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Knorr J, Lone Z, Werneburg G, Adler A, Agudelo J, Suryavanshi M, Campbell RA, Ericson K, Qiu H, Bajic P, Haber GP, Weight CJ, Ahern PP, Almassi N, Miller AW, Lee BH. An exploratory study investigating the impact of the bladder tumor microbiome on Bacillus Calmette Guerin (BCG) response in non-muscle invasive bladder cancer. Urol Oncol 2024; 42:291.e1-291.e11. [PMID: 38664180 DOI: 10.1016/j.urolonc.2024.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/29/2024] [Accepted: 04/09/2024] [Indexed: 06/23/2024]
Abstract
PURPOSE Intravesical Bacillus Calmette-Guerin (BCG) is standard of care for intermediate- and high-risk non-muscle invasive bladder cancer (NMIBC). The effect of the bladder microbiome on response to BCG is unclear. We sought to characterize the microbiome of bladder tumors in BCG-responders and non-responders and identify potential mechanisms that drive treatment response. MATERIALS AND METHODS Patients with archival pre-treatment biopsy samples (2012-2018) were identified retrospectively. Prospectively, urine and fresh tumor samples were collected from individuals with high-risk NMIBC (2020-2023). BCG response was defined as tumor-free 2 years from induction therapy. Extracted DNA was sequenced for 16S rRNA and shotgun metagenomics. Primary outcomes were species richness (α-diversity) and microbial composition (β-diversity). Paired t-tests were performed for α-diversity (Observed species/Margalef). Statistical analysis for β-diversity (weighted and unweighted UniFrac distances, weighted Bray-Curtis dissimilarity) were conducted through Permanova, with 999 permutations. RESULTS Microbial species richness (P < 0.001) and composition (P = 0.001) differed between BCG responders and non-responders. Lactobacillus spp. were significantly enriched in BCG-responders. Shotgun metagenomics identified possible mechanistic pathways such as assimilatory sulfate reduction. CONCLUSION A compositional difference exists in the tumor microbiome of BCG responders and non-responders with Lactobacillus having increased abundance in BCG responders.
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Affiliation(s)
- Jacob Knorr
- Cleveland Clinic Glickman Urological and Kidney Institute, Cleveland, OH
| | - Zaeem Lone
- Cleveland Clinic Lerner College of Medicine, Cleveland, OH
| | - Glenn Werneburg
- Cleveland Clinic Glickman Urological and Kidney Institute, Cleveland, OH
| | - Ava Adler
- Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Jose Agudelo
- Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | | | - Rebecca A Campbell
- Cleveland Clinic Glickman Urological and Kidney Institute, Cleveland, OH
| | - Kyle Ericson
- Univeristy Hospitals Department of Urology, Cleveland, OH
| | - Hong Qiu
- Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Petar Bajic
- Cleveland Clinic Glickman Urological and Kidney Institute, Cleveland, OH
| | | | | | - Philip P Ahern
- Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Nima Almassi
- Cleveland Clinic Glickman Urological and Kidney Institute, Cleveland, OH
| | - Aaron W Miller
- Cleveland Clinic Glickman Urological and Kidney Institute, Cleveland, OH; Cleveland Clinic Lerner Research Institute, Cleveland, OH.
| | - Byron H Lee
- University of Texas MD Anderson Cancer Center, Houston, TX.
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2
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Chen VS, James C, Khemmani M, Desai S, Doshi C, Rac G, Ellis JL, Patel HD, Barkan GA, Gupta GN, Flanigan RC, Wolfe AJ. A prospective evaluation of the prostate microbiome in malignant and benign tissue using transperineal biopsy. Prostate 2024; 84:1251-1261. [PMID: 38946139 DOI: 10.1002/pros.24763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/08/2024] [Accepted: 06/18/2024] [Indexed: 07/02/2024]
Abstract
BACKGROUND The link between the prostate microbiome and prostate cancer remains unclear. Few studies have analyzed the microbiota of prostate tissue, and these have been limited by potential contamination by transrectal biopsy. Transperineal prostate biopsy offers an alternative and avoids fecal cross-contamination. We aim to characterize the prostate microbiome using transperineal biopsy. METHODS Patients with clinical suspicion for prostate cancer who were to undergo transperineal prostate biopsy with magnetic resonance imaging (MRI) fusion guidance were prospectively enrolled from 2022 to 2023. Patients were excluded if they had Prostate Imaging Reporting and Data System lesions with scores ≤ 3, a history of prostate biopsy within 1 year, a history of prostate cancer, or antibiotic use within 30 days of biopsy. Tissue was collected from the MRI target lesions and nonneoplastic transitional zone. Bacteria were identified using 16S ribosomal RNA gene sequencing. RESULTS Across the 42 patients, 76% were found to have prostate cancer. Beta diversity indices differed significantly between the perineum, voided urine, and prostate tissue. There were no beta diversity differences between cancerous or benign tissue, or between pre- and postbiopsy urines. There appear to be unique genera more abundant in cancerous versus benign tissue. There were no differences in alpha diversity indices relative to clinical findings including cancer status, grade, and risk group. CONCLUSIONS We demonstrate a rigorous method to better characterize the prostate microbiome using transperineal biopsy and to limit contamination. These findings provide a framework for future large-scale studies of the microbiome of prostate cancer.
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Affiliation(s)
- Victor S Chen
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Christopher James
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Mark Khemmani
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Shalin Desai
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Chirag Doshi
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Goran Rac
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Jeffrey L Ellis
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Hiten D Patel
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Guliz A Barkan
- Department of Pathology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Gopal N Gupta
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Robert C Flanigan
- Department of Urology, Loyola University Medical Center, Maywood, Illinois, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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Balaouras G, Kostoulas P, Mikos T, Balaouras D, Chitzios D. The Study of Microbiome of the Female Genital Area in Relation to Pelvic Floor Dysfunction: A Systematic Review. Int Urogynecol J 2024; 35:1347-1362. [PMID: 38861007 DOI: 10.1007/s00192-024-05821-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/24/2024] [Indexed: 06/12/2024]
Abstract
INTRODUCTION AND HYPOTHESIS The aim of this article is to present a systematic literature review focused on microbiome diversity in women experiencing pelvic floor dysfunction. METHODS Utilizing PubMed/MedLine and Scopus, 25 pertinent studies were meticulously selected for this review. RESULTS A key theme identified is the potential of microbiomes as diagnostic tools. The findings consistently highlight Lactobacillus as recurrent microbiota. Additionally, Gardnerella, Streptococcus, Prevotella, Aerococcus, Staphylococcus, Proteus, and Bifidobacterium species were frequently observed. This suggests the influential role of these microorganisms in shaping female urological and reproductive health. A deeper understanding of these predominant bacterial genera could offer invaluable insights into healthy physiological states and various disorders. The complex relationship between microbial compositions and diverse health conditions paves the way for novel diagnostic and therapeutic approaches. As we further explore the complexities of microbiomes, their role becomes increasingly crucial in transforming women's health care. CONCLUSIONS These findings emphasize the need for personalized care, integrating the microbiome into a comprehensive health assessment and treatment framework. This review lays the groundwork for future medical strategies where the microbiome is a pivotal element in both preventive and therapeutic care.
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Affiliation(s)
- George Balaouras
- 1st Department of Obstetrics & Gynecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital, Thessaloniki, Greece
| | | | - Themistoklis Mikos
- 1st Department of Obstetrics & Gynecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital, Thessaloniki, Greece
| | - Dimitrios Balaouras
- Midwifery Department, International Hellenic University, Thessaloniki, Sindos, Greece
| | - Dimitrios Chitzios
- Midwifery Department, International Hellenic University, Thessaloniki, Sindos, Greece
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4
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Fu C, Zhang Y, Liang L, Lin H, Shan K, Liu F, Feng N. The microbiota in patients with interstitial cystitis/bladder pain syndrome: a systematic review. BJU Int 2024. [PMID: 38890150 DOI: 10.1111/bju.16439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
OBJECTIVE To comprehensively review and critically assess the literature on microbiota differences between patients with interstitial cystitis (IC)/bladder pain syndrome (BPS) and normal controls and to provide clinical practice guidelines. MATERIALS AND METHODS In this systematic review, we evaluated previous research on microbiota disparities between IC/BPS and normal controls, as well as distinctions among IC/BPS subgroups. A comprehensive literature search was conducted across PubMed/MEDLINE, EMBASE, Web of Science, and the Cochrane Central Register of Controlled Trials. Relevant studies were shortlisted based on predetermined inclusion and exclusion criteria, followed by quality assessment. The primary focus was identifying specific taxonomic variations among these cohorts. RESULTS A total of 12 studies met the selection criteria. Discrepancies were adjudicated by a third reviewer. The Newcastle-Ottawa Scale was used to assess study quality. Predominantly, the studies focused on disparities in urine microbiota between IC/BPS patients and normal controls, with one study examining gut microbiota differences between the groups, and two studies exploring vaginal microbiota distinctions. Unfortunately, analyses of discrepancies in other microbiota were limited. Our findings revealed evidence of distinct bacterial abundance variations, particularly involving Lactobacillus, alongside variations in specific metabolites among IC/BPS patients compared to controls. CONCLUSIONS Currently, there is evidence suggesting significant variations in the diversity and species composition of the urinary microbiota between individuals diagnosed with IC/BPS and control groups. In the foreseeable future, urologists should consider urine microbiota dysbiosis as a potential aetiology for IC, with potential clinical implications for diagnosis and treatment.
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Affiliation(s)
- Chaowei Fu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yuwei Zhang
- Nantong University Medical School, Nantong, China
| | - Linghui Liang
- Department of Urology, Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, China
| | - Hao Lin
- Department of Urology, Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, China
| | - Kai Shan
- School of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fengping Liu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Urology, Jiangnan University Medical Center, Wuxi, China
| | - Ninghan Feng
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Urology, Jiangnan University Medical Center, Wuxi, China
- Department of Urology, Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, China
- Nantong University Medical School, Nantong, China
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5
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Yurick S, Ray S, El-Nashar S, Brennand E, Kim-Fine S, Sanaee M, Regan S, Geoffrion R, Occhino J, Hijaz A, Sheyn D. Prediction of Postoperative Urinary Tract Infection Following Benign Gynecologic Surgery. Int Urogynecol J 2024; 35:1035-1043. [PMID: 38625604 DOI: 10.1007/s00192-024-05773-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/06/2024] [Indexed: 04/17/2024]
Abstract
INTRODUCTION AND HYPOTHESIS The objective was to develop a prediction model for urinary tract infection (UTI) after pelvic surgery. METHODS We utilized data from three tertiary care centers of women undergoing pelvic surgery. The primary outcome was a UTI within 8 weeks of surgery. Additional variables collected included procedural data, severity of prolapse, use of mesh, anti-incontinence surgery, EBL, diabetes, steroid use, estrogen use, postoperative catheter use, PVR, history of recurrent UTI, operative time, comorbidities, and postoperative morbidity including venous thromboembolism, surgical site infection. Two datasets were used for internal validation, whereas a third dataset was used for external validation. Algorithms that tested included the following: multivariable logistic regression, decision trees (DTs), naive Bayes (NB), random forest (RF), gradient boosting (GB), and multilayer perceptron (MP). RESULTS For the training dataset, containing both University of British Columbia and Mayo Clinic Rochester data, there were 1,657 patients, with 172 (10.4%) UTIs; whereas for the University of Calgary external validation data, there were a total of 392 patients with a UTI rate of 16.1% (n = 63). All models performed well; however, the GB, DT, and RF models all had an area under the curve (AUC) > 0.97. With external validation the model retained high discriminatory ability, DT: AUC = 0.88, RF: AUC = 0.88, and GB: AUC = 0.90. CONCLUSIONS A model with high discriminatory ability can predict UTI within 8 weeks of pelvic surgery. Future studies should focus on prospective validation and application of randomized trial models to test the utility of this model in the prevention of postoperative UTI.
