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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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Choi BI, Fontes Noronha M, Kaindl J, Wolfe AJ. Complete genome sequences of Aerococcus loyolae ATCC TSD-300 T, Aerococcus mictus ATCC TSD-301 T, and Aerococcus tenax ATCC TSD-302 T. Microbiol Resour Announc 2024; 13:e0015624. [PMID: 38651909 PMCID: PMC11237779 DOI: 10.1128/mra.00156-24] [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: 02/15/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Previously identified under the single designation of Aerococcus urinae, three distinct taxonomic species have been distinguished as Aerococcus loyolae, Aerococcus mictus, and Aerococcus tenax. Here, we present the complete genome sequences of the type strains of these species assembled via a combination of short-read and long-read sequencing techniques.Registered at ClinicalTrials.gov (NCT01166438).
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Affiliation(s)
- Brian I. Choi
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Melline Fontes Noronha
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Jacob Kaindl
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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Choi BI, Ene A, Du J, Johnson G, Putonti C, Schouw CH, Dargis R, Senneby E, Christensen JJ, Wolfe AJ. Taxonomic considerations on Aerococcus urinae with proposal of subdivision into Aerococcus urinae, Aerococcus tenax sp. nov., Aerococcus mictus sp. nov., and Aerococcus loyolae sp. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37755156 DOI: 10.1099/ijsem.0.006066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Average nucleotide identity analysis, based on whole genome sequences of 115 strains previously identified as Aerococcus urinae, an emerging uropathogen, discriminates at least six unique genomic taxa. The whole genome analysis affords clearer species boundaries over 16S rRNA gene sequencing and traditional phenotypic approaches for the identification and phylogenetic organization of Aerococcus species. The newly described species can be differentiated by matrix-assisted laser desorption ionization time-of-flight analysis of protein signatures. We propose the emendation of the description of A. urinae (type strain ATCC 51268T = CCUG 34223T=NCFB 2893) and the names of Aerococcus tenax sp. nov. (ATCC TSD-302T = DSM 115700T = CCUG 76531T=NR-58630T), Aerococcus mictus sp. nov. (ATCC TSD-301T = DSM 115699T = CCUG 76532T=NR-58629T), and Aerococcus loyolae sp. nov. (ATCC TSD-300T = DSM 115698T = CCUG 76533T=NR-58628T) for three of the newly identified genomic taxa.
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Affiliation(s)
- Brian I Choi
- Loyola University Chicago, Department of Microbiology & Immunology, Maywood IL, USA
| | - Adriana Ene
- Loyola University Chicago, Bioinformatics Program, Chicago IL, USA
| | - Jingjie Du
- Loyola University Chicago, Department of Microbiology & Immunology, Maywood IL, USA
| | | | - Catherine Putonti
- Loyola University Chicago, Department of Microbiology & Immunology, Maywood IL, USA
- Loyola University Chicago, Bioinformatics Program, Chicago IL, USA
- Loyola University Chicago, Department of Biology, Chicago IL, USA
| | - Christian H Schouw
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark
| | - Rimtas Dargis
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark
| | - Erik Senneby
- Lund University, Clinical Microbiology, Department of Translational Medicine, Lund, Sweden
| | - Jens J Christensen
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Alan J Wolfe
- Loyola University Chicago, Department of Microbiology & Immunology, Maywood IL, USA
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Nardos R, Leung ET, Dahl EM, Davin S, Asquith M, Gregory WT, Karstens L. Network-Based Differences in the Vaginal and Bladder Microbial Communities Between Women With and Without Urgency Urinary Incontinence. Front Cell Infect Microbiol 2022; 12:759156. [PMID: 35402312 PMCID: PMC8988226 DOI: 10.3389/fcimb.2022.759156] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/17/2022] [Indexed: 12/12/2022] Open
Abstract
Background Little is known about the relationship of proximal urogenital microbiomes in the bladder and the vagina and how this contributes to bladder health. In this study, we use a microbial ecology and network framework to understand the dynamics of interactions/co-occurrences of bacteria in the bladder and vagina in women with and without urgency urinary incontinence (UUI). Methods We collected vaginal swabs and catheterized urine specimens from 20 women with UUI (cases) and 30 women without UUI (controls). We sequenced the V4 region of the bacterial 16S rRNA gene and evaluated using alpha and beta diversity metrics. We used microbial network analysis to detect interactions in the microbiome and the betweenness centrality measure to identify central bacteria in the microbial network. Bacteria exhibiting maximum betweenness centrality are considered central to the microbe-wide networks and likely maintain the overall microbial network structure. Results There were no significant differences in the vaginal or bladder microbiomes between cases and controls using alpha and beta diversity. Silhouette metric analysis identified two distinct microbiome clusters in both the bladder and vagina. One cluster was dominated by Lactobacillus genus while the other was more diverse. Network-based analyses demonstrated that vaginal and bladder microbial networks were different between cases and controls. In the vagina, there were similar numbers of genera and subgroup clusters in each network for cases and controls. However, cases tend to have more unique bacterial co-occurrences. While Bacteroides and Lactobacillus were the central bacteria with the highest betweenness centrality in controls, Aerococcus had the highest centrality in cases and correlated with bacteria commonly associated with bacterial vaginosis. In the bladder, cases have less than half as many network clusters compared to controls. Lactobacillus was the central bacteria in both groups but associated with several known uropathogens in cases. The number of shared bacterial genera between the bladder and the vagina differed between cases and controls, with cases having larger overlap (43%) compared to controls (29%). Conclusion Our study shows overlaps in microbial communities of bladder and vagina, with higher overlap in cases. We also identified differences in the bacteria that are central to the overall community structure.
