Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms
Urinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs are commonly associated with colonization by Escherichia coli, members of this species also have been found within the bladder of individuals with no lower urinary tract symptoms (no LUTS), also known a...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
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Frontiers Media S.A.
2020-09-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2020.02094/full |
| _version_ | 1818306502188859392 |
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| author | Andrea Garretto Taylor Miller-Ensminger Adriana Ene Zubia Merchant Aashaka Shah Athina Gerodias Anthony Biancofiori Stacey Canchola Stephanie Canchola Emanuel Castillo Tasnim Chowdhury Nikita Gandhi Sarah Hamilton Kyla Hatton Syed Hyder Koty Krull Demetrios Lagios Thinh Lam Kennedy Mitchell Christine Mortensen Amber Murphy Joseph Richburg Meghan Rokas Suzanne Ryclik Pauline Sulit Thomas Szwajnos Manuel Widuch Jessica Willis Mary Woloszyn Bridget Brassil Genevieve Johnson Rita Mormando Laura Maskeri Mary Batrich Nicole Stark Jason W. Shapiro Cesar Montelongo Hernandez Swarnali Banerjee Alan J. Wolfe Catherine Putonti Catherine Putonti Catherine Putonti Catherine Putonti |
| author_facet | Andrea Garretto Taylor Miller-Ensminger Adriana Ene Zubia Merchant Aashaka Shah Athina Gerodias Anthony Biancofiori Stacey Canchola Stephanie Canchola Emanuel Castillo Tasnim Chowdhury Nikita Gandhi Sarah Hamilton Kyla Hatton Syed Hyder Koty Krull Demetrios Lagios Thinh Lam Kennedy Mitchell Christine Mortensen Amber Murphy Joseph Richburg Meghan Rokas Suzanne Ryclik Pauline Sulit Thomas Szwajnos Manuel Widuch Jessica Willis Mary Woloszyn Bridget Brassil Genevieve Johnson Rita Mormando Laura Maskeri Mary Batrich Nicole Stark Jason W. Shapiro Cesar Montelongo Hernandez Swarnali Banerjee Alan J. Wolfe Catherine Putonti Catherine Putonti Catherine Putonti Catherine Putonti |
| author_sort | Andrea Garretto |
| collection | DOAJ |
| description | Urinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs are commonly associated with colonization by Escherichia coli, members of this species also have been found within the bladder of individuals with no lower urinary tract symptoms (no LUTS), also known as asymptomatic bacteriuria. Prior studies have found that both uropathogenic E. coli (UPEC) strains and E. coli isolates that are not associated with UTIs encode for virulence factors. Thus, the reason(s) why E. coli sometimes causes UTI-like symptoms remain(s) elusive. In this study, the genomes of 66 E. coli isolates from adult female bladders were sequenced. These isolates were collected from four cohorts, including women: (1) without lower urinary tract symptoms, (2) overactive bladder symptoms, (3) urgency urinary incontinence, and (4) a clinical diagnosis of UTI. Comparative genomic analyses were conducted, including core and accessory genome analyses, virulence and motility gene analyses, and antibiotic resistance prediction and testing. We found that the genomic content of these 66 E. coli isolates does not correspond with the participant’s symptom status. We thus looked beyond the E. coli genomes to the composition of the entire urobiome and found that the presence of E. coli alone was not sufficient to distinguish between the urobiomes of individuals with UTI and those with no LUTS. Because E. coli presence, abundance, and genomic content appear to be weak predictors of UTI status, we hypothesize that UTI symptoms associated with detection of E. coli are more likely the result of urobiome composition. |
| first_indexed | 2024-12-13T06:43:30Z |
| format | Article |
| id | doaj.art-51d9d5fc02cc4d7ebbf112699803c490 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-13T06:43:30Z |
| publishDate | 2020-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-51d9d5fc02cc4d7ebbf112699803c4902022-12-21T23:56:21ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-09-011110.3389/fmicb.2020.02094566478Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract SymptomsAndrea Garretto0Taylor Miller-Ensminger1Adriana Ene2Zubia Merchant3Aashaka Shah4Athina Gerodias5Anthony Biancofiori6Stacey Canchola7Stephanie Canchola8Emanuel Castillo9Tasnim Chowdhury10Nikita Gandhi11Sarah Hamilton12Kyla Hatton13Syed Hyder14Koty Krull15Demetrios Lagios16Thinh Lam17Kennedy Mitchell18Christine Mortensen19Amber Murphy20Joseph Richburg21Meghan Rokas22Suzanne Ryclik23Pauline Sulit24Thomas Szwajnos25Manuel Widuch26Jessica Willis27Mary Woloszyn28Bridget Brassil29Genevieve Johnson30Rita Mormando31Laura