1
|
Ebrahimzadeh T, Basu U, Lutz KC, Gadhvi J, Komarovsky JV, Li Q, Zimmern PE, De Nisco NJ. Inflammatory markers for improved recurrent UTI diagnosis in postmenopausal women. Life Sci Alliance 2024; 7:e202302323. [PMID: 38331474 PMCID: PMC10853434 DOI: 10.26508/lsa.202302323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024] Open
Abstract
Recurrent urinary tract infection (rUTI) severely impacts postmenopausal women. The lack of rapid and accurate diagnostic tools is a major obstacle in rUTI management as current gold standard methods have >24-h diagnostic windows. Work in animal models and limited human cohorts have identified robust inflammatory responses activated during UTI. Consequently, urinary inflammatory cytokines secreted during UTI may function as diagnostic biomarkers. This study aimed to identify urinary cytokines that could accurately diagnose UTI in a controlled cohort of postmenopausal women. Women passing study exclusion criteria were classified into no UTI and active rUTI groups, and urinary cytokine levels were measured by immunoassay. Pro-inflammatory cytokines IL-8, IL-18, IL-1β, and monocyte chemoattractant protein-1 were significantly elevated in the active rUTI group, and anti-inflammatory cytokines IL-13 and IL-4 were elevated in women without UTI. We evaluated cytokine diagnostic performance and found that an IL-8, prostaglandin E2, and IL-13 multivariable model had the lowest misclassification rate and highest sensitivity. Our data identify urinary IL-8, prostaglandin E2, and IL-13 as candidate biomarkers that may be useful in the development of immunoassay-based UTI diagnostics.
Collapse
Affiliation(s)
- Tahmineh Ebrahimzadeh
- https://ror.org/049emcs32 Department of Biological Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Ujjaini Basu
- https://ror.org/049emcs32 Department of Biological Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Kevin C Lutz
- https://ror.org/049emcs32 Department of Mathematics, University of Texas at Dallas, Dallas, TX, USA
| | - Jashkaran Gadhvi
- https://ror.org/049emcs32 Department of Biological Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Jessica V Komarovsky
- https://ror.org/049emcs32 Department of Biological Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Qiwei Li
- https://ror.org/049emcs32 Department of Mathematics, University of Texas at Dallas, Dallas, TX, USA
| | - Philippe E Zimmern
- https://ror.org/05byvp690 Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nicole J De Nisco
- https://ror.org/049emcs32 Department of Biological Sciences, University of Texas at Dallas, Dallas, TX, USA
- https://ror.org/05byvp690 Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
2
|
Sawant NV, Chang SS, Pandit KA, Khekare P, Warner WR, Zimmern PE, De Nisco NJ. VesiX cetylpyridinium chloride is rapidly bactericidal and reduces uropathogenic Escherichia coli bladder epithelial cell invasion in vitro. Microbiol Spectr 2024; 12:e0271223. [PMID: 38240572 PMCID: PMC10913388 DOI: 10.1128/spectrum.02712-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/11/2023] [Indexed: 03/06/2024] Open
Abstract
Management of urinary tract infection (UTI) in postmenopausal women can be challenging. The recent rise in resistance to most of the available oral antibiotic options together with high recurrence rate in postmenopausal women has further complicated treatment of UTI. As such, intravesical instillations of antibiotics like gentamicin are being investigated as an alternative to oral antibiotic therapies. This study evaluates the efficacy of the candidate intravesical therapeutic VesiX, a solution containing the cationic detergent Cetylpyridinium chloride, against a broad range of uropathogenic bacterial species clinically isolated from postmenopausal women with recurrent UTI (rUTI). We also evaluate the cytotoxicity of VesiX against cultured bladder epithelial cells and find that low concentrations of 0.0063% and 0.0125% provide significant bactericidal effect toward diverse bacterial species including uropathogenic Escherichia coli (UPEC), Klebsiella pneumoniae, Enterococcus faecalis, Pseudomonas aeruginosa, and Proteus mirabilis while minimizing cytotoxic effects against cultured 5637 bladder epithelial cells. Lastly, to begin to evaluate the potential utility of using VesiX in combination therapy with existing intravesical therapies for rUTI, we investigate the combined effects of VesiX and the intravesical antibiotic gentamicin. We find that VesiX and gentamicin are not antagonistic and are able to reduce levels of intracellular UPEC in cultured bladder epithelial cells. IMPORTANCE When urinary tract infections (UTIs), which affect over 50% of women, become resistant to available antibiotic therapies dangerous complications like kidney infection and lethal sepsis can occur. New therapeutic paradigms are needed to expand our arsenal against these difficult to manage infections. Our study investigates VesiX, a Cetylpyridinium chloride (CPC)-based therapeutic, as a candidate broad-spectrum antimicrobial agent for use in bladder instillation therapy for antibiotic-resistant UTI. CPC is a cationic surfactant that is FDA-approved for use in mouthwashes and is used as a food additive but has not been extensively evaluated as a UTI therapeutic. Our study is the first to investigate its rapid bactericidal kinetics against diverse uropathogenic bacterial species isolated from postmenopausal women with recurrent UTI and host cytotoxicity. We also report that together with the FDA-approved bladder-instillation agent gentamicin, VesiX was able to significantly reduce intracellular populations of uropathogenic bacteria in cultured bladder epithelial cells.
Collapse
Affiliation(s)
- Namrata V. Sawant
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Samuel S. Chang
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Krutika A. Pandit
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Prachi Khekare
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | | | - Philippe E. Zimmern
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Nicole J. De Nisco
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
3
|
Nguyen VH, Sharon BM, Shipman BM, Zimmern PE, De Nisco NJ. Complete genomes of Limosilactobacillus portuensis and Limosilactobacillus vaginalis isolated from the urine of postmenopausal women. Microbiol Resour Announc 2024; 13:e0088323. [PMID: 38018964 PMCID: PMC10793329 DOI: 10.1128/mra.00883-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/22/2023] [Indexed: 11/30/2023] Open
Abstract
There is frequent evidence that Limosilactobacillus vaginalis colonizes female genitourinary tracts but few reports of Limosilactobacillus portuensis. Their role in urinary tract infection (UTI) is unclear. We present the first complete genome of L. portuensis and a complete genome of L. vaginalis isolated from postmenopausal women with varying UTI histories.
Collapse
Affiliation(s)
- Vivian H. Nguyen
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Belle M. Sharon
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Braden M. Shipman
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Philippe E. Zimmern
- Department of Urology, The University of Texas at Southwestern Medical Center, Dallas, Texas, USA
| | - Nicole J. De Nisco
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| |
Collapse
|
4
|
Sharon BM, Arute AP, Nguyen A, Tiwari S, Reddy Bonthu SS, Hulyalkar NV, Neugent ML, Palacios Araya D, Dillon NA, Zimmern PE, Palmer KL, De Nisco NJ. Genetic and functional enrichments associated with Enterococcus faecalis isolated from the urinary tract. mBio 2023; 14:e0251523. [PMID: 37962362 PMCID: PMC10746210 DOI: 10.1128/mbio.02515-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/05/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Urinary tract infection (UTI) is a global health issue that imposes a substantial burden on healthcare systems. Women are disproportionately affected by UTI, with >60% of women experiencing at least one UTI in their lifetime. UTIs can recur, particularly in postmenopausal women, leading to diminished quality of life and potentially life-threatening complications. Understanding how pathogens colonize and survive in the urinary tract is necessary to identify new therapeutic targets that are urgently needed due to rising rates of antimicrobial resistance. How Enterococcus faecalis, a bacterium commonly associated with UTI, adapts to the urinary tract remains understudied. Here, we generated a collection of high-quality closed genome assemblies of clinical urinary E. faecalis isolated from the urine of postmenopausal women that we used alongside detailed clinical metadata to perform a robust comparative genomic investigation of genetic factors that may be involved in E. faecalis survival in the urinary tract.
