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Jeries LM, Sysoeva TA, Karstens L, Kelly MS. Synthesis of current pediatric urinary microbiome research. Front Pediatr 2024; 12:1396408. [PMID: 38957777 PMCID: PMC11217333 DOI: 10.3389/fped.2024.1396408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/29/2024] [Indexed: 07/04/2024] Open
Abstract
The human urinary bladder hosts a complex microbial community of low biomass referred to as the urobiome. While the composition of the urobiome has been investigated in adults for over a decade now, only a few studies have considered the presence and composition of the urobiome in children. It is critical to explore how the urobiome develops throughout the life span and how it changes in the presence of various health conditions. Therefore, we set to review the available data on pediatric urobiome composition and its development with age and disease. In addition, we focused on identifying and reporting specific gaps in our knowledge of the pediatric urobiome that we hope will be addressed by future studies in this swiftly developing field with fast-improving methods and consensus.
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Affiliation(s)
- Layla M. Jeries
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, United States
| | - Tatyana A. Sysoeva
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, United States
| | - Lisa Karstens
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, United States
| | - Maryellen S. Kelly
- Division of Healthcare of Women and Children, School of Nursing, Duke University, Durham, NC, United States
- Department of Urology, Duke University Hospital, Durham, NC, United States
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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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Jia K, Huang S, Shen C, Li H, Zhang Z, Wang L, Zhao G, Wu Z, Lin Y, Xia H, Tang M, Yang H, Hu H. Enhancing urinary tract infection diagnosis for negative culture patients with metagenomic next-generation sequencing (mNGS). Front Cell Infect Microbiol 2023; 13:1119020. [PMID: 36936777 PMCID: PMC10020507 DOI: 10.3389/fcimb.2023.1119020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a promising technology that allows unbiased pathogen detection and is increasingly being used for clinical diagnoses. However, its application in urinary tract infection (UTI) is still scarce. Methods The medical records of 33 patients with suspected UTI who were admitted to the Second Hospital of Tianjin Medical University from March 2021 to July 2022 and received urine mNGS were retrospectively analyzed. The performance of mNGS and conventional urine culture in diagnosing infection and identifying causative organisms was compared, and the treatment effects were evaluated in terms of changes in urinalyses and urinary symptoms. Results In the detection of bacteria and fungi, mNGS detected at least one pathogen in 29 (87.9%) cases, including 19 (57.6%) with positive mNGS but negative culture results and 10 (30.3%) with both mNGS and culture positive results. The remaining 4 (12.1%) patients were negative by both tests. Overall, mNGS performed better than culture (87.9% vs. 30.3%, P < 0.001). Within the 10 double-positive patients, mNGS matched culture results exactly in 5 cases, partially in 4 cases, and not at all in 1 case. In addition, mNGS detected a broader pathogen spectrum, detecting 26 species compared to only 5 species found in culture. The most abundant bacteria detected by mNGS was Escherichia coli, detected in 9 (27.2%) patients. All anaerobic bacteria, Mycobacterium Tuberculosis and all mixed pathogens were detected by mNGS. The final clinical diagnosis of UTI was made in 25 cases, and the sensitivity of mNGS was significantly higher than culture (100.0% vs 40.0%; P < 0.001) when using the diagnosis as a reference standard; the positive predictive value, negative predictive value and specificity were 86.2%, 100% and 50.0%, respectively. Importantly, targeted antibiotic therapy based on mNGS resulted in significant improvement in urinalyses and urinary symptoms in patients. Conclusions mNGS is a technology that has shown clear advantages over culture, particularly in the context of mixed infections and UTIs that are difficult to diagnose and treat. It helps to improve the detection of pathogens, guide changes in treatment strategies, and is an effective complement to urine culture.
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Affiliation(s)
- Kaipeng Jia
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Shiwang Huang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Chong Shen
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Hongjun Li
- Department of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhe Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Lei Wang
- Department of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Gangjian Zhao
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhouliang Wu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yuda Lin
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Mingze Tang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Huifen Yang
- Department of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
- *Correspondence: Huifen Yang, ; Hailong Hu,
| | - Hailong Hu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- *Correspondence: Huifen Yang, ; Hailong Hu,
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Characterization of the Urinary Metagenome and Virome in Healthy Children. Biomedicines 2022; 10:biomedicines10102412. [PMID: 36289674 PMCID: PMC9599034 DOI: 10.3390/biomedicines10102412] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022] Open
Abstract
Recent advances in next-generation sequencing and metagenomic studies have provided insights into the microbial profile of different body sites. However, research on the microbial composition of urine is limited, particularly in children. The goal of this study was to optimize and develop reproducible metagenome and virome protocols using a small volume of urine samples collected from healthy children. We collected midstream urine specimens from 40 healthy children. Using the metagenomics shotgun approach, we tested various protocols. Different microbial roots such as Archaea, Bacteria, Eukaryota, and Viruses were successfully identified using our optimized urine protocol. Our data reflected much variation in the microbial fingerprints of children. Girls had significantly higher levels of Firmicutes, whereas boys had significantly higher levels of Actinobacteria. The genus Anaerococcus dominated the urinary bacteriome of healthy girls, with a significant increase in Anaerococcus prevotii, Anaerococcus vaginalis, and Veillonella parvula (p-value < 0.001) when compared with that of boys. An increased relative abundance of Xylanimonas and Arthrobacter, with a significantly high abundance of Arthrobacter sp. FB24 (p-value 0.0028) and Arthrobacter aurescences (p-value 0.015), was observed in boys. The urinary mycobiome showed a significant rise in the genus Malassezia and Malassezia globose fungus (p-value 0.009) in girls, whereas genus Saccharomyces (p-value 0.009) was significantly high in boys. The beta diversity of the urinary mycobiome was found to differ between different age groups. Boys had significantly more Mastadenovirus and Human mastadenovirus-A in their urinary virome than girls. With increasing age, we noticed an increase in the relative abundance of the order Caudovirales. Our optimized protocols allowed us to identify the unique microbes for each sex by using an adequate volume of urine (3−10 mL) to screen for the bacteriome, mycobiome, and virome profiles in the urine of healthy children. To the best of our knowledge, this is the first study to characterize the metagenomics profiles of urine in a healthy pediatric population.