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Affiliation(s)
- Sarah Yurick
- Case Western Reserve University College of Engineering, Cleveland, OH, USA
| | - Soumya Ray
- Case Western Reserve University College of Engineering, Cleveland, OH, USA
| | | | | | | | - May Sanaee
- University of Alberta, Edmonton, AB, Canada
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Occhino JA, Byrnes JN, Wu PY, Walther-Antonio MR, Chen J. Preoperative Vaginal Microbiome as a Predictor of Postoperative Urinary Tract Infection. RESEARCH SQUARE 2024:rs.3.rs-4069233. [PMID: 38659758 PMCID: PMC11042435 DOI: 10.21203/rs.3.rs-4069233/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
This is a single Institute, prospective cohort study. We collected twenty- two postmenopausal women with pelvic organ prolapse planning to undergo vaginal hysterectomy with transvaginal pelvic reconstructive surgery, with or without a concomitant anti-incontinence procedure. Vaginal swabs and urine samples were longitudinally collected at five time points: preoperative consult visit (T1), day of surgery prior to surgical scrub (T2), immediately postoperative (T3), day of hospital discharge (T4), and at the postoperative exam visit (T5). Women experiencing urinary tract infection symptoms provided a sample set prior to antibiotic administration (T6). Microbiome analysis on vaginal and urinary specimens at each time point. Region V3-V5 of the 16S ribosomal RNA gene was amplified and sequenced. Sample DNA was analyzed with visit T1, T2, T5 and T6. Six (27.3%) participants developed postoperative urinary tract infection whose vaginal sample at first clinical visit (T1) revealed beta-diversity analysis with significant differences in microbiome structure and composition. Women diagnosed with a postoperative urinary tract infection had a vaginal microbiome characterized by low abundance of Lactobacillus and high prevalence of Prevotella and Gardnerella species. In our cohort, preoperative vaginal swabs can predict who will develop a urinary tract infection following transvaginal surgery for pelvic organ prolapse.
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Affiliation(s)
| | | | - Pei-Ying Wu
- National Cheng Kung University Hospital, National Cheng Kung University
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7
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Zhang M, Zhou Y, Yao S, Zhao Y, Batool SS, Huang J, Jiang L, Yan D, Yan W, Yu Z. Effect of stress urinary incontinence on vaginal microbial communities. BMC Microbiol 2024; 24:112. [PMID: 38575862 PMCID: PMC10993610 DOI: 10.1186/s12866-024-03237-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/26/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Postpartum women often experience stress urinary incontinence (SUI) and vaginal microbial dysbiosis, which seriously affect women's physical and mental health. Understanding the relationship between SUI and vaginal microbiota composition may help to prevent vaginal diseases, but research on the potential association between these conditions is limited. RESULTS This study employed 16S rRNA gene sequencing to explore the association between SUI and vaginal dysbiosis. In terms of the vaginal microbiota, both species richness and evenness were significantly higher in the SUI group. Additionally, the results of NMDS and species composition indicated that there were differences in the composition of the vaginal microbiota between the two groups. Specifically, compared to postpartum women without SUI (Non-SUI), the relative abundance of bacteria associated with bacterial dysbiosis, such as Streptococcus, Prevotella, Dialister, and Veillonella, showed an increase, while the relative abundance of Lactobacillus decreased in SUI patients. Furthermore, the vaginal microbial co-occurrence network of SUI patients displayed higher connectivity, complexity, and clustering. CONCLUSION The study highlights the role of Lactobacillus in maintaining vaginal microbial homeostasis. It found a correlation between SUI and vaginal microbiota, indicating an increased risk of vaginal dysbiosis. The findings could enhance our understanding of the relationship between SUI and vaginal dysbiosis in postpartum women, providing valuable insights for preventing bacterial vaginal diseases and improving women's health.
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Affiliation(s)
- Man Zhang
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Yanhua Zhou
- Department of Rehabilitation Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Siqi Yao
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Yiming Zhao
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Syeda Sundas Batool
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Li Jiang
- Department of Rehabilitation Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Dayu Yan
- Department of Gynecology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Wenguang Yan
- Department of Rehabilitation Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.
| | - Zheng Yu
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China.
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Li J, Li Y, Zhou L, Li C, Liu J, Liu D, Fu Y, Wang Y, Tang J, Zhou L, Tan S, Wang L. The human microbiome and benign prostatic hyperplasia: Current understandings and clinical implications. Microbiol Res 2024; 281:127596. [PMID: 38215640 DOI: 10.1016/j.micres.2023.127596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/14/2024]
Abstract
The research of the human microbiome in the preceding decade has yielded novel perspectives on human health and diseases. Benign prostatic hyperplasia (BPH) is a common disease in middle-aged and elderly males, which negatively affects the life quality. Existing evidence has indicated that the human microbiome, including urinary, intra-prostate, gut, oral and blood microbiome may exert a significant impact on the natural progression of BPH. The dysbiosis of the microbiome may induce inflammation at either a local or systemic level, thereby affecting the BPH. Moreover, metabolic syndrome (MetS) caused by the microbiome can also be involved in the development of BPH. Additionally, alterations in the microbiome composition during the senility process may serve as another cause of the BPH. Here, we summarize the influence of human microbiome on BPH and explore how the microbiome is linked to BPH through inflammation, MetS, and senility. In addition, we propose promising areas of investigation and discuss the implications for advancing therapeutic approaches.
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Affiliation(s)
- Jiaren Li
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Youyou Li
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Liang Zhou
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Cheng Li
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jiahao Liu
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Dingwen Liu
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Yunlong Fu
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Yichuan Wang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jin Tang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Lei Zhou
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Shuo Tan
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Long Wang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China.
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9
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Du J, Khemmani M, Halverson T, Ene A, Limeira R, Tinawi L, Hochstedler-Kramer BR, Noronha MF, Putonti C, Wolfe AJ. Cataloging the phylogenetic diversity of human bladder bacterial isolates. Genome Biol 2024; 25:75. [PMID: 38515176 PMCID: PMC10958879 DOI: 10.1186/s13059-024-03216-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, such as the gut and oral cavity. RESULTS To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, we present a bladder-specific bacterial isolate reference collection comprising 1134 genomes, primarily from adult females. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial isolate reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2% of the genera found when re-examining previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis finds that the taxonomies and functions of the bladder microbiota share more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder Escherichia coli isolates and 387 gut Escherichia coli isolates support the hypothesis that phylogroup distribution and functions of Escherichia coli strains differ dramatically between these two very different niches. CONCLUSIONS This bladder-specific bacterial isolate reference collection is a unique resource that will enable bladder microbiota research and comparison to isolates from other anatomical sites.
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Affiliation(s)
- Jingjie Du
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Present address: Division of Nutritional Science, Cornell University, Ithaca, NY, 14850, USA
| | - Mark Khemmani
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Thomas Halverson
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Roberto Limeira
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Lana Tinawi
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Baylie R Hochstedler-Kramer
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Melline Fontes Noronha
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, 60660, USA
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Alan J Wolfe
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
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10
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Zheng H, Wang C, Yu X, Zheng W, An Y, Zhang J, Zhang Y, Wang G, Qi M, Lin H, Wang F. The Role of Metabolomics and Microbiology in Urinary Tract Infection. Int J Mol Sci 2024; 25:3134. [PMID: 38542107 PMCID: PMC10969911 DOI: 10.3390/ijms25063134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 08/25/2024] Open
Abstract
One of the common illnesses that affect women's physical and mental health is urinary tract infection (UTI). The disappointing results of empirical anti-infective treatment and the lengthy time required for urine bacterial culture are two issues. Antibiotic misuse is common, especially in females who experience recurrent UTI (rUTI). This leads to a higher prevalence of antibiotic resistance in the microorganisms that cause the infection. Antibiotic therapy will face major challenges in the future, prompting clinicians to update their practices. New testing techniques are making the potential association between the urogenital microbiota and UTIs increasingly apparent. Monitoring changes in female urinary tract (UT) microbiota, as well as metabolites, may be useful in exploring newer preventive treatments for UTIs. This review focuses on advances in urogenital microbiology and organismal metabolites relevant to the identification and handling of UTIs in an attempt to provide novel methods for the identification and management of infections of the UT. Particular attention is paid to the microbiota and metabolites in the patient's urine in relation to their role in supporting host health.
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Affiliation(s)
- Haoyu Zheng
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Chao Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Xiao Yu
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Wenxue Zheng
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Yiming An
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Jiaqi Zhang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Yuhan Zhang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Guoqiang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Mingran Qi
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Hongqiang Lin
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
| | - Fang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.Z.); (C.W.); (X.Y.); (W.Z.); (Y.A.); (J.Z.); (Y.Z.); (G.W.); (M.Q.); (H.L.)
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
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11
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Kustrimovic N, Bilato G, Mortara L, Baci D. The Urinary Microbiome in Health and Disease: Relevance for Bladder Cancer. Int J Mol Sci 2024; 25:1732. [PMID: 38339010 PMCID: PMC10855347 DOI: 10.3390/ijms25031732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/24/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
Bladder cancer (BC) constitutes one of the most diagnosed types of cancer worldwide. Advancements in and new methodologies for DNA sequencing, leading to high-throughput microbiota testing, have pinpointed discrepancies in urinary microbial fingerprints between healthy individuals and patients with BC. Although several studies suggest an involvement of microbiota dysbiosis in the pathogenesis, progression, and therapeutic response to bladder cancer, an established direct causal relationship remains to be elucidated due to the lack of standardized methodologies associated with such studies. This review compiles an overview of the microbiota of the human urinary tract in healthy and diseased individuals and discusses the evidence to date on microbiome involvement and potential mechanisms by which the microbiota may contribute to the development of BC. We also explore the potential profiling of urinary microbiota as a biomarker for risk stratification, as well as the prediction of the response to intravesical therapies and immunotherapy in BC patients. Further investigation into the urinary microbiome of BC patients is imperative to unravel the complexities of the role played by host-microbe interactions in shaping wellness or disease and yield valuable insights into and strategies for the prevention and personalized treatment of BC.
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Affiliation(s)
- Natasa Kustrimovic
- Center for Translational Research on Autoimmune and Allergic Disease—CAAD, Università del Piemonte Orientale, 28100 Novara, Italy;
| | - Giorgia Bilato
- Immunology and General Pathology Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy;
| | - Lorenzo Mortara
- Immunology and General Pathology Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy;
| | - Denisa Baci
- Immunology and General Pathology Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy;
- Molecular Cardiology Laboratory, IRCCS—Policlinico San Donato, 20097 Milan, Italy
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12
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Elsayed NS, Wolfe AJ, Burk RD. Urine microbiome in individuals with an impaired immune system. Front Cell Infect Microbiol 2024; 13:1308665. [PMID: 38274734 PMCID: PMC10808152 DOI: 10.3389/fcimb.2023.1308665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
With the advent of next generation sequencing, it is now appreciated that human urine is not sterile. Recent investigations of the urinary microbiome (urobiome) have provided insights into several urological diseases. Urobiome dysbiosis, defined as non-optimal urine microbiome composition, has been observed in many disorders; however, it is not clear whether this dysbiosis is the cause of urinary tract disorders or a consequence. In addition, immunologically altered disorders are associated with higher rates of urinary tract infections. These disorders include immunoproliferative and immunodeficiency diseases, cancer, and immunosuppressant therapy in transplant recipients. In this review, we examine the current state of knowledge of the urobiome in immunologically altered diseases, its composition and metabolomic consequences. We conclude that more data are required to describe the urobiome in immune altered states, knowledge that could facilitate understanding the role of the urobiome and its pathophysiological effects on urinary tract infections and other disorders of the urinary tract.
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Affiliation(s)
- Noha S. Elsayed
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Robert D. Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
- Departments of Microbiology and Immunology, Epidemiology and Population Health, and Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY, United States
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13
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Pfail J, Drobner J, Doppalapudi K, Saraiya B, Packiam V, Ghodoussipour S. The Role of Tumor and Host Microbiome on Immunotherapy Response in Urologic Cancers. JOURNAL OF CANCER IMMUNOLOGY 2024; 6:1-13. [PMID: 38846356 PMCID: PMC11156155 DOI: 10.33696/cancerimmunol.6.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Introduction & Objective The role of the microbiome in the development and treatment of genitourinary malignancies is just starting to be appreciated. Accumulating evidence suggests that the microbiome can modulate immunotherapy through signaling in the highly dynamic tumor microenvironment. Nevertheless, much is still unknown about the immuno-oncology-microbiome axis, especially in urologic oncology. The objective of this review is to synthesize our current understanding of the microbiome's role in modulating and predicting immunotherapy response to genitourinary malignancies. Methods A literature search for peer-reviewed publications about the microbiome and immunotherapy response in bladder, kidney, and prostate cancer was conducted. All research available in PubMed, Google Scholar, clinicaltrials.gov, and bioRxiv up to September 2023 was analyzed. Results Significant differences in urinary microbiota composition have been found in patients with genitourinary cancers compared to healthy controls. Lactic acid-producing bacteria, such as Bifidobacterium and Lactobacillus genera, may have value in augmenting BCG responsiveness to bladder cancer. BCG may also be a dynamic regulator of PD-L1. Thus, the combination of BCG and immune checkpoint inhibitors may be an effective strategy for bladder cancer management. In advanced renal cell carcinoma, studies show that recent antibiotic administration negatively impacts survival outcomes in patients undergoing immunotherapy, while administration of CBM588, a live bacterial product, is associated with improved progression-free survival. Specific bacterial taxa, such as Streptococcus salivarius, have been linked with response to pembrolizumab in metastatic castrate-resistant prostate cancer. Fecal microbiota transplant has been shown to overcome resistance and reduce toxicity to immunotherapy; it is currently being investigated for both kidney and prostate cancers. Conclusions Although the exact mechanism is unclear, several studies identify a symbiotic relationship between microbiota-centered interventions and immunotherapy efficacy. It is possible to improve immunotherapy responsiveness in genitourinary malignancies using the microbiome, but further research with more standardized methodology is warranted.
