Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant In Situ populations

Willner, Dana, Low, Serene, Steen, Jason A., George, Narelle, Nimmo, Graeme R., Schembri, Mark A. and Hugenholtz, Philip (2014) Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant In Situ populations. mBio, 5 2: e01064-13.1-e01064-13.10. doi:10.1128/mBio.01064-13


Author Willner, Dana
Low, Serene
Steen, Jason A.
George, Narelle
Nimmo, Graeme R.
Schembri, Mark A.
Hugenholtz, Philip
Title Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant In Situ populations
Journal name mBio   Check publisher's open access policy
ISSN 2150-7511
Publication date 2014-02-25
Year available 2014
Sub-type Article (original research)
DOI 10.1128/mBio.01064-13
Open Access Status DOI
Volume 5
Issue 2
Start page e01064-13.1
End page e01064-13.10
Total pages 10
Place of publication Washington DC, United States
Publisher American Society for Microbiology
Language eng
Abstract Urinary tract infections (UTIs) are one of the most commonly acquired bacterial infections in humans, and uropathogenic Escherichia coli strains are responsible for over 80% of all cases. The standard method for identification of uropathogens in clinical laboratories is cultivation, primarily using solid growth media under aerobic conditions, coupled with morphological and biochemical tests of typically a single isolate colony. However, these methods detect only culturable microorganisms, and characterization is phenotypic in nature. Here, we explored the genotypic identity of communities in acute uncomplicated UTIs from 50 individuals by using culture-independent amplicon pyrosequencing and whole-genome and metagenomic shotgun sequencing. Genus-level characterization of the UTI communities was achieved using the 16S rRNA gene (V8 region). Overall UTI community richness was very low in comparison to other human microbiomes. We strain-typed Escherichia-dominated UTIs using amplicon pyrosequencing of the fimbrial adhesin gene, fimH. There were nine highly abundant fimH types, and each UTI sample was dominated by a single type. Molecular analysis of the corresponding clinical isolates revealed that in the majority of cases the isolate was representative of the dominant taxon in the community at both the genus and the strain level. Shotgun sequencing was performed on a subset of eight E. coli urine UTI and isolate pairs. The majority of UTI microbial metagenomic sequences mapped to isolate genomes, confirming the results obtained using phylogenetic markers. We conclude that for the majority of acute uncomplicated E. coli-mediated UTIs, single cultured isolates are diagnostic of the infection.
Formatted abstract
Urinary tract infections (UTIs) are one of the most commonly acquired bacterial infections in humans, and uropathogenic Escherichia coli strains are responsible for over 80% of all cases. The standard method for identification of uropathogens in clinical laboratories is cultivation, primarily using solid growth media under aerobic conditions, coupled with morphological and biochemical tests of typically a single isolate colony. However, these methods detect only culturable microorganisms, and characterization is phenotypic in nature. Here, we explored the genotypic identity of communities in acute uncomplicated UTIs from 50 individuals by using culture-independent amplicon pyrosequencing and whole-genome and metagenomic shotgun sequencing. Genus-level characterization of the UTI communities was achieved using the 16S rRNA gene (V8 region). Overall UTI community richness was very low in comparison to other human microbiomes. We strain-typed Escherichia-dominated UTIs using amplicon pyrosequencing of the fimbrial adhesin gene, fimH. There were nine highly abundant fimH types, and each UTI sample was dominated by a single type. Molecular analysis of the corresponding clinical isolates revealed that in the majority of cases the isolate was representative of the dominant taxon in the community at both the genus and the strain level. Shotgun sequencing was performed on a subset of eight E. coli urine UTI and isolate pairs. The majority of UTI microbial metagenomic sequences mapped to isolate genomes, confirming the results obtained using phylogenetic markers. We conclude that for the majority of acute uncomplicated E. coli-mediated UTIs, single cultured isolates are diagnostic of the infection.
Keyword Microbiology
Microbiology
MICROBIOLOGY
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID APP1005315
DP120103498
FT100100662
Institutional Status UQ

 
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