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Ruța F, Pribac M, Mardale E, Suciu S, Maior R, Bogdan S, Avram C. Associations between Gut Microbiota Dysbiosis and Other Risk Factors in Women with a History of Urinary Tract Infections. Nutrients 2024; 16:1753. [PMID: 38892685 PMCID: PMC11174854 DOI: 10.3390/nu16111753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
(1) Background: Urinary tract infections (UTIs) are among otherwise healthy women represent a problem that requires additional understanding and approaches. Evidencing the link between dysbiosis and UTIs and the associated potential risk factors could lead to therapeutic approaches with increased efficiency under the conditions of reducing the risks associated with antibiotic treatments. The purpose of this study was to evaluate dysbiosis and other potential risk factors in women with a history of urinary tract infections; (2) Methods: Fecal dysbiosis tests were performed comparatively in two groups of women. The first group in-cluded women with recurrent urinary tract infections (rUTI) who had either two or more symp-tomatic episodes of UTI in the previous six months. The second group included women with spo-radic UTIs who did not have >1 UTI during a 12-month period and who did not have another UTI in the last 12 months; (3) Results: An association was shown between intestinal dysbiosis and recurrences of urinary tract infections. Increased body weight was associated with intestinal dysbiosis. Also, the lack of knowledge regarding the risk of using antibiotics and the benefits of probiotics was associated with both dysbiosis and recurrences of urinary tract infections; (4) Conclusions: Dysbiosis can have an impact on the recurrence of urinary tract infections. The risk factors for rUTI and dysbiosis in the sphere of lifestyle are potentially controllable, broadening the perspective for new approaches and changing the paradigm in the treatment of urinary tract infections.
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Affiliation(s)
- Florina Ruța
- George Emil Palade University of Medicine Pharmacy, Science and Technology of Targu Mures, 540142 Targu Mures, Romania; (F.R.); (S.S.)
| | - Mirela Pribac
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania
| | | | - Sara Suciu
- George Emil Palade University of Medicine Pharmacy, Science and Technology of Targu Mures, 540142 Targu Mures, Romania; (F.R.); (S.S.)
| | - Raluca Maior
- Anti-Aging Nutrition Clinic, 540142 Targu Mures, Romania;
| | | | - Călin Avram
- George Emil Palade University of Medicine Pharmacy, Science and Technology of Targu Mures, 540142 Targu Mures, Romania; (F.R.); (S.S.)
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2
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Young MG, Straub TJ, Worby CJ, Metsky HC, Gnirke A, Bronson RA, van Dijk LR, Desjardins CA, Matranga C, Qu J, Villicana JB, Azimzadeh P, Kau A, Dodson KW, Schreiber HL, Manson AL, Hultgren SJ, Earl AM. Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582780. [PMID: 38463963 PMCID: PMC10925322 DOI: 10.1101/2024.02.29.582780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Low-abundance members of microbial communities are difficult to study in their native habitats. This includes Escherichia coli, a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urinary tract, where it is the primary pathogen. While multi-omic analyses have detailed critical interactions between uropathogenic Escherichia coli (UPEC) and the bladder that mediate UTI outcome, comparatively little is known about UPEC in its pre-infection reservoir, partly due to its low abundance there (<1% relative abundance). To accurately and sensitively explore the genomes and transcriptomes of diverse E. coli in gastrointestinal communities, we developed E. coli PanSelect which uses a set of probes designed to specifically recognize and capture E. coli's broad pangenome from sequencing libraries. We demonstrated the ability of E. coli PanSelect to enrich, by orders of magnitude, sequencing data from diverse E. coli using a mock community and a set of human stool samples collected as part of a cohort study investigating drivers of recurrent urinary tract infections (rUTI). Comparisons of genomes and transcriptomes between E. coli residing in the gastrointestinal tracts of women with and without a history of rUTI suggest that rUTI gut E. coli are responding to increased levels of oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of native in vivo biology of E. coli in other environments where it is at low relative abundance, and the framework described here has broad applicability to other highly diverse, low abundance organisms.
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Affiliation(s)
- Mark G Young
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Timothy J Straub
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Colin J Worby
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Hayden C Metsky
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Andreas Gnirke
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Ryan A Bronson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Lucas R van Dijk
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands
| | | | - Christian Matranga
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - James Qu
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Jesús Bazan Villicana
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Philippe Azimzadeh
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew Kau
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Karen W Dodson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Henry L Schreiber
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Abigail L Manson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashlee M Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
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3
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Shea AE, Forsyth VS, Stocki JA, Mitchell TJ, Frick-Cheng AE, Smith SN, Hardy SL, Mobley HLT. Emerging roles for ABC transporters as virulence factors in uropathogenic Escherichia coli. Proc Natl Acad Sci U S A 2024; 121:e2310693121. [PMID: 38607934 PMCID: PMC11032443 DOI: 10.1073/pnas.2310693121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 03/07/2024] [Indexed: 04/14/2024] Open
Abstract
Urinary tract infections (UTI) account for a substantial financial burden globally. Over 75% of UTIs are caused by uropathogenic Escherichia coli (UPEC), which have demonstrated an extraordinarily rapid growth rate in vivo. This rapid growth rate appears paradoxical given that urine and the human urinary tract are relatively nutrient-restricted. Thus, we lack a fundamental understanding of how uropathogens propel growth in the host to fuel pathogenesis. Here, we used large in silico, in vivo, and in vitro screens to better understand the role of UPEC transport mechanisms and their contributions to uropathogenesis. In silico analysis of annotated transport systems indicated that the ATP-binding cassette (ABC) family of transporters was most conserved among uropathogenic bacterial species, suggesting their importance. Consistent with in silico predictions, we determined that the ABC family contributed significantly to fitness and virulence in the urinary tract: these were overrepresented as fitness factors in vivo (37.2%), liquid media (52.3%), and organ agar (66.2%). We characterized 12 transport systems that were most frequently defective in screening experiments by generating in-frame deletions. These mutant constructs were tested in urovirulence phenotypic assays and produced differences in motility and growth rate. However, deletion of multiple transport systems was required to achieve substantial fitness defects in the cochallenge murine model. This is likely due to genetic compensation among transport systems, highlighting the centrality of ABC transporters in these organisms. Therefore, these nutrient uptake systems play a concerted, critical role in pathogenesis and are broadly applicable candidate targets for therapeutic intervention.
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Affiliation(s)
- Allyson E. Shea
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Valerie S. Forsyth
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Jolie A. Stocki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Taylor J. Mitchell
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Arwen E. Frick-Cheng
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Sara N. Smith
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
| | - Sicily L. Hardy
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, AL36688
| | - Harry L. T. Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI48109
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4
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Du J, Khemmani M, Halverson T, Ene A, Limeira R, Tinawi L, Hochstedler-Kramer BR, Noronha MF, Putonti C, Wolfe AJ. Cataloging the phylogenetic diversity of human bladder bacterial isolates. Genome Biol 2024; 25:75. [PMID: 38515176 PMCID: PMC10958879 DOI: 10.1186/s13059-024-03216-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, such as the gut and oral cavity. RESULTS To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, we present a bladder-specific bacterial isolate reference collection comprising 1134 genomes, primarily from adult females. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial isolate reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2% of the genera found when re-examining previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis finds that the taxonomies and functions of the bladder microbiota share more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder Escherichia coli isolates and 387 gut Escherichia coli isolates support the hypothesis that phylogroup distribution and functions of Escherichia coli strains differ dramatically between these two very different niches. CONCLUSIONS This bladder-specific bacterial isolate reference collection is a unique resource that will enable bladder microbiota research and comparison to isolates from other anatomical sites.
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Affiliation(s)
- Jingjie Du
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Present address: Division of Nutritional Science, Cornell University, Ithaca, NY, 14850, USA
| | - Mark Khemmani
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Thomas Halverson
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Roberto Limeira
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Lana Tinawi
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Baylie R Hochstedler-Kramer
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Melline Fontes Noronha
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, 60660, USA
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Alan J Wolfe
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
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5
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Sheng N, Mårell L, Sitaram RT, Svensäter G, Westerlund A, Strömberg N. Human PRH1, PRH2 susceptibility and resistance and Streptococcus mutans virulence phenotypes specify different microbial profiles in caries. EBioMedicine 2024; 101:105001. [PMID: 38364699 PMCID: PMC10878843 DOI: 10.1016/j.ebiom.2024.105001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Lifestyle- and sucrose-dependent polymicrobial ecological shifts are a primary cause of caries in populations with high caries prevalence. In populations with low prevalence, PRH1, PRH2 susceptibility and resistance phenotypes may interact with the Streptococcus mutans adhesin cariogenicity phenotype to affect caries progression, but studies are lacking on how these factors affect the microbial profile of caries. METHODS We analysed how the residency and infection profiles of S. mutans adhesin (SpaP A/B/C and Cnm/Cbm) phenotypes and commensal streptococci and lactobacilli influenced caries progression in a prospective case-referent sample of 452 Swedish adolescents with high (P4a), moderate (P6), and low (P1) caries PRH1, PRH2 phenotypes. Isolates of S. mutans from participants were analysed for adhesin expression and glycosylation and in vitro and in situ mechanisms related to caries activity. FINDINGS Among adolescents with the resistant (P1) phenotype, infection with S. mutans high-virulence phenotypes was required for caries progression. In contrast, with highly (P4a) or moderately (P6) susceptible phenotypes, caries developed from a broader polymicrobial flora that included moderately cariogenic oral commensal streptococci and lactobacilli and S. mutans phenotypes. High virulence involved unstable residency and fluctuating SpaP ABC, B-1, or Cnm expression/glycosylation phenotypes, whereas low/moderate virulence involved SpaP A phenotypes with stable residency. Adhesin phenotypes did not display changes in individual host residency but were paired within individuals and geographic regions. INTERPRETATION These results suggest that receptor PRH1, PRH2 susceptibility and resistance and S. mutans adhesin virulence phenotypes specify different microbial profiles in caries. FUNDING Swedish Research Council and funding bodies listed in the acknowledgement section.
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Affiliation(s)
- Nongfei Sheng
- Department of Odontology/Cariology, Umeå University, 901 87, Umeå, Sweden
| | - Lena Mårell
- Department of Odontology/Cariology, Umeå University, 901 87, Umeå, Sweden
| | | | | | - Anna Westerlund
- Department of Orthodontics, Sahlgrenska Academy, University of Gothenburg, 413 90, Göteborg, Sweden
| | - Nicklas Strömberg
- Department of Odontology/Cariology, Umeå University, 901 87, Umeå, Sweden.
