Exploring Condition-Specific Variability in the Ureteral Stent Microbiome
Abstract
:1. Introduction
2. Materials and Methods
2.1. Patient Population
2.2. Sample Processing
2.3. Microbial Profiling
2.4. Bioinformatic Processing, Quality Control, and Reporting
2.5. Data Analysis
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Lange, D.; Scotland, K.B. (Eds.) The Role of Bacteria in Urology, 2nd ed.; Springer: Cham, Switzerland, 2019; ISBN 978-3-030-17542-9. [Google Scholar]
- Siddiqui, H.; Nederbragt, A.J.; Lagesen, K.; Jeansson, S.L.; Jakobsen, K.S. Assessing Diversity of the Female Urine Microbiota by High Throughput Sequencing of 16S rDNA Amplicons. BMC Microbiol. 2011, 11, 244. [Google Scholar] [CrossRef] [PubMed]
- Wolfe, A.J.; Toh, E.; Shibata, N.; Rong, R.; Kenton, K.; Fitzgerald, M.; Mueller, E.R.; Schreckenberger, P.; Dong, Q.; Nelson, D.E.; et al. Evidence of Uncultivated Bacteria in the Adult Female Bladder. J. Clin. Microbiol. 2012, 50, 1376–1383. [Google Scholar] [CrossRef]
- Fouts, D.E.; Pieper, R.; Szpakowski, S.; Pohl, H.; Knoblach, S.; Suh, M.-J.; Huang, S.-T.; Ljungberg, I.; Sprague, B.M.; Lucas, S.K.; et al. Integrated Next-Generation Sequencing of 16S rDNA and Metaproteomics Differentiate the Healthy Urine Microbiome from Asymptomatic Bacteriuria in Neuropathic Bladder Associated with Spinal Cord Injury. J. Transl. Med. 2012, 10, 174. [Google Scholar] [CrossRef]
- Hills, R.; Pontefract, B.; Mishcon, H.; Black, C.; Sutton, S.; Theberge, C. Gut Microbiome: Profound Implications for Diet and Disease. Nutrients 2019, 11, 1613. [Google Scholar] [CrossRef]
- Brubaker, L.; Putonti, C.; Dong, Q.; Wolfe, A.J. The Human Urobiome. Mamm. Genome 2021, 32, 232–238. [Google Scholar] [CrossRef]
- Neugent, M.L.; Hulyalkar, N.V.; Nguyen, V.H.; Zimmern, P.E.; De Nisco, N.J. Advances in Understanding the Human Urinary Microbiome and Its Potential Role in Urinary Tract Infection. mBio 2020, 11, e00218-20. [Google Scholar] [CrossRef]
- Scotland, K.B.; Kung, S.H.; Chew, B.H.; Lange, D. Uropathogens Preferrentially Interact with Conditioning Film Components on the Surface of Indwelling Ureteral Stents Rather than Stent Material. Pathogens 2020, 9, 764. [Google Scholar] [CrossRef]
- Scotland, K.B.; Lo, J.; Grgic, T.; Lange, D. Ureteral Stent-Associated Infection and Sepsis: Pathogenesis and Prevention: A Review. Biofouling 2019, 35, 117–127. [Google Scholar] [CrossRef]
- Robert, M.; Boularan, A.-M.; El Sandid, M.; Grasset, D. Double-J Ureteric Stent Encrustations: Clinical Study on Crystal Formation on Polyurethane Stents. Urol. Int. 1997, 58, 100–104. [Google Scholar] [CrossRef]
- Khoddami, S.; Chew, B.H.; Lange, D. Problems and Solutions of Stent Biofilm and Encrustations: A Review of Literature. Turk. J. Urol. 2020, 46, S11–S18. [Google Scholar] [CrossRef]
- Al, K.F.; Denstedt, J.D.; Daisley, B.A.; Bjazevic, J.; Welk, B.K.; Pautler, S.E.; Gloor, G.B.; Reid, G.; Razvi, H.; Burton, J.P. Ureteral Stent Microbiota Is Associated with Patient Comorbidities but Not Antibiotic Exposure. Cell Rep. Med. 2020, 1, 100094. [Google Scholar] [CrossRef]
- Ripa, F.; Pietropaolo, A.; Montanari, E.; Hameed, B.M.Z.; Gauhar, V.; Somani, B.K. Association of Kidney Stones and Recurrent UTIs: The Chicken and Egg Situation. A Systematic Review of Literature. Curr. Urol. Rep. 2022, 23, 165–174. [Google Scholar] [CrossRef]
