Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota

From BugSigDB
Needs review
study design
prospective cohort
Citation
PMID
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
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


Needs review

Curated date: 2021/09/17

Curator: Mmarin

Revision editor(s): LGeistlinger, Mmarin, WikiWorks753

Subjects

Location of subjects Country from which study subjects were recruited
Switzerland
Host species Species from which microbiome was sampled (if applicable)
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
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
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 Experimental technique used for quantifying microbial abundance
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

Statistical test Statistical test or computational tool used for differential abundance testing
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)?
Yes


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

Needs review

Curated date: 2021/09/23

Curator: Mmarin

Revision editor(s): Mmarin

Source: Figure 3

Description: Families and genera differentially represented between before and after antibiotic treatment. Boxes were coloured red and blue to indicate decrease and increase, respectively. CP: ciprofloxacin group, CRL: control group; CTCP: household members of ciprofloxacin group; NF: nitrofurantoin group

Abundance in Group 1: decreased abundance in ciprofloxacin treated

NCBI Links
Bifidobacteriaceae
Faecalibacterium
Oscillospira
Ruminococcus
Oscillospiraceae

Revision editor(s): Mmarin

Signature 2

Needs review

Curated date: 2021/09/23

Curator: Mmarin

Revision editor(s): Mmarin

Source: Figure 3

Description: Families and genera differentially represented between before and after antibiotic treatment. Boxes were coloured red and blue to indicate decrease and increase, respectively. CP: ciprofloxacin group, CRL: control group; CTCP: household members of ciprofloxacin group; NF: nitrofurantoin group

Abundance in Group 1: increased abundance in ciprofloxacin treated

NCBI Links
Bacteroidaceae
Blautia
Clostridium
Eubacterium
Lachnospiraceae
Roseburia

Revision editor(s): Mmarin

Experiment 2


Needs review

Curated date: 2021/09/23

Curator: Mmarin

Revision editor(s): LGeistlinger, Mmarin, WikiWorks753

Subjects

Location of subjects Country from which study subjects were recruited
Switzerland
Host species Species from which microbiome was sampled (if applicable)
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
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
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 Experimental technique used for quantifying microbial abundance
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05


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

Needs review

Curated date: 2021/09/23

Curator: Mmarin

Revision editor(s): Mmarin

Source: Figure 3

Description: Families and genera differentially represented between before and after antibiotic treatment. Boxes were coloured red and blue to indicate decrease and increase, respectively. CP: ciprofloxacin group, CRL: control group; CTCP: household members of ciprofloxacin group; NF: nitrofurantoin group

Abundance in Group 1: decreased abundance in Nitrofurantoin treated

NCBI Links
Clostridiaceae

Revision editor(s): Mmarin

Signature 2

Needs review

Curated date: 2021/09/23

Curator: Mmarin

Revision editor(s): Mmarin

Source: Figure 3

Description: Families and genera differentially represented between before and after antibiotic treatment. Boxes were coloured red and blue to indicate decrease and increase, respectively. CP: ciprofloxacin group, CRL: control group; CTCP: household members of ciprofloxacin group; NF: nitrofurantoin group

Abundance in Group 1: increased abundance in Nitrofurantoin treated

NCBI Links
Faecalibacterium

Revision editor(s): Mmarin

Experiment 3


incomplete

Curated date: 2021/09/23

Curator: Mmarin

Revision editor(s): LGeistlinger, Mmarin, WikiWorks753

Subjects

Location of subjects Country from which study subjects were recruited
Switzerland
Host species Species from which microbiome was sampled (if applicable)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
urinary tract infection INFECTION, URINARY TRACT,TRACT, INFECTION OF URINARY,urinary tract infection,urinary tract infection (disease)
Group 0 name Corresponds to the control (unexposed) group for case-control studies
without antibiotic treatment
Group 0 sample size Number of subjects in the control (unexposed) 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 Experimental technique used for quantifying microbial abundance
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05


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

Experiment 4


incomplete

Curated date: 2021/09/23

Curator: Mmarin

Revision editor(s): LGeistlinger, Mmarin, WikiWorks753

Subjects

Location of subjects Country from which study subjects were recruited
Switzerland
Host species Species from which microbiome was sampled (if applicable)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
urinary tract infection INFECTION, URINARY TRACT,TRACT, INFECTION OF URINARY,urinary tract infection,urinary tract infection (disease)
Group 0 name Corresponds to the control (unexposed) group for case-control studies
adult household contact for each patient treated with ciprofloxacin
Group 0 sample size Number of subjects in the control (unexposed) group
10
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
controls received no antibiotics during the study period or 2 months before it.

