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Hu YY, Lo IH, Hsiao JT, Sheu F. Real-time PCR-based quantitative microbiome profiling elucidates the microbial dynamic succession in backslopping fermentation of Taiwanese pickled cabbage. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38925544 DOI: 10.1002/jsfa.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Microbiota succession determines the flavor and quality of fermented foods. Quantitative PCR-based quantitative microbiome profiling (QMP) has been applied broadly for microbial analysis from absolute abundance perspectives, transforming microbiota ratios into counts by normalizing 16S ribosomal RNA (16S rRNA) gene sequencing data with gene copies quantified by quantitative PCR. However, the application of QMP in fermented foods is still limited. RESULTS QMP elucidated microbial succession of Taiwanese pickled cabbage. In the spontaneous first-round fermentation (FR), the 16S rRNA gene copies of total bacteria increased from 6.1 to 10 log copies mL-1. The dominant lactic acid bacteria genera were successively Lactococcus, Leuconostoc and Lactiplantibacillus. Despite the decrease in the proportion of Lactococcus during the succession, the absolute abundance of Lactococcus still increased. In the backslopping second-round fermentation (SR), the total bacteria 16S rRNA gene copies increased from 7.6 to 9.9 log copies mL-1. The addition of backslopping starter and vinegar rapidly led to a homogenous microbial community dominated by Lactiplantibacillus. The proportion of Lactiplantibacillus remained consistently around 90% during SR, whereas its absolute abundance exhibited a continuous increase. In SR without vinegar, Leuconostoc consistently dominated the fermentation. CONCLUSION The present study highlights that compositional analysis would misinterpret microbial dynamics, whereas QMP reflected the real succession profiles and unveiled the essential role of vinegar in promoting Lactiplantibacillus dominance in backslopping fermentation of Taiwanese pickled cabbage. Quantitative microbiome profiling (QMP) was found to be a more promising approach for the detailed observation of microbiome succession in food fermentation compared to compositional analysis. © 2024 Society of Chemical Industry.
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Affiliation(s)
- You-Yun Hu
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - I-Hsuan Lo
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Jhih-Ting Hsiao
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Fuu Sheu
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
- Center for Biotechnology, National Taiwan University, Taipei, Taiwan
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2
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Malhotra M, Bello S, Gupta RS. Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus. Syst Appl Microbiol 2024; 47:126499. [PMID: 38428338 DOI: 10.1016/j.syapm.2024.126499] [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: 09/19/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/03/2024]
Abstract
To clarify the evolutionary relationships among Peptoniphilus species, whose members show association with increased risk for prostate cancer, detailed phylogenomic and comparative analyses were conducted on their genome sequences. In phylogenetic trees based on core genome proteins and 16S rRNA gene sequences, Peptoniphilus species formed eight distinct clades, with Aedoeadaptatus and Anaerosphaera species branching between them. The observed clades designated as Peptoniphilus sensu stricto (encompassing its type species), Harei, Lacrimalis, Duerdenii, Mikwangii, Stercorisuis, Catoniae and Aedoeadaptatus, show genus level divergence based on 16S rRNA similarity and average amino acid identity (AAI). The Genome Taxonomy Database also assigns most of these clades to distinct taxa. Several Peptoniphilus species (viz. P. coxii, P. ivorii, P. nemausensis and some non-validly published species) grouped reliably with the type species of Aedoeadaptatus (A. acetigenes) and are affiliated to this genus based on 16S rRNA similarity, AAI, and multiple uniquely shared molecular signatures. Hence, we are proposing the transfer of these species into the emended genus Aedoeadaptatus. Our analyses on protein sequences from Peptoniphilus genomes have also identified 54 novel molecular markers consisting of conserved signature indels (CSIs), which are specific for different Peptoniphilus species clades and provide reliable means for their demarcation in molecular terms. Lastly, we also show that based on the shared presence of these CSIs in the genomes of uncharacterized Peptoniphilus spp. (cultured and uncultured), their affiliations to the specific Peptoniphilus clades can be accurately predicted. These results should prove useful in understanding the potential involvement of Peptoniphilus-related species in diseases.