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6
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Isali I, Wong TR, Batur AF, Wu CHW, Schumacher FR, Pope R, Hijaz A, Sheyn D. Recurrent urinary tract infection genetic risk: a systematic review and gene network analysis. Int Urogynecol J 2024; 35:259-271. [PMID: 37917182 DOI: 10.1007/s00192-023-05671-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/11/2023] [Indexed: 11/04/2023]
Abstract
INTRODUCTION AND HYPOTHESIS The development of recurrent urinary tract infections (rUTIs) is not completely understood. This review is aimed at investigating the connection between genetics and rUTIs and summarizing the results of studies that have documented variations in gene expression among individuals with rUTIs compared with healthy individuals. METHODS A systematic search was conducted in Cochrane, Ovid, and PubMed, limiting the results to articles published between 1 January 2000, and 5 July 2022. Only studies comparing the difference in gene expression between individuals with rUTI and healthy individuals utilizing molecular techniques to measure gene expression in blood or urine samples were included in this systematic review. Gene network and pathways analyses were performed using Cytoscape software, with input data obtained from our systematic review of differentially expressed genes in rUTIs. RESULTS Six studies met our criteria for inclusion. The selected studies used molecular biology methods to quantify gene expression data from blood specimens. The analysis revealed that gene expressions of CXCR1 and TLR4 decreased, whereas CXCR2, TRIF, and SIGIRR increased in patients with rUTI compared with healthy controls. The analysis demonstrated that the most significant pathways were associated with TLR receptor signaling and tolerance, I-kappa B kinase/NF-kappa B signaling, and MyD88-independent TLR signaling. CONCLUSIONS This systematic review uncovered gene expression variations in several candidate genes and identified a number of underlying biological pathways associated with rUTIs. These findings could shift the treatment and prevention strategies for rUTIs.
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Affiliation(s)
- Ilaha Isali
- Department of Urology, University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
| | - Thomas R Wong
- Department of Urology, University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
| | - Ali Furkan Batur
- Department of Urology, University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
| | - Chen-Han Wilfred Wu
- Department of Urology, University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Fredrick R Schumacher
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Rachel Pope
- Department of Urology, University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
| | - Adonis Hijaz
- Department of Urology, University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
| | - David Sheyn
- Department of Urology, University Hospitals, Cleveland Medical Center, Cleveland, OH, USA.
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7
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Sampson T. Microbial amyloids in neurodegenerative amyloid diseases. FEBS J 2023:10.1111/febs.17023. [PMID: 38041542 PMCID: PMC11144261 DOI: 10.1111/febs.17023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/13/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023]
Abstract
Human-disease associated amyloidogenic proteins are not unique in their ability to form amyloid fibrillar structures. Numerous microbes produce amyloidogenic proteins that have distinct functions for their physiology in their amyloid form, rather than solely detrimental. Emerging data indicate associations between various microbial organisms, including those which produce functional amyloids, with neurodegenerative diseases. Here, we review some of the evidence suggesting that microbial amyloids impact amyloid disease in host organisms. Experimental data are building a foundation for continued lines of enquiry and suggest that that direct or indirect interactions between microbial and host amyloids may be a contributor to amyloid pathologies. Inhibiting microbial amyloids or their interactions with the host may therefore represent a tangible target to limit various amyloid pathologies.
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Affiliation(s)
- Timothy Sampson
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
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8
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Moglad E, Altayb HN. Genomic characterization of extended spectrum beta lactamases producing multidrug-resistant Escherichia coli clinically isolated harboring chromosomally mediated CTX-M-15 from Alkharj, KSA. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105526. [PMID: 37977421 DOI: 10.1016/j.meegid.2023.105526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Extended Spectrum Beta Lactamases (ESBLs) are the most prevalent enzymes conferring resistance to beta-lactams encoded on plasmids and rarely in chromosomes. This genomic study aims to characterize Escherichia coli to identify antimicrobial resistance genes (ARG), virulence factors, and phylogenetic relationships among ESBL-positive and negative isolates of E. coli obtained from Al-Kharj, Riyadh region, Saudi Arabia. Three clinical isolates from urine and vaginal swabs were obtained and subjected to whole genome sequencing, minimum inhibitory concentration, and antibiotic sensitivity tests. The pathogenicity and ARG were discovered, and the raw genomic sequences were assembled and annotated. Two isolates (E5 and E15) were MDR and ESBLs producers; the sequence type (ST) for E5 was 58, while those for E15 and E21 were 106. Most of the virulence genes were detected as plasmid-mediated; E21 was identified with a hyper-virulent plasmid (pH 2332-166) carrying different virulence factors (TraJ, traT, iss, etsC, hlyF, and iron acquisition associated proteins), plasmids (IncFII, IncFIB, and IncFIA), and insertion sequences (ISEc31). While most of the antimicrobial resistance genes were chromosomally mediated, a rare chromosome insertion of qnrS1 and blaCTX-M-15 with co-occurrence of Tn2 and ISKpn19 was identified in the E5 isolate. The consistent preservation of these genetic elements on bacterial chromosomes and plasmids could enhance the spread of Multidrug-Resistant (MDR) strains across various Enterobacteriaceae Species. This poses a significant threat to the effectiveness of existing antimicrobial treatments.
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Affiliation(s)
- Ehssan Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, P.O. Box 173, Alkharj 11942, Saudi Arabia.
| | - Hisham N Altayb
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 23589, Saudi Arabia
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9
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Mulder M, Notermans DW, Wielders CCH, Bos J, Witteveen S, Ganesh VA, Landman F, de Haan A, Schneeberger-van der Linden C, Hendrickx APA. OXA-48-Producing Uropathogenic Escherichia coli Sequence Type 127, the Netherlands, 2015-2022. Emerg Infect Dis 2023; 29:2563-2565. [PMID: 37987600 PMCID: PMC10683799 DOI: 10.3201/eid2912.231114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023] Open
Abstract
During 2015-2022, a genetic cluster of OXA-48-producing uropathogenic Escherichia coli sequence type 127 spread throughout the Netherlands. The 20 isolates we investigated originated mainly from urine, belonged to Clermont phylotype B2, and carried 18 genes encoding putative uropathogenicity factors. The isolates were susceptible to first-choice antimicrobial drugs for urinary tract infections.
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10
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Chagneau CV, Payros D, Goman A, Goursat C, David L, Okuno M, Bordignon PJ, Séguy C, Massip C, Branchu P, Ogura Y, Nougayrède JP, Marenda M, Oswald E. HlyF, an underestimated virulence factor of uropathogenic Escherichia coli. Clin Microbiol Infect 2023; 29:1449.e1-1449.e9. [PMID: 37532127 DOI: 10.1016/j.cmi.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
OBJECTIVES Urinary tract infections (UTIs) are primarily caused by uropathogenic Escherichia coli (UPEC). This study aims to elucidate the role of the virulence factor HlyF in the epidemiology and pathophysiology of UTIs and investigate the dissemination of plasmids carrying the hlyF gene. METHODS An epidemiological analysis was conducted on a representative collection of 225 UPEC strains isolated from community-acquired infections. Selected hlyF+ strains were fully sequenced using a combination of Illumina and Nanopore technologies. To investigate the impact of HlyF, a murine model of UTI was utilized to compare clinical signs, bacterial loads in the bladder, kidney, and spleen, onset of bacteraemia, and inflammation through cytokine quantification among wild-type hlyF+ strains, isogenic mutants, and complemented mutants. RESULTS Our findings demonstrate that 20% of UPEC encode the HlyF protein. These hlyF+ UPEC strains exhibited enhanced virulence, frequently leading to pyelonephritis accompanied by bloodstream infections. Unlike typical UPEC strains, hlyF+ UPEC strains demonstrate a broader phylogroup distribution and possess a unique array of virulence factors and antimicrobial resistance genes, primarily carried by ColV-like plasmids. In the murine UTI model, expression of HlyF was linked to the UPECs' capacity to induce urosepsis and elicit an exacerbated inflammatory response, setting them apart from typical UPEC strains. DISCUSSION Overall, our results strongly support the notion that HlyF serves as a significant virulence factor for UPECs, and the dissemination of ColV-like plasmids encoding HlyF warrants further investigation.
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Affiliation(s)
- Camille V Chagneau
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France; Service de Bactériologie-Hygiène, Univerity Hospital of Toulouse, Hôpital Purpan, Toulouse, France
| | - Delphine Payros
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Audrey Goman
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Cécile Goursat
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Laure David
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Pierre-Jean Bordignon
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Carine Séguy
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Clémence Massip
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France; Service de Bactériologie-Hygiène, Univerity Hospital of Toulouse, Hôpital Purpan, Toulouse, France
| | - Priscilla Branchu
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Yoshitoshi Ogura
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Jean-Philippe Nougayrède
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France
| | - Marc Marenda
- Melbourne Veterinary School, Faculty of Science, University of Melbourne, Melbourne, Australia
| | - Eric Oswald
- Digestive Health Research Institute (IRSD), National Institute of Health and Medical Research (INSERM), Université de Toulouse Paul Sabatier, National Research Institute for Agriculture, Food and the Environment (INRAE), National Veterinary School of Toulouse (ENVT), Toulouse, France; Service de Bactériologie-Hygiène, Univerity Hospital of Toulouse, Hôpital Purpan, Toulouse, France.
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11
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Ljubetic BM, Mohammad A, Durrani B, Dobberfuhl AD. Pathophysiologic Insights into the Transition from Asymptomatic Bacteriuria to Urinary Tract Infection. Curr Urol Rep 2023; 24:533-540. [PMID: 37856072 DOI: 10.1007/s11934-023-01183-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2023] [Indexed: 10/20/2023]
Abstract
PURPOSE OF REVIEW Asymptomatic bacteriuria (ASB) can be found in the general population but it is more common in catheterized patients. Some patients develop urinary tract infections (UTI) and others stay asymptomatic throughout time. The scientific community lacks a pathophysiologic explanation of why asymptomatic bacteriuria stays asymptomatic most of the time, and why and how it sometimes transitions to UTI. In an attempt to bridge this gap in knowledge, a summary of the current literature is conducted on the pathophysiologic differences between ASB and UTI, beyond their clinical differences. RECENT FINDINGS ASB and UTI cannot be differentiated just by their phylogroup or number of virulence factors. The difference may be in their metabolism gene expression. The literature lacks a pathophysiological explanation of the transition from ASB to UTI, and recent discoveries suggest that metabolic gene expression may hold the key.
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Affiliation(s)
- Bernardita M Ljubetic
- Department of Urology, Center for Academic Medicine, Urology-5656, Stanford University School of Medicine, 453 Quarry Road, Palo Alto, CA, 94304, USA
| | - Ashu Mohammad
- Department of Urology, Center for Academic Medicine, Urology-5656, Stanford University School of Medicine, 453 Quarry Road, Palo Alto, CA, 94304, USA
| | - Butool Durrani
- Department of Internal Medicine, Aga Khan University Hospital, National Stadium Rd, Karachi, Karachi City, Pakistan
| | - Amy D Dobberfuhl
- Department of Urology, Center for Academic Medicine, Urology-5656, Stanford University School of Medicine, 453 Quarry Road, Palo Alto, CA, 94304, USA.