Collapse
Affiliation(s)
- Belle M. Sharon
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Amanda P. Arute
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Amber Nguyen
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Suman Tiwari
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | | | - Neha V. Hulyalkar
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Michael L. Neugent
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Dennise Palacios Araya
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Nicholas A. Dillon
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Philippe E. Zimmern
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kelli L. Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Nicole J. De Nisco
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
5
|
Hagge LM, Shahrivarkevishahi A, Al-Kharji NM, Chen Z, Brohlin OR, Trashi I, Tumac A, C Herbert F, Adlooru AV, Lee H, Firouzi HR, Cornelius SA, De Nisco NJ, Gassensmith JJ. Intracellular delivery of virus-like particles using a sheddable linker. J Mater Chem B 2023. [PMID: 37401235 DOI: 10.1039/d3tb00696d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Intracellular targeting is essential for the efficient delivery of drugs and nanotherapeutics. Transporting nanomaterials into cells' cytoplasm for therapeutic purposes can be challenging due to the endosomal trap and lysosomal degradation of cargo. To overcome this issue, we utilized chemical synthesis to design a functional carrier that can escape the endosome and deliver biological materials into the cytoplasm. We synthesized a thiol-sensitive maleimide linker that connects the well-known mitochondria targeting lipophilic triphenylphosphonium cation (TPP) to the surface of a proteinaceous nanoparticle based on the engineered virus-like particle (VLP) Qβ. TPP facilitates endosomal escape by its lipophilic and cationic nature, which disrupts the endosomal membrane. Once in the cytosol, glutathione reacts with the thiol-sensitive maleimide linkers, severs the TPP from the nanoparticle, halting its trafficking to the mitochondria, and marooning it in the cytosol. We successfully demonstrated cytosolic delivery of a VLP loaded with Green Fluorescent Protein (GFP) in vitro and small-ultrared fluorescent protein (smURFP) in vivo, where evenly distributed fluorescence is observed in A549 human lung adenocarcinoma cells and the epithelial cells of BALB/c mice lungs. As a proof of concept, we encapsulated luciferase-targeted siRNA (siLuc) inside the VLP decorated with the maleimide-TPP (M-TPP) linker. We observed enhanced luminescence silencing in luciferase-expressing HeLa cells using our sheddable TPP linker compared to control VLPs.
Collapse
Affiliation(s)
- Laurel M Hagge
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Arezoo Shahrivarkevishahi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Noora M Al-Kharji
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Zhuo Chen
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Olivia R Brohlin
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Ikeda Trashi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Alisia Tumac
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Fabian C Herbert
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Abhinay Varma Adlooru
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Hamilton Lee
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Hamid Reza Firouzi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Samuel A Cornelius
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Nicole J De Nisco
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Jeremiah J Gassensmith
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
- Department of Bioengineering, The University of Texas at Dallas, Richardson, Texas 75080, USA
| |
Collapse
|
6
|
Sharon BM, Hulyalkar NV, Zimmern PE, Palmer KL, De Nisco NJ. Inter-species diversity and functional genomic analyses of closed genome assemblies of clinically isolated, megaplasmid-containing Enterococcus raffinosus Er676 and ATCC49464. Access Microbiol 2023; 5:acmi000508.v3. [PMID: 37424546 PMCID: PMC10323788 DOI: 10.1099/acmi.0.000508.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/10/2023] [Indexed: 07/11/2023] Open
Abstract
Enterococcus raffinosus is an understudied member of its genus possessing a characteristic megaplasmid contributing to a large genome size. Although less commonly associated with human infection compared to other enterococci, this species can cause disease and persist in diverse niches such as the gut, urinary tract, blood and environment. Few complete genome assemblies have been published to date for E. raffinosus . In this study, we report the complete assembly of the first clinical urinary E. raffinosus strain, Er676, isolated from a postmenopausal woman with history of recurrent urinary tract infection. We additionally completed the assembly of clinical type strain ATCC49464. Comparative genomic analyses reveal inter-species diversity driven by large accessory genomes. The presence of a conserved megaplasmid indicates it is a ubiquitous and vital genetic feature of E. raffinosus . We find that the E. raffinosus chromosome is enriched for DNA replication and protein biosynthesis genes while the megaplasmid is enriched for transcription and carbohydrate metabolism genes. Prophage analysis suggests that diversity in the chromosome and megaplasmid sequences arises, in part, from horizontal gene transfer. Er676 demonstrated the largest genome size reported to date for E. raffinosus and the highest probability of human pathogenicity. Er676 also possesses multiple antimicrobial resistance genes, of which all but one are encoded on the chromosome, and has the most complete prophage sequences. Complete assembly and comparative analyses of the Er676 and ATCC49464 genomes provide important insight into the inter-species diversity of E. raffinosus that gives it its ability to colonize and persist in the human body. Investigating genetic factors that contribute to the pathogenicity of this species will provide valuable tools to combat diseases caused by this opportunistic pathogen.
Collapse
Affiliation(s)
- Belle M. Sharon
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Neha V. Hulyalkar
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Philippe E. Zimmern
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kelli L. Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Nicole J. De Nisco
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
7
|
Sharon BM, Arute AP, Nguyen A, Tiwari S, Bonthu SSR, Hulyalkar NV, Neugent ML, Araya DP, Dillon NA, Zimmern PE, Palmer KL, De Nisco NJ. Functional and genetic adaptations contributing to Enterococcus faecalis persistence in the female urinary tract. bioRxiv 2023:2023.05.18.541374. [PMID: 37293065 PMCID: PMC10245761 DOI: 10.1101/2023.05.18.541374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Enterococcus faecalis is the leading Gram-positive bacterial species implicated in urinary tract infection (UTI). An opportunistic pathogen, E. faecalis is a commensal of the human gastrointestinal tract (GIT) and its presence in the GIT is a predisposing factor for UTI. The mechanisms by which E. faecalis colonizes and survives in the urinary tract (UT) are poorly understood, especially in uncomplicated or recurrent UTI. The UT is distinct from the GIT and is characterized by a sparse nutrient landscape and unique environmental stressors. In this study, we isolated and sequenced a collection of 37 clinical E. faecalis strains from the urine of primarily postmenopausal women. We generated 33 closed genome assemblies and four highly contiguous draft assemblies and conducted a comparative genomics to identify genetic features enriched in urinary E. faecalis with respect to E. faecalis isolated from the human GIT and blood. Phylogenetic analysis revealed high diversity among urinary strains and a closer relatedness between urine and gut isolates than blood isolates. Plasmid replicon (rep) typing further underscored possible UT-GIT interconnection identifying nine shared rep types between urine and gut E. faecalis . Both genotypic and phenotypic analysis of antimicrobial resistance among urinary E. faecalis revealed infrequent resistance to front-line UTI antibiotics nitrofurantoin and fluoroquinolones and no vancomycin resistance. Finally, we identified 19 candidate genes enriched among urinary strains that may play a role in adaptation to the UT. These genes are involved in the core processes of sugar transport, cobalamin import, glucose metabolism, and post-transcriptional regulation of gene expression. IMPORTANCE Urinary tract infection (UTI) is a global health issue that imposes substantial burden on healthcare systems. Women are disproportionately affected by UTI with >60% of women experiencing at least one UTI in their lifetime. UTIs can recur, particularly in postmenopausal women, leading to diminished quality of life and potentially life-threatening complications. Understanding how pathogens colonize and survive in the urinary tract is necessary to identify new therapeutic targets that are urgently needed due to rising rates of antimicrobial resistance. How Enterococcus faecalis , a bacterium commonly associated with UTI, adapts to the urinary tract remains understudied. Here, we generated a collection of high-quality closed genome assemblies of clinical urinary E. faecalis isolated from the urine of postmenopausal women that we used alongside detailed clinical metadata to perform a robust comparative genomic investigation of genetic factors that may mediate urinary E. faecalis adaptation to the female urinary tract.