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Affiliation(s)
- Megha Malhotra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Sarah Bello
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
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3
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Nhu NTK, Phan MD, Hancock SJ, Peters KM, Alvarez-Fraga L, Forde BM, Andersen SB, Miliya T, Harris PNA, Beatson SA, Schlebusch S, Bergh H, Turner P, Brauner A, Westerlund-Wikström B, Irwin AD, Schembri MA. High-risk Escherichia coli clones that cause neonatal meningitis and association with recrudescent infection. eLife 2024; 12:RP91853. [PMID: 38622998 PMCID: PMC11021048 DOI: 10.7554/elife.91853] [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] [Indexed: 04/17/2024] Open
Abstract
Neonatal meningitis is a devastating disease associated with high mortality and neurological sequelae. Escherichia coli is the second most common cause of neonatal meningitis in full-term infants (herein NMEC) and the most common cause of meningitis in preterm neonates. Here, we investigated the genomic relatedness of a collection of 58 NMEC isolates spanning 1974-2020 and isolated from seven different geographic regions. We show NMEC are comprised of diverse sequence types (STs), with ST95 (34.5%) and ST1193 (15.5%) the most common. No single virulence gene profile was conserved in all isolates; however, genes encoding fimbrial adhesins, iron acquisition systems, the K1 capsule, and O antigen types O18, O75, and O2 were most prevalent. Antibiotic resistance genes occurred infrequently in our collection. We also monitored the infection dynamics in three patients that suffered recrudescent invasive infection caused by the original infecting isolate despite appropriate antibiotic treatment based on antibiogram profile and resistance genotype. These patients exhibited severe gut dysbiosis. In one patient, the causative NMEC isolate was also detected in the fecal flora at the time of the second infection episode and after treatment. Thus, although antibiotics are the standard of care for NMEC treatment, our data suggest that failure to eliminate the causative NMEC that resides intestinally can lead to the existence of a refractory reservoir that may seed recrudescent infection.
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Affiliation(s)
- Nguyen Thi Khanh Nhu
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Minh-Duy Phan
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Steven J Hancock
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Kate M Peters
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Laura Alvarez-Fraga
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Brian M Forde
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
| | - Stacey B Andersen
- Genome Innovation Hub, The University of QueenslandBrisbaneAustralia
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
| | - Patrick NA Harris
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Pathology Queensland, Queensland HealthBrisbaneAustralia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
| | - Sanmarie Schlebusch
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Pathology Queensland, Queensland HealthBrisbaneAustralia
- Q-PHIRE Genomics and Public Health Microbiology, Forensic and Scientific Services, Coopers PlainsBrisbaneAustralia
| | - Haakon Bergh
- Pathology Queensland, Queensland HealthBrisbaneAustralia
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Annelie Brauner
- Department of Microbiology, Tumor and Cell Biology, Division of Clinical Microbiology, Karolinska Institutet and Karolinska University HospitalStockholmSweden
| | | | - Adam D Irwin
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
- University of Queensland Centre for Clinical Research, The University of QueenslandBrisbaneAustralia
- Infection Management Prevention Service, Queensland Children's HospitalBrisbaneAustralia
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), The University of QueenslandBrisbaneAustralia
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbaneAustralia
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbaneAustralia
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Campbell K, Brinkley C, Malm-Buatsi E. The Urinary Microbiome Composition in Infants. Urology 2024; 186:172-179. [PMID: 38350552 DOI: 10.1016/j.urology.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Affiliation(s)
- Katherine Campbell
- University Missouri School of Medicine, Columbia, MO; Division of Urology, Department of Surgery, University of Missouri, Columbia, MO.
| | - Clayton Brinkley
- University Missouri School of Medicine, Columbia, MO; Division of Urology, Department of Surgery, University of Missouri, Columbia, MO.
| | - Elizabeth Malm-Buatsi
- University Missouri School of Medicine, Columbia, MO; Division of Urology, Department of Surgery, University of Missouri, Columbia, MO.