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12
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Salamzade R, McElheny CL, Manson AL, Earl AM, Shaikh N, Doi Y. Genomic epidemiology and antibiotic susceptibility profiling of uropathogenic Escherichia coli among children in the United States. mSphere 2023; 8:e0018423. [PMID: 37581436 PMCID: PMC10597468 DOI: 10.1128/msphere.00184-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/15/2023] [Indexed: 08/16/2023] Open
Abstract
Escherichia coli is the most common cause of urinary tract infections (UTIs) in children, and yet the underlying mechanisms of virulence and antibiotic resistance and the overall population structure of the species is poorly understood within this age group. To investigate whether uropathogenic E. coli (UPEC) from children who developed pyelonephritis carried specific genetic markers, we generated whole-genome sequence data for 96 isolates from children with UTIs. This included 57 isolates from children with either radiologically confirmed pyelonephritis or cystitis and 27 isolates belonging to the well-known multidrug-resistant sequence type ST131, selected to investigate their population structure and antibiotic resistance characteristics. We observed a UPEC population structure that is similar to those reported in adults. In comparison with prior investigations, we found that the full pap operon was more common among UPEC from pediatric cases of pyelonephritis. Further, in contrast with recent reports that the P-fimbriae adhesin-encoding papGII allele is substantially more prevalent in invasive UPEC from adults, we found papGII was common to both invasive and non-invasive UPEC from children. Among the set of ST131 isolates from children with UTIs, we found antibiotic resistance was correlated with known genetic markers of resistance, as in adults. Unexpectedly, we observed that fimH30, an allele of the fimbrial gene fimH often used as a proxy to type ST131 isolates into the most drug-resistant subclade C, was carried by some of the subclade A and subclade B isolates, suggesting that the fimH30 allele could confer a selective advantage for UPEC. IMPORTANCE Urinary tract infections (UTIs), which are most often caused by Escherichia coli, are not well studied in children. Here, we examine genetic characteristics that differentiate UTI-causing bacteria in children that either remain localized to the bladder or are involved in more serious kidney infections. We also examine patterns of antibiotic resistance among strains from children that are part of E. coli sequence type 131, a group of bacteria that commonly cause UTIs and are known to have high levels of drug resistance. This work provides new insight into the virulence and antibiotic resistance characteristics of the bacteria that cause UTIs in children.
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Affiliation(s)
- Rauf Salamzade
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Christi L. McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Abigail L. Manson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Ashlee M. Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Nader Shaikh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Fujita Health University School of Medicine, Aichi, Japan
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13
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Hogins J, Xuan Z, Zimmern PE, Reitzer L. The distinct transcriptome of virulence-associated phylogenetic group B2 Escherichia coli. Microbiol Spectr 2023; 11:e0208523. [PMID: 37724859 PMCID: PMC10580932 DOI: 10.1128/spectrum.02085-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/28/2023] [Indexed: 09/21/2023] Open
Abstract
Escherichia coli strains of phylogenetic group B2 are often associated with urinary tract infections (UTIs) and several other diseases. Recent genomic and transcriptomic analyses have not suggested or identified specific genes required for virulence, but have instead suggested multiple virulence strategies and complex host-pathogen interactions. Previous analyses have not compared core gene expression between phylogenetic groups or between pathogens and nonpathogens within phylogenetic groups. We compared the core gene expression of 35 strains from three phylogenetic groups that included both pathogens and nonpathogens after growth in a medium that allowed comparable growth of both types of strains. K-means clustering suggested a B2 cluster with 17 group B2 strains and two group A strains; an AD cluster with six group A strains, five group D strains and one B2 strain; and four outliers which included the highly studied model uropathogenic E. coli strains UTI89 and CFT073. Half of the core genes were differentially expressed between B2 and AD cluster strains, including transcripts of genes for all aspects of macromolecular synthesis-replication, transcription, translation, and peptidoglycan synthesis-energy metabolism, and environmental-sensing transcriptional regulators. Notably, core gene expression between nonpathogenic and uropathogenic transcriptomes within phylogenetic groups did not differ. If differences between pathogens and nonpathogens exist, then the differences do not require transcriptional reprogramming. In summary, B2 cluster strains have a distinct transcription pattern that involves hundreds of genes. We propose that this transcription pattern is one factor that contributes to virulence. IMPORTANCE Escherichia coli is a diverse species and an opportunistic pathogen that is associated with various diseases, such as urinary tract infections. When examined, phylogenetic group B2 strains are more often associated with these diseases, but the specific properties that contribute to their virulence are not known. From a comparative transcriptomic analysis, we found that group B2 strains grown in a nutrient-rich medium had a distinct transcription pattern, which is the first evidence that core gene expression differs between phylogenetic groups. Understanding the consequences of group B2 transcription pattern will provide important information on basic E. coli biology, the basis for E. coli virulence, and possibly for developing therapies for a majority of urinary tract infections and other group B2-associated diseases.
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Affiliation(s)
- Jacob Hogins
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Philippe E. Zimmern
- Department of Urology, The University of Texas Southwestern, Dallas, Texas, USA
| | - Larry Reitzer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
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14
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Azam MW, Zarrilli R, Khan AU. Updates on the Virulence Factors Produced by Multidrug-Resistant Enterobacterales and Strategies to Control Their Infections. Microorganisms 2023; 11:1901. [PMID: 37630461 PMCID: PMC10456890 DOI: 10.3390/microorganisms11081901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/06/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
The Enterobacterales order is a massive group of Gram-negative bacteria comprised of pathogenic and nonpathogenic members, including beneficial commensal gut microbiota. The pathogenic members produce several pathogenic or virulence factors that enhance their pathogenic properties and increase the severity of the infection. The members of Enterobacterales can also develop resistance against the common antimicrobial agents, a phenomenon called antimicrobial resistance (AMR). Many pathogenic Enterobacterales members are known to possess antimicrobial resistance. This review discusses the virulence factors, pathogenicity, and infections caused by multidrug-resistant Enterobacterales, especially E. coli and some other bacterial species sharing similarities with the Enterobacterales members. We also discuss both conventional and modern approaches used to combat the infections caused by them. Understanding the virulence factors produced by the pathogenic bacteria will help develop novel strategies and methods to treat infections caused by them.
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Affiliation(s)
- Mohd W. Azam
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy
| | - Asad U. Khan
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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15
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Jiao L, Cao X, Wang C, Chen F, Zou H, Yue L, Wang Z. Crosstalk between in situ root exudates and rhizobacteria to promote rice growth by selenium nanomaterials. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:163175. [PMID: 37003329 DOI: 10.1016/j.scitotenv.2023.163175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/25/2023] [Accepted: 03/26/2023] [Indexed: 05/13/2023]
Abstract
Maximizing the potential of plant-microbe systems offers great opportunities to confront sustainability issues in agroecosystems. However, the dialog between root exudates and rhizobacteria remains largely unknown. As a novel nanofertilizer, nanomaterials (NMs) have significant potential to improve agricultural productivity due to their unique properties. Here, soil amendment with 0.1 mg·kg-1 selenium (Se) NMs (30-50 nm) significantly promoted rice seedling growth. Differences in root exudates and rhizobacteria were evident. At an earlier time point (3rd week), Se NMs increased the relative content of malic and citric acid by 15.4- and 8.1-fold, respectively. Meanwhile, the relative abundances of Streptomyces and Sphingomonas were increased by 164.6 % and 38.3 %, respectively. As the exposure time increased, succinic acid (40.5-fold) at the 4th week and salicylic acid (4.7-fold) and indole-3-acetic (7.0-fold) at the 5th week were enhanced, while Pseudomonas and Bacillus increased at the 4th (112.3 % and 50.2 %) and 5th weeks (190.8 % and 53.1 %), respectively. Further analysis indicated that (1) Se NMs directly enhanced the synthesis and secretion of malic and citric acids by upregulating their biosynthesis and transporter genes and then recruited Bacillus and Pseudomonas; (2) Se NMs upregulated the chemotaxis and flagellar genes of Sphingomonas for more interaction with rice plants, thereby promoting rice growth and stimulating root exudate secretion. This crosstalk of root exudates and rhizobacteria enhanced nutrient uptake, resulting in promoted rice growth. Our study offers insights into the crosstalk between root exudates and rhizobacteria by NMs and provides new insights into rhizosphere regulation in nano-enabled agriculture.
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Affiliation(s)
- Liya Jiao
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Xuesong Cao
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Chuanxi Wang
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Feiran Chen
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Hua Zou
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Le Yue
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China.
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
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16
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Morales G, Abelson B, Reasoner S, Miller J, Earl AM, Hadjifrangiskou M, Schmitz J. The Role of Mobile Genetic Elements in Virulence Factor Carriage from Symptomatic and Asymptomatic Cases of Escherichia coli Bacteriuria. Microbiol Spectr 2023; 11:e0471022. [PMID: 37195213 PMCID: PMC10269530 DOI: 10.1128/spectrum.04710-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/01/2023] [Indexed: 05/18/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is extremely diverse genotypically and phenotypically. Individual strains can variably carry diverse virulence factors, making it challenging to define a molecular signature for this pathotype. For many bacterial pathogens, mobile genetic elements (MGEs) constitute a major mechanism of virulence factor acquisition. For urinary E. coli, the total distribution of MGEs and their role in the acquisition of virulence factors is not well defined, including in the context of symptomatic infection versus asymptomatic bacteriuria (ASB). In this work, we characterized 151 isolates of E. coli, derived from patients with either urinary tract infection (UTI) or ASB. For both sets of E. coli, we catalogued the presence of plasmids, prophage, and transposons. We analyzed MGE sequences for the presence of virulence factors and antimicrobial resistance genes. These MGEs were associated with only ~4% of total virulence associated genes, while plasmids contributed to ~15% of antimicrobial resistance genes under consideration. Our analyses suggests that, across strains of E. coli, MGEs are not a prominent driver of urinary tract pathogenesis and symptomatic infection. IMPORTANCE Escherichia coli is the most common etiological agent of urinary tract infections (UTIs), with UTI-associated strains designated "uropathogenic" E. coli or UPEC. Across urinary strains of E. coli, the global landscape of MGEs and its relationship to virulence factor carriage and clinical symptomatology require greater clarity. Here, we demonstrate that many of the putative virulence factors of UPEC are not associated with acquisition due to MGEs. The current work enhances our understanding of the strain-to-strain variability and pathogenic potential of urine-associated E. coli and points toward more subtle genomic differences distinguishing ASB from UTI isolates.
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Affiliation(s)
- Grace Morales
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Benjamin Abelson
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seth Reasoner
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jordan Miller
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Maria Hadjifrangiskou
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, Tennessee, USA
| | - Jonathan Schmitz
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, Tennessee, USA
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17
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Du J, Khemmani M, Halverson T, Ene A, Limeira R, Tinawi L, Hochstedler-Kramer BR, Noronha MF, Putonti C, Wolfe AJ. Cataloging the Phylogenetic Diversity of Human Bladder Bacterial Isolates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541916. [PMID: 37292924 PMCID: PMC10245883 DOI: 10.1101/2023.05.23.541916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, e.g., the gut and oral cavity. To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, here we present a bladder-specific bacterial reference collection comprised of 1134 genomes. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2 % of the genera found when we reexamined previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis found that the taxonomies and functions of the bladder microbiota shared more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder E. coli isolates and 387 gut E. coli isolates supports the hypothesis that phylogroup distribution and functions of E. coli strains differ dramatically between these two very different niches. This bladder-specific bacterial reference collection is a unique resource that will enable hypothesis-driven bladder microbiota research and comparison to isolates from other anatomical sites.
