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Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections

Recurrent urinary tract infection (rUTI) remains a major problem for many women and therefore the pursuit for genomic and phenotypic traits which could define rUTI has been ongoing. The present study applied a genomic approach to investigate recurrent urinary tract infections by comparative analyses...

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Autores principales: Nielsen, Karen Leth, Stegger, Marc, Kiil, Kristoffer, Lilje, Berit, Ejrnæs, Karen, Leihof, Rikke Fleron, Skjøt-Rasmussen, Line, Godfrey, Paul, Monsen, Tor, Ferry, Sven, Hammerum, Anette M., Frimodt-Møller, Niels
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8303582/
https://www.ncbi.nlm.nih.gov/pubmed/34209190
http://dx.doi.org/10.3390/microorganisms9071416
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author Nielsen, Karen Leth
Stegger, Marc
Kiil, Kristoffer
Lilje, Berit
Ejrnæs, Karen
Leihof, Rikke Fleron
Skjøt-Rasmussen, Line
Godfrey, Paul
Monsen, Tor
Ferry, Sven
Hammerum, Anette M.
Frimodt-Møller, Niels
author_facet Nielsen, Karen Leth
Stegger, Marc
Kiil, Kristoffer
Lilje, Berit
Ejrnæs, Karen
Leihof, Rikke Fleron
Skjøt-Rasmussen, Line
Godfrey, Paul
Monsen, Tor
Ferry, Sven
Hammerum, Anette M.
Frimodt-Møller, Niels
author_sort Nielsen, Karen Leth
collection PubMed
description Recurrent urinary tract infection (rUTI) remains a major problem for many women and therefore the pursuit for genomic and phenotypic traits which could define rUTI has been ongoing. The present study applied a genomic approach to investigate recurrent urinary tract infections by comparative analyses of recurrent and non-recurrent Escherichia coli isolates from general practice. From whole-genome sequencing data, phylogenetic clustering and genomic traits were studied on a collection of isolates which caused recurrent infection compared to non-recurrent isolates. In addition, genomic variation between the 1st and following infection was studied on a subset of the isolates. Evidence of limited adaptation between the recurrent infections based on single nucleotide polymorphism analyses with a range of 0–13 non-synonymous single nucleotide polymorphisms (SNPs) between the paired isolates. This included an overrepresentation of SNPs in metabolism genes. We identified several genes which were more common in rUTI isolates, including nine fimbrial genes, however, not significantly after false-discovery rate. Finally, the results show that recurrent isolates of the present dataset are not distinctive by variation in the core genome, and thus, did not cluster distinct from non-rUTI isolates in a SNP phylogeny.
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spelling pubmed-83035822021-07-25 Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections Nielsen, Karen Leth Stegger, Marc Kiil, Kristoffer Lilje, Berit Ejrnæs, Karen Leihof, Rikke Fleron Skjøt-Rasmussen, Line Godfrey, Paul Monsen, Tor Ferry, Sven Hammerum, Anette M. Frimodt-Møller, Niels Microorganisms Article Recurrent urinary tract infection (rUTI) remains a major problem for many women and therefore the pursuit for genomic and phenotypic traits which could define rUTI has been ongoing. The present study applied a genomic approach to investigate recurrent urinary tract infections by comparative analyses of recurrent and non-recurrent Escherichia coli isolates from general practice. From whole-genome sequencing data, phylogenetic clustering and genomic traits were studied on a collection of isolates which caused recurrent infection compared to non-recurrent isolates. In addition, genomic variation between the 1st and following infection was studied on a subset of the isolates. Evidence of limited adaptation between the recurrent infections based on single nucleotide polymorphism analyses with a range of 0–13 non-synonymous single nucleotide polymorphisms (SNPs) between the paired isolates. This included an overrepresentation of SNPs in metabolism genes. We identified several genes which were more common in rUTI isolates, including nine fimbrial genes, however, not significantly after false-discovery rate. Finally, the results show that recurrent isolates of the present dataset are not distinctive by variation in the core genome, and thus, did not cluster distinct from non-rUTI isolates in a SNP phylogeny. MDPI 2021-06-30 /pmc/articles/PMC8303582/ /pubmed/34209190 http://dx.doi.org/10.3390/microorganisms9071416 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Nielsen, Karen Leth
Stegger, Marc
Kiil, Kristoffer
Lilje, Berit
Ejrnæs, Karen
Leihof, Rikke Fleron
Skjøt-Rasmussen, Line
Godfrey, Paul
Monsen, Tor
Ferry, Sven
Hammerum, Anette M.
Frimodt-Møller, Niels
Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections
title Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections
title_full Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections
title_fullStr Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections
title_full_unstemmed Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections
title_short Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections
title_sort escherichia coli causing recurrent urinary tract infections: comparison to non-recurrent isolates and genomic adaptation in recurrent infections
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8303582/
https://www.ncbi.nlm.nih.gov/pubmed/34209190
http://dx.doi.org/10.3390/microorganisms9071416
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