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Affiliation(s)
- John Pfail
- Section of Urologic Oncology, Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Jake Drobner
- Section of Urologic Oncology, Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Krishna Doppalapudi
- Section of Urologic Oncology, Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Biren Saraiya
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Vignesh Packiam
- Section of Urologic Oncology, Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Saum Ghodoussipour
- Section of Urologic Oncology, Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
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Roth RS, Liden M, Huttner A. The urobiome in men and women: a clinical review. Clin Microbiol Infect 2023; 29:1242-1248. [PMID: 36028087 DOI: 10.1016/j.cmi.2022.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Antibiotic therapy alone is unable to control recurrent urinary tract infection (UTI); uropathogens have become multiresistant, and alternative strategies are needed. Far from sterile, the urinary tract contains various low-biomass microbiota, some of whose members appear to protect against clinical UTI. OBJECTIVES This narrative review summarizes (a) the current knowledge of male and female urobiomes in healthy and diseased states, as well as their interplay among sexual partners and (b) clinical trials to date assessing probiotic and other nonantibiotic measures to reduce UTI. SOURCES We used the PubMed interface to search Ovid Medline for articles describing urogenital flora, UTI, UTI dysbiosis, the effects of sexual intercourse on urogenital flora, and clinical trials of probiotics as UTI prophylaxis. CONTENT The healthy urobiome of women contains several Lactobacillus species, some of which may impede Escherichia coli growth in the urinary tract. Although Lactobacilli have been found in male urethral microbiota, their presence in male bladder microbiota is less certain. Distal male urethral and vaginal microbiomes of male and sexual female partners influence one another, but more research is needed on the direct interplay of their full urobiomes. Clinical trials assessing the therapeutic potential of Lactobacilli have been largely underpowered and highly varied in tested formulations and routes and frequencies of administration; as such, they have failed to show a clear benefit. Faecal microbiota transplantation for recurrent Clostridium difficile infection was shown, in a retrospective study of seven patients, to reduce recurrent UTI as a side effect. IMPLICATIONS The urobiome in men and women is complex, variable, and still understudied. Although there is hope that Lactobacilli and faecal microbial transplantation could be future nonantibiotic options for recurrent UTI, both require more pharmacologic and clinical research to identify optimal preparations and routes of administration.
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Affiliation(s)
- Romain S Roth
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Mia Liden
- University of Geneva, Faculty of Medicine, Geneva, Switzerland
| | - Angela Huttner
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland; University of Geneva, Faculty of Medicine, Geneva, Switzerland; Center for Clinical Research, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland.
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15
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Cole EB, Khemmani M, Liu H, Halverson TM, Noronha MF, Forster CS, Wolfe AJ, Shaikh N. Urogenital urobiome of healthy children does not differ from that of children with bladder and bowel dysfunction. J Pediatr Urol 2023; 19:368.e1-368.e8. [PMID: 37117081 PMCID: PMC10524508 DOI: 10.1016/j.jpurol.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/30/2023] [Accepted: 04/10/2023] [Indexed: 04/30/2023]
Abstract
INTRODUCTION The pediatric urinary microbiome (urobiome) has been studied in the context of healthy children and children with genitourinary pathologies including neuropathic bladder, urinary tract infection (UTI) and nephrolithiasis. Little is known about the urobiome of children with bladder and bowel dysfunction (BBD), a condition that is an established risk factor of UTI. We hypothesized that the symptoms of a child with BBD may be related to urobiome composition. OBJECTIVE To evaluate the urogenital urobiome's role in BBD, we compared the urogenital urobiomes of children with and without BBD. STUDY DESIGN We performed a prospective case-control pilot study at a single large, academic children's hospital. Cases included toilet trained prepubertal females over 2 years of age with BBD established through a validated scoring system and controls included asymptomatic, presumably healthy, children. Children were excluded if they had symptoms or lab work consistent with a concurrent UTI or antibiotic course for any reason within the prior 14 days. We performed 16 S ribosomal RNA gene sequencing and expanded quantitative urine culture on clean catch urine samples. To compare within sample (alpha) diversity, we used the Kruskal-Wallis test. To compare between sample (beta) diversity, we calculated the Bray-Curtis distance and performed the PERMANOVA test. RESULTS Data from 25 children with BBD and 8 asymptomatic controls were analyzed. The demographic and clinical characteristics of the two comparison groups were similar, though a higher proportion of Black children were included in the asymptomatic control group. Neither alpha diversity nor beta diversity was significantly different between the two groups. The core microbiome of the BBD group included all the genera in the core urogenital urobiome of the controls, plus additional genera associated with opportunistic infection and/or UTI, including Escherichia, Campylobacter and Streptococcus. DISCUSSION The results of both the 16 S sequencing and expanded quantitative urine culture in this small study suggest that the urogenital urobiomes of children with BBD do not differ significantly from those of asymptomatic children. However, the core urogenital urobiome of children with BBD included genera associated with opportunistic infection and/or UTI. This study was limited by the sample collection method ("clean catch" midstream voided urine samples, which introduce the possibility of vulvovaginal contamination), small sample size, and unequal balance of patient characteristics between the two study groups. CONCLUSION The urogenital urobiomes of children with and without BBD do not appear to significantly differ. Larger studies are needed to confirm these findings.
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Affiliation(s)
- Elisabeth B Cole
- Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
| | - Mark Khemmani
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| | - Hui Liu
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Thomas M Halverson
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| | - Melline Fontes Noronha
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| | - Catherine S Forster
- Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| | - Nader Shaikh
- Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
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16
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Kim DS, Lee JW. Urinary Tract Infection and Microbiome. Diagnostics (Basel) 2023; 13:diagnostics13111921. [PMID: 37296773 DOI: 10.3390/diagnostics13111921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/23/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Urinary tract infection is one of the most common bacterial infections and can cause major burdens, not only to individuals but also to an entire society. Current knowledge of the microbial communities in the urinary tract has increased exponentially due to next-generation sequencing and expanded quantitative urine culture. We now acknowledge a dynamic urinary tract microbiome that we once thought was sterile. Taxonomic studies have identified the normal core microbiota of the urinary tract, and studies on the changes in microbiome due to sexuality and age have set the foundation for microbiome studies in pathologic states. Urinary tract infection is not only caused by invading uropathogenic bacteria but also by changes to the uromicrobiome milieu, and interactions with other microbial communities can also contribute. Recent studies have provided insights into the pathogenesis of recurrent urinary tract infections and antimicrobial resistance. New therapeutic options for urinary tract infections also show promise; however, further research is needed to fully understand the implications of the urinary microbiome in urinary tract infections.
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Affiliation(s)
- Dong Soo Kim
- Department of Urology, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul 02447, Republic of Korea
| | - Jeong Woo Lee
- Department of Urology, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul 02447, Republic of Korea
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17
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Weng X, Liu Y, Hu H, Wang M, Huang X. Changes of microbiota level in urinary tract infections: A meta-analysis. Open Med (Wars) 2023; 18:20230702. [PMID: 37251539 PMCID: PMC10224615 DOI: 10.1515/med-2023-0702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 05/31/2023] Open
Abstract
No consensus has been reached on the dysbiosis signs of microbiota in patients with urinary tract infections (UTIs). This meta-analysis aimed to verify the relationship between microbiota levels and UTIs. PubMed, Web of Science, and Embase databases were retrieved for related articles published from inception until October 20, 2021. The standardized mean difference (SMD) and its related 95% confidence intervals (CIs) of the microbiota diversity and abundance were pooled under a random-effects model. Twelve studies were included in this meta-analysis. The pooled analysis revealed that the microbiota diversity was lower in patients with UTIs than in healthy individuals (SMD = -0.655, 95% CI = -1.290, -0.021, I 2 = 81.0%, P = 0.043). The abundance of specific bacteria was higher in UTI subjects compared with healthy control individuals (SMD = 0.41, 95% CI = 0.07-0.74, P = 0.017), especially in North America patients with UTIs. Similar results were also found in studies with the total sample size being greater than 30. Importantly, Escherichia coli levels were increased in patients with UTI, whereas Lactobacillus levels decreased. E. coli and Lactobacilli have huge prospects as potential microbiota markers in the treatment of UTIs.
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Affiliation(s)
- Xia Weng
- Urology Department, Zhejiang Hospital, Hangzhou310013, Zhejiang Province, China
| | - Yajun Liu
- Neurosurgery Department, Zhejiang Provincial Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
| | - Haiping Hu
- Urology Department, Zhejiang Hospital, Hangzhou310013, Zhejiang Province, China
| | - Meichai Wang
- Urology Department, Zhejiang Hospital, Hangzhou310013, Zhejiang Province, China
| | - Xiaoqin Huang
- Orthopedics Department, Zhejiang Hospital, No. 1229, Gudun Road, Hangzhou 310013, Zhejiang Province, China
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Du J, Khemmani M, Halverson T, Ene A, Limeira R, Tinawi L, Hochstedler-Kramer BR, Noronha MF, Putonti C, Wolfe AJ. Cataloging the Phylogenetic Diversity of Human Bladder Bacterial Isolates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541916. [PMID: 37292924 PMCID: PMC10245883 DOI: 10.1101/2023.05.23.541916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, e.g., the gut and oral cavity. To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, here we present a bladder-specific bacterial reference collection comprised of 1134 genomes. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2 % of the genera found when we reexamined previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis found that the taxonomies and functions of the bladder microbiota shared more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder E. coli isolates and 387 gut E. coli isolates supports the hypothesis that phylogroup distribution and functions of E. coli strains differ dramatically between these two very different niches. This bladder-specific bacterial reference collection is a unique resource that will enable hypothesis-driven bladder microbiota research and comparison to isolates from other anatomical sites.
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Affiliation(s)
- Jingjie Du
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Mark Khemmani
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Thomas Halverson
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660
| | - Roberto Limeira
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Lana Tinawi
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Baylie R. Hochstedler-Kramer
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Melline Fontes Noronha
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660
- Department of Biology, Loyola University Chicago, Chicago, IL 60660
| | - Alan J. Wolfe
- Department of Microbiology & Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153
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Hyun J, Ha MS, Oh SY, Tae JH, Chi BH, Chang IH, Kim TH, Myung SC, Nguyen TT, Kim JH, Kim JW, Lee YS, Lee J, Choi SY. Urinary tract infection after radiation therapy or radical prostatectomy on the prognosis of patients with prostate cancer: a population-based study. BMC Cancer 2023; 23:395. [PMID: 37138203 PMCID: PMC10157974 DOI: 10.1186/s12885-023-10869-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/20/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND We aimed to assess the trends in urinary tract infections (UTIs) and prognosis of patients with prostate cancer after radical prostatectomy (RP) and radiation therapy (RT) as definitive treatment options. METHODS The data of patients diagnosed with prostate cancer between 2007 and 2016 were collected from the National Health Insurance Service database. The incidence of UTIs was evaluated in patients treated with RT, open/laparoscopic RP, and robot-assisted RP. The proportional hazard assumption test was performed using the scaled Schoenfeld residuals based on a multivariable Cox proportional hazard model. Kaplan-Meier analysis were performed to assess survival. RESULTS A total of 28,887 patients were treated with definitive treatment. In the acute phase (< 3 months), UTIs were more frequent in RP than in RT; in the chronic phase (> 12 months), UTIs were more frequent in RT than in RP. In the early follow-up period, the risk of UTIs was higher in the open/laparoscopic RP group (aHR, 1.63; 95% CI, 1.44-1.83; p < 0.001) and the robot-assisted RP group (aHR, 1.26; 95% CI, 1.11-1.43; p < 0.001), compared to the RT group. The robot-assisted RP group had a lower risk of UTIs than the open/laparoscopic RP group in the early (aHR, 0.77; 95% CI, 0.77-0.78; p < 0.001) and late (aHR, 0.90; 95% CI, 0.89-0.91; p < 0.001) follow-up periods. In patients with UTI, Charlson Comorbidity Index score, primary treatment, age at UTI diagnosis, type of UTI, hospitalization, and sepsis from UTI were risk factors for overall survival. CONCLUSIONS In patients treated with RP or RT, the incidence of UTIs was higher than that in the general population. RP posed a higher risk of UTIs than RT did in early follow-up period. Robot-assisted RP had a lower risk of UTIs than open/laparoscopic RP group in total period. UTI characteristics might be related to poor prognosis.