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Chorbińska J, Krajewski W, Nowak Ł, Małkiewicz B, Del Giudice F, Szydełko T. Urinary Microbiome in Bladder Diseases-Review. Biomedicines 2023; 11:2816. [PMID: 37893189 PMCID: PMC10604329 DOI: 10.3390/biomedicines11102816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/01/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
The microbiome is the totality of microorganisms found in a specific biological niche. It has been proven that in the human body, the microbiome is responsible for its proper functioning. Dysbiosis, i.e., a disturbance in the composition of the microbiome, may be associated with the pathogenesis of many human diseases. Until recently, studies did not focus on the microbiome of the urinary tract, because, since the 19th century, there had been a dogma that urine in healthy people is sterile. Yet, advances in molecular biology techniques have allowed this dogma to be overthrown. The use of DNA sequencing has shown that the urinary tract has its own endogenous microbiome. This discovery enabled further research on the characteristics of the urine microbiomes of healthy people, as well as on the role of the urine microbiome in the pathogenesis of many urological diseases, including bladder diseases. The aim of this review is to summarize the current knowledge on the urinary microbiome in bladder diseases and to identify potential directions for further research.
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Affiliation(s)
- Joanna Chorbińska
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wrocław Medical University, 50-367 Wrocław, Poland; (W.K.); (Ł.N.); (B.M.)
| | - Wojciech Krajewski
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wrocław Medical University, 50-367 Wrocław, Poland; (W.K.); (Ł.N.); (B.M.)
| | - Łukasz Nowak
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wrocław Medical University, 50-367 Wrocław, Poland; (W.K.); (Ł.N.); (B.M.)
| | - Bartosz Małkiewicz
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wrocław Medical University, 50-367 Wrocław, Poland; (W.K.); (Ł.N.); (B.M.)
| | - Francesco Del Giudice
- Department of Maternal Infant and Urologic Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy;
| | - Tomasz Szydełko
- University Center of Excellence in Urology, Wrocław Medical University, 50-367 Wrocław, Poland;
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Abbott IJ, Peel TN, Cairns KA, Stewardson AJ. Antibiotic management of urinary tract infections in the post-antibiotic era: a narrative review highlighting diagnostic and antimicrobial stewardship. Clin Microbiol Infect 2023; 29:1254-1266. [PMID: 35640839 DOI: 10.1016/j.cmi.2022.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 12/22/2022]
Abstract
BACKGROUND As one of the most common indications for antimicrobial prescription in the community, the management of urinary tract infections (UTIs) is both complicated by, and a driver of, antimicrobial resistance. OBJECTIVES To highlight the key clinical decisions involved in the diagnosis and treatment of UTIs in adult women, focusing on clinical effectiveness and both diagnostic and antimicrobial stewardship as we approach the post-antimicrobial era. SOURCES Literature reviewed via directed PubMed searches and manual searching of the reference list for included studies to identify key references to respond to the objectives. A strict time limit was not applied. We prioritised recent publications, randomised trials, and systematic reviews (with or without meta-analyses) where available. Searches were limited to English language articles. A formal quality assessment was not performed; however, the strengths and limitations of each paper were reviewed by the authors throughout the preparation of this manuscript. CONTENT We discuss the management of UTIs in ambulatory adult women, with particular focus on uncomplicated infections. We address the diagnosis of UTIs, including the following: definition and categorisation; bedside assessments and point-of-care tests; and the indications for, and use of, laboratory tests. We then discuss the treatment of UTIs, including the following: indications for treatment, antimicrobial sparing approaches, key considerations when selecting a specific antimicrobial agent, specific treatment scenarios, and duration of treatment. We finally outline emerging areas of interest in this field. IMPLICATIONS The steady increase in antimicrobial resistance among common uropathogens has had a substantial affect on the management of UTIs. Regarding both diagnosis and treatment, the clinician must consider both the patient (clinical effectiveness and adverse effects, including collateral damage) and the community more broadly (population-level antimicrobial selection pressure).