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Affiliation(s)
- Rahel Nardos
- Division of Urogynecology, Oregon Health and Science University, Portland, OR, United States
- Division of Female Pelvic Medicine and Reconstructive Surgery, University of Minnesota, Minneapolis, MN, United States
- *Correspondence: Rahel Nardos,
| | - Eric T. Leung
- Division of Bioinformatics and Computational Biomedicine, Oregon Health and Science University, Portland, OR, United States
| | - Erin M. Dahl
- Division of Bioinformatics and Computational Biomedicine, Oregon Health and Science University, Portland, OR, United States
| | - Sean Davin
- Division of Arthritis and Rheumatology, Oregon Health and Science University, Portland, OR, United States
| | - Mark Asquith
- Division of Arthritis and Rheumatology, Oregon Health and Science University, Portland, OR, United States
| | - W. Thomas Gregory
- Division of Urogynecology, Oregon Health and Science University, Portland, OR, United States
| | - Lisa Karstens
- Division of Urogynecology, Oregon Health and Science University, Portland, OR, United States
- Division of Bioinformatics and Computational Biomedicine, Oregon Health and Science University, Portland, OR, United States
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Gilbert NM, Choi B, Du J, Collins C, Lewis AL, Putonti C, Wolfe AJ. A mouse model displays host and bacterial strain differences in Aerococcus urinae urinary tract infection. Biol Open 2021; 10:271827. [PMID: 34387311 PMCID: PMC8380466 DOI: 10.1242/bio.058931] [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: 07/09/2021] [Accepted: 07/15/2021] [Indexed: 11/30/2022] Open
Abstract
In recent years, the clinical significance of Aerococcus urinae has been increasingly recognized. A. urinae has been implicated in cases of urinary tract infection (UTI; acute cystitis and pyelonephritis) in both male and female patients, ranging from children to older adults. Aerococcus urinae can also be invasive, causing urosepsis, endocarditis, and musculoskeletal infections. Mechanisms of pathogenesis in A. urinae infections are poorly understood, largely due to the lack of an animal model system. In response to this gap, we developed a model of A. urinae urinary tract infection in mice. We compared A. urinae UTI in female C3H/HeN and C57BL/6 mice and compared four clinical isolates of A. urinae isolated from patients with UTI, urgency urinary incontinence, and overactive bladder. Our data demonstrate that host genetic background modulates A. urinae UTI. Female C57BL/6 female mice rapidly cleared the infection. Female C3H/HeN mice, which have inherent vesicoureteral reflux that flushes urine from the bladder up into the kidneys, were susceptible to prolonged bacteriuria. This result is consistent with the fact that A. urinae infections most frequently occur in patients with underlying urinary tract abnormalities or disorders that make them susceptible to bacterial infection. Unlike uropathogens such as E. coli, which cause infection and inflammation both of the bladder and kidneys in C3H/HeN mice, A. urinae displayed tropism for the kidney, persisting in kidney tissue even after clearance of bacteria from the bladder. Aerococcus urinae strains from different genetic clades displayed varying propensities to cause persistent kidney infection. Aerococcus urinae infected kidneys displayed histological inflammation, neutrophil recruitment and increased pro-inflammatory cytokines. These results set the stage for future research that interrogates host-pathogen interactions between A. urinae and the urinary tract. Summary:Aerococcus urinae clinical isolates are genetically diverse and display differential capacity to cause UTI in a mouse model. Infection was rapidly cleared from the bladder, but persisted and caused inflammation in the kidney.