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Affiliation(s)
- Jihye Hyun
- Department of Applied Statistics, Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea
| | - Moon Soo Ha
- Department of Urology, Hyundae General Hospital, Chung-Ang University College of Medicine, 21 Bonghyeon-ro, Gyeonggi-Do, 12013, Namyangju-si, Republic of Korea
| | - Seung Young Oh
- Department of Urology, Hyundae General Hospital, Chung-Ang University College of Medicine, 21 Bonghyeon-ro, Gyeonggi-Do, 12013, Namyangju-si, Republic of Korea
| | - Jong Hyun Tae
- Department of Urology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, 102, Heukseok-Ro, Dongjak-Gu, 06973, Seoul, Republic of Korea
| | - Byung Hoon Chi
- Department of Urology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, 102, Heukseok-Ro, Dongjak-Gu, 06973, Seoul, Republic of Korea
| | - In Ho Chang
- Department of Urology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, 102, Heukseok-Ro, Dongjak-Gu, 06973, Seoul, Republic of Korea
| | - Tae-Hyoung Kim
- Department of Urology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, 102, Heukseok-Ro, Dongjak-Gu, 06973, Seoul, Republic of Korea
| | - Soon Chul Myung
- Department of Urology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, 102, Heukseok-Ro, Dongjak-Gu, 06973, Seoul, Republic of Korea
| | - Tuan Thanh Nguyen
- Department of Urology, Cho Ray Hospital, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Jung Hoon Kim
- Department of Urology, Chung-Ang University Gwangmyeong Hospital, Chung-Ang University College of Medicine, 110, Deokan-ro, Gyeonggi-Do, 14353, Gwangmyeong-si, Republic of Korea
| | - Jin Wook Kim
- Department of Urology, Chung-Ang University Gwangmyeong Hospital, Chung-Ang University College of Medicine, 110, Deokan-ro, Gyeonggi-Do, 14353, Gwangmyeong-si, Republic of Korea
| | - Yong Seong Lee
- Department of Urology, Chung-Ang University Gwangmyeong Hospital, Chung-Ang University College of Medicine, 110, Deokan-ro, Gyeonggi-Do, 14353, Gwangmyeong-si, Republic of Korea
| | - Jooyoung Lee
- Department of Applied Statistics, Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, 06974, Seoul, Republic of Korea.
| | - Se Young Choi
- Department of Urology, Chung-Ang University Hospital, Chung-Ang University College of Medicine, 102, Heukseok-Ro, Dongjak-Gu, 06973, Seoul, Republic of Korea.
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Crum E, Merchant Z, Ene A, Miller-Ensminger T, Johnson G, Wolfe AJ, Putonti C. Coliphages of the human urinary microbiota. PLoS One 2023; 18:e0283930. [PMID: 37053131 PMCID: PMC10101464 DOI: 10.1371/journal.pone.0283930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Due to its frequent association with urinary tract infections (UTIs), Escherichia coli is the best characterized constituent of the urinary microbiota (urobiome). However, uropathogenic E. coli is just one member of the urobiome. In addition to bacterial constituents, the urobiome of both healthy and symptomatic individuals is home to a diverse population of bacterial viruses (bacteriophages). A prior investigation found that most bacterial species in the urobiome are lysogens, harboring one or more phages integrated into their genome (prophages). Many of these prophages are temperate phages, capable of entering the lytic cycle and thus lysing their bacterial host. This transition from the lysogenic to lytic life cycle can impact the bacterial diversity of the urobiome. While many phages that infect E. coli (coliphages) have been studied for decades in the laboratory setting, the coliphages within the urobiome have yet to be cataloged. Here, we investigated the diversity of urinary coliphages by first identifying prophages in all publicly available urinary E. coli genomes. We detected 3,038 intact prophage sequences, representative of 1,542 unique phages. These phages include both novel species as well as species also found within the gut microbiota. Ten temperate phages were isolated from urinary E. coli strains included in our analysis, and we assessed their ability to infect and lyse urinary E. coli strains. We also included in these host range assays other urinary coliphages and laboratory coliphages. The temperate phages and other urinary coliphages were successful in lysing urinary E. coli strains. We also observed that coliphages from non-urinary sources were most efficient in killing urinary E. coli strains. The two phages, T2 and N4, were capable of lysing 83.5% (n = 86) of strains isolated from females with UTI symptoms. In conclusion, our study finds a diverse community of coliphages in the urobiome, many of which are predicted to be temperate phages, ten of which were confirmed here. Their ability to infect and lyse urinary E. coli strains suggests that urinary coliphages may play a role in modulating the E. coli strain diversity of the urobiome.
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Affiliation(s)
- Elias Crum
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Zubia Merchant
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Taylor Miller-Ensminger
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Genevieve Johnson
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
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Park MG, Cho S, Oh MM. Menopausal Changes in the Microbiome-A Review Focused on the Genitourinary Microbiome. Diagnostics (Basel) 2023; 13:diagnostics13061193. [PMID: 36980501 PMCID: PMC10047399 DOI: 10.3390/diagnostics13061193] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/01/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
A balanced interaction between the host and its microbiome is crucial to health. Research regarding the significance of the gut and vaginal microbiomes in female health is substantial. However, less data regarding the urinary microbiome are available. Interactions between the gut, vaginal, and urinary microbiomes are also currently being researched. Hormone-induced dysbiosis after menopause is believed to have effects on physical changes and health consequences. Postmenopausal changes in the gut microbiome are associated with increased short-chain fatty acids and hydrogen sulfide levels. Increased vaginal pH caused by reduced estrogen alters the vaginal microbiome, resulting in reduced levels of Lactobacillus. Such changes influence the vaginal structure and functions, contributing to the onset of genitourinary syndrome of menopause. A dysbiosis of the urinary microbiome is associated with urgency and urinary incontinence and also related to interstitial cystitis/bladder pain syndrome and neuropathic bladder. As these diseases commonly affect postmenopausal women, hormone-induced changes in the microbiome may play a role. Menopause increases the alpha diversity of the urinary microbiome and lowers the percentage of Lactobacillus in urine, and such changes precede recurrent cystitis. More research regarding the effects of changes in the urinary microbiome due to menopause on urinary tract diseases is needed.
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Affiliation(s)
- Min Gu Park
- Department of Urology, Inje University Seoul Paik Hospital, 9 Mareunnae-ro, Jung-gu, Seoul 04551, Republic of Korea
| | - Seok Cho
- Department of Urology, Inje University Ilsan Paik Hospital, 170 Juhwa-ro, Ilsanseo-gu, Goyang-si 10380, Republic of Korea
| | - Mi Mi Oh
- Department of Urology, Korea University Guro Hospital, 148 Gurodong-ro, Guro-gu, Seoul 08308, Republic of Korea
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22
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Maffucci F, Chang C, Simhan J, Cohn JA. Is There Any Benefit to the Use of Antibiotics with Indwelling Catheters after Urologic Surgery in Adults. Antibiotics (Basel) 2023; 12:156. [PMID: 36671357 PMCID: PMC9854512 DOI: 10.3390/antibiotics12010156] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
Antibiotic stewardship in urologic reconstruction is critically important, as many patients will require indwelling catheters for days to weeks following surgery and thus are at risk of both developing catheter-associated urinary tract infections (CAUTI) as well as multi-drug resistant (MDR) uropathogens. Accordingly, limiting antibiotic use, when safe, should help reduce antibiotic resistance and the prevalence of MDR organisms. However, there is significant heterogeneity in how antibiotics are prescribed to patients who need indwelling urethral catheters post-operatively. We performed a literature review to determine if there are benefits in the use of antibiotics for various clinical scenarios that require post-operative indwelling catheters for greater than 24 h. In general, for patients undergoing prostatectomy, transurethral resection of the prostate, and/or urethroplasty, antibiotic administration may be limited without increased risk of CAUTI. However, more work is needed to identify optimal antibiotic regimens for these and alternative urologic procedures, whether certain sub-populations benefit from longer courses of antibiotics, and effective non-antibiotic or non-systemic therapies.
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Affiliation(s)
- Fenizia Maffucci
- Department of Urology, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA 19111, USA
| | | | | | - Joshua A. Cohn
- Department of Urology, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA 19111, USA
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23
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Kustrimovic N, Bombelli R, Baci D, Mortara L. Microbiome and Prostate Cancer: A Novel Target for Prevention and Treatment. Int J Mol Sci 2023; 24:ijms24021511. [PMID: 36675055 PMCID: PMC9860633 DOI: 10.3390/ijms24021511] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
Growing evidence of the microbiome's role in human health and disease has emerged since the creation of the Human Microbiome Project. Recent studies suggest that alterations in microbiota composition (dysbiosis) may play an essential role in the occurrence, development, and prognosis of prostate cancer (PCa), which remains the second most frequent male malignancy worldwide. Current advances in biological technologies, such as high-throughput sequencing, transcriptomics, and metabolomics, have enabled research on the gut, urinary, and intra-prostate microbiome signature and the correlation with local and systemic inflammation, host immunity response, and PCa progression. Several microbial species and their metabolites facilitate PCa insurgence through genotoxin-mediated mutagenesis or by driving tumor-promoting inflammation and dysfunctional immunosurveillance. However, the impact of the microbiome on PCa development, progression, and response to treatment is complex and needs to be fully understood. This review addresses the current knowledge on the host-microbe interaction and the risk of PCa, providing novel insights into the intraprostatic, gut, and urinary microbiome mechanisms leading to PCa carcinogenesis and treatment response. In this paper, we provide a detailed overview of diet changes, gut microbiome, and emerging therapeutic approaches related to the microbiome and PCa. Further investigation on the prostate-related microbiome and large-scale clinical trials testing the efficacy of microbiota modulation approaches may improve patient outcomes while fulfilling the literature gap of microbial-immune-cancer-cell mechanistic interactions.
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Affiliation(s)
- Natasa Kustrimovic
- Center for Translational Research on Autoimmune and Allergic Disease—CAAD, Università del Piemonte Orientale, 28100 Novara, Italy
| | - Raffaella Bombelli
- Immunology and General Pathology Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
| | - Denisa Baci
- Immunology and General Pathology Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Lorenzo Mortara
- Immunology and General Pathology Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, 21100 Varese, Italy
- Correspondence:
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Aggarwal N, Kitano S, Puah GRY, Kittelmann S, Hwang IY, Chang MW. Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies. Chem Rev 2023; 123:31-72. [PMID: 36317983 PMCID: PMC9837825 DOI: 10.1021/acs.chemrev.2c00431] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Indexed: 01/12/2023]
Abstract
The human microbiome is composed of a collection of dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, the coevolution of the microbiome with the host has resulted in these communities playing a profound role in promoting human health. Consequently, perturbations in the human microbiome can cause or exacerbate several diseases. In this Review, we present our current understanding of the relationship between human health and disease development, focusing on the microbiomes found across the digestive, respiratory, urinary, and reproductive systems as well as the skin. We further discuss various strategies by which the composition and function of the human microbiome can be modulated to exert a therapeutic effect on the host. Finally, we examine technologies such as multiomics approaches and cellular reprogramming of microbes that can enable significant advancements in microbiome research and engineering.
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Affiliation(s)
- Nikhil Aggarwal
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Shohei Kitano
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Ginette Ru Ying Puah
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Wilmar
International Limited, Singapore 138568, Singapore
| | - Sandra Kittelmann
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Wilmar
International Limited, Singapore 138568, Singapore
| | - In Young Hwang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Singapore
Institute of Technology, Singapore 138683, Singapore
| | - Matthew Wook Chang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
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Wawrysiuk S, Rechberger T, Kubik-Komar A, Kolodynska A, Naber K, Miotla P. Postoperative Prevention of Urinary Tract Infections in Patients after Urogynecological Surgeries-Nonantibiotic Herbal (Canephron) versus Antibiotic Prophylaxis (Fosfomycin Trometamol): A Parallel-Group, Randomized, Noninferiority Experimental Trial. Pathogens 2022; 12:pathogens12010027. [PMID: 36678373 PMCID: PMC9864930 DOI: 10.3390/pathogens12010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
INTRODUCTION AND HYPOTHESIS Urinary tract infections (UTIs) are one of the most common complications of urogynecological surgeries. The risk of UTIs is increased by the catheterization of the bladder, intraoperative cystoscopy, and urine retention after the procedure. Due to increasing antibiotic resistance, there is a need to search for new methods of postoperative UTI prevention. Canephron is a mixture of century herbs, lovage roots, and rosemary leaves with diuretic, spasmolytic, anti-inflammatory, antibacterial, and nephroprotective properties. The aim of this study is to demonstrate the noninferiority of Canephron versus antibiotic prophylaxis with fosfomycin trometamol (FT), based on the collective results of postoperative urine culture analyses. METHODS One hundred and twenty-five female patients were randomized into two groups before undergoing urogynecological surgeries, including a control group (n = 67), which received one dose of 3 g of FT the day after the procedure, and a study group (n = 58), which received Canephron three times a day for 14 days, starting the day after the procedure. All the patients were assessed using the Acute Cystitis Symptom Score (ACSS). RESULTS UTIs were observed in 6.4% of the patients. There was no statistically significant difference between the use of FT and Canephron in terms of UTIs (Chi^2 N-1 = 0.8837; p = ns). Additional factors, such as menopausal status and the type of procedure performed, increased the risk of developing a UTI. Factors such as the body mass index (BMI) and parity had no correlation. CONCLUSIONS Canephron is noninferior to FT in the prevention of postoperative UTIs. The use of such a phytotherapeutic drug may help to decrease antibiotic consumption, which is closely connected to the growing trend of antibiotic resistance.