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Affiliation(s)
- Iain J Abbott
- Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia; Microbiology Unit, Alfred Health, Melbourne, Victoria, Australia.
| | - Trisha N Peel
- Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Kelly A Cairns
- Pharmacy Department, Alfred Health, Melbourne, Victoria, Australia
| | - Andrew J Stewardson
- Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
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7
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Jaworska MM, Pecyna P, Jaskiewicz K, Rydzanicz M, Kaluzna M, Pawlaczyk K, Ploski R, Nowak-Malczewska DM, Karolak JA, Gajecka M. Differences in the composition of the bacterial element of the urinary tract microbiome in patients undergoing dialysis and patients after kidney transplantation. Front Microbiol 2023; 14:1187625. [PMID: 37350786 PMCID: PMC10282556 DOI: 10.3389/fmicb.2023.1187625] [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: 03/16/2023] [Accepted: 05/16/2023] [Indexed: 06/24/2023] Open
Abstract
Introduction The development of molecular biology methods and their application in microbial research allowed the detection of many new pathogens that cause urinary tract infections (UTIs). Despite the advances of using new research techniques, the etiopathogenesis of UTIs, especially in patients undergoing dialysis and patients after kidney transplantation, is still not fully understood. Methods This study aimed to characterize and compare the composition of the bacterial element of the urinary tract microbiome between the groups of patients undergoing dialysis (n = 50) and patients after kidney transplantation (n = 50), with positive or negative urine culture, compared to healthy individuals (n = 50). Results Asymptomatic bacteriuria was observed in 30% of the urine cultures of patients undergoing dialysis and patients after kidney transplantation, with Escherichia coli as the most dominant microorganism (73%) detected with the use of classical microbiology techniques. However, differences in the bacterial composition of the urine samples between the evaluated patient groups were demonstrated using the amplicon sequencing. Finegoldia, Leptotrichia, and Corynebacterium were found to be discriminative bacteria genera in patients after dialysis and kidney transplantation compared to the control group. In addition, in all of urine samples, including those without bacteriuria in classical urine culture, many types of bacteria have been identified using 16S rRNA sequencing. Discussion The revealed microbial characteristics may form the basis in searching for new diagnostic markers in treatment of patients undergoing dialysis and patients after kidney transplantation.
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Affiliation(s)
- Marcelina M. Jaworska
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Paulina Pecyna
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | | | | | - Malgorzata Kaluzna
- Chair and Department of Endocrinology, Metabolism and Internal Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Krzysztof Pawlaczyk
- Department of Nephrology, Transplantology and Internal Medicine, Poznan University of Medical Sciences, Poznań, Poland
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Dorota M. Nowak-Malczewska
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marzena Gajecka
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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8
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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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Kim WB. Differences in Urine Microbiome of Acute Cystitis and Chronic Recurrent Cystitis in Women. UROGENITAL TRACT INFECTION 2023; 18:1-7. [DOI: 10.14777/uti.2023.18.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 09/01/2023]
Affiliation(s)
- Woong Bin Kim
- Department of Urology, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
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10
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Pallares-Mendez R, Cervantes-Miranda DE, Gonzalez-Colmenero AD, Ochoa-Arvizo MA, Gutierrez-Gonzalez A. A Perspective of the Urinary Microbiome in Lower Urinary Tract Infections - A Review. Curr Urol Rep 2022; 23:235-244. [PMID: 36053406 DOI: 10.1007/s11934-022-01108-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2022] [Indexed: 11/24/2022]
Abstract
PURPOSE OF REVIEW Greater availability of sequencing methods has broadened the knowledge of the urinary microbiome in an environment previously believed to be sterile. This review discusses internal and external influences that promote either a balance or a dysbiosis of the urinary tract and the future perspectives in understanding lower urinary tract infections. RECENT FINDINGS Efforts have been made to identify a "core" urinary microbiome in which Firmicutes and Bacteroidetes account for most of the bacterial representations. A shift to a Proteobacteria-dominant representation shapes the fingerprint of the infectious urinary microbiome; furthermore, the virome and the mycobiome are important modulators of the urinary microbiome, which have been recently explored to determine their role in the health-disease process of the lower urinary tract. A disturbance of bacterial representation and diversity triggers a transition from health to disease; conversely, a functional cooperative interplay between the host and microbiome allows for basic metabolic and immune functions to take place.