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Affiliation(s)
- Jingjie Du
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Mark Khemmani
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Thomas Halverson
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660
| | - Roberto Limeira
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Lana Tinawi
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Baylie R. Hochstedler-Kramer
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Melline Fontes Noronha
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660
- Department of Biology, Loyola University Chicago, Chicago, IL 60660
| | - Alan J. Wolfe
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
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18
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Host-pathogen biology intertwines in recurrent UTI. Nat Microbiol 2023; 8:749-750. [PMID: 37142687 DOI: 10.1038/s41564-023-01391-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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19
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de la Fuente R, Díaz-Villanueva W, Arnau V, Moya A. Genomic Signature in Evolutionary Biology: A Review. BIOLOGY 2023; 12:biology12020322. [PMID: 36829597 PMCID: PMC9953303 DOI: 10.3390/biology12020322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023]
Abstract
Organisms are unique physical entities in which information is stored and continuously processed. The digital nature of DNA sequences enables the construction of a dynamic information reservoir. However, the distinction between the hardware and software components in the information flow is crucial to identify the mechanisms generating specific genomic signatures. In this work, we perform a bibliometric analysis to identify the different purposes of looking for particular patterns in DNA sequences associated with a given phenotype. This study has enabled us to make a conceptual breakdown of the genomic signature and differentiate the leading applications. On the one hand, it refers to gene expression profiling associated with a biological function, which may be shared across taxa. This signature is the focus of study in precision medicine. On the other hand, it also refers to characteristic patterns in species-specific DNA sequences. This interpretation plays a key role in comparative genomics, identifying evolutionary relationships. Looking at the relevant studies in our bibliographic database, we highlight the main factors causing heterogeneities in genome composition and how they can be quantified. All these findings lead us to reformulate some questions relevant to evolutionary biology.
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Affiliation(s)
- Rebeca de la Fuente
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
- Correspondence:
| | - Wladimiro Díaz-Villanueva
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
| | - Vicente Arnau
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
| | - Andrés Moya
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), 46020 Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), 28029 Madrid, Spain
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20
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Zou Z, Potter RF, McCoy WH, Wildenthal JA, Katumba GL, Mucha PJ, Dantas G, Henderson JP. E. coli catheter-associated urinary tract infections are associated with distinctive virulence and biofilm gene determinants. JCI Insight 2023; 8:e161461. [PMID: 36512427 PMCID: PMC9977300 DOI: 10.1172/jci.insight.161461] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
Urinary catheterization facilitates urinary tract colonization by E. coli and increases infection risk. Here, we aimed to identify strain-specific characteristics associated with the transition from colonization to infection in catheterized patients. In a single-site study population, we compared E. coli isolates from patients with catheter-associated asymptomatic bacteriuria (CAASB) to those with catheter-associated urinary tract infection (CAUTI). CAUTI isolates were dominated by a phylotype B2 subclade containing the multidrug-resistant ST131 lineage relative to CAASB isolates, which were phylogenetically more diverse. A distinctive combination of virulence-associated genes was present in the CAUTI-associated B2 subclade. Catheter-associated biofilm formation was widespread among isolates and did not distinguish CAUTI from CAASB strains. Preincubation with CAASB strains could inhibit catheter colonization by multiple ST131 CAUTI isolates. Comparative genomic analysis identified a group of variable genes associated with high catheter biofilm formation present in both CAUTI and CAASB strains. Among these, ferric citrate transport (Fec) system genes were experimentally associated with enhanced catheter biofilm formation using reporter and fecA deletion strains. These results are consistent with a variable role for catheter biofilm formation in promoting CAUTI by ST131-like strains or resisting CAUTI by lower-risk strains that engage in niche exclusion.
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Affiliation(s)
- Zongsen Zou
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
| | - Robert F. Potter
- The Edison Family Center for Genome Sciences and Systems Biology
- Department of Pathology and Immunology, and
| | - William H. McCoy
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Dermatology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John A. Wildenthal
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
| | - George L. Katumba
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
| | - Peter J. Mucha
- Department of Mathematics, Dartmouth College, Hanover, New Hampshire, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology
- Department of Pathology and Immunology, and
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, Missouri, USA
| | - Jeffrey P. Henderson
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
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21
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Tan A, Alsenani Q, Lanz M, Birchall C, Drage LKL, Picton D, Mowbray C, Ali A, Harding C, Pickard RS, Hall J, Aldridge PD. Evasion of toll-like receptor recognition by Escherichia coli is mediated via population level regulation of flagellin production. Front Microbiol 2023; 14:1093922. [PMID: 37032848 PMCID: PMC10078357 DOI: 10.3389/fmicb.2023.1093922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
Uropathogenic Escherichia coli is a major cause of urinary tract infections. Analysis of the innate immune response in immortalized urothelial cells suggests that the bacterial flagellar subunit, flagellin, is key in inducing host defenses. A panel of 48 clinical uro-associated E. coli isolates recovered from either cystitis, pyelonephritis asymptomatic bacteriuria (ABU) or UTI-associated bacteraemia infections were characterized for motility and their ability to induce an innate response in urothelial cells stably transfected with a NF-κB luciferase reporter. Thirty-two isolates (67%) were identified as motile with strains recovered from cystitis patients exhibiting an uneven motility distribution pattern; seven of the cystitis isolates were associated with a > 5-fold increase in NF-κB signaling. To explore whether the NF-κB signaling response reflected antigenic variation, flagellin was purified from 14 different isolates. Purified flagellin filaments generated comparable NF-κB signaling responses, irrespective of either the source of the isolate or H-serotype. These data argued against any variability between isolates being related to flagellin itself. Investigations also argued that neither TLR4 dependent recognition of bacterial lipopolysaccharide nor growth fitness of the isolates played key roles in leading to the variable host response. To determine the roles, if any, of flagellar abundance in inducing these variable responses, flagellar hook numbers of a range of cystitis and ABU isolates were quantified. Images suggested that up to 60% of the isolate population exhibited flagella with the numbers averaging between 1 and 2 flagella per bacterial cell. These data suggest that selective pressures exist in the urinary tract that allow uro-associated E. coli strains to maintain motility, but exploit population heterogeneity, which together function to prevent host TLR5 recognition and bacterial killing.
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Affiliation(s)
- Aaron Tan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Qusai Alsenani
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marcello Lanz
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christopher Birchall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lauren K. L. Drage
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David Picton
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Catherine Mowbray
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ased Ali
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christopher Harding
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Urology Department, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Robert S. Pickard
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Urology Department, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Judith Hall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- *Correspondence: Judith Hall,
| | - Phillip D. Aldridge
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Phillip D. Aldridge,
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22
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Phenotypic Assessment of Clinical Escherichia coli Isolates as an Indicator for Uropathogenic Potential. mSystems 2022; 7:e0082722. [PMID: 36445110 PMCID: PMC9765037 DOI: 10.1128/msystems.00827-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
For women in the United States, urinary tract infections (UTIs) are the most frequent diagnosis in emergency departments, comprising 21.3% of total visits. Uropathogenic Escherichia coli (UPEC) causes ~80% of uncomplicated UTIs. To combat this public health issue, it is vital to characterize UPEC strains as well as to differentiate them from commensal strains to reduce the overuse of antibiotics. It has been challenging to determine a consistent genetic signature that clearly distinguishes UPEC from other E. coli strains. Therefore, we examined whether phenotypic data could be predictive of uropathogenic potential. We screened 13 clinical strains of UPEC, isolated from cases of uncomplicated UTI in young otherwise healthy women, in a series of microbiological phenotypic assays using UPEC prototype strain CFT073 and nonpathogenic E. coli strain MG1655 K-12 as controls. Phenotypes included adherence, iron acquisition, biofilm formation, human serum resistance, motility, and stress resistance. By use of a well-established experimental mouse model of UTI, these data were able to predict the severity of the bacterial burden in both the urine and bladders. Multiple linear regression using three different phenotypic assays, i.e., growth in minimal medium, siderophore production, and type 1 fimbrial expression, was predictive of bladder colonization (adjusted R2 = 0.6411). Growth in ex vivo human urine, hemagglutination of red blood cells, and motility modeled urine colonization (adjusted R2 = 0.4821). These results showcase the utility of phenotypic characterization to predict the severity of infection that these strains may cause. We predict that these methods will also be applicable to other complex, genetically redundant, pathogens. IMPORTANCE Urinary tract infections are the second leading infectious disease worldwide, occurring in over half of the female population during their lifetime. Most infections are caused by uropathogenic Escherichia coli (UPEC) strains. These strains can establish a reservoir in the gut, in which they do not cause disease but, upon introduction to the urinary tract, can infect the host and elicit pathogenesis. Clinically, it would be beneficial to screen patient E. coli strains to understand their pathogenic potential, which may lead to the administration of prophylactic antibiotic treatment for those with increased risk. Others have proposed the use of PCR-based genetic screening methods to detect UPEC strains and differentiate them from other E. coli pathotypes; however, this method has not yielded a consistent uropathogenic genetic signature. Here, we used phenotypic characteristics such as growth rate, siderophore production, and expression of fimbriae to better predict uropathogenic potential.
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23
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Geurtsen J, de Been M, Weerdenburg E, Zomer A, McNally A, Poolman J. Genomics and pathotypes of the many faces of Escherichia coli. FEMS Microbiol Rev 2022; 46:6617594. [PMID: 35749579 PMCID: PMC9629502 DOI: 10.1093/femsre/fuac031] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli's infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.
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Affiliation(s)
- Jeroen Geurtsen
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | - Mark de Been
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | | | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, the Netherlands
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Jan Poolman
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
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24
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Sturov NV, Popov SV, Zhukov VA, Lyapunova TV, Rusanova EI, Kobylyanu GN, Kobylyanu GN. Intestinal Microbiota Correction in the Treatment and Prevention of Urinary Tract Infection. Turk J Urol 2022; 48:406-414. [PMID: 36416330 PMCID: PMC9797784 DOI: 10.5152/tud.2022.22119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Intestinal microbiota is a topical subject of modern research. The maintenance of a healthy intestinal micro biota is an important component of homeostasis, and violations of its composition and functions, called dysbiosis, are associated with a number of diseases, including urinary tract infections. Antimicrobial therapy leads to significant changes in the intestinal microbiota and causes the possibility of urinary tract infection recurrence. In this regard, it is important to study methods of microbiota correction in order to restore its structural and functional integrity.
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Affiliation(s)
- Nikolay V. Sturov
- General Medical Practice Department, RUDN University (Peoples’ Friendship University of Russia), Moscow, Russian Federation
| | - Sergey V. Popov
- General Medical Practice Department, RUDN University (Peoples’ Friendship University of Russia), Moscow, Russian Federation
| | - Vladimir A. Zhukov
- General Medical Practice Department, RUDN University (Peoples’ Friendship University of Russia), Moscow, Russian Federation,Corresponding author:Vladimir A. ZhukovE-mail:
| | - Tatiana V. Lyapunova
- Medical Informatics and Telemedicine Department, RUDN University (Peoples’ Friendship University of Russia), Moscow, Russian Federation
| | - Ekaterina I. Rusanova
- General Medical Practice Department, RUDN University (Peoples’ Friendship University of Russia), Moscow, Russian Federation
| | - Georgy N. Kobylyanu
- General Medical Practice Department, RUDN University (Peoples’ Friendship University of Russia), Moscow, Russian Federation
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25
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Cho YH, Renouf MJ, Omotoso O, McPhee JB. Inflammatory bowel disease-associated adherent-invasive Escherichia coli have elevated host-defense peptide resistance. FEMS Microbiol Lett 2022; 369:6754321. [PMID: 36208952 DOI: 10.1093/femsle/fnac098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/28/2022] [Accepted: 10/06/2022] [Indexed: 12/13/2022] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) are isolated from inflammatory bowel disease (IBD) patients at a higher rate than from control patients. Using a collection of E. coli strains collected from Crohn's disease (CD), ulcerative colitis (UC), or non-IBD control patients, antibiotic and resistance to the antimicrobial peptides HBD-3 and LL-37 was assessed. Carriage of bacterial-encoded omptin protease genes was assessed by PCR and omptin protease activity was measured using a whole-cell based fluorescence assay. Elevated resistance to antibiotics and host defense peptides in IBD-associated AIEC were observed. IBD-associated strains showed increased (but statistically non-significant) antibiotic resistance. CD-associated strains showed greater (but statistically non-significant) resistance to HBD3-mediated killing while UC-associated strains showed statistically greater resistance to LL-37 mediated killing. High-level resistance to LL-37 was associated with carriage of omptin protease genes and with increased omptin protease activity. Antimicrobial host defense peptide resistance may be an adaptive feature of AIEC leading to enhanced pathogenesis during the initiation or progression of IBD.