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Affiliation(s)
- Sara Wawrysiuk
- 2nd Department of Gynaecology, Medical University of Lublin, ul. Jaczewskiego 8, 20-954 Lublin, Poland
- Correspondence:
| | - Tomasz Rechberger
- 2nd Department of Gynaecology, Medical University of Lublin, ul. Jaczewskiego 8, 20-954 Lublin, Poland
| | - Agnieszka Kubik-Komar
- Department of Applied Mathematics and Computer Science, University of Life Sciences in Lublin, ul. Głęboka 28, 20-950 Lublin, Poland
| | - Aleksandra Kolodynska
- 2nd Department of Gynaecology, Medical University of Lublin, ul. Jaczewskiego 8, 20-954 Lublin, Poland
| | - Kurt Naber
- Department of Urology, Technical University of Munich, Arcisstrasse 21, 80333 Munich, Germany
| | - Pawel Miotla
- 2nd Department of Gynaecology, Medical University of Lublin, ul. Jaczewskiego 8, 20-954 Lublin, Poland
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Reduction in Rates of Symptomatic Urinary Tract Infection After Pelvic Reconstructive Surgery: A Quality Improvement Analysis. UROGYNECOLOGY (HAGERSTOWN, MD.) 2022; 28:763-769. [PMID: 36288115 DOI: 10.1097/spv.0000000000001242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
IMPORTANCE Urinary tract infections contribute to high health care costs. OBJECTIVE This study aimed to determine if a combination of interventions was successful at reducing the rate of postoperative symptomatic urinary tract infections (SUTIs) in a female pelvic medicine and reconstructive surgery (FPMRS) practice. STUDY DESIGN Observational, retrospective quality improvement analysis looking at the rate of postoperative SUTI within 30 days of surgery in women who underwent gynecologic surgery performed by an FPMRS surgeon from October 2015 to October 2019. Symptomatic urinary tract infection was defined by symptoms and urinalysis, positive urine culture, or treatment for cystitis or urethritis within 30 days of surgery. Interventions were implemented between 2015 and 2016: perioperative cranberry use, intraoperative protocols for catheterization, and postoperative protocols for urinary retention management. In 2018, we added metronidazole to cefazolin for antibiotic prophylaxis. We developed a multivariable logistic regression to determine if postoperative SUTI rates decreased over the study period with adjustment for clustering by surgeons, patient factors, and surgery type. RESULTS Of 2,389 procedures performed, 284 (11.8%) involved patients who had an SUTI within 30 days of surgery. The annual infection rate decreased 50% (year 1, 14.7%; year 4, 7.3%). Adjusting for age, race, body mass index, length of stay, surgery type, and surgeon, the odds of SUTI decreased 19% each year (odds ratio [OR], 0.81; 95% confidence interval [CI], 0.72-0.91; P < 0.001). Compared with women who had other gynecologic procedures, those who underwent vaginal prolapse surgery with or without incontinence procedures (OR, 2.75; 95% CI, 1.35-5.54; P = 0.01) or incontinence surgery alone (OR, 2.65; 95% CI, 1.25-5.62; P = 0.01) were more likely to have an SUTI. CONCLUSION Combining interventions can be highly effective in reducing postoperative SUTI rates.
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Hong SY, Yang YY, Xu JZ, Xia QD, Wang SG, Xun Y. The renal pelvis urobiome in the unilateral kidney stone patients revealed by 2bRAD-M. J Transl Med 2022; 20:431. [PMID: 36153619 PMCID: PMC9509602 DOI: 10.1186/s12967-022-03639-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/14/2022] [Indexed: 11/27/2022] Open
Abstract
Background The pathogenesis of kidney stone disease (KSD) is not fully understood, and potential contributing factors remain to be explored. Several studies have revealed that the urinary microbiome (urobiome) of stone formers was distinct from that of healthy individuals using 16S rRNA gene sequencing, most of which only provided microbial identification at the genus level. 2bRAD sequencing for Microbiome (2bRAD-M) is a novel sequencing technique that enables accurate characterization of the low-biomass microbiome at the species resolution. We aimed to apply 2bRAD-M to profile the renal pelvis urobiome of unilateral kidney stone patients and compared the urobiome with and without stone(s). Method A total of 30 patients with unilateral stones were recruited, and their renal pelvis urine from both sides was collected. A ureteroscope was inserted into the renal pelvis with stone(s) and a ureteral catheter was placed into the ureteroscope to collect renal pelvis urine. This procedure was repeated again with new devices to collect the urine of the other side. 2bRAD-M was performed to characterize the renal pelvis urobiome of unilateral stone formers to explore whether microbial differences existed between the stone side and the non-stone side. Results The microbial community composition of the stone side was similar to that of the non-stone side. Paired comparison showed that Corynebacterium was increased and Prevotella and Lactobacillus were decreased in the stone side. Four species (Prevotella bivia, Lactobacillus iners, Corynebacterium aurimucosum, and Pseudomonas sp_286) were overrepresented in the non-stone side. 24 differential taxa were also identified between two groups by linear discriminant analysis effect size (LEfSe). Extensive and close connections among genera and species were observed in the correlation analysis. Moreover, a random forest classifier was constructed using specific enriched species, which can distinguish the stone side from the non-stone side with an accuracy of 71.2%. Conclusion This first 2bRAD-M microbiome survey gave an important hint towards the potential role of urinary dysbiosis in KSD and provided a better understanding of mechanism of stone formation. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03639-6.
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The Bladder Microbiome, Metabolome, Cytokines, and Phenotypes in Patients with Systemic Lupus Erythematosus. Microbiol Spectr 2022; 10:e0021222. [PMID: 35913213 PMCID: PMC9620774 DOI: 10.1128/spectrum.00212-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Emerging studies reveal unique bacterial communities in the human bladder, with alteration of composition associated to disease states. Systemic lupus erythematosus (SLE) is a complex autoimmune disease that is characterized by frequent impairment of the kidney. Here, we explored the bladder microbiome, metabolome, and cytokine profiles in SLE patients, as well as correlations between microbiome and metabolome, cytokines, and disease profiles. We recruited a group of 50 SLE patients and 50 individually matched asymptomatic controls. We used transurethral catheterization to collect urine samples, 16S rRNA gene sequencing to profile bladder microbiomes, and liquid chromatography-tandem mass spectrometry to perform untargeted metabolomic profiling. Compared to controls, SLE patients possessed unique bladder microbial communities and increased alpha diversity. These differences were accompanied by differences in urinary metabolomes, cytokines, and patients’ disease profiles. The SLE-enriched genera, including Bacteroides, were positively correlated with several SLE-enriched metabolites, including olopatadine. The SLE-depleted genera, such as Pseudomonas, were negatively correlated to SLE-depleted cytokines, including interleukin-8. Alteration of the bladder microbiome was associated with disease profile. For example, the genera Megamonas and Phocaeicola were negatively correlated with serum complement component 3, and Streptococcus was positively correlated with IgG. Our present study reveals associations between the bladder microbiome and the urinary metabolome, cytokines, and disease phenotypes. Our results could help identify biomarkers for SLE. IMPORTANCE Contrary to dogma, the human urinary bladder possesses its own unique bacterial community with alteration of composition associated with disease states. Systemic lupus erythematosus (SLE) is a complex autoimmune disease often characterized by kidney impairment. Here, we explored the bladder microbiome, metabolome, and cytokine profiles in SLE patients, as well as correlations between the microbiome and metabolome, cytokines, and disease profiles. Compared to controls, SLE patients possessed a unique bladder microbial community and elevated alpha diversity. These differences were accompanied by differences in bladder metabolomes, cytokines, and patients’ disease profiles. SLE-enriched genera were positively correlated with several SLE-enriched metabolites. SLE-depleted genera were negatively correlated to SLE-depleted cytokines. Alteration of the bladder microbiome was associated with disease profile. Thus, our study reveals associations between the bladder microbiome and the bladder metabolome, cytokines, and disease phenotypes. These results could help identify biomarkers for SLE.
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29
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Zerdan MB, Moukarzel R, Naji NS, Bilen Y, Nagarajan A. The Urogenital System’s Role in Diseases: A Synopsis. Cancers (Basel) 2022; 14:cancers14143328. [PMID: 35884388 PMCID: PMC9319963 DOI: 10.3390/cancers14143328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The urinary tract microbiome has come under a lot of scrutiny, and this has led to the rejection of the pre-established concept of sterility in the urinary bladder. Microbial communities in the urinary tract have been implicated in the maintenance of health. Thus, alterations in their composition have also been associated with different urinary pathologies, such as urinary tract infections. For that reason, tackling the urinary microbiome of healthy individuals, as well as its involvement in disease through the proliferation of opportunistic pathogens, could open a potential field of study, leading to new insights into prevention, diagnosis, and treatment strategies for different diseases. Abstract The human microbiota contains ten times more microbial cells than human cells contained by the human body, constituting a larger genetic material than the human genome itself. Emerging studies have shown that these microorganisms represent a critical determinant in human health and disease, and the use of probiotic products as potential therapeutic interventions to modulate homeostasis and treat disease is being explored. The gut is a niche for the largest proportion of the human microbiota with myriad studies suggesting a strong link between the gut microbiota composition and disease development throughout the body. More specifically, there is mounting evidence on the relevance of gut microbiota dysbiosis in the development of urinary tract disease including urinary tract infections (UTIs), chronic kidney disease, and kidney stones. Fewer emerging reports, however, are suggesting that the urinary tract, which has long been considered ‘sterile’, also houses its unique microbiota that might have an important role in urologic health and disease. The implications of this new paradigm could potentially change the therapeutic perspective in urological disease.
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Affiliation(s)
- Maroun Bou Zerdan
- Department of Internal Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA;
- Department of Hematology and Oncology, Cleveland Clinic Florida, Weston, FL 33331, USA
| | - Rita Moukarzel
- Faculty of Medicine, Lebanese American University Medical Center, Lebanese American University, Beirut 1102, Lebanon;
| | - Nour Sabiha Naji
- Faculty of Medicine, American University of Beirut, Beirut 2020, Lebanon;
| | - Yara Bilen
- Department of Internal Medicine, Cleveland Clinic Foundation, Cleveland, OH 44195, USA;
| | - Arun Nagarajan
- Department of Hematology and Oncology, Cleveland Clinic Florida, Weston, FL 33331, USA
- Correspondence:
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30
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Johnson JA, Delaney LF, Ojha V, Rudraraju M, Hintze KR, Siddiqui NY, Sysoeva TA. Commensal Urinary Lactobacilli Inhibit Major Uropathogens In Vitro With Heterogeneity at Species and Strain Level. Front Cell Infect Microbiol 2022; 12:870603. [PMID: 35811675 PMCID: PMC9260849 DOI: 10.3389/fcimb.2022.870603] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
The human urinary microbiome is thought to affect the development and progression of urinary tract infections (UTI), particularly recurrent UTIs in aging populations of women. To understand the possible interactions of urinary pathogens with commensal bacteria inhabiting the aging bladder, we conducted an initial functional assessment of a representative set of urinary lactobacilli that dominate this niche in postmenopausal women. We created a repository of urinary bladder bacteria isolated via Enhanced Quantitative Urinary Culture (EQUC) from healthy postmenopausal women, as well as those with a culture-proven recurrent UTI (rUTI) diagnosis. This repository contains lactobacilli strains from eight different species. As many other lactobacilli are known to inhibit human pathogens, we hypothesized that some urinary lactobacilli will have similar abilities to inhibit the growth of typical uropathogens and thus, provide a link between the urinary microbiome and the predisposition to the rUTI. Therefore, we screened the urinary lactobacilli in our repository for their ability to inhibit model uropathogens in vitro. We observed that many urinary isolates strongly inhibit model strains of gram-negative Escherichia coli and Klebsiella pneumoniae but demonstrate less inhibition of gram-positive Enterococcus faecalis. The observed inhibition affected model strains of uropathogens as well as clinical and multidrug-resistant isolates of those species. Our preliminary analysis of inhibition modes suggests a combination of pH-dependent and cell-dependent inhibition. Overall, inhibition strongly varies among species and strains of urinary lactobacilli. While the strength of the inhibition is not predictive of health outcomes in this limited repository, there is a high level of species and strain diversity that warrants future detailed investigations.