Collapse
|
8
|
Trashi I, Durbacz MZ, Trashi O, Wijesundara YH, Ehrman RN, Chiev AC, Darwin CB, Herbert FC, Gadhvi J, De Nisco NJ, Nielsen SO, Gassensmith JJ. Self-assembly of a fluorescent virus-like particle for imaging in tissues with high autofluorescence. J Mater Chem B 2023; 11:4445-4452. [PMID: 37144595 DOI: 10.1039/d3tb00469d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Virus-like particles (VLPs) are engineered nanoparticles that mimic the properties of viruses-like high tolerance to heat and proteases-but lack a viral genome, making them non-infectious. They are easily modified chemically and genetically, making them useful in drug delivery, enhancing vaccine efficacy, gene delivery, and cancer immunotherapy. One such VLP is Qβ, which has an affinity towards an RNA hairpin structure found in its viral RNA that drives the self-assembly of the capsid. It is possible to usurp the native way infectious Qβ self-assembles to encapsidate its RNA to place enzymes inside the VLP's lumen as a protease-resistant cage. Further, using RNA templates that mimic the natural self-assembly of the native capsid, fluorescent proteins (FPs) have been placed inside VLPs in a "one pot" expression system. Autofluorescence in tissues can lead to misinterpretation of results and unreliable science, so we created a single-pot expression system that uses the fluorescent protein smURFP, which avoids autofluorescence and has spectral properties compatible with standard commercial filter sets on confocal microscopes. In this work, we were able to simplify the existing "one-pot" expression system while creating high-yielding fluorescent VLP nanoparticles that could easily be imaged inside lung epithelial tissue.
Collapse
Affiliation(s)
- Ikeda Trashi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Mateusz Z Durbacz
- Department of Molecular Biology and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Orikeda Trashi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Yalini H Wijesundara
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Ryanne N Ehrman
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Alyssa C Chiev
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Cary B Darwin
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Fabian C Herbert
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Jashkaran Gadhvi
- Department of Biological Science, The University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Nicole J De Nisco
- Department of Biological Science, The University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Steven O Nielsen
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
| | - Jeremiah J Gassensmith
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, USA.
- Department of Bioengineering, The University of Texas at Dallas, Richardson, Texas 75080, USA
| |
Collapse
|
9
|
Colbert JF, Kirsch JM, Erzen CL, Langouët-Astrié CJ, Thompson GE, McMurtry SA, Kofonow JM, Robertson CE, Kovacs EJ, Sullivan RC, Hippensteel JA, Sawant NV, De Nisco NJ, McCollister BD, Schwartz RS, Horswill AR, Frank DN, Duerkop BA, Schmidt EP. Aging-Associated Augmentation of Gut Microbiome Virulence Capability Drives Sepsis Severity. mBio 2023:e0005223. [PMID: 37102874 DOI: 10.1128/mbio.00052-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
Prior research has focused on host factors as mediators of exaggerated sepsis-associated morbidity and mortality in older adults. This focus on the host, however, has failed to identify therapies that improve sepsis outcomes in the elderly. We hypothesized that the increased susceptibility of the aging population to sepsis is not only a function of the host but also reflects longevity-associated changes in the virulence of gut pathobionts. We utilized two complementary models of gut microbiota-induced experimental sepsis to establish the aged gut microbiome as a key pathophysiologic driver of heightened disease severity. Further murine and human investigations into these polymicrobial bacterial communities demonstrated that age was associated with only subtle shifts in ecological composition but also an overabundance of genomic virulence factors that have functional consequence on host immune evasion. IMPORTANCE Older adults suffer more frequent and worse outcomes from sepsis, a critical illness secondary to infection. The reasons underlying this unique susceptibility are incompletely understood. Prior work in this area has focused on how the immune response changes with age. The current study, however, focuses instead on alterations in the community of bacteria that humans live with within their gut (i.e., the gut microbiome). The central concept of this paper is that the bacteria in our gut evolve along with the host and "age," making them more efficient at causing sepsis.
Collapse
Affiliation(s)
- James F Colbert
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado, USA
| | - Joshua M Kirsch
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Christopher L Erzen
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | | | - Sarah A McMurtry
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jennifer M Kofonow
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Charles E Robertson
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Elizabeth J Kovacs
- Department of Surgery, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Ryan C Sullivan
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Joseph A Hippensteel
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Namrata V Sawant
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Nicole J De Nisco
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bruce D McCollister
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Robert S Schwartz
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
- Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado, USA
| | - Alexander R Horswill
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado, USA
| | - Daniel N Frank
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Eric P Schmidt
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| |
Collapse
|
10
|
Neugent ML, Hulyalkar NV, Kumar A, Xing C, Zimmern PE, Shulaev V, De Nisco NJ. Urinary Glycosaminoglycans Are Associated with Recurrent UTI and Urobiome Ecology in Postmenopausal Women. ACS Infect Dis 2023; 9:1022-1032. [PMID: 36942838 PMCID: PMC10111421 DOI: 10.1021/acsinfecdis.3c00027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Glycosaminoglycans (GAGs) are linear, negatively charged polysaccharides composed of repeating disaccharide units of uronic acid and amino sugars. The luminal surface of the bladder epithelium is coated with a GAG layer. These urothelial GAGs are thought to provide a protective barrier and serve as a potential interaction site with the urinary microbiome (urobiome). Previous studies have profiled urinary GAG composition in mixed cohorts, but the urinary GAG composition in postmenopausal women remains undefined. To investigate the relationship between GAGs and recurrent urinary tract infection (rUTI), we profiled urinary GAGs in a controlled cohort of postmenopausal women. We found that chondroitin sulfate (CS) is the major urinary GAG in postmenopausal women and that urinary CS was elevated in women with active rUTI. We also associated urinary GAGs with urobiome composition and identified bacterial species that significantly associated with urinary GAG concentration. Corynebacterium amycolatum, Porphyromonas somerae, and Staphylococcus pasteuri were positively associated with heparin sulfate or hyaluronic acid, and bacterial species associated with vaginal dysbiosis were negatively correlated with urinary CS. Altogether, this work defines changes in urinary GAG composition associated with rUTI and identifies new associations between urinary GAGs and the urobiome that may play a role in rUTI pathobiology.
Collapse
Affiliation(s)
- Michael L Neugent
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Neha V Hulyalkar
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
- Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Philippe E Zimmern
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Vladimir Shulaev
- Department of Biological Sciences, The University of North Texas, Denton, Texas 76203, United States
- Advanced Environmental Research Institute, The University of North Texas, Denton, Texas 76203, United States
| | - Nicole J De Nisco
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| |
Collapse
|
11
|
Zimmern PE, Sawant NV, Chang SS, Warner RW, De Nisco NJ. Intravesical VesiX as a Last Resort Therapy in Women With Antibiotic-Refractory Recurrent Urinary Tract Infections Contemplating Bladder Removal: A Preliminary Report. Ann Pharmacother 2023; 57:350-351. [PMID: 35838251 DOI: 10.1177/10600280221112111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
12
|
Neugent ML, Hulyalkar NV, Kumar A, Xing C, Zimmern PE, Shulaev V, De Nisco NJ. Urinary Glycosaminoglycans are Associated with Recurrent UTI and Urobiome Ecology in Postmenopausal Women. bioRxiv 2023:2023.01.11.523678. [PMID: 36711817 PMCID: PMC9882061 DOI: 10.1101/2023.01.11.523678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Glycosaminoglycans (GAGs) are linear, negatively charged polysaccharides composed of repeating disaccharide units of uronic acid and amino sugars. The luminal surface of the bladder epithelium is coated with a GAG layer. These urothelial GAGs are thought to provide a protective barrier and serve as a potential interaction site with the urinary microbiome (urobiome). Previous studies have profiled urinary GAG composition in mixed cohorts, but the urinary GAG composition in postmenopausal women remains undefined. To investigate the relationship between GAGs and recurrent UTI (rUTI), we profiled urinary GAGs in a controlled cohort of postmenopausal women. We found that chondroitin sulfate (CS) is the major urinary GAG in postmenopausal women and that urinary CS was elevated in women with active rUTI. We also associated urinary GAGs with urobiome composition and identified bacterial species that significantly associated with urinary GAG concentration. Corynebacterium amycolatum, Porphyromonas somerae , and Staphylococcus pasteuri were positively associated with heparin sulfate or hyaluronic acid and bacterial species associated with vaginal dysbiosis were negatively correlated to urinary CS. Altogether, this work defines changes in urinary GAG composition associated with rUTI and identifies new associations between urinary GAGs and the urobiome that may play a role in rUTI pathobiology.