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Affiliation(s)
- Youn Hee Cho
- Department of Chemistry and Biology, Toronto Metropolitan University (Formerly Ryerson University), 350 Victoria St., Toronto, ON M5B 2K3, Canada
| | - Michael J Renouf
- Department of Chemistry and Biology, Toronto Metropolitan University (Formerly Ryerson University), 350 Victoria St., Toronto, ON M5B 2K3, Canada
| | - Oluwafikemi Omotoso
- Department of Chemistry and Biology, Toronto Metropolitan University (Formerly Ryerson University), 350 Victoria St., Toronto, ON M5B 2K3, Canada
| | - Joseph B McPhee
- Department of Chemistry and Biology, Toronto Metropolitan University (Formerly Ryerson University), 350 Victoria St., Toronto, ON M5B 2K3, Canada
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26
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Bacterial Growth of Uropathogenic Escherichia coli in Pooled Urine Is Much Higher than Predicted from the Average Growth in Individual Urine Samples. Microbiol Spectr 2022; 10:e0201622. [PMID: 36154127 PMCID: PMC9603375 DOI: 10.1128/spectrum.02016-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Urinary tract infections (UTIs), mostly caused by uropathogenic E. coli (UPEC), affect most women, and often recur. Genomic and transcriptomic analyses have not identified a common set of virulence genes, which has suggested complex host-pathogen interactions and multiple virulence mechanisms. One aspect of the host-pathogen interaction is rapid UPEC growth in urine in vivo. When bacterial growth in urine is studied in vitro, urine is pooled, which is assumed to diminish individual variation. We grew one nonpathogenic and two pathogenic E. coli strains in urine from individuals who never had a UTI, had a UTI history but no current infection, and had a UTI history with a current infection. Bacterial growth showed large variations in individual urine samples, and pooled urine often supported significantly more growth than the average growth from individual urine samples. Total nutrient content tended to be higher in current group urine samples than the never and history grouped samples urine. We propose that pooling optimizes a nutrient mixture in the never and history group urine samples, which are often studied, whereas urine from current group individuals may have a more optimal nutrient mixture because of additional nutrient sources. We conclude that a pooled urine is not "an average urine sample," and that the best comparisons of results between labs using pooled urine would also include results with a standardized synthetic urine. IMPORTANCE Urinary tract infections (UTIs) will affect most women, can recur especially in postmenopausal women, and can become antibiotic recalcitrant. Escherichia coli causes most community-acquired UTIs and recurrent UTIs. Current theories of virulence, based on studies of UTI-associated E. coli, propose multiple virulence mechanisms and complex host-pathogen interactions. Studies of bacterial growth in urine samples-one aspect of the host-pathogen interaction-invariably involve pooled urine that are assumed to eliminate variations between individuals. Our results show that a pooled urine is not necessarily an average urine sample, and we suggest that quantitative and qualitative variations in nutrient content are the basis for this discrepancy. Knowledge of growth-promoting urinary components is important for understanding host-pathogen interactions during UTIs and could contribute to developing nonantibiotic-based therapies.
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27
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Notermans DW, Schoffelen AF, Landman F, Wielders CCH, Witteveen S, Ganesh VA, van Santen-Verheuvel M, de Greeff SC, Kuijper EJ, Hendrickx APA. A genetic cluster of OXA-244 carbapenemase-producing Escherichia coli ST38 with putative uropathogenicity factors in the Netherlands. J Antimicrob Chemother 2022; 77:3205-3208. [PMID: 36171716 PMCID: PMC9616543 DOI: 10.1093/jac/dkac307] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Indexed: 12/02/2022] Open
Affiliation(s)
- Daan W Notermans
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Annelot F Schoffelen
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Fabian Landman
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Cornelia C H Wielders
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Sandra Witteveen
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Varisha A Ganesh
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Marga van Santen-Verheuvel
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Sabine C de Greeff
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Ed J Kuijper
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
| | - Antoni P A Hendrickx
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721 MA, Bilthoven, the Netherlands
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28
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Brauer AL, Learman BS, Taddei SM, Deka N, Hunt BC, Armbruster CE. Preferential catabolism of l- vs d-serine by Proteus mirabilis contributes to pathogenesis and catheter-associated urinary tract infection. Mol Microbiol 2022; 118:125-144. [PMID: 35970717 PMCID: PMC9486832 DOI: 10.1111/mmi.14968] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/24/2022] [Accepted: 07/30/2022] [Indexed: 11/29/2022]
Abstract
Proteus mirabilis is a common cause of urinary tract infection, especially in catheterized individuals. Amino acids are the predominant nutrient for bacteria during growth in urine, and our prior studies identified several amino acid import and catabolism genes as fitness factors for P. mirabilis catheter-associated urinary tract infection (CAUTI), particularly those for d- and l-serine. In this study, we sought to determine the hierarchy of amino acid utilization by P. mirabilis and to examine the relative importance of d- vs l-serine catabolism for critical steps in CAUTI development and progression. Herein, we show that P. mirabilis preferentially catabolizes l-serine during growth in human urine, followed by d-serine, threonine, tyrosine, glutamine, tryptophan, and phenylalanine. Independently disrupting catabolism of either d- or l-serine has minimal impact on in vitro phenotypes while completely disrupting both pathways decreases motility, biofilm formation, and fitness due to perturbation of membrane potential and cell wall biosynthesis. In a mouse model of CAUTI, loss of either serine catabolism system decreased fitness, but disrupting l-serine catabolism caused a greater fitness defect than disrupting d-serine catabolism. We, therefore, conclude that the hierarchical utilization of amino acids may be a critical component of P. mirabilis colonization and pathogenesis within the urinary tract.
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Affiliation(s)
- Aimee L. Brauer
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Brian S. Learman
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Steven M. Taddei
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Namrata Deka
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Benjamin C. Hunt
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
| | - Chelsie E. Armbruster
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, United States
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29
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Vendrik KEW, de Meij TGJ, Bökenkamp A, Ooijevaar RE, Groenewegen B, Hendrickx APA, Terveer EM, Kuijper EJ, van Prehn J. Transmission of Antibiotic-Susceptible Escherichia coli Causing Urinary Tract Infections in a Fecal Microbiota Transplantation Recipient: Consequences for Donor Screening? Open Forum Infect Dis 2022; 9:ofac324. [PMID: 35899275 PMCID: PMC9314704 DOI: 10.1093/ofid/ofac324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
Fecal microbiota transplantation (FMT) has been reported to decrease the incidence of recurrent urinary tract infections (UTIs), presumably by restoring microbiome diversity and/or uropathogen competition. We report a 16-year-old female with recurrent UTIs caused by multidrug-resistant Klebsiella pneumoniae, for which frequent intravenous broad-spectrum antibiotic treatment was necessary. The patient was treated with FMT from a well-screened healthy donor without multidrug-resistant bacteria in the feces. After FMT, she developed several UTIs with an antibiotic-susceptible Escherichia coli that could be treated orally. The uropathogenic E. coli could be cultured from donor feces, and whole genome sequencing confirmed donor-to-recipient transmission. Our observation should stimulate discussion on long-term follow-up of all infections after FMT and donor fecal screening for antibiotic-susceptible Enterobacterales.
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Affiliation(s)
- Karuna E W Vendrik
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Tim G J de Meij
- Department of Pediatrics, Amsterdam University Medical Centers, Emma Children's Hospital, Amsterdam, The Netherlands
| | - Arend Bökenkamp
- Department of Pediatric Nephrology, Amsterdam Medical Centers, Emma Children's Hospital, Amsterdam, The Netherlands
| | - Rogier E Ooijevaar
- Netherlands Donor Feces Bank, Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Bas Groenewegen
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Antoni P A Hendrickx
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Elisabeth M Terveer
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Joffrey van Prehn
- Department of Medical Microbiology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
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30
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Groves RA, Mapar M, Aburashed R, Ponce LF, Bishop SL, Rydzak T, Drikic M, Bihan DG, Benediktsson H, Clement F, Gregson DB, Lewis IA. Methods for Quantifying the Metabolic Boundary Fluxes of Cell Cultures in Large Cohorts by High-Resolution Hydrophilic Liquid Chromatography Mass Spectrometry. Anal Chem 2022; 94:8874-8882. [PMID: 35700271 PMCID: PMC9244871 DOI: 10.1021/acs.analchem.2c00078] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Metabolomics is a
mainstream approach for investigating the metabolic
underpinnings of complex biological phenomena and is increasingly
being applied to large-scale studies involving hundreds or thousands
of samples. Although metabolomics methods are robust in smaller-scale
studies, they can be challenging to apply to larger cohorts due to
the inherent variability of liquid chromatography mass spectrometry
(LC-MS). Much of this difficulty results from the time-dependent changes
in the LC-MS system, which affects both the qualitative and quantitative
performances of the instrument. Herein, we introduce an analytical
strategy for addressing this problem in large-scale microbial studies.
Our approach quantifies microbial boundary fluxes using two zwitterionic
hydrophilic interaction liquid chromatography (ZIC-HILIC) columns
that are plumbed to enable offline column equilibration. Using this
strategy, we show that over 397 common metabolites can be resolved
in 4.5 min per sample and that metabolites can be quantified with
a median coefficient of variation of 0.127 across 1100 technical replicates.
We illustrate the utility of this strategy via an analysis of 960
strains of Staphylococcus aureus isolated
from bloodstream infections. These data capture the diversity of metabolic
phenotypes observed in clinical isolates and provide an example of
how large-scale investigations can leverage our novel analytical strategy.