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Affiliation(s)
- James A. Johnson
- Department of Biology, University of Alabama in Huntsville, Huntsville, AL, United States
| | - Lydia F. Delaney
- Department of Biology, University of Alabama in Huntsville, Huntsville, AL, United States
| | - Vaishali Ojha
- Department of Biology, University of Alabama in Huntsville, Huntsville, AL, United States
| | - Medha Rudraraju
- Department of Biology, University of Alabama in Huntsville, Huntsville, AL, United States
| | - Kaylie R. Hintze
- Department of Biology, University of Alabama in Huntsville, Huntsville, AL, United States
| | - Nazema Y. Siddiqui
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Obstetrics and Gynecology, Duke University, Durham, NC, United States
| | - Tatyana A. Sysoeva
- Department of Biology, University of Alabama in Huntsville, Huntsville, AL, United States
- *Correspondence: Tatyana A. Sysoeva,
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Joyce C, Halverson T, Gonzalez C, Brubaker L, Wolfe AJ. The Urobiomes of Adult Women With Various Lower Urinary Tract Symptoms Status Differ: A Re-Analysis. Front Cell Infect Microbiol 2022; 12:860408. [PMID: 35755842 PMCID: PMC9218574 DOI: 10.3389/fcimb.2022.860408] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/11/2022] [Indexed: 01/26/2023] Open
Abstract
The discovery of the urinary microbiome (urobiome) has created opportunities for urinary health researchers who study a wide variety of human health conditions. This manuscript describes an analysis of catheterized urine samples obtained from 1,004 urobiome study participants with the goal of identifying the most abundant and/or prevalent (common) taxa in five clinically relevant cohorts: unaffected adult women (n=346, 34.6%), urgency urinary incontinence (UUI) (n=255, 25.5%), stress urinary incontinence (SUI) (n=50, 5.0%), urinary tract infection (UTI) (n=304, 30.4%), and interstitial cystitis/painful bladder syndrome (IC/PBS) (n=49, 4.9%). Urine was collected via transurethral catheter and assessed for microbes with the Expanded Quantitative Urine Culture (EQUC) technique. For this combined analytic cohort, the mean age was 59 ± 16; most were Caucasian (n=704, 70.2%), Black (n=137, 13.7%), or Hispanic (n=130, 13.0%), and the mean BMI was 30.4 ± 7.7. Whereas many control or IC/PBS cohort members were EQUC-negative (42.4% and 39.8%, respectively), members of the other 3 cohorts were extremely likely to have detectable microbes. The detected urobiomes of the controls and IC/PBS did not differ by alpha diversity or genus level composition and differed by only a few species. The other 3 cohorts differed significantly from the controls. As expected, Escherichia was both prevalent and highly abundant in the UTI cohort, but other taxa also were prevalent at more moderate abundances, including members of the genera Lactobacillus, Streptococcus, Staphylococcus, Corynebacterium, Actinomyces, and Aerococcus. Members of these genera were also prevalent and highly abundant in members of the UUI cohort, especially Streptococcus anginosus. Intriguingly, these taxa were also detected in controls but at vastly lower levels of both prevalence and abundance, suggesting the possibility that UUI-associated symptoms could be the result of an overabundance of typical urobiome constituents. Finally, prevalence and abundance of microbes in the SUI cohort were intermediate to those of the UUI and control cohorts. These observations can inform the next decade of urobiome research, with the goal of clarifying the mechanisms of urobiome community composition and function. There is tremendous potential to improve diagnosis, evaluation and treatment for individuals affected with a wide variety of urinary tract disorders.
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Affiliation(s)
- Cara Joyce
- Dept. of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Thomas Halverson
- Dept. of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Caroline Gonzalez
- Dept. of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Linda Brubaker
- Dept. of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, CA, United States
| | - Alan J. Wolfe
- Dept. of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States,*Correspondence: Alan J. Wolfe,
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Storm DW, Copp HL, Halverson TM, Du J, Juhr D, Wolfe AJ. A Child's urine is not sterile: A pilot study evaluating the Pediatric Urinary Microbiome. J Pediatr Urol 2022; 18:383-392. [PMID: 35337731 DOI: 10.1016/j.jpurol.2022.02.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/03/2022] [Accepted: 02/24/2022] [Indexed: 10/18/2022]
Abstract
INTRODUCTION A bladder microbiome (urobiome) exists in adults. Data supports the effects of the adult urobiome on urinary tract health with associations between dysbiotic urobiomes and lower urinary tract disorders. Understanding urobiome origin is important since other microbiomes establish around birth and microbiome alterations are linked to disease development. However, the pediatric urobiome has not been well studied. OBJECTIVES We sought to determine the age when the urobiome develops, compare the pediatric urobiome to microbiomes of adjacent urogenital niches, and compare the urobiomes between boys and girls and across age groups. STUDY DESIGN Seventy-four children less than 18 years of age without recent antibiotic exposure were recruited, including 48 males and 26 females, aged 2 weeks to 209 months of age. Transurethral catheterized urine samples and samples from the perineum, urethra, vagina, and foreskin were collected. Specimens were assessed using the expanded quantitative urine culture protocol and by 16S rRNA gene sequencing. Dada2 was used to profile microbial compositions, and BLCA was used to identify microbial taxa. RESULTS Bacteria were detected in 90.5% of urine samples and identified in children as young as 2 weeks of age. Microbial communities and compositions of the female bladder and other urogenital niches (urethra, perineum, and vagina) differed significantly by age. Lactobacillus predominated the bladder, urethral, and vaginal microbiomes in post-pubertal girls. Compared to female urinary microbiomes, those of males differed less substantially. Only perineal microbiomes differed significantly by age, whereas male urethral and foreskin microbiomes did not differ significantly. DISCUSSION We identified that a urinary microbiome is established as early as infancy. In addition, the female urobiome changes throughout childhood, until the post-pubertal bacterial taxa becomes consistent with that seen in adult females. Whereas in boys, the urinary microbiome changed very little over time. In addition, the surrounding urogenital microbiomes differed less in boys as compared to females. Microbiomes established at a young age may have long-term influences on immune, metabolic, and neurobehavioral traits. The same may be true for the urobiome. Our study provides a foundation for future research to determine the influence of the pediatric urobiome on the development of urinary and even non-urinary disorders. CONCLUSIONS A pediatric urobiome exists, with differences between males and females and can be detected at a young age with changes occurring throughout childhood. Similarities and differences are also seen between the pediatric urobiome and adjacent niches.
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Affiliation(s)
- Douglas W Storm
- Department of Urology, University of Iowa, 200 Hawkins Dr., 3RCP, Iowa City, IA, 52242, USA.
| | - Hillary L Copp
- Department of Urology, University of California San Francisco Medical Center, 400 Parnassus Ave., San Francisco, CA, 94143, USA.
| | - Thomas M Halverson
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University, 2160 1st Ave., Maywood, IL, 60153, USA
| | - Jingjie Du
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University, 2160 1st Ave., Maywood, IL, 60153, USA.
| | - Denise Juhr
- Department of Urology, University of Iowa, 200 Hawkins Dr., 3RCP, Iowa City, IA, 52242, USA.
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University, 2160 1st Ave., Maywood, IL, 60153, USA.
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Hiyama Y. Editorial Comment to Proactive discontinuation of postoperative antibiotic prophylaxis after urethroplasty. Int J Urol 2022; 29:711-712. [PMID: 35477930 DOI: 10.1111/iju.14909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoshiki Hiyama
- Department of Urology, NTT East Medical Center Sapporo, Sapporo, Hokkaido, Japan
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The Urobiome and Its Role in Overactive Bladder. Int Neurourol J 2022; 26:190-200. [PMID: 35468617 PMCID: PMC9537439 DOI: 10.5213/inj.2244016.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/25/2022] [Indexed: 12/04/2022] Open
Abstract
Urine is no longer considered to be sterile. After the existence of the microbiome was revealed through metagenomic analysis using next-generation sequencing, the relationship between characteristics of the microbiome and diseases have been studied and published in various journals. A microbiome exists in the urinary tract and is associated with urinary tract infection, malignancy of the genitourinary tract, and lower urinary tract symptoms. Based on the urine sampling method, sampling site, culture method, and sex, the characteristics of the microbiome vary. Most of the Lactobacillus species are identified mainly in women, and various other species are identified in men. These microorganisms can cause or prevent various diseases. Variations in the microbiome are seen in those with and without disease, and an asymptomatic status does not indicate the absence of microbes. This microbiome has been implicated in a variety of lower urinary tract symptoms and diseases, in particular, overactive bladder. The microbiome differs between patients with urgency and urge urinary incontinence and healthy individuals. There are many aspects of the microbiome yet to be studied in relation to other lower urinary tract symptoms.
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Roth M, Jaquet V, Lemeille S, Bonetti EJ, Cambet Y, François P, Krause KH. Transcriptomic Analysis of E. coli after Exposure to a Sublethal Concentration of Hydrogen Peroxide Revealed a Coordinated Up-Regulation of the Cysteine Biosynthesis Pathway. Antioxidants (Basel) 2022; 11:antiox11040655. [PMID: 35453340 PMCID: PMC9026346 DOI: 10.3390/antiox11040655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022] Open
Abstract
Hydrogen peroxide (H2O2) is a key defense component of host-microbe interaction. However, H2O2 concentrations generated by immune cells or epithelia are usually insufficient for bacterial killing and rather modulate bacterial responses. Here, we investigated the impact of sublethal H2O2 concentration on gene expression of E. coli BW25113 after 10 and 60 min of exposure. RNA-seq analysis revealed that approximately 12% of bacterial genes were strongly dysregulated 10 min following exposure to 2.5 mM H2O2. H2O2 exposure led to the activation of a specific antioxidant response and a general stress response. The latter was characterized by a transient down-regulation of genes involved in general metabolism, such as nucleic acid biosynthesis and translation, with a striking and coordinated down-regulation of genes involved in ribosome formation, and a sustained up-regulation of the SOS response. We confirmed the rapid transient and specific response mediated by the transcription factor OxyR leading to up-regulation of antioxidant systems, including the catalase-encoding gene (katG), that rapidly degrade extracellular H2O2 and promote bacterial survival. We documented a strong and transient up-regulation of genes involved in sulfur metabolism and cysteine biosynthesis, which are under the control of the transcription factor CysB. This strong specific transcriptional response to H2O2 exposure had no apparent impact on bacterial survival, but possibly replenishes the stores of oxidized cysteine and glutathione. In summary, our results demonstrate that different stress response mechanisms are activated by H2O2 exposure and highlight the cysteine synthesis as an antioxidant response in E. coli.
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Affiliation(s)
- Myriam Roth
- Department of Pathology and Immunology, Medical School, University of Geneva, 1211 Geneva, Switzerland; (V.J.); (S.L.); (K.-H.K.)
- Correspondence: ; Tel.: +41-223-794-257
| | - Vincent Jaquet
- Department of Pathology and Immunology, Medical School, University of Geneva, 1211 Geneva, Switzerland; (V.J.); (S.L.); (K.-H.K.)
- REaders, Assay Development & Screening Unit (READS Unit), Faculty of Medecine, University of Geneva, 1211 Geneva, Switzerland;
| | - Sylvain Lemeille
- Department of Pathology and Immunology, Medical School, University of Geneva, 1211 Geneva, Switzerland; (V.J.); (S.L.); (K.-H.K.)
| | - Eve-Julie Bonetti
- Genomic Research Laboratory, Infectious Diseases Service, University Hospitals Geneva Medical Center, Michel-Servet 1, 1211 Geneva, Switzerland; (E.-J.B.); (P.F.)
| | - Yves Cambet
- REaders, Assay Development & Screening Unit (READS Unit), Faculty of Medecine, University of Geneva, 1211 Geneva, Switzerland;
| | - Patrice François
- Genomic Research Laboratory, Infectious Diseases Service, University Hospitals Geneva Medical Center, Michel-Servet 1, 1211 Geneva, Switzerland; (E.-J.B.); (P.F.)
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Medical School, University of Geneva, 1211 Geneva, Switzerland; (V.J.); (S.L.); (K.-H.K.)