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Affiliation(s)
- Nicole M Gilbert
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian Choi
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Jingjie Du
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Christina Collins
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amanda L Lewis
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego School of Medicine, La Jolla, CA 92093, 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 and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
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Validation of a Gradient Diffusion Method (Etest) for Testing of Antimicrobial Susceptibility of Aerococcus urinae to Fluoroquinolones. J Clin Microbiol 2021; 59:e0025921. [PMID: 34076476 DOI: 10.1128/jcm.00259-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aerococcus urinae is a urinary pathogen with well-described resistance to fluoroquinolones. This study aimed to validate the gradient diffusion (GD) method (Etest) on cation-adjusted Mueller-Hinton agar with 5% sheep blood for testing the susceptibilities of Aerococcus urinae to the antimicrobial agents ciprofloxacin and levofloxacin and to compare the Etest to the broth microdilution (BMD) method from CLSI document M45-A3. Agar dilution (AD), as recommended by EUCAST, was used as an alternative reference method to arbitrate discrepancies or address technical issues. Aerococcus urinae isolates from urinary specimens were prospectively collected between June 2016 and December 2017 from six hospitals in Quebec, Canada, and identifications were confirmed using Vitek MS with the IVD 3.0 database. Of the 207 isolates tested using BMD, 37 (17.9%) showed trailing and 19 (9.2%) showed insufficient growth; these were tested using AD. Also, 38 isolates (18.4%) for ciprofloxacin and 13 isolates (6.3%) for levofloxacin showed a lack of essential or categorical agreement between the Etest and BMD and were also tested by AD. By use of a combined reference method (BMD or AD), the susceptibility rates of Aerococcus urinae were 82.6% and 81.6% for ciprofloxacin and levofloxacin, respectively. Categorical agreement between GD and the combined reference methods was 95.2% for ciprofloxacin and 97.1% for levofloxacin, with no very major error identified. Major and minor error rates were 0.6% and 4.3% for ciprofloxacin and 1.2% and 1.9% for levofloxacin. Overall, antimicrobial susceptibility testing (AST) using the Etest on sheep blood agar showed good agreement with the reference methods and can be considered by clinical laboratories wishing to perform AST on Aerococcus urinae isolates.
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Evaluation of the relationship of cholinergic metabolites in urine and urgency urinary incontinence. Int Urogynecol J 2021; 33:1165-1174. [PMID: 33818647 PMCID: PMC8020620 DOI: 10.1007/s00192-021-04785-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/24/2021] [Indexed: 12/02/2022]
Abstract
Introduction and hypothesis To investigate differences in urine cholinergic metabolites in women with urinary urgency incontinence (UUI) and responders (R) and non-responders (NR) to anti-cholinergic medications (AC). Methods Patients with UUI and age-matched controls were evaluated pre- and post-treatment using OABSS, UDI-6 and IIQ-7. Controls were defined as having a cumulative OABSS of zero. Patients with UUI were treated with AC and followed for 12 weeks. Responders were those with a > 50% decrease in the total OABSS score. Urine samples were collected from all participants for evaluation. Metabolite detection was accomplished using commercial assay kits. Wilcoxon-rank sum test and Fisher’s exact test were used to express differences between groups. Spearman’s rho correlation coefficient was used to determine the relationship between acetylcholine (Ach), choline (Ch), acetylcholinesterase (AchE) and questionnaire scores. Results We recruited 39 with UUI and 33 controls. We found concentrations of Ch [29.0 (IQR: 24.2–42.5) μmol vs. 15.2 (IQR: 7.5–24.1) μmol] and Ach [65.8 (IQR: 30.4–101.8) nmol and 33.1 (IQR: 11.9–43.8) nmol] were higher in the UUI group compared to controls (p = 0.003 and p < 0.001, respectively] and no differences in AchE concentrations. In the UUI group, 43.6% responded to AC after 12 weeks of therapy. There were no differences in Ch or AchE levels between R and NR; Ach levels were higher in the R group [82.1 nmol (IQR: 54.8–118.1) vs. 50.3 nmol (IQR: 29.9–68.2), p = 0.007]. Ch and Ach were positively associated with pre-treatment OABSS parameters. Conclusions Urine Ach is higher in responders to anti-cholinergic therapy, and urine cholinergic metabolites were higher in the UUI patients compared to controls.