Maskeri32Mary Batrich33Nicole Stark34Jason W. Shapiro35Cesar Montelongo Hernandez36Swarnali Banerjee37Alan J. Wolfe38Catherine Putonti39Catherine Putonti40Catherine Putonti41Catherine Putonti42Bioinformatics Program, Loyola University Chicago, Chicago, IL, United StatesBioinformatics Program, Loyola University Chicago, Chicago, IL, United StatesBioinformatics Program, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesBioinformatics Program, Loyola University Chicago, Chicago, IL, United StatesBioinformatics Program, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesNeuroscience Program, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesBioinformatics Program, Loyola University Chicago, Chicago, IL, United StatesBioinformatics Program, Loyola University Chicago, Chicago, IL, United StatesBioinformatics Program, Loyola University Chicago, Chicago, IL, United StatesNiehoff School of Nursing, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United StatesDepartment of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, United StatesDepartment of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United StatesBioinformatics Program, Loyola University Chicago, Chicago, IL, United StatesDepartment of Biology, Loyola University Chicago, Chicago, IL, United StatesDepartment of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United StatesDepartment of Computer Science, Loyola University Chicago, Chicago, IL, United StatesUrinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs are commonly associated with colonization by Escherichia coli, members of this species also have been found within the bladder of individuals with no lower urinary tract symptoms (no LUTS), also known as asymptomatic bacteriuria. Prior studies have found that both uropathogenic E. coli (UPEC) strains and E. coli isolates that are not associated with UTIs encode for virulence factors. Thus, the reason(s) why E. coli sometimes causes UTI-like symptoms remain(s) elusive. In this study, the genomes of 66 E. coli isolates from adult female bladders were sequenced. These isolates were collected from four cohorts, including women: (1) without lower urinary tract symptoms, (2) overactive bladder symptoms, (3) urgency urinary incontinence, and (4) a clinical diagnosis of UTI. Comparative genomic analyses were conducted, including core and accessory genome analyses, virulence and motility gene analyses, and antibiotic resistance prediction and testing. We found that the genomic content of these 66 E. coli isolates does not correspond with the participant’s symptom status. We thus looked beyond the E. coli genomes to the composition of the entire urobiome and found that the presence of E. coli alone was not sufficient to distinguish between the urobiomes of individuals with UTI and those with no LUTS. Because E. coli presence, abundance, and genomic content appear to be weak predictors of UTI status, we hypothesize that UTI symptoms associated with detection of E. coli are more likely the result of urobiome composition.https://www.frontiersin.org/article/10.3389/fmicb.2020.02094/fullE. coliUPECUTIurinary microbiomeurobiome |
| spellingShingle | Andrea Garretto Taylor Miller-Ensminger Adriana Ene Zubia Merchant Aashaka Shah Athina Gerodias Anthony Biancofiori Stacey Canchola Stephanie Canchola Emanuel Castillo Tasnim Chowdhury Nikita Gandhi Sarah Hamilton Kyla Hatton Syed Hyder Koty Krull Demetrios Lagios Thinh Lam Kennedy Mitchell Christine Mortensen Amber Murphy Joseph Richburg Meghan Rokas Suzanne Ryclik Pauline Sulit Thomas Szwajnos Manuel Widuch Jessica Willis Mary Woloszyn Bridget Brassil Genevieve Johnson Rita Mormando Laura Maskeri Mary Batrich Nicole Stark Jason W. Shapiro Cesar Montelongo Hernandez Swarnali Banerjee Alan J. Wolfe Catherine Putonti Catherine Putonti Catherine Putonti Catherine Putonti Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms Frontiers in Microbiology E. coli UPEC UTI urinary microbiome urobiome |
| title | Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms |
| title_full | Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms |
| title_fullStr | Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms |
| title_full_unstemmed | Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms |
| title_short | Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms |
| title_sort | genomic survey of e coli from the bladders of women with and without lower urinary tract symptoms |
| topic | E. coli UPEC UTI urinary microbiome urobiome |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2020.02094/full |
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