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Giannattasio-Ferraz S, Ene A, Gomes VJ, Queiroz CO, Maskeri L, Oliveira AP, Putonti C, Barbosa-Stancioli EF. Escherichia coli and Pseudomonas aeruginosa Isolated From Urine of Healthy Bovine Have Potential as Emerging Human and Bovine Pathogens. Front Microbiol 2022; 13:764760. [PMID: 35330764 PMCID: PMC8940275 DOI: 10.3389/fmicb.2022.764760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The study of livestock microbiota has immediate benefits for animal health as well as mitigating food contamination and emerging pathogens. While prior research has indicated the gastrointestinal tract of cattle as the source for many zoonoses, including Shiga-toxin producing Escherichia coli and antibiotic resistant bacteria, the bovine urinary tract microbiota has yet to be thoroughly investigated. Here, we describe 5 E. coli and 4 Pseudomonas aeruginosa strains isolated from urine of dairy Gyr cattle. While both species are typically associated with urinary tract infections and mastitis, all of the animals sampled were healthy. The bovine urinary strains were compared to E. coli and P. aeruginosa isolates from other bovine samples as well as human urinary samples. While the bovine urinary E. coli isolates had genomic similarity to isolates from the gastrointestinal tract of cattle and other agricultural animals, the bovine urinary P. aeruginosa strains were most similar to human isolates suggesting niche adaptation rather than host adaptation. Examination of prophages harbored by these bovine isolates revealed similarity with prophages within distantly related E. coli and P. aeruginosa isolates from the human urinary tract. This suggests that related urinary phages may persist and/or be shared between mammals. Future studies of the bovine urinary microbiota are needed to ascertain if E. coli and P. aeruginosa are resident members of this niche and/or possible sources for emerging pathogens in humans.
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Affiliation(s)
- Silvia Giannattasio-Ferraz
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Vitor Júnio Gomes
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Cid Oliveira Queiroz
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Laura Maskeri
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | | | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Edel F. Barbosa-Stancioli
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Abstract
Regular health monitoring can result in early detection of disease, accelerate the delivery of medical care and, therefore, considerably improve patient outcomes for countless medical conditions that affect public health. A substantial unmet need remains for technologies that can transform the status quo of reactive health care to preventive, evidence-based, person-centred care. With this goal in mind, platforms that can be easily integrated into people's daily lives and identify a range of biomarkers for health and disease are desirable. However, urine - a biological fluid that is produced in large volumes every day and can be obtained with zero pain, without affecting the daily routine of individuals, and has the most biologically rich content - is discarded into sewers on a regular basis without being processed or monitored. Toilet-based health-monitoring tools in the form of smart toilets could offer preventive home-based continuous health monitoring for early diagnosis of diseases while being connected to data servers (using the Internet of Things) to enable collection of the health status of users. In addition, machine learning methods can assist clinicians to classify, quantify and interpret collected data more rapidly and accurately than they were able to previously. Meanwhile, challenges associated with user acceptance, privacy and test frequency optimization should be considered to facilitate the acceptance of smart toilets in society.
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Affiliation(s)
- Savas Tasoglu
- Department of Mechanical Engineering, Koc University, Istanbul, Turkey. .,Koç University Translational Medicine Research Center (KUTTAM), Koç University, Sarıyer, Istanbul, Turkey. .,Boğaziçi Institute of Biomedical Engineering, Boğaziçi University, Çengelköy, Istanbul, Turkey. .,Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart, Germany.
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Schiereck T, Yeldan S, Kranz J, Schneidewind L, Wagenlehner F, Wieters I, Vehreschild MJGT, Otto T, Barski D. [Urinary bladder microbiome analysis and probiotic treatment options for women with recurrent urinary tract infections]. Urologe A 2022; 61:41-51. [PMID: 34424357 PMCID: PMC8381347 DOI: 10.1007/s00120-021-01621-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2021] [Indexed: 11/29/2022]
Abstract
Novel preventive measures and therapeutic approaches are needed to reduce the frequency of recurrent urinary tract infections (rUTI) and the associated emergence of multidrug-resistant uropathogens. The aim of this review is to systematically present the available evidence on the urinary bladder microbiome of healthy women and those with rUTIs. In addition, relevant studies on the efficacy of probiotics in rUTIs are presented in a structured manner. This will provide an overview on the current state of research and an outlook on treatment strategies beyond the usual antimicrobial options.
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Affiliation(s)
- T Schiereck
- Urologische Klinik, Lukaskrankenhaus Neuss, Rheinland Klinikum, Preussenstr. 84, 41464, Neuss, Deutschland.
| | - S Yeldan
- Urologische Klinik, Lukaskrankenhaus Neuss, Rheinland Klinikum, Preussenstr. 84, 41464, Neuss, Deutschland
| | - J Kranz
- Klinik für Urologie und Kinderurologie, St.-Antonius-Hospital Eschweiler, Akademisches Lehrkrankenhaus der RWTH Aachen, Eschweiler, Deutschland
- Universitätsklinik und Poliklinik für Urologie, Universitätsklinikum Halle (Saale), Halle (Saale), Deutschland
| | - L Schneidewind
- Urologische Klinik und Poliklinik, Universitätsmedizin Rostock, Ernst-Heydemann-Str. 6, 18055, Rostock, Deutschland
| | - F Wagenlehner
- Klinik für Urologie, Kinderurologie und Andrologie, Universitätsklinikum Gießen, Gießen, Deutschland
| | - I Wieters
- Zentrum für Innere Medizin, Infektiologie, Universitätsklinikum Frankfurt, Goethe Universität Frankfurt, Frankfurt am Main, Deutschland
| | - M J G T Vehreschild
- Zentrum für Innere Medizin, Infektiologie, Universitätsklinikum Frankfurt, Goethe Universität Frankfurt, Frankfurt am Main, Deutschland
| | - T Otto
- Urologische Klinik, Lukaskrankenhaus Neuss, Rheinland Klinikum, Preussenstr. 84, 41464, Neuss, Deutschland
- Universität Duisburg-Essen, Essen, Deutschland
| | - D Barski
- Urologische Klinik, Lukaskrankenhaus Neuss, Rheinland Klinikum, Preussenstr. 84, 41464, Neuss, Deutschland
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39
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The urobiome, urinary tract infections, and the need for alternative therapeutics. Microb Pathog 2021; 161:105295. [PMID: 34801647 DOI: 10.1016/j.micpath.2021.105295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/26/2021] [Accepted: 11/15/2021] [Indexed: 12/16/2022]
Abstract
Improvements in bacterial culturing and DNA sequencing techniques have revealed a diverse, and hitherto unknown, urinary tract microbiome (urobiome). The potential role of this microbial community in contributing to health and disease, particularly in the context of urinary tract infections (UTIs) is of significant clinical importance. However, while several studies have confirmed the existence of a core urobiome, the role of its constituent microbes is not yet fully understood, particularly in the context of health and disease. Herein, we review the current state of the art, concluding that the urobiome represents an important component of the body's innate immune defences, and a potentially rich resource for the development of alternative treatment and control strategies for UTIs.
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40
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Jayalath S, Magana-Arachchi D. Dysbiosis of the Human Urinary Microbiome and its Association to Diseases Affecting the Urinary System. Indian J Microbiol 2021; 62:153-166. [DOI: 10.1007/s12088-021-00991-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/02/2021] [Indexed: 12/15/2022] Open
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41
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Huang X, Pan T, Yan L, Jin T, Zhang R, Chen B, Feng J, Duan T, Xiang Y, Zhang M, Chen X, Yang Z, Zhang W, Ding X, Xie T, Sui X. The inflammatory microenvironment and the urinary microbiome in the initiation and progression of bladder cancer. Genes Dis 2021; 8:781-797. [PMID: 34522708 PMCID: PMC8427242 DOI: 10.1016/j.gendis.2020.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/24/2022] Open
Abstract
Accumulating evidence suggests that chronic inflammation may play a critical role in various malignancies, including bladder cancer. This hypothesis stems in part from inflammatory cells observed in the urethral microenvironment. Chronic inflammation may drive neoplastic transformation and the progression of bladder cancer by activating a series of inflammatory molecules and signals. Recently, it has been shown that the microbiome also plays an important role in the development and progression of bladder cancer, which can be mediated through the stimulation of chronic inflammation. In effect, the urinary microbiome can play a role in establishing the inflammatory urethral microenvironment that may facilitate the development and progression of bladder cancer. In other words, chronic inflammation caused by the urinary microbiome may promote the initiation and progression of bladder cancer. Here, we provide a detailed and comprehensive account of the link between chronic inflammation, the microbiome and bladder cancer. Finally, we highlight that targeting the urinary microbiome might enable the development of strategies for bladder cancer prevention and personalized treatment.
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Affiliation(s)
- Xingxing Huang
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Ting Pan
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Lili Yan
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Ting Jin
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Ruonan Zhang
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Bi Chen
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Jiao Feng
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Ting Duan
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Yu Xiang
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Mingming Zhang
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Xiaying Chen
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Zuyi Yang
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Wenzheng Zhang
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Xia Ding
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, PR China
| | - Tian Xie
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
| | - Xinbing Sui
- Department of Medical Oncology, the Affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 310015, PR China
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang Province, 311121, PR China
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, PR China
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42
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Hoffman C, Siddiqui NY, Fields I, Gregory WT, Simon HM, Mooney MA, Wolfe AJ, Karstens L. Species-Level Resolution of Female Bladder Microbiota from 16S rRNA Amplicon Sequencing. mSystems 2021; 6:e0051821. [PMID: 34519534 PMCID: PMC8547459 DOI: 10.1128/msystems.00518-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/18/2021] [Indexed: 01/04/2023] Open
Abstract
The human bladder contains bacteria, even in the absence of infection. Interest in studying these bacteria and their association with bladder conditions is increasing. However, the chosen experimental method can limit the resolution of the taxonomy that can be assigned to the bacteria found in the bladder. 16S rRNA amplicon sequencing is commonly used to identify bacteria in urinary specimens, but it is typically restricted to genus-level identification. Our primary aim here was to determine if accurate species-level identification of bladder bacteria is possible using 16S rRNA amplicon sequencing. We evaluated the ability of different classification schemes, each consisting of combinations of a reference database, a 16S rRNA gene variable region, and a taxonomic classification algorithm to correctly classify bladder bacteria. We show that species-level identification is possible and that the reference database chosen is the most important component, followed by the 16S variable region sequenced. IMPORTANCE Accurate species-level identification from culture-independent techniques is of importance for microbial niches that are less well characterized, such as that of the bladder. 16S rRNA amplicon sequencing, a common culture-independent way to identify bacteria, is often critiqued for lacking species-level resolution. Here, we extensively evaluate classification schemes for species-level bacterial annotation of 16S amplicon data from bladder bacteria. Our results show that the proper choice of taxonomic database and variable region of the 16S rRNA gene sequence makes species level identification possible. We also show that this improvement can be achieved through the more careful application of existing methods and resources. Species-level information may deepen our understanding of associations between bacteria in the bladder and bladder conditions such as lower urinary tract symptoms and urinary tract infections.
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Affiliation(s)
- Carter Hoffman
- Division of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
| | - Nazema Y. Siddiqui
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Obstetrics and Gynecology, Duke University, Durham, North Carolina, USA
| | - Ian Fields
- Division of Urogynecology, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
| | - W. Thomas Gregory
- Division of Urogynecology, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
| | | | - Michael A. Mooney
- Division of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
| | - Alan J. Wolfe
- Department of Microbiology & Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Lisa Karstens
- Division of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA
- Division of Urogynecology, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
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Xiao X, Sun H, Liu X, Guo Z, Zheng S, Xu J, Sun J, Lan Y, Shao C, Sun W. Qualitative and quantitative proteomic and metaproteomic analyses of healthy human urine sediment. Proteomics Clin Appl 2021; 16:e2100007. [PMID: 34687263 DOI: 10.1002/prca.202100007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 09/30/2021] [Accepted: 10/17/2021] [Indexed: 11/07/2022]
Abstract
PURPOSE The healthy human urine sediment proteome and metaproteome are investigated, to shed light on the variations of urine sediment proteins and metaproteins associated with sex and age. EXPERIMENTAL DESIGN Urine sediment samples are collected from 19 healthy subjects. Protein identification and quantification are performed by liquid chromatography coupled high-resolution mass spectrometry. RESULTS A total of 2736 human proteins were identified, which were primarily associated with inflammatory response and energy metabolism. For the metaproteome, 65 genera were identified that were primarily involved in translation and carbohydrate metabolic processes. The median biological coefficient variation of the proteome/metaproteome of human urine sediment was 0.5/0.72, similar to the proteome of human urine supernatant. In addition, sex and age were observed to affect the proteome and metaproteome of healthy human urine sediment. CONCLUSION AND CLINICAL RELEVANCE The healthy human urine sediment were characterized, indicating that urine sediment might represent an alternative resource for disease research in addition to urine supernatant, but the influence of sex and age must be considered in the study design process.
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Affiliation(s)
- XiaoLian Xiao
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Haidan Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyan Liu
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhengguang Guo
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuxin Zheng
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiyu Xu
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiameng Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Lan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chen Shao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Wei Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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Abstract
The introduction of next generation sequencing techniques has enabled the characterization of the urinary tract microbiome, which resulted in the rejection of the long-held notion of urinary bladder sterility. Since the discovery and confirmation of the human bladder microbiome, an increasing number of studies have defined this microbial community and understand better its relationship to urinary pathologies. The composition of microbial communities in the urinary tract is linked to a variety of urinary diseases. The purpose of this review is to provide an overview of current information about the urinary microbiome and diseases as well as the development of novel treatment methods.