Collapse
|
13
|
Colbert JF, Kirsch JM, Erzen CL, Langouët-Astrié CJ, Thompson GE, McMurtry SA, Kofonow JM, Robertson CE, Kovacs EJ, Sullivan RC, Hippensteel JA, Sawant NV, De Nisco NJ, McCollister BD, Schwartz RS, Horswill AR, Frank DN, Duerkop BA, Schmidt EP. Aging-associated augmentation of gut microbiome virulence capability drives sepsis severity. bioRxiv 2023:2023.01.10.523523. [PMID: 36711447 PMCID: PMC9882086 DOI: 10.1101/2023.01.10.523523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Prior research has focused on host factors as mediators of exaggerated sepsis-associated morbidity and mortality in older adults. This focus on the host, however, has failed to identify therapies that improve sepsis outcomes in the elderly. We hypothesized that the increased susceptibility of the aging population to sepsis is not only a function of the host, but also reflects longevity-associated changes in the virulence of gut pathobionts. We utilized two complementary models of gut microbiota-induced experimental sepsis to establish the aged gut microbiome as a key pathophysiologic driver of heightened disease severity. Further murine and human investigations into these polymicrobial bacterial communities demonstrated that age was associated with only subtle shifts in ecological composition, but an overabundance of genomic virulence factors that have functional consequence on host immune evasion. One Sentence Summary The severity of sepsis in the aged host is in part mediated by longevity-associated increases in gut microbial virulence.
Collapse
|
14
|
Wijesundara YH, Herbert FC, Trashi O, Trashi I, Brohlin OR, Kumari S, Howlett T, Benjamin CE, Shahrivarkevishahi A, Diwakara SD, Perera SD, Cornelius SA, Vizuet JP, Balkus KJ, Smaldone RA, De Nisco NJ, Gassensmith JJ. Carrier gas triggered controlled biolistic delivery of DNA and protein therapeutics from metal-organic frameworks. Chem Sci 2022; 13:13803-13814. [PMID: 36544734 PMCID: PMC9710232 DOI: 10.1039/d2sc04982a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/24/2022] [Indexed: 12/24/2022] Open
Abstract
The efficacy and specificity of protein, DNA, and RNA-based drugs make them popular in the clinic; however, these drugs are often delivered via injection, requiring skilled medical personnel, and producing biohazardous waste. Here, we report an approach that allows for their controlled delivery, affording either a burst or slow release without altering the formulation. We show that when encapsulated within zeolitic-imidazolate framework eight (ZIF-8), the biomolecules are stable in powder formulations and can be inoculated with a low-cost, gas-powered "MOF-Jet" into living animal and plant tissues. Additionally, their release profiles can be modulated through judicious selection of the carrier gas used in the MOF-Jet. Our in vitro and in vivo studies reveal that when CO2 is used, it creates a transient and weakly acidic local environment that causes a near-instantaneous release of the biomolecules through an immediate dissolution of ZIF-8. Conversely, when air is used, ZIF-8 biodegrades slowly, releasing the biomolecules over a week. This is the first example of controlled-biolistic delivery of biomolecules using ZIF-8, which provides a powerful tool for fundamental and applied science research.
Collapse
Affiliation(s)
- Yalini H. Wijesundara
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Fabian C. Herbert
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Orikeda Trashi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Ikeda Trashi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Olivia R. Brohlin
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Sneha Kumari
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Thomas Howlett
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Candace E. Benjamin
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Arezoo Shahrivarkevishahi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Shashini D. Diwakara
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Sachini D. Perera
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Samuel A. Cornelius
- Department of Biological Sciences, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Juan P. Vizuet
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Kenneth J. Balkus
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Ronald A. Smaldone
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Nicole J. De Nisco
- Department of Biological Sciences, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| | - Jeremiah J. Gassensmith
- Department of Chemistry and Biochemistry, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA,Department of Biomedical Engineering, The University of Texas at Dallas800 West Campbel RdRichardson 75080TXUSA
| |
Collapse
|
15
|
Ganguly A, Ebrahimzadeh T, Komarovsky J, Zimmern PE, De Nisco NJ, Prasad S. DigEST
: Digital plug‐n‐probe disease Endotyping Sensor Technology. Bioeng Transl Med 2022. [DOI: 10.1002/btm2.10437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Antra Ganguly
- Department of Bioengineering University of Texas at Dallas Richardson Texas USA
| | - Tahmineh Ebrahimzadeh
- Department of Biological Sciences University of Texas at Dallas Richardson Texas USA
| | - Jessica Komarovsky
- Department of Biological Sciences University of Texas at Dallas Richardson Texas USA
| | - Philippe E. Zimmern
- Department of Urology University of Texas Southwestern Medical Center Dallas Texas USA
| | - Nicole J. De Nisco
- Department of Biological Sciences University of Texas at Dallas Richardson Texas USA
| | - Shalini Prasad
- Department of Bioengineering University of Texas at Dallas Richardson Texas USA
| |
Collapse
|
16
|
Neugent ML, Kumar A, Hulyalkar NV, Lutz KC, Nguyen VH, Fuentes JL, Zhang C, Nguyen A, Sharon BM, Kuprasertkul A, Arute AP, Ebrahimzadeh T, Natesan N, Xing C, Shulaev V, Li Q, Zimmern PE, Palmer KL, De Nisco NJ. Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome. Cell Rep Med 2022; 3:100753. [PMID: 36182683 PMCID: PMC9588997 DOI: 10.1016/j.xcrm.2022.100753] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/28/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022]
Abstract
Postmenopausal women are severely affected by recurrent urinary tract infection (rUTI). The urogenital microbiome is a key component of the urinary environment. However, changes in the urogenital microbiome underlying rUTI susceptibility are unknown. Here, we perform shotgun metagenomics and advanced culture on urine from a controlled cohort of postmenopausal women to identify urogenital microbiome compositional and function changes linked to rUTI susceptibility. We identify candidate taxonomic biomarkers of rUTI susceptibility in postmenopausal women and an enrichment of lactobacilli in postmenopausal women taking estrogen hormone therapy. We find robust correlations between Bifidobacterium and Lactobacillus and urinary estrogens in women without urinary tract infection (UTI) history. Functional analyses reveal distinct metabolic and antimicrobial resistance gene (ARG) signatures associated with rUTI. Importantly, we find that ARGs are enriched in the urogenital microbiomes of women with rUTI history independent of current UTI status. Our data suggest that rUTI and estrogen shape the urogenital microbiome in postmenopausal women.
Collapse
Affiliation(s)
- Michael L Neugent
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Neha V Hulyalkar
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Kevin C Lutz
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Vivian H Nguyen
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Jorge L Fuentes
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cong Zhang
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Amber Nguyen
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Belle M Sharon
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Amy Kuprasertkul
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amanda P Arute
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Tahmineh Ebrahimzadeh
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Nitya Natesan
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vladimir Shulaev
- Department of Biological Sciences, The University of North Texas, Denton, TX, USA; Advanced Environmental Research Institute, The University of North Texas, Denton, TX, USA
| | - Qiwei Li
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Philippe E Zimmern
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kelli L Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Nicole J De Nisco
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA; Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
17
|
Abstract
The gut microbiome is a critical modulator of systemic physiology, including infectious disease susceptibility. Although this niche is a reservoir for uropathogenic Escherichia coli, knowledge of its role in urinary tract infections (UTIs) is limited. We discuss two recent studies, Thänert et al. (2022) and Worby et al. (2022), that interrogate the roles of the gut-bladder axis in UTIs.
