Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant <italic toggle="yes">In Situ</italic> Populations

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, primari...

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Autores principales:	Dana Willner, Serene Low, Jason A. Steen, Narelle George, Graeme R. Nimmo, Mark A. Schembri, Philip Hugenholtz
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2014
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/4863aac139174975b23aa3b4ced9ea6c
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spelling	oai:doaj.org-article:4863aac139174975b23aa3b4ced9ea6c2021-11-15T15:45:13ZSingle Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant <italic toggle="yes">In Situ</italic> Populations10.1128/mBio.01064-132150-7511https://doaj.org/article/4863aac139174975b23aa3b4ced9ea6c2014-05-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01064-13https://doaj.org/toc/2150-7511ABSTRACT 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. IMPORTANCE In clinical practice, the diagnosis and treatment of acute uncomplicated urinary tract infection (UTI) are based on analysis of a single bacterial isolate cultured from urine, and it is assumed that this isolate represents the dominant UTI pathogen. However, these methods detect only culturable bacteria, and the existence of multiple pathogens as well as strain diversity within a single infection is not examined. Here, we explored bacteria present in acute uncomplicated UTIs using culture-independent sequence-based methods. Escherichia coli was the most common organism identified, and analysis of E. coli dominant UTI samples and their paired clinical isolates revealed that in the majority of infections the cultured isolate was representative of the dominant taxon at both the genus and the strain level. Our data demonstrate that in most cases single cultured isolates are diagnostic of UTI and are consistent with the notion of bottlenecks that limit strain diversity during UTI pathogenesis.Dana WillnerSerene LowJason A. SteenNarelle GeorgeGraeme R. NimmoMark A. SchembriPhilip HugenholtzAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 5, Iss 2 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Dana Willner Serene Low Jason A. Steen Narelle George Graeme R. Nimmo Mark A. Schembri Philip Hugenholtz Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant <italic toggle="yes">In Situ</italic> Populations
description	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. IMPORTANCE In clinical practice, the diagnosis and treatment of acute uncomplicated urinary tract infection (UTI) are based on analysis of a single bacterial isolate cultured from urine, and it is assumed that this isolate represents the dominant UTI pathogen. However, these methods detect only culturable bacteria, and the existence of multiple pathogens as well as strain diversity within a single infection is not examined. Here, we explored bacteria present in acute uncomplicated UTIs using culture-independent sequence-based methods. Escherichia coli was the most common organism identified, and analysis of E. coli dominant UTI samples and their paired clinical isolates revealed that in the majority of infections the cultured isolate was representative of the dominant taxon at both the genus and the strain level. Our data demonstrate that in most cases single cultured isolates are diagnostic of UTI and are consistent with the notion of bottlenecks that limit strain diversity during UTI pathogenesis.
format	article
author	Dana Willner Serene Low Jason A. Steen Narelle George Graeme R. Nimmo Mark A. Schembri Philip Hugenholtz
author_facet	Dana Willner Serene Low Jason A. Steen Narelle George Graeme R. Nimmo Mark A. Schembri Philip Hugenholtz
author_sort	Dana Willner
title	Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant <italic toggle="yes">In Situ</italic> Populations
title_short	Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant <italic toggle="yes">In Situ</italic> Populations
title_full	Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant <italic toggle="yes">In Situ</italic> Populations
title_fullStr	Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant <italic toggle="yes">In Situ</italic> Populations
title_full_unstemmed	Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant <italic toggle="yes">In Situ</italic> Populations
title_sort	single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant <italic toggle="yes">in situ</italic> populations
publisher	American Society for Microbiology
publishDate	2014
url	https://doaj.org/article/4863aac139174975b23aa3b4ced9ea6c
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Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant <italic toggle="yes">In Situ</italic> Populations

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