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Affiliation(s)
- Ryan A Groves
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Maryam Mapar
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Raied Aburashed
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Luis F Ponce
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Stephanie L Bishop
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Thomas Rydzak
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Marija Drikic
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Dominique G Bihan
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Hallgrimur Benediktsson
- Cumming School of Medicine, Department of Pathology and Laboratory Medicine, University of Calgary, Calgary T2N 1N4, Canada.,Alberta Precision Laboratories, Calgary T2L 2K8, Canada
| | - Fiona Clement
- Cumming School of Medicine, Department of Community Health Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Daniel B Gregson
- Cumming School of Medicine, Department of Pathology and Laboratory Medicine, University of Calgary, Calgary T2N 1N4, Canada.,Alberta Precision Laboratories, Calgary T2L 2K8, Canada.,Cumming School of Medicine, Department of Medicine, University of Calgary, Calgary T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
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31
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A Three-Year Look at the Phylogenetic Profile, Antimicrobial Resistance, and Associated Virulence Genes of Uropathogenic Escherichia coli. Pathogens 2022; 11:pathogens11060631. [PMID: 35745485 PMCID: PMC9227886 DOI: 10.3390/pathogens11060631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/19/2022] [Accepted: 05/28/2022] [Indexed: 12/04/2022] Open
Abstract
Uropathogenic Escherichia coli is the most common cause of urinary tract infections, resulting in about 150 million reported annual cases. With multidrug resistance on the rise and the need for global and region surveillance, this investigation looks at the UPEC isolates collected for a 3-year period, with a view of ascertaining their antimicrobial susceptibility patterns and associated virulence determinants. The identification of bacteria isolates, antimicrobial susceptibility, and extended-spectrum beta-lactamases (ESBLs) production was determined with a Vitek 2 Compact Automated System (BioMerieux, Marcy L’Etoile, France). ESBLs were confirmed by the combined disc test (CDT) and basic biochemical test. The isolates were distributed into A (11%), B1 (6%), B2 (62.4%), and D (20.6%). Resistance to the penicillin group was high, between 88% and 100%. Additionally, resistance was high to cephalosporins (100%) in 2017 and 2018. The isolates were all sensitive to tigecycline, while resistance against imipenem and meropenem was low, at 4–12% in 2017 and 2018 and 0% in 2019. The results also showed that ESBL isolates were seen in 2017 and 2018. They were confirmed positive to CTX/CLA (88.5%) and CAZ/CLA (85%). By 2019, the number of resistant isolates reduced, showing only 4% ESBL isolates. Two virulence genes, fimH (46%) and papE/F (15%), were detected among the isolates by PCR. In conclusion, this study found that phylogroups B2 and D carried the most virulence genes as well as MDR and ESBL characteristics, suggesting the UPEC strains to be extraintestinal pathogens responsible for UTIs.
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32
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Sanchez BC, Heckmann ER, Green SI, Clark JR, Kaplan HB, Ramig RF, Muldrew KL, Hines-Munson C, Skelton F, Trautner BW, Maresso AW. Development of Phage Cocktails to Treat E. coli Catheter-Associated Urinary Tract Infection and Associated Biofilms. Front Microbiol 2022; 13:796132. [PMID: 35620093 PMCID: PMC9127763 DOI: 10.3389/fmicb.2022.796132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/04/2022] [Indexed: 11/16/2022] Open
Abstract
High rates of antimicrobial resistance and formation of biofilms makes treatment of Escherichia coli catheter-associated urinary tract infections (CAUTI) particularly challenging. CAUTI affect 1 million patients per year in the United States and are associated with morbidity and mortality, particularly as an etiology for sepsis. Phage have been proposed as a potential therapeutic option. Here, we report the development of phage cocktails that lyse contemporary E. coli strains isolated from the urine of patients with spinal cord injury (SCI) and display strong biofilm-forming properties. We characterized E. coli phage against biofilms in two in vitro CAUTI models. Biofilm viability was measured by an MTT assay that determines cell metabolic activity and by quantification of colony forming units. Nine phage decreased cell viability by >80% when added individually to biofilms of two E. coli strains in human urine. A phage cocktail comprising six phage lyses 82% of the strains in our E. coli library and is highly effective against young and old biofilms and against biofilms on silicon catheter materials. Using antibiotics together with our phage cocktail prevented or decreased emergence of E. coli resistant to phage in human urine. We created an anti-biofilm phage cocktail with broad host range against E. coli strains isolated from urine. These phage cocktails may have therapeutic potential against CAUTI.
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Affiliation(s)
- Belkys C. Sanchez
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Emmaline R. Heckmann
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Sabrina I. Green
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Justin R. Clark
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Heidi B. Kaplan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth Houston, Houston, TX, United States
| | - Robert F. Ramig
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Kenneth L. Muldrew
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States,Pathology and Laboratory Medicine, Michael E. DeBakey VA Medical Center, Houston, TX, United States,Section of Infectious Diseases, Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Casey Hines-Munson
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States
| | - Felicia Skelton
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States,H. Ben Taub Department of Physical Medicine and Rehabilitation, Baylor College of Medicine, Houston, TX, United States
| | - Barbara W. Trautner
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States,Department of Medicine and Surgery, Baylor College of Medicine, Houston, TX, United States,Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey VA Medical Center, Houston, TX, United States
| | - Anthony W. Maresso
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States,*Correspondence: Anthony W. Maresso,
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Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women. Nat Microbiol 2022; 7:630-639. [PMID: 35505248 DOI: 10.1038/s41564-022-01107-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/18/2022] [Indexed: 12/13/2022]
Abstract
Recurrent urinary tract infections (rUTIs) are a major health burden worldwide, with history of infection being a significant risk factor. While the gut is a known reservoir for uropathogenic bacteria, the role of the microbiota in rUTI remains unclear. We conducted a year-long study of women with (n = 15) and without (n = 16) history of rUTI, from whom we collected urine, blood and monthly faecal samples for metagenomic and transcriptomic interrogation. During the study 24 UTIs were reported, with additional samples collected during and after infection. The gut microbiome of individuals with a history of rUTI was significantly depleted in microbial richness and butyrate-producing bacteria compared with controls, reminiscent of other inflammatory conditions. However, Escherichia coli gut and bladder populations were comparable between cohorts in both relative abundance and phylogroup. Transcriptional analysis of peripheral blood mononuclear cells revealed expression profiles indicative of differential systemic immunity between cohorts. Altogether, these results suggest that rUTI susceptibility is in part mediated through the gut-bladder axis, comprising gut dysbiosis and differential immune response to bacterial bladder colonization, manifesting in symptoms.
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A Biomimetic Porcine Urothelial Model for Assessing Escherichia coli Pathogenicity. Microorganisms 2022; 10:microorganisms10040783. [PMID: 35456833 PMCID: PMC9029248 DOI: 10.3390/microorganisms10040783] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/20/2022] [Accepted: 04/01/2022] [Indexed: 02/01/2023] Open
Abstract
Urinary tract infections can be severe, sometimes fatal, diseases whose etiological pathogens are predominantly uropathogenic strains of E. coli (UPEC). To investigate the UPEC pathogenesis, several models have already been established with minor or major disadvantages. The aim was to develop a simple, fast, and inexpensive biomimetic in vitro model based on normal porcine urothelial (NPU) cells that are genetically and physiologically similar to human bladder urothelium and to perform basic studies of E. coli pathogenicity. Initially, the model was tested using a set of control E. coli strains and, subsequently, with human E. coli strains isolated either from patients with urinary infections or from the feces of healthy individuals. A drop in viability of NPU cells was used as a measure of the pathogenicity of the individual strain tested. To visualize the subcellular events, transmission and scanning electron microscopy was performed. The strains were tested for the presence of different virulence-associated genes, phylogroup, type of core lipid, O-serotype, and type of lipopolysaccharide and a statistical analysis of possible correlations between strains’ characteristics and the effect on the model was performed. Results showed that our model has the discriminatory power to distinguish pathogenic from non-pathogenic E. coli strains, and to identify new, potentially pathogenic strains.
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35
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van Dijk LR, Walker BJ, Straub TJ, Worby CJ, Grote A, Schreiber HL, Anyansi C, Pickering AJ, Hultgren SJ, Manson AL, Abeel T, Earl AM. StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities. Genome Biol 2022; 23:74. [PMID: 35255937 PMCID: PMC8900328 DOI: 10.1186/s13059-022-02630-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 02/09/2022] [Indexed: 01/21/2023] Open
Abstract
Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify strains at 0.1x coverage and detect variants for multiple conspecific strains within a sample from coverages as low as 0.5x.
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Affiliation(s)
- Lucas R. van Dijk
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA ,grid.5292.c0000 0001 2097 4740Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE The Netherlands
| | - Bruce J. Walker
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA ,Applied Invention, Cambridge, MA USA
| | - Timothy J. Straub
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Colin J. Worby
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA
| | - Alexandra Grote
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA
| | - Henry L. Schreiber
- grid.4367.60000 0001 2355 7002Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Women’s Infectious Disease Research (CWIDR), Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Christine Anyansi
- grid.5292.c0000 0001 2097 4740Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE The Netherlands
| | - Amy J. Pickering
- grid.47840.3f0000 0001 2181 7878Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA 94720 USA ,grid.429997.80000 0004 1936 7531Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA USA
| | - Scott J. Hultgren
- grid.4367.60000 0001 2355 7002Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110 USA ,grid.4367.60000 0001 2355 7002Center for Women’s Infectious Disease Research (CWIDR), Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Abigail L. Manson
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA
| | - Thomas Abeel
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA ,grid.5292.c0000 0001 2097 4740Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE The Netherlands
| | - Ashlee M. Earl
- grid.66859.340000 0004 0546 1623Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA 02142 USA
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36
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Kenneally C, Murphy CP, Sleator RD, Culligan EP. The Urinary Microbiome and Biological Therapeutics: Novel Therapies For Urinary Tract Infections. Microbiol Res 2022; 259:127010. [DOI: 10.1016/j.micres.2022.127010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/12/2022]
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Worby CJ, Olson BS, Dodson KW, Earl AM, Hultgren SJ. Establishing the role of the gut microbiota in susceptibility to recurrent urinary tract infections. J Clin Invest 2022; 132:158497. [PMID: 35229729 PMCID: PMC8884912 DOI: 10.1172/jci158497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Colin J Worby
- Broad Institute of MIT and Harvard, Infectious Disease and Microbiome Program, Cambridge, Massachusetts, USA
| | - Benjamin S Olson
- Department of Molecular Microbiology and.,Center for Women's Infectious Disease Research (cWIDR), Washington University School of Medicine, St. Louis, Missouri, USA
| | - Karen W Dodson
- Department of Molecular Microbiology and.,Center for Women's Infectious Disease Research (cWIDR), Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Infectious Disease and Microbiome Program, Cambridge, Massachusetts, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology and.,Center for Women's Infectious Disease Research (cWIDR), Washington University School of Medicine, St. Louis, Missouri, USA
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38
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Similarities in Virulence and Extended Spectrum Beta-Lactamase Gene Profiles among Cefotaxime-Resistant Escherichia coli Wastewater and Clinical Isolates. Antibiotics (Basel) 2022; 11:antibiotics11020260. [PMID: 35203862 PMCID: PMC8868091 DOI: 10.3390/antibiotics11020260] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 12/10/2022] Open
Abstract
The World Health Organization has identified antibiotic resistance as one of the largest threats to human health and food security. In this study, we compared antibiotic resistance patterns between ESBL-producing Escherichia coli from human clinical diseases and cefotaxime-resistant environmental strains, as well as their potential to be pathogenic. Antibiotic susceptibility was tested amongst clinical isolates (n = 11), hospital wastewater (n = 22), and urban wastewater (n = 36, both influent and treated effluents). Multi-drug resistance predominated (>70%) among hospitalwastewater and urban wastewater influent isolates. Interestingly, isolates from clinical and urban treated effluents showed similar multi-drug resistance rates (~50%). Most hospital wastewater isolates were Phylogroup A, while clinical isolates were predominately B2, with a more diverse phylogroup population in urban wastewater. ESBL characterization of cefotaxime-resistant populations identified blaCTX-M-1 subgroup as the most common, whereby blaKPC was more associated with ceftazidime and ertapenem resistance. Whole-genome sequencing of a carbapenemase-producing hospital wastewater E. coli strain revealed plasmid-mediated blaKPC-2. Among cefotaxime-resistant populations, over 60% of clinical and 30% of treated effluent E. coli encoded three or more virulence genes exhibiting a pathogenic potential. Together, the similarity among treated effluent E. coli populations and clinical strains suggest effluents could serve as a reservoir for future multi-drug resistant E. coli clinical infections.