Collapse
Affiliation(s)
- Arnold M Salazar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael L Neugent
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Nicole J De Nisco
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA; Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Indira U Mysorekar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center of Aging, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
18
|
Nguyen VH, Khan F, Shipman BM, Neugent ML, Hulyalkar NV, Cha NY, Zimmern PE, De Nisco NJ. A Semi-Quantitative Assay to Measure Glycosaminoglycan Degradation by the Urinary Microbiota. Front Cell Infect Microbiol 2022; 11:803409. [PMID: 35047421 PMCID: PMC8762050 DOI: 10.3389/fcimb.2021.803409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/30/2021] [Indexed: 11/28/2022] Open
Abstract
Glycosaminoglycans (GAGs) are linear polysaccharides and are among the primary components of mucosal surfaces in mammalian systems. The GAG layer lining the mucosal surface of the urinary tract is thought to play a critical role in urinary tract homeostasis and provide a barrier against urinary tract infection (UTI). This key component of the host-microbe interface may serve as a scaffolding site or a nutrient source for the urinary microbiota or invading pathogens, but its exact role in UTI pathogenesis is unclear. Although members of the gut microbiota have been shown to degrade GAGs, the utilization and degradation of GAGs by the urinary microbiota or uropathogens had not been investigated. In this study, we developed an in vitro plate-based assay to measure GAG degradation and utilization and used this assay to screen a library of 37 urinary bacterial isolates representing both urinary microbiota and uropathogenic species. This novel assay is more rapid, inexpensive, and quantitative compared to previously developed assays, and can measure three of the major classes of human GAGs. Our findings demonstrate that this assay captures the well-characterized ability of Streptococcus agalactiae to degrade hyaluronic acid and partially degrade chondroitin sulfate. Additionally, we present the first known report of chondroitin sulfate degradation by Proteus mirabilis, an important uropathogen and a causative agent of acute, recurrent, and catheter-associated urinary tract infections (CAUTI). In contrast, we observed that uropathogenic Escherichia coli (UPEC) and members of the urinary microbiota, including lactobacilli, were unable to degrade GAGs.
Collapse
Affiliation(s)
- Vivian H Nguyen
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, United States
| | - Fatima Khan
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, United States
| | - Braden M Shipman
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, United States
| | - Michael L Neugent
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, United States
| | - Neha V Hulyalkar
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, United States
| | - Natalie Y Cha
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, United States
| | - Philippe E Zimmern
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Nicole J De Nisco
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, United States.,Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| |
Collapse
|
19
|
Ganguly A, Ebrahimzadeh T, Zimmern P, De Nisco NJ, Prasad S. Label-Free, Novel Electrofluidic Capacitor Biosensor for Prostaglandin E2 Detection toward Early and Rapid Urinary Tract Infection Diagnosis. ACS Sens 2022; 7:186-198. [PMID: 34928577 DOI: 10.1021/acssensors.1c01951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Urine Prostaglandin E2 (PGE2) has been identified as an attractive diagnostic and prognostic biomarker for urinary tract infection (UTI). This work demonstrates the use of PGE2 as a biomarker for rapid and label-free testing for UTI. In this work, we have developed a novel electrofluidic capacitor-based biosensor that can used for home-based UTI management with high accuracy in less than 5 min for small volume urine samples (<60 μL). The PGE2 biosensor works on the principle of affinity capture using highly specific monoclonal PGE2 antibody and relies on non-faradaic electrical impedance spectroscopy (EIS) and Mott-Schottky (MS) for quantifying subtle variations in PGE2 levels expressed in human urine (pH 5-8). Dynamic light scattering experiments were performed to characterize surface charge properties and the impact of bulk interferents on the interfacial modulation of electrical properties due to binding and urine pH variations. Binding chemistry between the key elements of the immunosensor stack was validated using attenuated total reflectance-Fourier transform infrared spectroscopy and surface plasmon resonance studies. Linear calibration dose responses were obtained for PGE2 for both EIS and MS. The sensor reliably distinguished between UTI negative and UTI positive cases for both artificial (pH 5-8) and pooled human urine samples. The sensor was not found to cross-react with Prostaglandin D2, a structurally similar interferent, and other abundant urine interferents (urea and creatinine). Human subject studies confirmed the validity of the sensor for robust and accurate UTI diagnosis. This work can be extended to achieve easy, reliable, and rapid home-based UTI management, which can consequently help physicians with timely and appropriate administration of therapy to improve patient outcomes and treatment success.
Collapse
Affiliation(s)
- Antra Ganguly
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Tahmineh Ebrahimzadeh
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Philippe Zimmern
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Nicole J. De Nisco
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Shalini Prasad
- Department of Bioengineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| |
Collapse
|
20
|
Luzuriaga MA, Herbert FC, Brohlin OR, Gadhvi J, Howlett T, Shahrivarkevishahi A, Wijesundara YH, Venkitapathi S, Veera K, Ehrman R, Benjamin CE, Popal S, Burton MD, Ingersoll MA, De Nisco NJ, Gassensmith JJ. Metal-Organic Framework Encapsulated Whole-Cell Vaccines Enhance Humoral Immunity against Bacterial Infection. ACS Nano 2021; 15:17426-17438. [PMID: 34546723 DOI: 10.1021/acsnano.1c03092] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The increasing rate of resistance of bacterial infection against antibiotics requires next generation approaches to fight potential pandemic spread. The development of vaccines against pathogenic bacteria has been difficult owing, in part, to the genetic diversity of bacteria. Hence, there are many potential target antigens and little a priori knowledge of which antigen/s will elicit protective immunity. The painstaking process of selecting appropriate antigens could be avoided with whole-cell bacteria; however, whole-cell formulations typically fail to produce long-term and durable immune responses. These complications are one reason why no vaccine against any type of pathogenic E. coli has been successfully clinically translated. As a proof of principle, we demonstrate a method to enhance the immunogenicity of a model pathogenic E. coli strain by forming a slow releasing depot. The E. coli strain CFT073 was biomimetically mineralized within a metal-organic framework (MOF). This process encapsulates the bacteria within 30 min in water and at ambient temperatures. Vaccination with this formulation substantially enhances antibody production and results in significantly enhanced survival in a mouse model of bacteremia compared to standard inactivated formulations.
Collapse
|
21
|
Shahrivarkevishahi A, Luzuriaga MA, Herbert FC, Tumac AC, Brohlin OR, Wijesundara YH, Adlooru AV, Benjamin C, Lee H, Parsamian P, Gadhvi J, De Nisco NJ, Gassensmith JJ. PhotothermalPhage: A Virus-Based Photothermal Therapeutic Agent. J Am Chem Soc 2021; 143:16428-16438. [PMID: 34551259 DOI: 10.1021/jacs.1c05090] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Virus-like particles (VLPs) are multifunctional nanocarriers that mimic the architecture of viruses. They can serve as a safe platform for specific functionalization and immunization, which provides benefits in a wide range of biomedical applications. In this work, a new generation immunophotothermal agent is developed that adjuvants photothermal ablation using a chemically modified VLP called bacteriophage Qβ. The design is based on the conjugation of near-infrared absorbing croconium dyes to lysine residues located on the surface of Qβ, which turns it to a powerful NIR-absorber called PhotothermalPhage. This system can generate more heat upon 808 nm NIR laser radiation than free dye and possesses a photothermal efficiency comparable to gold nanostructures, yet it is biodegradable and acts as an immunoadjuvant combined with the heat it produces. The synergistic combination of thermal ablation with the mild immunogenicity of the VLP leads to effective suppression of primary tumors, reduced lung metastasis, and increased survival time.
