at timepoint 2
Abundance in Group 1: increased abundance in Ciprofloxacin treated group (timepoint 2)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Lachnospiraceae | ||
| Oscillospira | ||
| Parabacteroides | ||
| Porphyromonadaceae | ||
| Rikenellaceae | ||
| Roseburia | ||
| Ruminococcus | ||
| Veillonellaceae |
Revision editor(s): Mmarin, Claregrieve1
Experiment 7
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/3
Curated date: 2021/10/15
Curator: Mmarin
Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Mmarin, Victoria
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls (timepoint 2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- nitrofurantoin treated group (timepoint 2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- nitrofurantoin-treated group at end of treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/3
Source: Table S2
Description: Differential microbial abundance between the control group and nitrofurantoin-treated group at timepoint 2
Abundance in Group 1: increased abundance in nitrofurantoin treated group (timepoint 2)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroidales | ||
| Bacteroidia | ||
| Bacteroidota | ||
| Faecalibacterium | ||
| Rikenellaceae |
Revision editor(s): Mmarin, Claregrieve1
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