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Hernández-Hernández D, Padilla-Fernández B, Ortega-González MY, Castro-Díaz DM. Recurrent Urinary Tract Infections and Asymptomatic Bacteriuria in Adults. CURRENT BLADDER DYSFUNCTION REPORTS 2021; 17:1-12. [PMID: 34868442 PMCID: PMC8634747 DOI: 10.1007/s11884-021-00638-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2021] [Indexed: 12/14/2022]
Abstract
Purpose of review Our goal was to summarize recent evidence regarding recurrent urinary tract infections and asymptomatic bacteriuria in different adult populations. Recent findings Several research groups are focused on the description of resident bacterial flora in the bladder and urinary dysbiosis in the microbiome era. Even the definitions might change in light of these discoveries. However, the role of urinary microbiome and bacterial interference has still to be determined. Summary Systematic treatment of asymptomatic bacteriuria is not recommended and even classic indications such as asymptomatic bacteriuria in pregnant women are controversial. In fact, its treatment is associated with a higher probability of symptomatic UTI and a higher prevalence of antibiotic-resistant bacteria. Improving the diagnosis of asymptomatic bacteriuria and optimizing the management of recurrent urinary tract infections, especially through non-antibiotics measures, are needed in order to minimise antimicrobial resistance.
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Affiliation(s)
| | - Bárbara Padilla-Fernández
- Department of Urology, Complejo Hospitalario Universitario de Canarias, La Laguna, Tenerife Spain.,Departamento de Cirugía, Facultad de Medicina, Universidad de La Laguna, Tenerife, Spain
| | | | - David Manuel Castro-Díaz
- Department of Urology, Complejo Hospitalario Universitario de Canarias, La Laguna, Tenerife Spain.,Departamento de Cirugía, Facultad de Medicina, Universidad de La Laguna, Tenerife, Spain
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40
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Josephs-Spaulding J, Krogh TJ, Rettig HC, Lyng M, Chkonia M, Waschina S, Graspeuntner S, Rupp J, Møller-Jensen J, Kaleta C. Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs. Front Cell Infect Microbiol 2021; 11:562525. [PMID: 34368008 PMCID: PMC8340884 DOI: 10.3389/fcimb.2021.562525] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Urinary tract infections (UTIs) are frequent in humans, affecting the upper and lower urinary tract. Present diagnosis relies on the positive culture of uropathogenic bacteria from urine and clinical markers of inflammation of the urinary tract. The bladder is constantly challenged by adverse environmental stimuli which influence urinary tract physiology, contributing to a dysbiotic environment. Simultaneously, pathogens are primed by environmental stressors such as antibiotics, favoring recurrent UTIs (rUTIs), resulting in chronic illness. Due to different confounders for UTI onset, a greater understanding of the fundamental environmental mechanisms and microbial ecology of the human urinary tract is required. Such advancements could promote the tandem translation of bench and computational studies for precision treatments and clinical management of UTIs. Therefore, there is an urgent need to understand the ecological interactions of the human urogenital microbial communities which precede rUTIs. This review aims to outline the mechanistic aspects of rUTI ecology underlying dysbiosis between both the human microbiome and host physiology which predisposes humans to rUTIs. By assessing the applications of next generation and systems level methods, we also recommend novel approaches to elucidate the systemic consequences of rUTIs which requires an integrated approach for successful treatment. To this end, we will provide an outlook towards the so-called 'uncomplicated environment of UTIs', a holistic and systems view that applies ecological principles to define patient-specific UTIs. This perspective illustrates the need to withdraw from traditional reductionist perspectives in infection biology and instead, a move towards a systems-view revolving around patient-specific pathophysiology during UTIs.
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Affiliation(s)
- Jonathan Josephs-Spaulding
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
| | - Thøger Jensen Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hannah Clara Rettig
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Mark Lyng
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mariam Chkonia
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Silvio Waschina
- Research Group Nutriinformatics, Institute of Human Nutrition and Food Science, Christian-Albrechts-Universität, Kiel, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
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Li X, Zhou K, Wang J, Guo J, Cao Y, Ren J, Guan T, Sheng W, Zhang M, Yao Z, Wang Q. Diagnostic Value of the Fimbriae Distribution Pattern in Localization of Urinary Tract Infection. Front Med (Lausanne) 2021; 8:602691. [PMID: 34222269 PMCID: PMC8249706 DOI: 10.3389/fmed.2021.602691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 05/26/2021] [Indexed: 01/16/2023] Open
Abstract
Urinary tract infections (UTIs) are one of the most common infectious diseases. UTIs are mainly caused by uropathogenic Escherichia coli (UPEC), and are either upper or lower according to the infection site. Fimbriae are necessary for UPEC to adhere to the host uroepithelium, and are abundant and diverse in UPEC strains. Although great progress has been made in determining the roles of different types of fimbriae in UPEC colonization, the contributions of multiple fimbriae to site-specific attachment also need to be considered. Therefore, the distribution patterns of 22 fimbrial genes in 90 UPEC strains from patients diagnosed with upper or lower UTIs were analyzed using PCR. The distribution patterns correlated with the infection sites, an XGBoost model with a mean accuracy of 83.33% and a mean area under the curve (AUC) of the receiver operating characteristic (ROC) of 0.92 demonstrated that fimbrial gene distribution patterns could predict the localization of upper and lower UTIs.
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Affiliation(s)
- Xiao Li
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Xuzhou Key Laboratory of Laboratory Diagnostics, School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Kaichen Zhou
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jingyu Wang
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jiahe Guo
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yang Cao
- Department of Clinical Laboratory, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Jie Ren
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tao Guan
- China Unicom Software Research Institute, Xi'an, China
| | - Wenchao Sheng
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Mingyao Zhang
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhi Yao
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Medical University, Tianjin, China
| | - Quan Wang
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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Genome profiling of fluoroquinolone-resistant uropathogenic Escherichia coli isolates from Brazil. Braz J Microbiol 2021; 52:1067-1075. [PMID: 34105110 DOI: 10.1007/s42770-021-00513-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 04/27/2021] [Indexed: 10/21/2022] Open
Abstract
Urinary tract infections (UTIs) are a major public health concern in both community and hospital settings worldwide. Uropathogenic Escherichia coli (UPEC) is the main causative agent of UTI and increasingly associated with antibiotic resistance. Herein, we report the draft genome sequence of 9 fluoroquinolone-resistant UPEC isolates from Brazil and examine selected major phenotypic features, such as antimicrobial resistance profile, phylogroup, serotype, sequence type (ST), virulence genes, and resistance marks. Besides the quinolone resistance, beta-lactams, ESBL production, aminoglycosides, and tetracycline resistance were observed. High prevalence of 20 virulence genes was detected in all isolates, such as those encoding type 1 fimbriae, acid tolerance system, and hemolysin E, particularly within E. coli B2 phylogroup, as ST131 and ST1193 strains, among other genomic analyses as genomic islands, resistance plasmids, and integron identification.
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Sharapatov Y, Turgunov Y, Lavrinenko A. Pathogenic Mechanisms of Acute Obstructive Pyelonephritis. Open Access Maced J Med Sci 2021. [DOI: 10.3889/oamjms.2021.5876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Among urological diseases, the most relevant is infection of the urinary tract. Pyelonephritis is on the 5th place in kidney diseases, and obstructive pyelonephritis occurs in 84% of all pyelonephritis. In the world, among the adult population, 100 people per 100,000 of the population suffer from pyelonephritis. In addition, from year to year, there is an increase in purulent forms of acute pyelonephritis by 4–5 times. This pathology is a separated manifestation of such an important urological problem as complicated urinary tract infection, which accounts for 84–86% of all infections. In acute obstructive pyelonephritis, more severe complications such as bacteriotoxic shock and urosepsis may develop. The mortality rate from these dangerous complications reaches 70–90%. In addition, the number of patients with urosepsis and bacteriotoxic shock has increased 4–6 times in recent years. The review presents current literature data on acute obstructive pyelonephritis. The main causes and pathogenetic mechanisms of the disease development are presented.
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Babar A, Moore L, Leblanc V, Dudonné S, Desjardins Y, Lemieux S, Bochard V, Guyonnet D, Dodin S. High dose versus low dose standardized cranberry proanthocyanidin extract for the prevention of recurrent urinary tract infection in healthy women: a double-blind randomized controlled trial. BMC Urol 2021; 21:44. [PMID: 33757474 PMCID: PMC7986024 DOI: 10.1186/s12894-021-00811-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/26/2021] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Our objective was to assess the efficacy of a high dose cranberry proanthocyanidin extract for the prevention of recurrent urinary tract infection. MATERIAL AND METHODS We recruited 145 healthy, adult women with a history of recurrent urinary tract infection, defined as ≥ 2 in the past 6 months or ≥ 3 in the past 12 months in this randomized, controlled, double-blind clinical trial. Participants were randomized to receive a high dose of standardized, commercially available cranberry proanthocyanidins (2 × 18.5 mg daily, n = 72) or a control low dose (2 × 1 mg daily, n = 73) for a 24-week period. During follow-up, symptomatic women provided urine samples for detection of pyuria and/or bacteriuria and received an appropriate antibiotic prescription. The primary outcome for the trial was the mean number of new symptomatic urinary tract infections during a 24-week intervention period. Secondary outcomes included symptomatic urinary tract infection with pyuria or bacteriuria. RESULTS In response to the intervention, a non-significant 24% decrease in the number of symptomatic urinary tract infections was observed between groups (Incidence rate ratio 0.76, 95%CI 0.51-1.11). Post-hoc analyses indicated that among 97 women who experienced less than 5 infections in the year preceding enrolment, the high dose was associated with a significant decrease in the number of symptomatic urinary tract infections reported compared to the low dose (age-adjusted incidence rate ratio 0.57, 95%CI 0.33-0.99). No major side effects were reported. CONCLUSION High dose twice daily proanthocyanidin extract was not associated with a reduction in the number of symptomatic urinary tract infections when compared to a low dose proanthocyanidin extract. Our post-hoc results reveal that this high dose of proanthocyanidins may have a preventive impact on symptomatic urinary tract infection recurrence in women who experienced less than 5 infections per year. TRIAL REGISTRATION Clinicaltrials.gov, identifier NCT02572895.
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Affiliation(s)
- Asma Babar
- CHU de Québec-Laval University Research Center, Québec City, Canada.,Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Québec City, Canada
| | - Lynne Moore
- Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Québec City, Canada
| | - Vicky Leblanc
- Institute of Nutrition and Functional Foods, Laval University, Québec City, Canada
| | - Stéphanie Dudonné
- Institute of Nutrition and Functional Foods, Laval University, Québec City, Canada
| | - Yves Desjardins
- Institute of Nutrition and Functional Foods, Laval University, Québec City, Canada
| | - Simone Lemieux
- Institute of Nutrition and Functional Foods, Laval University, Québec City, Canada
| | | | | | - Sylvie Dodin
- CHU de Québec-Laval University Research Center, Québec City, Canada. .,Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Québec City, Canada. .,Department of Obstetrics and Gynecology, Saint-Francois D'Assise Hospital, Laval University, 10 Espinay Road, Québec City, G1V 0A6, Canada.