Collapse
Affiliation(s)
- Arezoo Shahrivarkevishahi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Michael A Luzuriaga
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Fabian C Herbert
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Alisia C Tumac
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Olivia R Brohlin
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Yalini H Wijesundara
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Abhinay V Adlooru
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Candace Benjamin
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Hamilton Lee
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Perouza Parsamian
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Jashkaran Gadhvi
- Department of Biological Sciences, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Nicole J De Nisco
- Department of Biological Sciences, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| | - Jeremiah J Gassensmith
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States.,Department of Bioengineering, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States
| |
Collapse
|
22
|
Sharon BM, Hulyalkar NV, Nguyen VH, Zimmern PE, Palmer KL, De Nisco NJ. Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies. J Vis Exp 2021. [PMID: 34487123 DOI: 10.3791/62872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Complete genome sequences provide valuable data for the understanding of genetic diversity and unique colonization factors of urinary microbes. These data may include mobile genetic elements, such as plasmids and extrachromosomal phage, that contribute to the dissemination of antimicrobial resistance and further complicate treatment of urinary tract infection (UTI). In addition to providing fine resolution of genome structure, complete, closed genomes allow for the detailed comparative genomics and evolutionary analyses. The generation of complete genomes de novo has long been a challenging task due to limitations of available sequencing technology. Paired-end Next Generation Sequencing (NGS) produces high quality short reads often resulting in accurate but fragmented genome assemblies. On the contrary, Nanopore sequencing provides long reads of lower quality normally leading to error-prone complete assemblies. Such errors may hamper genome-wide association studies or provide misleading variant analysis results. Therefore, hybrid approaches combining both short and long reads have emerged as reliable methods to achieve highly accurate closed bacterial genomes. Reported herein is a comprehensive method for the culture of diverse urinary bacteria, species identification by 16S rRNA gene sequencing, extraction of genomic DNA (gDNA), and generation of short and long reads by NGS and Nanopore platforms, respectively. Additionally, this method describes a bioinformatic pipeline of quality control, assembly, and gene prediction algorithms for the generation of annotated complete genome sequences. Combination of bioinformatic tools enables the selection of high quality read data for hybrid genome assembly and downstream analysis. The streamlined approach for the hybrid de novo genome assembly described in this protocol may be adapted for the use in any culturable bacteria.
Collapse
Affiliation(s)
- Belle M Sharon
- Department of Biological Sciences, University of Texas at Dallas
| | - Neha V Hulyalkar
- Department of Biological Sciences, University of Texas at Dallas
| | - Vivian H Nguyen
- Department of Biological Sciences, University of Texas at Dallas
| | | | - Kelli L Palmer
- Department of Biological Sciences, University of Texas at Dallas
| | | |
Collapse
|
23
|
Ebrahimzadeh T, Kuprasertkul A, Neugent ML, Lutz KC, Fuentes JL, Gadhvi J, Khan F, Zhang C, Sharon BM, Orth K, Li Q, Zimmern PE, De Nisco NJ. Urinary prostaglandin E2 as a biomarker for recurrent UTI in postmenopausal women. Life Sci Alliance 2021; 4:4/7/e202000948. [PMID: 33958485 PMCID: PMC8200289 DOI: 10.26508/lsa.202000948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/11/2023] Open
Abstract
This work uses controlled human cohorts to investigate urinary prostaglandin E2, the product of cyclooxygenase-2, as both a diagnostic and prognostic biomarker of recurrent UTI postmenopausal women. Urinary tract infection (UTI) is one of the most common adult bacterial infections and exhibits high recurrence rates, especially in postmenopausal women. Studies in mouse models suggest that cyclooxygenase-2 (COX-2)–mediated inflammation sensitizes the bladder to recurrent UTI (rUTI). However, COX-2–mediated inflammation has not been robustly studied in human rUTI. We used human cohorts to assess urothelial COX-2 production and evaluate its product, PGE2, as a biomarker for rUTI in postmenopausal women. We found that the percentage of COX-2–positive cells was elevated in inflamed versus uninflamed bladder regions. We analyzed the performance of urinary PGE2 as a biomarker for rUTI in a controlled cohort of 92 postmenopausal women and PGE2 consistently outperformed all other tested clinical variables as a predictor of rUTI status. Furthermore, time-to-relapse analysis indicated that the risk of rUTI relapse was 3.6 times higher in women with above median urinary PGE2 levels than with below median levels. Taken together, these data suggest that urinary PGE2 may be a clinically useful diagnostic and prognostic biomarker for rUTI in postmenopausal women.
Collapse
Affiliation(s)
- Tahmineh Ebrahimzadeh
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
| | - Amy Kuprasertkul
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael L Neugent
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
| | - Kevin C Lutz
- Depatment of Mathematics, University of Texas at Dallas, Richardson, TX, USA
| | - Jorge L Fuentes
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jashkaran Gadhvi
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
| | - Fatima Khan
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
| | - Cong Zhang
- Depatment of Mathematics, University of Texas at Dallas, Richardson, TX, USA
| | - Belle M Sharon
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qiwei Li
- Depatment of Mathematics, University of Texas at Dallas, Richardson, TX, USA
| | - Philippe E Zimmern
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nicole J De Nisco
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
| |
Collapse
|
24
|
De Nisco NJ, Casey AK, Kanchwala M, Lafrance AE, Coskun FS, Kinch LN, Grishin NV, Xing C, Orth K. Manipulation of IRE1-Dependent MAPK Signaling by a Vibrio Agonist-Antagonist Effector Pair. mSystems 2021; 6:e00872-20. [PMID: 33563785 PMCID: PMC7883537 DOI: 10.1128/msystems.00872-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/19/2021] [Indexed: 12/05/2022] Open
Abstract
Diverse bacterial pathogens employ effector delivery systems to disrupt vital cellular processes in the host (N. M. Alto and K. Orth, Cold Spring Harbor Perspect Biol 4:a006114, 2012, https://doi.org/10.1101/cshperspect.a006114). The type III secretion system 1 of the marine pathogen Vibrio parahaemolyticus utilizes the sequential action of four effectors to induce a rapid, proinflammatory cell death uniquely characterized by a prosurvival host transcriptional response (D. L. Burdette, M. L. Yarbrough, A Orvedahl, C. J. Gilpin, and K. Orth, Proc Natl Acad Sci USA 105:12497-12502, 2008, https://doi.org/10.1073/pnas.0802773105; N. J. De Nisco, M. Kanchwala, P. Li, J. Fernandez, C. Xing, and K. Orth, Sci Signal 10:eaa14501, 2017, https://doi.org/10.1126/scisignal.aal4501). Herein, we show that this prosurvival response is caused by the action of the channel-forming effector VopQ that targets the host V-ATPase, resulting in lysosomal deacidification and inhibition of lysosome-autophagosome fusion. Recent structural studies have shown how VopQ interacts with the V-ATPase and, while in the ER, a V-ATPase assembly intermediate can interact with VopQ, causing a disruption in membrane integrity. Additionally, we observed that VopQ-mediated disruption of the V-ATPase activates the IRE1 branch of the unfolded protein response (UPR), resulting in an IRE1-dependent activation of ERK1/2 MAPK signaling. We also find that this early VopQ-dependent induction of ERK1/2 phosphorylation is terminated by the VopS-mediated inhibitory AMPylation of Rho GTPase signaling. Since VopS dampens VopQ-induced IRE1-dependent ERK1/2 activation, we propose that IRE1 activates ERK1/2 phosphorylation at or above the level of Rho GTPases. This study illustrates how temporally induced effectors can work as in tandem as agonist/antagonist to manipulate host signaling and reveals new connections between V-ATPase function, UPR, and MAPK signaling.IMPORTANCE Vibrio parahaemolyticus is a seafood-borne pathogen that encodes two type 3 secretion systems (T3SS). The first system, T3SS1, is thought to be maintained in all strains of V. parahaemolyticus to maintain survival in the environment, whereas the second system, T3SS2, is linked to clinical isolates and disease in humans. Here, we found that first system targets evolutionarily conserved signaling systems to manipulate host cells, eventually causing a rapid, orchestrated cells death within 3 h. We have found that the T3SS1 injects virulence factors that temporally manipulate host signaling. Within the first hour of infection, the effector VopQ acts first by activating host survival signals while diminishing the host cell apoptotic machinery. Less than an hour later, another effector, VopS, reverses activation and inhibition of these signaling systems, ultimately leading to death of the host cell. This work provides example of how pathogens have evolved to manipulate the interplay between T3SS effectors to regulate host signaling pathways.