Lab analysis

Sequencing type Experimental technique used for quantifying microbial abundance
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
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)?
Yes


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

Experiment 5


incomplete

Curated date: 2021/09/30

Curator: Mmarin

Revision editor(s): LGeistlinger, Mmarin, WikiWorks753

Subjects

Location of subjects Country from which study subjects were recruited
Switzerland
Host species Species from which microbiome was sampled (if applicable)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
urinary tract infection INFECTION, URINARY TRACT,TRACT, INFECTION OF URINARY,urinary tract infection,urinary tract infection (disease)
Group 0 name Corresponds to the control (unexposed) group for case-control studies
baseline of the fosfomycin treated
Group 1 name Corresponds to the case (exposed) group for case-control studies
fosfomycin treated
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
UTI patients treated with fosfomycin, one 3g dose
Group 0 sample size Number of subjects in the control (unexposed) group
2
Group 1 sample size Number of subjects in the case (exposed) group
2
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 Experimental technique used for quantifying microbial abundance
16S

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
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)?
Yes


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

Experiment 6


Needs review

Curated date: 2021/10/15

Curator: Mmarin

Revision editor(s): LGeistlinger, Mmarin, WikiWorks753

Subjects

Location of subjects Country from which study subjects were recruited
Switzerland
Host species Species from which microbiome was sampled (if applicable)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
urinary tract infection INFECTION, URINARY TRACT,TRACT, INFECTION OF URINARY,urinary tract infection,urinary tract infection (disease)
Group 0 name Corresponds to the control (unexposed) group for case-control studies
CRL2
Group 1 name Corresponds to the case (exposed) group for case-control studies
CP2
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
ciprofloxacin group, between antibiotic treatment
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

Lab analysis

Sequencing type Experimental technique used for quantifying microbial abundance
16S

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
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)?
Yes


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

Needs review

Curated date: 2021/10/15

Curator: Mmarin

Revision editor(s): Mmarin

Source: Table S2

Description: Median values of taxa abundance.Taxa with median proportion >0.5% in at least one of two significantly different (P<0.05) groups of samples are presented. The statistical analysis method used was a Wilcoxon signed-rank test ('paired') and Wilcoxon rank sum ('non paired').

Abundance in Group 1: increased abundance in CP2

NCBI Links
Alistipes
Lachnospiraceae
Oscillospira
Parabacteroides
Porphyromonadaceae
Rikenellaceae
Roseburia
Ruminococcus
Veillonellaceae

Revision editor(s): Mmarin

Experiment 7


Needs review

Curated date: 2021/10/15

Curator: Mmarin

Revision editor(s): LGeistlinger, Mmarin, WikiWorks753

Subjects

Location of subjects Country from which study subjects were recruited
Switzerland
Host species Species from which microbiome was sampled (if applicable)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
urinary tract infection INFECTION, URINARY TRACT,TRACT, INFECTION OF URINARY,urinary tract infection,urinary tract infection (disease)
Group 0 name Corresponds to the control (unexposed) group for case-control studies
CRL2
Group 1 name Corresponds to the case (exposed) group for case-control studies
NF2
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
nitrofurantoin group between antibiotic treatment
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

Lab analysis

Sequencing type Experimental technique used for quantifying microbial abundance
16S

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
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)?
Yes


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

Needs review

Curated date: 2021/10/15

Curator: Mmarin

Revision editor(s): Mmarin

Source: Table S2

Description: Median values of taxa abundance.Taxa with median proportion >0.5% in at least one of two significantly different (P<0.05) groups of samples are presented. The statistical analysis method used was a Wilcoxon signed-rank test ('paired') and Wilcoxon rank sum ('non paired').

Abundance in Group 1: increased abundance in NF2

NCBI Links
Alistipes
Bacteroidales
Bacteroidetes
Bacteroidia
Faecalibacterium
Rikenellaceae

Revision editor(s): Mmarin