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Straub TJ, Chou WC, Manson AL, Schreiber HL, Walker BJ, Desjardins CA, Chapman SB, Kaspar KL, Kahsai OJ, Traylor E, Dodson KW, Hullar MAJ, Hultgren SJ, Khoo C, Earl AM. Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections. BMC Microbiol 2021; 21:53. [PMID: 33596852 PMCID: PMC7890861 DOI: 10.1186/s12866-021-02106-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/28/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Urinary tract infections (UTIs) affect 15 million women each year in the United States, with > 20% experiencing frequent recurrent UTIs. A recent placebo-controlled clinical trial found a 39% reduction in UTI symptoms among recurrent UTI sufferers who consumed a daily cranberry beverage for 24 weeks. Using metagenomic sequencing of stool from a subset of these trial participants, we assessed the impact of cranberry consumption on the gut microbiota, a reservoir for UTI-causing pathogens such as Escherichia coli, which causes > 80% of UTIs. RESULTS The overall taxonomic composition, community diversity, carriage of functional pathways and gene families, and relative abundances of the vast majority of observed bacterial taxa, including E. coli, were not changed significantly by cranberry consumption. However, one unnamed Flavonifractor species (OTU41), which represented ≤1% of the overall metagenome, was significantly less abundant in cranberry consumers compared to placebo at trial completion. Given Flavonifractor's association with negative human health effects, we sought to determine OTU41 characteristic genes that may explain its differential abundance and/or relationship to key host functions. Using comparative genomic and metagenomic techniques, we identified genes in OTU41 related to transport and metabolism of various compounds, including tryptophan and cobalamin, which have been shown to play roles in host-microbe interactions. CONCLUSION While our results indicated that cranberry juice consumption had little impact on global measures of the microbiome, we found one unnamed Flavonifractor species differed significantly between study arms. This suggests further studies are needed to assess the role of cranberry consumption and Flavonifractor in health and wellbeing in the context of recurrent UTI. TRIAL REGISTRATION Clinical trial registration number: ClinicalTrials.gov NCT01776021 .
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Affiliation(s)
- Timothy J Straub
- Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Wen-Chi Chou
- Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Abigail L Manson
- Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Henry L Schreiber
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Bruce J Walker
- Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher A Desjardins
- Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Sinéad B Chapman
- Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | | | - Orsalem J Kahsai
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elizabeth Traylor
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Karen W Dodson
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Meredith A J Hullar
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Ashlee M Earl
- Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA.
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Damalanka VC, Maddirala AR, Janetka JW. Novel approaches to glycomimetic design: development of small molecular weight lectin antagonists. Expert Opin Drug Discov 2021; 16:513-536. [PMID: 33337918 DOI: 10.1080/17460441.2021.1857721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Introduction: The direct binding of carbohydrates or those presented on glycoproteins or glycolipids to proteins is the primary effector of many biological responses. One class of carbohydrate-binding proteins, lectins are important in all forms of life. Their functions in animals include regulating cell adhesion, glycoprotein synthesis, metabolism, and mediating immune system response while in bacteria and viruses a lectin-mediated carbohydrate-protein interaction between host cells and the pathogen initiates pathogenesis of the infection.Areas covered: In this review, the authors outline the structural and functional pathogenesis of lectins from bacteria, amoeba, and humans. Mimics of a carbohydrate are referred to as glycomimetics, which are much smaller in molecular weight and are devised to mimic the key binding interactions of the carbohydrate while also allowing additional contacts with the lectin. This article emphasizes the various approaches used over the past 10-15 years in the rational design of glycomimetic ligands.Expert opinion: Medicinal chemistry efforts enabled by X-ray structural biology have identified small-molecule glycomimetic lectin antagonists that have entered or are nearing clinical trials. A common theme in these strategies is the use of biaryl ring systems to emulate the carbohydrate interactions with the lectin.
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Affiliation(s)
- Vishnu C Damalanka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis USA
| | - Amarendar Reddy Maddirala
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis USA
| | - James W Janetka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis USA
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Hashimoto M, Ma YF, Wang ST, Chen CS, Teng CH. Iron Acquisition of Urinary Tract Infection Escherichia coli Involves Pathogenicity in Caenorhabditis elegans. Microorganisms 2021; 9:microorganisms9020310. [PMID: 33540892 PMCID: PMC7913171 DOI: 10.3390/microorganisms9020310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/16/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is a major bacterial pathogen that causes urinary tract infections (UTIs). The mouse is an available UTI model for studying the pathogenicity; however, Caenorhabditis elegans represents as an alternative surrogate host with the capacity for high-throughput analysis. Then, we established a simple assay for a UPEC infection model with C. elegans for large-scale screening. A total of 133 clinically isolated E. coli strains, which included UTI-associated and fecal isolates, were applied to demonstrate the simple pathogenicity assay. From the screening, several virulence factors (VFs) involved with iron acquisition (chuA, fyuA, and irp2) were significantly associated with high pathogenicity. We then evaluated whether the VFs in UPEC were involved in the pathogenicity. Mutants of E. coli UTI89 with defective iron acquisition systems were applied to a solid killing assay with C. elegans. As a result, the survival rate of C. elegans fed with the mutants significantly increased compared to when fed with the parent strain. The results demonstrated, the simple assay with C. elegans was useful as a UPEC infectious model. To our knowledge, this is the first report of the involvement of iron acquisition in the pathogenicity of UPEC in a C. elegans model.
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Affiliation(s)
- Masayuki Hashimoto
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan;
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 70101, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; (S.-T.W.); (C.-S.C.)
- Correspondence: (M.H.); (C.-H.T.)
| | - Yi-Fen Ma
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan;
| | - Sin-Tian Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; (S.-T.W.); (C.-S.C.)
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chang-Shi Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; (S.-T.W.); (C.-S.C.)
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ching-Hao Teng
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan;
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 70101, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan; (S.-T.W.); (C.-S.C.)
- Center of Allergy and Clinical Immunology Research (ACIR), National Cheng Kung University, Tainan 70101, Taiwan
- Correspondence: (M.H.); (C.-H.T.)
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Ramakrishnan V, Marialouis XA, Sankarasubramanian J, Santhanam A, Balakrishnan AS. Whole Genomic analysis of a clinical isolate of Uropathogenic Escherichia coli strain of Sequence Type - 101 carrying the drug resistance NDM-7 in IncX3 plasmid. Bioinformation 2021; 17:126-131. [PMID: 34393427 PMCID: PMC8340689 DOI: 10.6026/97320630017126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/31/2020] [Accepted: 01/26/2021] [Indexed: 11/30/2022] Open
Abstract
The emerging NDM-producing Enterobactereciae is a major threat to public health. The association of NDM-7 with sequence type 101 E.coli is identified in very few numbers. Therefore, it is of interest to analyse the whole genome sequence of NDM-producing uropathogenic
E. coli XA31 that was found to carry numerous drug resistance genes of different antibiotic classes. The isolate E. coli belongs to ST-101 carrying blaNDM-7 coexisting with several resistance genes blaOXA-1, blaTEM1-A, blaCTX-M15, aac(6')-Ib-cr, catB3, tetB. Resfinder
predicts this and four other plasmid replicons were identified using the Plasfinder in the CGE platform. The high transferable IncX3 plasmid was found to carry the NDM-7 gene. Thus, we the report the combination of NDM-7-ST101-IncX3 in India. The combination of this
epidemic clone with NDM-7 is highly required to develop an effective infection control strategy.
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Affiliation(s)
- Venkatesan Ramakrishnan
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Xavier Alexander Marialouis
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.,National Institute of Pharmaceutical Education and Research, 168, Manicktala Main Road, Kolkata 700054, West Bengal, India
| | - Jagadesan Sankarasubramanian
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Amutha Santhanam
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.,National Centre for Nanoscience and Nanotechnology, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
| | - Anand Setty Balakrishnan
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
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49
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The Role of Gut, Vaginal, and Urinary Microbiome in Urinary Tract Infections: From Bench to Bedside. Diagnostics (Basel) 2020; 11:diagnostics11010007. [PMID: 33375202 PMCID: PMC7822161 DOI: 10.3390/diagnostics11010007] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/16/2022] Open
Abstract
The current paradigm of urinary tract infection (UTI) pathogenesis takes into account the contamination of the periurethral space by specific uropathogens residing in the gut, which is followed by urethral colonization and pathogen ascension to the urinary bladder. Consequently, studying the relationship between gut microbiota and the subsequent development of bacteriuria and UTI represents an important field of research. However, the well-established diagnostic and therapeutic paradigm for urinary tract infections (UTIs) has come into question with the discovery of a multifaceted, symbiotic microbiome in the healthy urogenital tract. More specifically, emerging data suggest that vaginal dysbiosis may result in Escherichia coli colonization and prompt recurrent UTIs, while urinary microbiome perturbations may precede the development of UTIs and other pathologic conditions of the urinary system. The question is whether these findings can be exploited for risk reduction and treatment purposes. This review aimed to appraise the three aforementioned specific microbiomes regarding their potential influence on UTI development by focusing on the recent studies in the field and assessing the potential linkages between these different niches, as well as evaluating the state of translational research for novel therapeutic and preventative approaches.
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50
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O'Brien VP, Joens MS, Lewis AL, Gilbert NM. Recurrent Escherichia coli Urinary Tract Infection Triggered by Gardnerella vaginalis Bladder Exposure in Mice. J Vis Exp 2020. [PMID: 33346201 DOI: 10.3791/61967] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Recurrent urinary tract infections (rUTI) caused by uropathogenic Escherichia coli (UPEC) are common and costly. Previous articles describing models of UTI in male and female mice have illustrated the procedures for bacterial inoculation and enumeration in urine and tissues. During an initial bladder infection in C57BL/6 mice, UPEC establish latent reservoirs inside bladder epithelial cells that persist following clearance of UPEC bacteriuria. This model builds on these studies to examine rUTI caused by the emergence of UPEC from within latent bladder reservoirs. The urogenital bacterium Gardnerella vaginalis is used as the trigger of rUTI in this model because it is frequently present in the urogenital tracts of women, especially in the context of vaginal dysbiosis that has been associated with UTI. In addition, a method for in situ bladder fixation followed by scanning electron microscopy (SEM) analysis of bladder tissue is also described, with potential application to other studies involving the bladder.
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Affiliation(s)
- Valerie P O'Brien
- Department of Molecular Microbiology, Washington University School of Medicine in Saint Louis; Center for Women's Infectious Disease Research, Washington University School of Medicine in Saint Louis; Fred Hutchinson Cancer Research Center
| | - Matthew S Joens
- Center for Cellular Imaging, Washington University School of Medicine in Saint Louis; TESCAN USA, Inc
| | - Amanda L Lewis
- Department of Molecular Microbiology, Washington University School of Medicine in Saint Louis; Center for Women's Infectious Disease Research, Washington University School of Medicine in Saint Louis; Department of Obstetrics and Gynecology, Washington University School of Medicine in Saint Louis; University of California San Diego
| | - Nicole M Gilbert
- Center for Women's Infectious Disease Research, Washington University School of Medicine in Saint Louis; Department of Pediatrics, Washington University School of Medicine in Saint Louis;
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