<i>Escherichia coli</i> 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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| Format: | Article |
| Language: | English |
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MDPI AG
2021-06-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/7/1416 |
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| author | Karen Leth Nielsen Marc Stegger Kristoffer Kiil Berit Lilje Karen Ejrnæs Rikke Fleron Leihof Line Skjøt-Rasmussen Paul Godfrey Tor Monsen Sven Ferry Anette M. Hammerum Niels Frimodt-Møller |
| author_facet | Karen Leth Nielsen Marc Stegger Kristoffer Kiil Berit Lilje Karen Ejrnæs Rikke Fleron Leihof Line Skjøt-Rasmussen Paul Godfrey Tor Monsen Sven Ferry Anette M. Hammerum Niels Frimodt-Møller |
| author_sort | Karen Leth Nielsen |
| collection | DOAJ |
| 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 <i>Escherichia coli</i> 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. |
| first_indexed | 2024-03-10T09:54:51Z |
| format | Article |
| id | doaj.art-8434f52b32ac428fb0f8145a29cf3489 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T09:54:51Z |
| publishDate | 2021-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-8434f52b32ac428fb0f8145a29cf34892023-11-22T02:26:57ZengMDPI AGMicroorganisms2076-26072021-06-0197141610.3390/microorganisms9071416<i>Escherichia coli</i> Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent InfectionsKaren Leth Nielsen0Marc Stegger1Kristoffer Kiil2Berit Lilje3Karen Ejrnæs4Rikke Fleron Leihof5Line Skjøt-Rasmussen6Paul Godfrey7Tor Monsen8Sven Ferry9Anette M. Hammerum10Niels Frimodt-Møller11Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, DenmarkDepartment of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, DenmarkDepartment of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, DenmarkDepartment of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, DenmarkDepartment of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, DenmarkDepartment of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, DenmarkDepartment of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, DenmarkGenome Sequencing and Analysis Program, Institute of Technology, Broad Institute of Harvard and Massachusetts, Cambridge, MA 02142, USADepartment of Clinical Microbiology, University of Umeå, 901 04 Umeå, SwedenDepartment of Clinical Microbiology, University of Umeå, 901 04 Umeå, SwedenDepartment of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, DenmarkDepartment of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, DenmarkRecurrent 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 <i>Escherichia coli</i> 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.https://www.mdpi.com/2076-2607/9/7/1416whole-genome sequencingurinary tract infectionmobilomesingle nucleotide polymorphismsadaptationgenomics |
| spellingShingle | Karen Leth Nielsen Marc Stegger Kristoffer Kiil Berit Lilje Karen Ejrnæs Rikke Fleron Leihof Line Skjøt-Rasmussen Paul Godfrey Tor Monsen Sven Ferry Anette M. Hammerum Niels Frimodt-Møller <i>Escherichia coli</i> Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections Microorganisms whole-genome sequencing urinary tract infection mobilome single nucleotide polymorphisms adaptation genomics |
| title | <i>Escherichia coli</i> Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections |
| title_full | <i>Escherichia coli</i> Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections |
| title_fullStr | <i>Escherichia coli</i> Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections |
| title_full_unstemmed | <i>Escherichia coli</i> Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections |
| title_short | <i>Escherichia coli</i> Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections |
| title_sort | i escherichia coli i causing recurrent urinary tract infections comparison to non recurrent isolates and genomic adaptation in recurrent infections |
| topic | whole-genome sequencing urinary tract infection mobilome single nucleotide polymorphisms adaptation genomics |
| url | https://www.mdpi.com/2076-2607/9/7/1416 |
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