- Agarwal, D.K.; Krambeck, A.E.; Sharma, V.; Maldonado, F.J.; Westerman, M.E.; Knoedler, J.J.; Rivera, M.E. Treatment of Non-Obstructive, Non-Struvite Urolithiasis Is Effective in Treatment of Recurrent Urinary Tract Infections. World J. Urol. 2020, 38, 2029–2033. [Google Scholar] [CrossRef]
- Sawinski, D.; Blumberg, E.A. Infection in Renal Transplant Recipients. In Chronic Kidney Disease, Dialysis, and Transplantation; Elsevier: Amsterdam, The Netherlands, 2019; pp. 621–638.e6. ISBN 978-0-323-52978-5. [Google Scholar]
- Mangus, R.S.; Haag, B.W. Stented versus Nonstented Extravesical Ureteroneocystostomy in Renal Transplantation: A Metaanalysis. Am. J. Transplant. 2004, 4, 1889–1896. [Google Scholar] [CrossRef]
- Ackerman, A.L.; Anger, J.T.; Khalique, M.U.; Ackerman, J.E.; Tang, J.; Kim, J.; Underhill, D.M.; Freeman, M.R.; the NIH Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP). Optimization of DNA Extraction from Human Urinary Samples for Mycobiome Community Profiling. PLoS ONE 2019, 14, e0210306. [Google Scholar] [CrossRef]
- Liss, M.A.; Reveles, K.R.; Tipton, C.D.; Gelfond, J.; Tseng, T. Comparative Effectiveness Randomized Clinical Trial Using Next-Generation Microbial Sequencing to Direct Prophylactic Antibiotic Choice Before Urologic Stone Lithotripsy Using an Interprofessional Model. Eur. Urol. Open Sci. 2023, 57, 74–83. [Google Scholar] [CrossRef]
- Jongjitaree, K.; Sheetz, T.; Finegan, J.; Bechis, S.K.; Sur, R.L.; Monga, M. The Application of Next-Generation Sequencing in Preoperative Evaluation for Urologic Stone Surgery. J. Endourol. 2024, 38, 908–915. [Google Scholar] [CrossRef]
- Callahan, B.J.; McMurdie, P.J.; Rosen, M.J.; Han, A.W.; Johnson, A.J.A.; Holmes, S.P. DADA2: High-Resolution Sample Inference from Illumina Amplicon Data. Nat. Methods 2016, 13, 581–583. [Google Scholar] [CrossRef]
- Tipton, C.D.; Wolcott, R.D.; Sanford, N.E.; Miller, C.; Pathak, G.; Silzer, T.K.; Sun, J.; Fleming, D.; Rumbaugh, K.P.; Little, T.D.; et al. Patient Genetics Is Linked to Chronic Wound Microbiome Composition and Healing. PLoS Pathog. 2020, 16, e1008511. [Google Scholar] [CrossRef]
- Mandal, S.; Van Treuren, W.; White, R.A.; Eggesbø, M.; Knight, R.; Peddada, S.D. Analysis of Composition of Microbiomes: A Novel Method for Studying Microbial Composition. Microb. Ecol. Health Dis. 2015, 26, 27663. [Google Scholar] [CrossRef]
- Paick, S.H.; Park, H.K.; Oh, S.-J.; Kim, H.H. Characteristics of Bacterial Colonization and Urinary Tract Infection after Indwelling of Double-J Ureteral Stent. Urology 2003, 62, 214–217. [Google Scholar] [CrossRef] [PubMed]
- Shabeena, K.; Bhargava, R.; Manzoor, M.A.P.; Mujeeburahiman, M. Characteristics of Bacterial Colonization after Indwelling Double-J Ureteral Stents for Different Time Duration. Urol. Ann. 2018, 10, 71. [Google Scholar] [CrossRef]
- Ch’ng, J.-H.; Chong, K.K.L.; Lam, L.N.; Wong, J.J.; Kline, K.A. Biofilm-Associated Infection by Enterococci. Nat. Rev. Microbiol. 2019, 17, 82–94. [Google Scholar] [CrossRef]
- Wasfi, R.; Hamed, S.M.; Amer, M.A.; Fahmy, L.I. Proteus Mirabilis Biofilm: Development and Therapeutic Strategies. Front. Cell Infect. Microbiol. 2020, 10, 414. [Google Scholar] [CrossRef]
- Șchiopu, P.; Toc, D.A.; Colosi, I.A.; Costache, C.; Ruospo, G.; Berar, G.; Gălbău, Ș.G.; Ghilea, A.C.; Botan, A.; Pană, A.G.; et al. An Overview of the Factors Involved in Biofilm Production by the Enterococcus Genus. Int. J. Mol. Sci. 2023, 24, 11577. [Google Scholar] [CrossRef]