Collapse
Affiliation(s)
- Nicole J De Nisco
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Amanda K Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Mohammed Kanchwala
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Alexander E Lafrance
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Fatma S Coskun
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Chao Xing
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
25
|
Neugent ML, Gadhvi J, Palmer KL, Zimmern PE, De Nisco NJ. Detection of Tissue-resident Bacteria in Bladder Biopsies by 16S rRNA Fluorescence In Situ Hybridization. J Vis Exp 2019. [PMID: 31680675 DOI: 10.3791/60458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Visualization of the interaction of bacteria with host mucosal surfaces and tissues can provide valuable insight into mechanisms of pathogenesis. While visualization of bacterial pathogens in animal models of infection can rely on bacterial strains engineered to express fluorescent proteins such as GFP, visualization of bacteria within the mucosa of biopsies or tissue obtained from human patients requires an unbiased method. Here, we describe an efficient method for the detection of tissue-associated bacteria in human biopsy sections. This method utilizes fluorescent in situ hybridization (FISH) with a fluorescently labeled universal oligonucleotide probe for 16S rRNA to label tissue-associated bacteria within bladder biopsy sections acquired from patients suffering from recurrent urinary tract infection. Through use of a universal 16S rRNA probe, bacteria can be detected without prior knowledge of species, genera, or biochemical characteristics, such as lipopolysaccharide (LPS), that would be required for detection by immunofluorescence experiments. We describe a complete protocol for 16S rRNA FISH from biopsy fixation to imaging by confocal microscopy. This protocol can be adapted for use in almost any type of tissue and represents a powerful tool for the unbiased visualization of clinically-relevant bacterial-host interactions in patient tissue. Furthermore, using species or genera-specific probes, this protocol can be adapted for the detection of specific bacterial pathogens within patient tissue.
Collapse
Affiliation(s)
| | - Jashkaran Gadhvi
- Department of Biological Sciences, University of Texas at Dallas
| | - Kelli L Palmer
- Department of Biological Sciences, University of Texas at Dallas
| | | | | |
Collapse
|
26
|
De Nisco NJ, Neugent M, Mull J, Chen L, Kuprasertkul A, de Souza Santos M, Palmer KL, Zimmern P, Orth K. Direct Detection of Tissue-Resident Bacteria and Chronic Inflammation in the Bladder Wall of Postmenopausal Women with Recurrent Urinary Tract Infection. J Mol Biol 2019; 431:4368-4379. [PMID: 31002774 DOI: 10.1016/j.jmb.2019.04.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/05/2019] [Accepted: 04/05/2019] [Indexed: 02/02/2023]
Abstract
Urinary tract infections (UTIs) are the most commonly reported infections in adult women and have high rates of recurrence, especially in postmenopausal women. Recurrent UTI (RUTI) greatly reduces quality of life, places a significant burden on the healthcare system, and contributes to antimicrobial resistance. Because treatment of RUTI by long-term antibiotic therapy is often ineffective or poorly tolerated in elderly women, new therapies must be developed. The molecular basis of RUTI, especially in postmenopausal women, has remained unclear because modeling RUTI in mice is difficult, and human data are limited. Invasion of the urothelium and induction of host inflammation are hypothesized to be key mechanisms by which bacterial pathogens cause RUTI. To further our understanding of RUTI in humans, we performed a systematic analysis of urine and bladder biopsy samples from postmenopausal women undergoing cystoscopy with fulguration of trigonitis in the advanced management of antibiotic-refractory RUTI. We provide direct evidence that bacteria reside in the bladder wall of postmenopausal RUTI patients and that diverse bacterial species can be isolated from the bladder tissue. Histopathological scoring revealed significant edema and alterations of urothelial architecture in RUTI patient biopsies. Lymphocytes, including plasma B-cells, were detected within the mesenchyme, urothelium, and follicular aggregates in the majority of patients, indicating that the local adaptive immune response is active during human RUTI. These data provide conclusive evidence that bacteria invade the human urothelium and suggest that diverse bacterial species and the adaptive immune response play important roles in RUTI in humans.
Collapse
Affiliation(s)
- Nicole J De Nisco
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Michael Neugent
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Jason Mull
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luming Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Amy Kuprasertkul
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marcela de Souza Santos
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kelli L Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Philippe Zimmern
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
27
|
De Nisco NJ, Kanchwala M, Li P, Fernandez J, Xing C, Orth K. The cytotoxic type 3 secretion system 1 of Vibrio rewires host gene expression to subvert cell death and activate cell survival pathways. Sci Signal 2017; 10:10/479/eaal4501. [PMID: 28512145 DOI: 10.1126/scisignal.aal4501] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bacterial effectors potently manipulate host signaling pathways. The marine bacterium Vibrio parahaemolyticus (V. para) delivers effectors into host cells through two type 3 secretion systems (T3SSs). T3SS1 is vital for V. para survival in the environment, whereas T3SS2 causes acute gastroenteritis in human hosts. Although the natural host is undefined, T3SS1 effectors attack highly conserved cellular processes and pathways to orchestrate nonapoptotic cell death. To understand how the concerted action of T3SS1 effectors globally affects host cell signaling, we compared gene expression changes over time in primary fibroblasts infected with V. para that have a functional T3SS1 (T3SS1+) to those in cells infected with V. para lacking T3SS1 (T3SS1-). Overall, the host transcriptional response to both T3SS1+ and T3SS1-V. para was rapid, robust, and temporally dynamic. T3SS1 rewired host gene expression by specifically altering the expression of 398 genes. Although T3SS1 effectors targeted host cells at the posttranslational level to cause cytotoxicity, V. para T3SS1 also precipitated a host transcriptional response that initially activated cell survival and repressed cell death networks. The increased expression of several key prosurvival transcripts mediated by T3SS1 depended on a host signaling pathway that is silenced posttranslationally later in infection. Together, our analysis reveals a complex interplay between the roles of T3SS1 as both a transcriptional and posttranslational manipulator of host cell signaling.
Collapse
Affiliation(s)
- Nicole J De Nisco
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mohammed Kanchwala
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Peng Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jessie Fernandez
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chao Xing
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. .,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
28
|
De Nisco NJ, Orth K, VanHook AM. Science Signaling Podcast for 16 May 2017: Vibrio rewires host cells. Sci Signal 2017; 10:10/479/eaan5621. [PMID: 28512146 DOI: 10.1126/scisignal.aan5621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
This Podcast features a conversation with Kim Orth and Nicole De Nisco, authors of a Research Resource that appears in the 16 May 2017 issue of Science Signaling, about how the marine bacterium Vibrio parahaemolyticus rewires host cell signaling networks. V. parahaemolyticus thrives in warm brackish waters and infects both shellfish and finfish. This bacterium causes gastroenteritis when humans consume contaminated seafood that is raw or undercooked. V. parahaemolyticus delivers virulence factors into host cells through two different type 3 secretion systems (T3SSes). Whereas T3SS2 mediates gastroenteritis, T3SS1 is required for the bacterium to survive in its natural environment and delivers virulence factors that target conserved cellular processes. De Nisco et al examined transcriptional changes in human cells infected with a strain of V. parahaemolyticus that lacked T3SS2 but had an intact T3SS1. They found that the virulence factors delivered through T3SS1 initially induced transcriptional changes that promoted cell survival, then later repressed prosurvival signaling to induce cell death.Listen to Podcast.
