Intestinal microbiome as a risk factor for urinary tract infections in children

From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-10
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Paalanne N, Husso A, Salo J, Pieviläinen O, Tejesvi MV, Koivusaari P, Pirttilä AM, Pokka T, Mattila S, Jyrkäs J, Turpeinen A, Uhari M, Renko M, Tapiainen T
Journal
European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology
Year
2018
As urinary tract infection (UTI) pathogens originate from the gut, we hypothesized that the gut environment reflected by intestinal microbiome influences the risk of UTI. Our prospective case-control study compared the intestinal microbiomes of 37 children with a febrile UTI with those of 69 healthy children. We sequenced the regions of the bacterial 16S rRNA gene and used the LefSe algorithm to calculate the size of the linear discriminant analysis (LDA) effect. We measured fecal lactoferrin and iron concentrations and quantitative PCR for Escherichia coli. At the phylum level, there were no significant differences. At the genus level, Enterobacter was more abundant in UTI patients with an LDA score > 3 (log 10), while Peptostreptococcaceae were more abundant in healthy subjects with an LDA score > 3 (log 10). In total, 20 OTUs with significantly different abundances were observed. Previous use of antimicrobials did not associate with intestinal microbiome. The relative abundance of E. coli was 1.9% in UTI patients and 0.5% in controls (95% CI of the difference-0.8 to 3.6%). The mean concentration of E.coli in quantitative PCR was 0.14 ng/μl in the patients and 0.08 ng/μl in the controls (95% CI of the difference-0.04 to 0.16). Fecal iron and lactoferrin concentrations were similar between the groups. At the family and genus level, we noted several differences in the intestinal microbiome between children with UTI and healthy children, which may imply that the gut environment is linked with the risk of UTI in children.

Experiment 1


Reviewed Marked as Reviewed by Atrayees on 2023-7-10

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): LGeistlinger, Chloe, WikiWorks, Atrayees

Subjects

Location of subjects
Finland
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
Urinary tract infection 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
healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
urinary tract infection
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
urinary tract infection
Group 0 sample size Number of subjects in the control (unexposed) group
69
Group 1 sample size Number of subjects in the case (exposed) group
37

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4-V5
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Ion Torrent

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
LEfSe
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
3
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
3
Matched on Factors on which subjects have been matched on in a case-control study
age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-7-10

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

Source: Figure 2

Description: Comaprison between UTI patients and Health controls using linear discriminant analysis

Abundance in Group 1: increased abundance in urinary tract infection

NCBI Quality ControlLinks
Enterobacter
Holdemania massiliensis
Priestia flexa
Enterocloster asparagiformis
Enterococcus dispar
Blautia glucerasea

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-10

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Fatima, WikiWorks

Source: Figure 2

Description: Comaprison between UTI patients and Health controls using linear discriminant analysis

Abundance in Group 1: decreased abundance in urinary tract infection

NCBI Quality ControlLinks
Clostridium tertium
Dialister
Finegoldia
Finegoldia magna
Haemophilus
Haemophilus parainfluenzae
Massilia
Oxalobacteraceae
Pasteurellaceae
Pasteurellales
Peptostreptococcaceae
Hoylesella timonensis
Massilia aurea
Romboutsia lituseburensis

Revision editor(s): Fatima, WikiWorks