- Scavone, P.; Iribarnegaray, V.; González, M.J.; Navarro, N.; Caneles-Huerta, N.; Jara-Wilde, J.; Härtel, S.; Zunino, P. Role of Proteus mirabilis Flagella in Biofilm Formation. Rev. Argent. Microbiol. 2023, 55, 226–234. [Google Scholar] [CrossRef]
- Scavone, P.; Iribarnegaray, V.; Caetano, A.L.; Schlapp, G.; Härtel, S.; Zunino, P. Fimbriae Have Distinguishable Roles in Proteus mirabilis Biofilm Formation. Pathog. Dis. 2016, 74, ftw033. [Google Scholar] [CrossRef]
- Rani, A.; Ranjan, R.; McGee, H.S.; Andropolis, K.E.; Panchal, D.V.; Hajjiri, Z.; Brennan, D.C.; Finn, P.W.; Perkins, D.L. Urinary Microbiome of Kidney Transplant Patients Reveals Dysbiosis with Potential for Antibiotic Resistance. Transl. Res. 2017, 181, 59–70. [Google Scholar] [CrossRef]
- Guerra, M.E.S.; Destro, G.; Vieira, B.; Lima, A.S.; Ferraz, L.F.C.; Hakansson, A.P.; Darrieux, M.; Converso, T.R. Klebsiella pneumoniae Biofilms and Their Role in Disease Pathogenesis. Front. Cell. Infect. Microbiol. 2022, 12, 877995. [Google Scholar] [CrossRef]
- Yildiz, F.H.; Visick, K.L. Vibrio Biofilms: So Much the Same yet so Different. Trends Microbiol. 2009, 17, 109–118. [Google Scholar] [CrossRef] [PubMed]
- Yadav, P.; Verma, S.; Bauer, R.; Kumari, M.; Dua, M.; Johri, A.K.; Yadav, V.; Spellerberg, B. Deciphering Streptococcal Biofilms. Microorganisms 2020, 8, 1835. [Google Scholar] [CrossRef] [PubMed]
- Leighton, R.E.; Xiong, L.; Anderson, G.K.; Astarita, G.M.; Cai, G.; Norman, R.S.; Decho, A.W. Vibrio parahaemolyticus and Vibrio vulnificus in Vitro Biofilm Dispersal from Microplastics Influenced by Simulated Human Environment. Front. Microbiol. 2023, 14, 1236471. [Google Scholar] [CrossRef]
- Sanches-Fernandes, G.M.M.; Sá-Correia, I.; Costa, R. Vibriosis Outbreaks in Aquaculture: Addressing Environmental and Public Health Concerns and Preventive Therapies Using Gilthead Seabream Farming as a Model System. Front. Microbiol. 2022, 13, 904815. [Google Scholar] [CrossRef]
- Kunitomo, K.; Uemura, N.; Shimizu, T.; Hayano, S.; Tsuji, T. Skin and Soft Tissue Infections and Bacteremia Caused by Vibrio cincinnatiensis. IDCases 2022, 29, e01564. [Google Scholar] [CrossRef]
- Brayton, P.R.; Bode, R.B.; Colwell, R.R.; MacDonell, M.T.; Hall, H.L.; Grimes, D.J.; West, P.A.; Bryant, T.N. Vibrio cincinnatiensis sp. nov., a New Human Pathogen. J. Clin. Microbiol. 1986, 23, 104–108. [Google Scholar] [CrossRef]
- Mougin, J.; Midelet, G.; Leterme, S.; Best, G.; Ells, T.; Joyce, A.; Whiley, H.; Brauge, T. Benzalkonium Chloride Disinfectant Residues Stimulate Biofilm Formation and Increase Survival of Vibrio Bacterial Pathogens. Front. Microbiol. 2024, 14, 1309032. [Google Scholar] [CrossRef]
- Merchel Piovesan Pereira, B.; Tagkopoulos, I. Benzalkonium Chlorides: Uses, Regulatory Status, and Microbial Resistance. Appl. Environ. Microbiol. 2019, 85, e00377-19. [Google Scholar] [CrossRef]
- Szell, T.; Dressler, F.F.; Goelz, H.; Bluemel, B.; Miernik, A.; Brandstetter, T.; Scherag, F.; Schoeb, D.S. In Vitro Effects of a Novel Coating Agent on Bacterial Biofilm Development on Ureteral Stents. J. Endourol. 2019, 33, 225–231. [Google Scholar] [CrossRef]
- Walker, J.N.; Flores-Mireles, A.L.; Lynch, A.J.L.; Pinkner, C.; Caparon, M.G.; Hultgren, S.J.; Desai, A. High-Resolution Imaging Reveals Microbial Biofilms on Patient Urinary Catheters despite Antibiotic Administration. World J. Urol. 2020, 38, 2237–2245. [Google Scholar] [CrossRef]