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Affiliation(s)
- Rigoberto Pallares-Mendez
- Department of Urology, Hospital Universitario "Dr. José Eleuterio González", Universidad Autonoma de Nuevo Leon, Monterrey, Mexico.
| | - Daniel E Cervantes-Miranda
- Department of Urology, Hospital Universitario "Dr. José Eleuterio González", Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | | | - Mario A Ochoa-Arvizo
- Department of Urology, Hospital Universitario "Dr. José Eleuterio González", Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Adrian Gutierrez-Gonzalez
- Department of Urology, Hospital Universitario "Dr. José Eleuterio González", Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
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Cole E, Shaikh N, Forster CS. The pediatric urobiome in genitourinary conditions: a narrative review. Pediatr Nephrol 2022; 37:1443-1452. [PMID: 34654953 DOI: 10.1007/s00467-021-05274-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/13/2021] [Accepted: 08/09/2021] [Indexed: 12/19/2022]
Abstract
The microbial ecosystem within the bladder that can be measured within the urine, or urobiome, is an emerging field of study with little published data regarding children. However, investigations into urobiome research have the potential to significantly impact the understanding of the pathophysiology of genitourinary conditions, as well as potentially identify novel therapeutics. Therefore, both researchers and clinicians should be aware of pediatric urobiome research. The purpose of this review is to highlight the literature around urobiome research in urinary tract infections, nephrolithiasis, and neurogenic bladder; comment on pediatric-specific considerations when reading and interpreting the urobiome literature; and to identify new potential areas of research.
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Affiliation(s)
- Elisabeth Cole
- Department of Pediatrics, University of Pittsburgh School of Medicine, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - Nader Shaikh
- Department of Pediatrics, University of Pittsburgh School of Medicine, 4401 Penn Ave, Pittsburgh, PA, 15224, USA
| | - Catherine S Forster
- Department of Pediatrics, University of Pittsburgh School of Medicine, 4401 Penn Ave, Pittsburgh, PA, 15224, USA.