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Sun Q, Li L, Zhou H, Wu Y, Gao Y, Wu B, Qiu Y, Zhou Z, Song Q, Zhao J, Wu P. The detection of urinary viruses is associated with aggravated symptoms and altered bacteriome in female with overactive bladder. Front Microbiol 2022; 13:984234. [PMID: 36212847 PMCID: PMC9537457 DOI: 10.3389/fmicb.2022.984234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/11/2022] [Indexed: 11/15/2022] Open
Abstract
Although it is known that changes in bacterial components of the urinary microbiome are associated with overactive bladder (OAB), the specific role of viruses is still insufficiently investigated. The aim of the present study is to evaluate the role of urinary viruses in woman with OAB, and analyze the potential relationship between viruses, bacteria and disease. Catheterized urine samples were collected from 55 women with OAB and 18 control individuals. OAB patients fulfilling the following criteria were considered eligible for this study: female, 18 years of age or older; presented with classic OAB symptoms defined by the International Continence Society; and OAB Symptom Score (OABSS) total score ≥ 3 points and question 3 (urgency) score ≥ 2 points. Based on results of metagenomic next-generation sequencing (mNGS), all participants were divided into virus-infected and virus-uninfected groups for analysis. The results of mNGS showed that the diversity of the OAB group was lower than that of the control group when focused on bacterial sequences, which was consistent with our previous study. According to the questionnaire filled out by the patients, OABSS and 8-item OAB questionnaire, female OAB patients who had viruses detected in their urine had more severe symptoms. In parallel, John Cunningham virus (mainly subtype 7 and subtype 2) was the most frequently detected virus in urine. Correlation analysis indicated that risk factors for virus infection in OAB patients include age, habit of holding urine and pelvic surgery history. Given our preliminary data, viral infection can aggravate OAB severity and affect the composition of bacterial. Further research is required to explain how viral infections can aggravate OAB patient symptoms and cause bacterial changes.
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Affiliation(s)
- Qi Sun
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Leqian Li
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hao Zhou
- Department of Hospital Infection Management, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ying Wu
- School of Public Health, Southern Medical University, Guangzhou, China
| | - Yubo Gao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bingyi Wu
- Medical Research Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yifeng Qiu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhipeng Zhou
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qixiang Song
- Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Qixiang Song,
| | - Jie Zhao
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- Jie Zhao,
| | - Peng Wu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Peng Wu,
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Sen T, Thummer RP. The Impact of Human Microbiotas in Hematopoietic Stem Cell and Organ Transplantation. Front Immunol 2022; 13:932228. [PMID: 35874759 PMCID: PMC9300833 DOI: 10.3389/fimmu.2022.932228] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
The human microbiota heavily influences most vital aspects of human physiology including organ transplantation outcomes and transplant rejection risk. A variety of organ transplantation scenarios such as lung and heart transplantation as well as hematopoietic stem cell transplantation is heavily influenced by the human microbiotas. The human microbiota refers to a rich, diverse, and complex ecosystem of bacteria, fungi, archaea, helminths, protozoans, parasites, and viruses. Research accumulating over the past decade has established the existence of complex cross-species, cross-kingdom interactions between the residents of the various human microbiotas and the human body. Since the gut microbiota is the densest, most popular, and most studied human microbiota, the impact of other human microbiotas such as the oral, lung, urinary, and genital microbiotas is often overshadowed. However, these microbiotas also provide critical and unique insights pertaining to transplantation success, rejection risk, and overall host health, across multiple different transplantation scenarios. Organ transplantation as well as the pre-, peri-, and post-transplant pharmacological regimens patients undergo is known to adversely impact the microbiotas, thereby increasing the risk of adverse patient outcomes. Over the past decade, holistic approaches to post-transplant patient care such as the administration of clinical and dietary interventions aiming at restoring deranged microbiota community structures have been gaining momentum. Examples of these include prebiotic and probiotic administration, fecal microbial transplantation, and bacteriophage-mediated multidrug-resistant bacterial decolonization. This review will discuss these perspectives and explore the role of different human microbiotas in the context of various transplantation scenarios.
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Affiliation(s)
| | - Rajkumar P. Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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