Collapse
Affiliation(s)
- Nicole J De Nisco
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Annalisa M VanHook
- Associate Editor, Science Signaling, American Association for the Advancement of Science, 1200 New York Avenue, NW, Washington, DC 20005, USA
| |
Collapse
|
29
|
Pini F, De Nisco NJ, Ferri L, Penterman J, Fioravanti A, Brilli M, Mengoni A, Bazzicalupo M, Viollier PH, Walker GC, Biondi EG. Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti. PLoS Genet 2015; 11:e1005232. [PMID: 25978424 PMCID: PMC4433202 DOI: 10.1371/journal.pgen.1005232] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/21/2015] [Indexed: 01/23/2023] Open
Abstract
In all domains of life, proper regulation of the cell cycle is critical to coordinate genome replication, segregation and cell division. In some groups of bacteria, e.g. Alphaproteobacteria, tight regulation of the cell cycle is also necessary for the morphological and functional differentiation of cells. Sinorhizobium meliloti is an alphaproteobacterium that forms an economically and ecologically important nitrogen-fixing symbiosis with specific legume hosts. During this symbiosis S. meliloti undergoes an elaborate cellular differentiation within host root cells. The differentiation of S. meliloti results in massive amplification of the genome, cell branching and/or elongation, and loss of reproductive capacity. In Caulobacter crescentus, cellular differentiation is tightly linked to the cell cycle via the activity of the master regulator CtrA, and recent research in S. meliloti suggests that CtrA might also be key to cellular differentiation during symbiosis. However, the regulatory circuit driving cell cycle progression in S. meliloti is not well characterized in both the free-living and symbiotic state. Here, we investigated the regulation and function of CtrA in S. meliloti. We demonstrated that depletion of CtrA cause cell elongation, branching and genome amplification, similar to that observed in nitrogen-fixing bacteroids. We also showed that the cell cycle regulated proteolytic degradation of CtrA is essential in S. meliloti, suggesting a possible mechanism of CtrA depletion in differentiated bacteroids. Using a combination of ChIP-Seq and gene expression microarray analysis we found that although S. meliloti CtrA regulates similar processes as C. crescentus CtrA, it does so through different target genes. For example, our data suggest that CtrA does not control the expression of the Fts complex to control the timing of cell division during the cell cycle, but instead it negatively regulates the septum-inhibiting Min system. Our findings provide valuable insight into how highly conserved genetic networks can evolve, possibly to fit the diverse lifestyles of different bacteria. In order to propagate, all living cells must ensure that their genetic material is faithfully copied and properly partitioned into the daughter cells before division. These coordinated processes of DNA replication and cell division are termed the “cell cycle” and are controlled by a complex network of regulatory proteins in all organisms. In the class Alphaproteobacteria, the regulation of the cell cycle is closely linked to cellular differentiation processes that are vital for survival in the environment. In these bacteria, the cell cycle regulator CtrA is thought to serve as the primary link between the coordination of the cell cycle and cellular differentiation. The alphaproteobacterium, Sinorhizobium meliloti, an important model symbiont of alfalfa plants, undergoes a striking cellular differentiation that is vital to the formation of an efficient symbiosis dedicated to the conversion of atmospheric nitrogen to biologically available organic nitrogen. However, the link between cellular differentiation and cell cycle control in S. meliloti has not been made. In this study, we showed that S. meliloti cells without CtrA are similar to the symbiotic form. By the identification of the genes whose expression is directly and indirectly controlled by CtrA, we found that CtrA regulates vital cell cycle processes, including DNA replication and cell division, but through different genetic pathways than in other alphaproteobacteria. We importantly show that the levels of CtrA protein are governed by an essential cell cycle regulated proteolysis, which may also be an important mode of CtrA down-regulation during symbiosis to drive cellular differentiation.
Collapse
Affiliation(s)
- Francesco Pini
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS—Université de Lille, Villeneuve d'Ascq, France
| | - Nicole J. De Nisco
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Lorenzo Ferri
- Meyer Children Hospital, University of Florence, Firenze, Italy
| | - Jon Penterman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Antonella Fioravanti
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS—Université de Lille, Villeneuve d'Ascq, France
| | - Matteo Brilli
- Fondazione Edmund Mach/CRI, Functional genomics, San Michele all'Adige, Italy
| | | | | | - Patrick H. Viollier
- Dept. Microbiology & Molecular Medicine, University of Geneva, Genève, Switzerland
| | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Emanuele G. Biondi
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS—Université de Lille, Villeneuve d'Ascq, France
- * E-mail:
| |
Collapse
|
30
|
Pini F, Frage B, Ferri L, De Nisco NJ, Mohapatra SS, Taddei L, Fioravanti A, Dewitte F, Galardini M, Brilli M, Villeret V, Bazzicalupo M, Mengoni A, Walker GC, Becker A, Biondi EG. The DivJ, CbrA and PleC system controls DivK phosphorylation and symbiosis in Sinorhizobium meliloti. Mol Microbiol 2013; 90:54-71. [PMID: 23909720 DOI: 10.1111/mmi.12347] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2013] [Indexed: 01/09/2023]
Abstract
Sinorhizobium meliloti is a soil bacterium that invades the root nodules it induces on Medicago sativa, whereupon it undergoes an alteration of its cell cycle and differentiates into nitrogen-fixing, elongated and polyploid bacteroid with higher membrane permeability. In Caulobacter crescentus, a related alphaproteobacterium, the principal cell cycle regulator, CtrA, is inhibited by the phosphorylated response regulator DivK. The phosphorylation of DivK depends on the histidine kinase DivJ, while PleC is the principal phosphatase for DivK. Despite the importance of the DivJ in C. crescentus, the mechanistic role of this kinase has never been elucidated in other Alphaproteobacteria. We show here that the histidine kinases DivJ together with CbrA and PleC participate in a complex phosphorylation system of the essential response regulator DivK in S. meliloti. In particular, DivJ and CbrA are involved in DivK phosphorylation and in turn CtrA inactivation, thereby controlling correct cell cycle progression and the integrity of the cell envelope. In contrast, the essential PleC presumably acts as a phosphatase of DivK. Interestingly, we found that a DivJ mutant is able to elicit nodules and enter plant cells, but fails to establish an effective symbiosis suggesting that proper envelope and/or low CtrA levels are required for symbiosis.
Collapse
Affiliation(s)
- Francesco Pini
- Interdisciplinary Research Institute USR3078, CNRS-Université Lille Nord de France, 50 avenue de Halley, Villeneuve d'Ascq Cedex, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Kobayashi H, De Nisco NJ, Chien P, Simmons LA, Walker GC. Sinorhizobium meliloti CpdR1 is critical for co-ordinating cell cycle progression and the symbiotic chronic infection. Mol Microbiol 2009; 73:586-600. [PMID: 19602145 DOI: 10.1111/j.1365-2958.2009.06794.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
ATP-driven proteolysis plays a major role in regulating the bacterial cell cycle, development and stress responses. In the nitro -fixing symbiosis with host plants, Sinorhizobium meliloti undergoes a profound cellular differentiation, including endoreduplication of the ome. The regulatory mechanisms governing the alterations of the S. meliloti cell cycle in planta are largely unknown. Here, we report the characterization of two cpdR homologues, cpdR1 and cpdR2, of S. meliloti that encode single-domain response regulators. In Caulobacter crescentus, CpdR controls the polar localization of the ClpXP protease, thereby mediating the regulated proteolysis of key protein(s), such as CtrA, involved in cell cycle progression. The S. meliloti cpdR1-null mutant can invade the host cytoplasm, however, the intracellular bacteria are unable to differentiate into bacteroids. We show that S. meliloti CpdR1 has a polar localization pattern and a role in ClpX positioning similar to C. crescentus CpdR, suggesting a conserved function of CpdR proteins among alpha-proteobacteria. However, in S. meliloti, free-living cells of the cpdR1-null mutant show a striking morphology of irregular coccoids and aberrant DNA replication. Thus, we demonstrate that CpdR1 mediates the co-ordination of cell cycle events, which are critical for both the free-living cell division and the differentiation required for the chronic intracellular infection.
Collapse
Affiliation(s)
- Hajime Kobayashi
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | | | | |
Collapse
|