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Zhang L, Chen T, Wang Y, Zhang S, Lv Q, Kong D, Jiang H, Zheng Y, Ren Y, Huang W, Liu P, Jiang Y. Comparison Analysis of Different DNA Extraction Methods on Suitability for Long-Read Metagenomic Nanopore Sequencing. Front Cell Infect Microbiol 2022; 12:919903. [PMID: 35837476 PMCID: PMC9273838 DOI: 10.3389/fcimb.2022.919903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is a novel useful strategy that is increasingly used for pathogens detection in clinic. Some emerging mNGS technologies with long-read ability are useful to decrease sequencing time and increase diagnosed accuracy, which is of great significance in rapid pathogen diagnosis. Reliable DNA extraction is considered critical for the success of sequencing; hence, there is thus an urgent need of gentle DNA extraction method to get unbiased and more integrate DNA from all kinds of pathogens. In this study, we systematically compared three DNA extraction methods (enzymatic cell lysis based on MetaPolyzyme, mechanical cell lysis based on bead beating, and the control method without pre-cell lysis, respectively) by assessing DNA yield, integrity, and the microbial diversity based on long-read nanopore sequencing of urine samples with microbial infections. Compared with the control method, the enzymatic-based method increased the average length of microbial reads by a median of 2.1-fold [Inter Quartile Range (IQR), 1.7-2.5; maximum, 4.8) in 18 of the 20 samples and the mapped reads proportion of specific species by a median of 11.8-fold (Inter Quartile Range (IQR), 6.9-32.2; maximum, 79.27]. Moreover, it provided fully (20 of 20) consistent diagnosed results to the clinical culture and more representative microbial profiles (P < 0.05), which all strongly proves the excellent performance of enzymatic-based method in long-read mNGS-based pathogen identification and potential diseases diagnosis of microbiome related.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ting Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
- The Fifth Medical Center of PLA General Hospital, The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Ye Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Shengwei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
- Department of Clinical Laboratory, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Qingyu Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuhao Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
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13
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Zhang L, Huang W, Zhang S, Li Q, Wang Y, Chen T, Jiang H, Kong D, Lv Q, Zheng Y, Ren Y, Liu P, Jiang Y, Chen Y. Rapid Detection of Bacterial Pathogens and Antimicrobial Resistance Genes in Clinical Urine Samples With Urinary Tract Infection by Metagenomic Nanopore Sequencing. Front Microbiol 2022; 13:858777. [PMID: 35655992 PMCID: PMC9152355 DOI: 10.3389/fmicb.2022.858777] [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: 01/20/2022] [Accepted: 04/11/2022] [Indexed: 12/24/2022] Open
Abstract
Urinary tract infections (UTIs) are among the most common acquired bacterial infections in humans. The current gold standard method for identification of uropathogens in clinical laboratories is cultivation. However, culture-based assays have substantial drawbacks, including long turnaround time and limited culturability of many potential pathogens. Nanopore sequencing technology can overcome these limitations and detect pathogens while also providing reliable predictions of drug susceptibility in clinical samples. Here, we optimized a metagenomic nanopore sequencing (mNPS) test for pathogen detection and identification in urine samples of 76 patients with acute uncomplicated UTIs. We first used twenty of these samples to show that library preparation by the PCR Barcoding Kit (PBK) led to the highest agreement of positive results with gold standard clinical culture tests, and enabled antibiotic resistance detection in downstream analyses. We then compared the detection results of mNPS with those of culture-based diagnostics and found that mNPS sensitivity and specificity of detection were 86.7% [95% confidence interval (CI), 73.5-94.1%] and 96.8% (95% CI, 82.4-99.9%), respectively, indicating that the mNPS method is a valid approach for rapid and specific detection of UTI pathogens. The mNPS results also performed well at predicting antibiotic susceptibility phenotypes. These results demonstrate that our workflow can accurately diagnose UTI-causative pathogens and enable successful prediction of drug-resistant phenotypes within 6 h of sample receipt. Rapid mNPS testing is thus a promising clinical diagnostic tool for infectious diseases, based on clinical urine samples from UTI patients, and shows considerable potential for application in other clinical infections.