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45
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Brown SE, Robinson CK, Shardell MD, Holm JB, Ravel J, Ghanem KG, Brotman RM. Assessing the Concordance Between Urogenital and Vaginal Microbiota: Can Urine Specimens Be Used as a Proxy for Vaginal Samples? Front Cell Infect Microbiol 2021; 11:671413. [PMID: 34268137 PMCID: PMC8276069 DOI: 10.3389/fcimb.2021.671413] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/28/2021] [Indexed: 01/04/2023] Open
Abstract
Background The vaginal microbiota play a key role in defense against reproductive tract infections; however, many population-based women's health studies do not collect vaginal samples. Molecular examinations of urine samples have revealed common vaginal bacteria. We sought to assess the extent that community state type assignments of archived random-catch and clean-catch urine samples agreed with the paired vaginal samples in both reproductive-age and peri/post-menopausal women. Results Using archived samples, we evaluated the microbiota concordance among women in three studies: two with paired mid-vaginal/random-catch urine (N=91 reproductive-age participants and N=13 peri/post-menopausal participants), and one with paired mid-vaginal/clean-catch urine (N=99 reproductive-age participants). Microbiota composition was characterized by sequencing amplicons of the 16S rRNA gene V3-V4 regions and assigned to community state types. Similarity of paired samples was gauged using agreement of community state types and Yue-Clayton θ indices. Analysis of Composition of Microbiomes II indicated which taxa were differently relatively abundant in paired vaginal and urine samples. In reproductive-age women, random-catch and clean-catch urines were 89.0% and 86.9% concordant on five community state types with paired mid-vaginal swabs, and Kappa statistics indicated almost perfect agreement (κrandom-catch=.85, κclean-catch=.81, p<0.0001). A small number of pairs of samples were discordant (23/190, 12%), and discordant pairs tended to be between samples classified to L. iners-dominated and/or low-Lactobacillus states. Concordance and agreement remained similar when dichotomizing the microbiota to Lactobacillus-dominated versus low-Lactobacillus microbiota, as well as when evaluating separately the three subtypes of the low-Lactobacillus community state type IV. Median similarity of paired urine/vaginal samples was high (θrandom-catch=.85, θclean-catch=.88), and a comparison of the random-catch and clean-catch similarity scores showed no significant difference (p=.80). Concordance and similarity were lower for peri/post-menopausal women, but agreement remained substantial (76.9% concordant, κrandom-catch= 0.64, θrandom-catch=.62). Taxonomic-level analysis confirmed these findings. Conclusions Random-catch and clean-catch urine samples showed substantial agreement on bacterial composition to paired mid-vaginal samples, indicating that the genitourinary microbiota may be a reliable proxy for assessing the overall composition of the vaginal microbiota via community state types. This data suggests that urine samples can, with proper interpretation, be utilized as a surrogate for developing preliminary data and hypothesis-generating studies.
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Affiliation(s)
- Sarah E. Brown
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Courtney K. Robinson
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Michelle D. Shardell
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Johanna B. Holm
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Khalil G. Ghanem
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rebecca M. Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, United States,*Correspondence: Rebecca M. Brotman,
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46
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Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection. Female Pelvic Med Reconstr Surg 2021; 28:20-26. [PMID: 33978602 DOI: 10.1097/spv.0000000000001051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The aim of this study was to describe effects of vaginal estrogen (VE) on the urogenital microbiome in postmenopausal women with recurrent urinary tract infections (rUTIs). METHODS This is a secondary analysis of 17 participants enrolled in a randomized controlled trial of VE versus placebo on urinary tract infection recurrence in postmenopausal women with rUTIs. Paired clean-catch urine samples were collected at baseline and after 6 months of VE and sequenced using 16S rRNA gene sequencing. Sequence reads were analyzed using Quantitative Insights Into Microbial Ecology 2. Changes in α diversity, β diversity, and differentially abundant genera were measured between paired baseline and 6-month samples and between those with a urinary tract infection at 6 months (failures) and those without (successes). RESULTS Of the 17 women, 11 were successes and 6 were failures after 6 months of VE treatment. There was a significant change in α diversity from baseline to month 6 in samples overall (Kruskal-Wallis χ2 = 3.47, P = 0.037) and in the treatment success group (Yuen T = -2.53, P = 0.035). The increase in relative abundance of Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus iners AB-1 was correlated with month 6. A relative bloom of L. crispatus compared with L. gasseri was associated with treatment success (Kruskal-Wallis χ2 = 4.9, P = 0.0014). CONCLUSIONS Lactobacillus increases in the urogenital microbiome of postmenopausal women with rUTI after 6 months of VE. However, only the relative increase in L. crispatus specifically may be associated with treatment success.
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Perez-Carrasco V, Soriano-Lerma A, Soriano M, Gutiérrez-Fernández J, Garcia-Salcedo JA. Urinary Microbiome: Yin and Yang of the Urinary Tract. Front Cell Infect Microbiol 2021; 11:617002. [PMID: 34084752 PMCID: PMC8167034 DOI: 10.3389/fcimb.2021.617002] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
The application of next generation sequencing techniques has allowed the characterization of the urinary tract microbiome and has led to the rejection of the pre-established concept of sterility in the urinary bladder. Not only have microbial communities in the urinary tract been implicated in the maintenance of health but alterations in their composition have also been associated with different urinary pathologies, such as urinary tract infections (UTI). Therefore, the study of the urinary microbiome in healthy individuals, as well as its involvement in disease through the proliferation of opportunistic pathogens, could open a potential field of study, leading to new insights into prevention, diagnosis and treatment strategies for urinary pathologies. In this review we present an overview of the current state of knowledge about the urinary microbiome in health and disease, as well as its involvement in the development of new therapeutic strategies.
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Affiliation(s)
- Virginia Perez-Carrasco
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Granada, Spain.,Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute (IBS.Granada), Granada, Spain
| | - Ana Soriano-Lerma
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Granada, Spain.,Department of Physiology, Faculty of Pharmacy, Institute of Nutrition and Food Technology "Jose' Mataix", University of Granada, Granada, Spain
| | - Miguel Soriano
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Granada, Spain.,Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAMBITAL), University of Almeria, Almeria, Spain
| | - José Gutiérrez-Fernández
- Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute (IBS.Granada), Granada, Spain
| | - Jose A Garcia-Salcedo
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Granada, Spain.,Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute (IBS.Granada), Granada, Spain
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48
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Zandbergen LE, Halverson T, Brons JK, Wolfe AJ, de Vos MGJ. The Good and the Bad: Ecological Interaction Measurements Between the Urinary Microbiota and Uropathogens. Front Microbiol 2021; 12:659450. [PMID: 34040594 PMCID: PMC8141646 DOI: 10.3389/fmicb.2021.659450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/09/2021] [Indexed: 01/16/2023] Open
Abstract
The human body harbors numerous populations of microorganisms in various ecological niches. Some of these microbial niches, such as the human gut and the respiratory system, are well studied. One system that has been understudied is the urinary tract, primarily because it has been considered sterile in the absence of infection. Thanks to modern sequencing and enhanced culture techniques, it is now known that a urinary microbiota exists. The implication is that these species live as communities in the urinary tract, forming microbial ecosystems. However, the interactions between species in such an ecosystem remains unknown. Various studies in different parts of the human body have highlighted the ability of the pre-existing microbiota to alter the course of infection by impacting the pathogenicity of bacteria either directly or indirectly. For the urinary tract, the effect of the resident microbiota on uropathogens and the phenotypic microbial interactions is largely unknown. No studies have yet measured the response of uropathogens to the resident urinary bacteria. In this study, we investigate the interactions between uropathogens, isolated from elderly individuals suffering from UTIs, and bacteria isolated from the urinary tract of asymptomatic individuals using growth measurements in conditioned media. We observed that bacteria isolated from individuals with UTI-like symptoms and bacteria isolated from asymptomatic individuals can affect each other's growth; for example, bacteria isolated from symptomatic individuals affect the growth of bacteria isolated from asymptomatic individuals more negatively than vice versa. Additionally, we show that Gram-positive bacteria alter the growth characteristics differently compared to Gram-negative bacteria. Our results are an early step in elucidating the role of microbial interactions in urinary microbial ecosystems that harbor both uropathogens and pre-existing microbiota.
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Affiliation(s)
- Laurens E. Zandbergen
- Microbial Eco-Evolutionary Medicine Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Thomas Halverson
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, United States
| | - Jolanda K. Brons
- Microbial Eco-Evolutionary Medicine Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, United States
| | - Marjon G. J. de Vos
- Microbial Eco-Evolutionary Medicine Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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Tarabal VS, Silva FG, Sinisterra RD, Gonçalves D, Silva J, Granjeiro JM, Speziali M, Granjeiro PA. Impact of DMPEI on Biofilm Adhesion on Latex Urinary Catheter. Recent Pat Biotechnol 2021; 15:51-66. [PMID: 33588743 DOI: 10.2174/1872208315666210215084127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/25/2020] [Accepted: 12/31/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Microorganisms can migrate from the external environment to the patient's organism through the insertion of catheters. Despite being indispensable medical device, the catheter surface can be colonized by microorganisms and become a starting point for biofilm formation. Therefore, new technologies are being developed in order to modify surfaces to prevent the adhesion and survival of microorganisms. Patents with the use of DMPEI have been filed. OBJECTIVE In the present work, we coated latex catheter surfaces with 2 mg mL-1 DMPEI in different solvents, evaluated the wettability of the surface and the anti- biofilm activity of the coated catheter against Escherichia coli, Staphylococcus aureus, and Candida albicans. METHODS We coated the inner and outer catheter surfaces with 2 mg mL-1 of DMPEI solubilized in butanol, dimethylformamide, and cyclohexanone and the surfaces were analyzed visually. Contact angle measurement allowed the analysis of the wettability of the surfaces. The CFU mL-1 count evaluated E. coli, S. aureus, and C. albicans adhesion onto the control and treated surfaces. RESULTS The contact angle decreased from 50.48º to 46.93º on the inner surface and from 55.83º to 50.91º on the outer surface of latex catheters coated with DMPEI. The catheter coated with DMPEI showed anti-biofilm activity of 83%, 88%, and 93% on the inner surface and 100%, 92%, and 86% on the outer surface for E. coli, S. aureus, and C. albicans, respectively. CONCLUSION Latex catheter coated with DMPEI efficiently impaired the biofilm formation both on the outer and inner surfaces, showing a potential antimicrobial activity along with a high anti-biofilm activity for medical devices.
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Affiliation(s)
- Vinícius S Tarabal
- Campus Centro-Oeste, Federal University of São João del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Flávia G Silva
- Chemistry Department, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ruben D Sinisterra
- Chemistry Department, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Daniel Gonçalves
- Campus Centro-Oeste, Federal University of São João del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Jose Silva
- Campus Centro-Oeste, Federal University of São João del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Jose M Granjeiro
- National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
| | - Marcelo Speziali
- Chemistry Department, Federal University of Ouro Preto, Minas Gerais, Brazil
| | - Paulo A Granjeiro
- Campus Centro-Oeste, Federal University of São João del-Rei, Divinópolis, Minas Gerais, Brazil
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50
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Brubaker L, Putonti C, Dong Q, Wolfe AJ. The human urobiome. Mamm Genome 2021; 32:232-238. [PMID: 33651197 DOI: 10.1007/s00335-021-09862-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/16/2021] [Indexed: 01/01/2023]
Abstract
Traditionally, the healthy urinary bladder has been considered to be sterile. Several teams have used metagenomic (DNA-dependent) and metaculturomic (culture-dependent) methods to debunk this longstanding dogma. In fact, resident microbial communities (urobiome) have been detected in both adult females and males. Although the field is young, several observations have been made. For example, the urobiome differs between men and women, likely due to anatomical and hormonal differences. Importantly, the urobiome has been associated with a variety of lower urinary tract disorders, including overactive bladder and post-operative urinary tract infection, raising the possibility that clinicians might one day treat symptoms by modifying the urobiome instead of killing the suspected uropathogen. Little is known concerning the relationship between the urobiome and host genetics; so far, only a single paper has reported such a study. However, major efforts have gone into understanding the genomics of the urobiome itself, a process facilitated by the fact that many urobiome studies have used metaculturomic methods to detect and identify microbes. In this narrative review, we will introduce the urobiome with separate sections on the female and male urobiomes, discuss challenges specific to the urobiome, describe newly discovered associations between the urobiome and lower urinary tract symptoms, and highlight the one study that has attempted to relate host genetics and the urobiome. We will finish with a section on how metagenomic surveys and whole genome sequencing of bacterial isolates are improving our understanding of the urobiome and its relationship to lower urinary tract health and disorders.
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Affiliation(s)
- L Brubaker
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - C Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Q Dong
- Department of Medicine and Center for Biomedical Informatics, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - A J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60089, USA.
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