- Shi, Y.-F.; Ju, W.-L.; Zhu, Y.-P.; Xia, S.-J.; Sun, X.-W. The Impact of Ureteral Stent Indwelling Time on the Treatment of Acute Infection Caused by Ureteral Calculi. Urolithiasis 2017, 45, 579–583. [Google Scholar] [CrossRef]
- Joshi, H.B.; Stainthorpe, A.; MacDONAGH, R.P.; Keeley, F.X.; Timoney, A.G. Indwelling Ureteral Stents: Evaluation of Symptoms, Quality of Life and Utility. J. Urol. 2003, 169, 1065–1069. [Google Scholar] [CrossRef] [PubMed]
- Klis, R.; Korczak-Kozakiewicz, E.; Denys, A.; Sosnowski, M.; Rozanski, W. Relationship Between Urinary Tract Infection and Self-Retaining Double-J Catheter Colonization. J. Endourol. 2009, 23, 1015–1019. [Google Scholar] [CrossRef] [PubMed]
- Xu, R.; Deebel, N.; Casals, R.; Dutta, R.; Mirzazadeh, M. A New Gold Rush: A Review of Current and Developing Diagnostic Tools for Urinary Tract Infections. Diagnostics 2021, 11, 479. [Google Scholar] [CrossRef] [PubMed]
- Nottingham, C.U.; Assmus, M.A.; Peters, A.W.; Large, T.; Agarwal, D.K.; Rivera, M.E.; Krambeck, A.E. Next Generation Sequencing in Patients with Nephrolithiasis: How Does It Perform Compared with Standard Urine and Stone Cultures? Ther. Adv. Urol. 2021, 13, 175628722199497. [Google Scholar] [CrossRef]
- Qin, J.; Shi, X.; Xu, J.; Yuan, S.; Zheng, B.; Zhang, E.; Huang, G.; Li, G.; Jiang, G.; Gao, S.; et al. Characterization of the Genitourinary Microbiome of 1,165 Middle-Aged and Elderly Healthy Individuals. Front. Microbiol. 2021, 12, 673969. [Google Scholar] [CrossRef]
- Vaughan, M.H.; Mao, J.; Karstens, L.A.; Ma, L.; Amundsen, C.L.; Schmader, K.E.; Siddiqui, N.Y. The Urinary Microbiome in Postmenopausal Women with Recurrent Urinary Tract Infections. J. Urol. 2021, 206, 1222–1231. [Google Scholar] [CrossRef]
Stone (N = 23) | Transplant (N = 23) | |||
---|---|---|---|---|
Variable | Category | N (%) | N (%) | p-Value |
Age | 25–49 | 4 (17.4) | 7 (30.4) | 0.3 |
50+ | 19 (82.6) | 16 (69.6) | 0.3 | |
Sex | Male | 8 (34.8) | 16 (69.6) | 0.018 |
Female | 15 (65.2) | 7 (30.4) | 0.018 | |
Race/Ethnicity | White | 12 (52.2) | 6 (26.1) | 0.07 |
Hispanic/Latino | 4 (17.4) | 9 (39.1) | 0.102 | |
Asian | 1 (4.3) | 4 (17.4) | 0.155 | |
Black/African American | 1 (4.3) | 4 (17.4) | 0.155 | |
Other | 1 (4.3) | 0 (0) | 0.312 | |
Declined to answer | 4 (17.4) | 0 (0) | 0.036 |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Mousavi, A.; Thaker, K.N.; Ackerman, J.E.; Diaz, N.; Martin, R.; Tipton, C.D.; Tallman, N.; Henao, L.M.; Nassiri, N.; Veale, J.; et al. Exploring Condition-Specific Variability in the Ureteral Stent Microbiome. Pathogens 2024, 13, 942. https://doi.org/10.3390/pathogens13110942
Mousavi A, Thaker KN, Ackerman JE, Diaz N, Martin R, Tipton CD, Tallman N, Henao LM, Nassiri N, Veale J, et al. Exploring Condition-Specific Variability in the Ureteral Stent Microbiome. Pathogens. 2024; 13(11):942. https://doi.org/10.3390/pathogens13110942
Chicago/Turabian StyleMousavi, Ava, Karan N. Thaker, James E. Ackerman, Niccole Diaz, Rick Martin, Craig D. Tipton, Nick Tallman, Lina Marcella Henao, Nima Nassiri, Jeffrey Veale, and et al. 2024. "Exploring Condition-Specific Variability in the Ureteral Stent Microbiome" Pathogens 13, no. 11: 942. https://doi.org/10.3390/pathogens13110942
APA StyleMousavi, A., Thaker, K. N., Ackerman, J. E., Diaz, N., Martin, R., Tipton, C. D., Tallman, N., Henao, L. M., Nassiri, N., Veale, J., Ackerman, A. L., & Scotland, K. B. (2024). Exploring Condition-Specific Variability in the Ureteral Stent Microbiome. Pathogens, 13(11), 942. https://doi.org/10.3390/pathogens13110942