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Kotásková I, Syrovátka V, Obručová H, Vídeňská P, Zwinsová B, Holá V, Blaštíková E, Růžička F, Freiberger T. Actinotignum schaalii: Relation to Concomitants and Connection to Patients' Conditions in Polymicrobial Biofilms of Urinary Tract Catheters and Urines. Microorganisms 2021; 9:microorganisms9030669. [PMID: 33807120 PMCID: PMC8004716 DOI: 10.3390/microorganisms9030669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/05/2021] [Accepted: 03/11/2021] [Indexed: 12/30/2022] Open
Abstract
Actinotignum schaalii is an emerging, opportunistic pathogen and its connection to non-infectious diseases and conditions, such as prostate or bladder cancer, or chronic inflammation has been proposed. Here, we analyzed 297 urine, ureteral and urinary catheter samples from 128 patients by Polymerase Chain Reaction followed by Denaturing Gradient Gel Electrophoresis and Sequencing (PCR-DGGE-S), and culture, and 29 of these samples also by 16S rRNA Illumina sequencing, to establish A. schaalii’s prevalence in urinary tract-related samples, its relation to other bacteria, and its potential association with patients’ conditions and samples’ characteristics. A. schaalii-positive samples were significantly more diverse than A. schaalii negative and between-group diversity was higher than intra-group. Propionimicrobium lymphophilum, Fusobacterium nucleatum, Veillonella sp., Morganella sp., and Aerococcus sp. were significantly more often present in A. schaalii-positive samples; thus, we suggest these species are A. schaalii’s concomitants, while Enterobacter and Staphylococcaceae were more often identified in A. schaalii-negative samples; therefore, we propose A. schaalii and these species are mutually exclusive. Additionally, a significantly higher A. schaalii prevalence in patients with ureter stricture associated hydronephrosis (p = 0.020) was noted. We suggest that A. schaalii could be an early polybacterial biofilm colonizer, together with concomitant species, known for pro-inflammatory features.
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Affiliation(s)
- Iva Kotásková
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 61600 Brno, Czech Republic; (I.K.); (H.O.); (E.B.)
- Department of Clinical Immunology and Allergology, Medical Faculty, Masaryk University, 61600 Brno, Czech Republic
- Research Centre for Toxic Compounds in the Environment, Masaryk University, 61600 Brno, Czech Republic; (P.V.); (B.Z.)
| | - Vít Syrovátka
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 61600 Brno, Czech Republic;
| | - Hana Obručová
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 61600 Brno, Czech Republic; (I.K.); (H.O.); (E.B.)
| | - Petra Vídeňská
- Research Centre for Toxic Compounds in the Environment, Masaryk University, 61600 Brno, Czech Republic; (P.V.); (B.Z.)
| | - Barbora Zwinsová
- Research Centre for Toxic Compounds in the Environment, Masaryk University, 61600 Brno, Czech Republic; (P.V.); (B.Z.)
| | - Veronika Holá
- Institute of Microbiology, Faculty of Medicine, St. Anne’s University Hospital, Masaryk University, 61600 Brno, Czech Republic; (V.H.); (F.R.)
| | - Eva Blaštíková
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 61600 Brno, Czech Republic; (I.K.); (H.O.); (E.B.)
| | - Filip Růžička
- Institute of Microbiology, Faculty of Medicine, St. Anne’s University Hospital, Masaryk University, 61600 Brno, Czech Republic; (V.H.); (F.R.)
| | - Tomáš Freiberger
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, 61600 Brno, Czech Republic; (I.K.); (H.O.); (E.B.)
- Department of Clinical Immunology and Allergology, Medical Faculty, Masaryk University, 61600 Brno, Czech Republic
- Correspondence:
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Bajic P, Wolfe AJ. The Microbiome of Male Infertility: Paving the Road Ahead. Eur Urol 2021; 79:837-838. [PMID: 33608155 DOI: 10.1016/j.eururo.2021.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/04/2021] [Indexed: 10/22/2022]
Affiliation(s)
- Petar Bajic
- Center for Men's Health, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
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