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Affiliation(s)
- Lei Zhang
- College of Life Science, Yantai University, Yantai, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Wenhua Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Shengwei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China.,Department of Clinical Laboratory, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Qian Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ye Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ting Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Decong Kong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Qingyu Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yuhao Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Ying Chen
- College of Life Science, Yantai University, Yantai, China
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14
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O’Callaghan JL, Willner D, Buttini M, Huygens F, Pelzer ES. Limitations of 16S rRNA Gene Sequencing to Characterize Lactobacillus Species in the Upper Genital Tract. Front Cell Dev Biol 2021; 9:641921. [PMID: 34395413 PMCID: PMC8359668 DOI: 10.3389/fcell.2021.641921] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/25/2021] [Indexed: 11/29/2022] Open
Abstract
The endometrial cavity is an upper genital tract site previously thought as sterile, however, advances in culture-independent, next-generation sequencing technology have revealed that this low-biomass site harbors a rich microbial community which includes multiple Lactobacillus species. These bacteria are considered to be the most abundant non-pathogenic genital tract commensals. Next-generation sequencing of the female lower genital tract has revealed significant variation amongst microbial community composition with respect to Lactobacillus sp. in samples collected from healthy women and women with urogenital conditions. The aim of this study was to evaluate our ability to characterize members of the genital tract microbial community to species-level taxonomy using variable regions of the 16S rRNA gene. Samples were interrogated for the presence of microbial DNA using next-generation sequencing technology that targets the V5-V8 regions of the 16S rRNA gene and compared to speciation using qPCR. We also performed re-analysis of published data using alternate variable regions of the 16S rRNA gene. In this analysis, we explore next-generation sequencing of clinical genital tract isolates as a method for high throughput identification to species-level of key Lactobacillus sp. Data revealed that characterization of genital tract taxa is hindered by a lack of a consensus protocol and 16S rRNA gene region target allowing comparison between studies.
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Affiliation(s)
- Jessica L. O’Callaghan
- Faculty of Health, Centre for Immunology and Infection Control, Queensland University of Technology, Brisbane, QLD, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Dana Willner
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, QLD, Australia
- Department of Computer Science, College of William & Mary, Williamsburg, VA, United States
| | | | - Flavia Huygens
- Faculty of Health, Centre for Immunology and Infection Control, Queensland University of Technology, Brisbane, QLD, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Elise S. Pelzer
- Faculty of Health, Centre for Immunology and Infection Control, Queensland University of Technology, Brisbane, QLD, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
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15
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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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16
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Mores CR, Price TK, Wolff B, Halverson T, Limeira R, Brubaker L, Mueller ER, Putonti C, Wolfe AJ. Genomic relatedness and clinical significance of Streptococcus mitis strains isolated from the urogenital tract of sexual partners. Microb Genom 2021; 7:mgen000535. [PMID: 33629947 PMCID: PMC8190612 DOI: 10.1099/mgen.0.000535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/31/2021] [Indexed: 11/29/2022] Open
Abstract
Research into the lower urinary tract (LUT) microbiota has primarily focused on its relationship to LUT symptoms (LUTS), taking snapshots of these communities in individuals with and without LUTS. While certain bacterial taxa have been associated with LUTS, or the lack thereof, the temporal dynamics of this community were largely unknown. Recently, we conducted a longitudinal study and found that vaginal intercourse resulted in a shift in species richness and diversity within the LUT microbiota. This is particularly relevant as frequent vaginal intercourse is a major risk factor for urinary tract infection (UTI) in premenopausal women (Aydin et al. Int Urogynecol J 2015;26:795-804). To further investigate the relationship between vaginal intercourse and LUT microbiota, here we present the results of a 3 week study in which daily urogenital specimens were collected from a female participant and her male sexual partner. Consistent with our previous findings, the LUT microbiota changed after vaginal intercourse, most notably a high abundance of Streptococcus mitis was observed post-coitus. We isolated and sequenced S. mitis from both sexual partners finding that: (i) the S. mitis isolates from the female partner's urogenital tract were genomically similar throughout the duration of the study, and (ii) they were related to one isolate from the male partner's oral cavity collected at the end of the study, suggesting transmission between the two individuals. We hypothesize that blooms in S. mitis after vaginal intercourse may play a role in coitus-related UTI. We found that a S. mitis isolate, in contrast to a Lactobacillus jensenii isolate displaced after vaginal intercourse, cannot inhibit the growth of uropathogenic Escherichia coli. Thus, this bloom in S. mitis may provide a window of opportunity for a uropathogen to colonize the LUT.
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Affiliation(s)
- Carine R. Mores
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
- Present address: Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Travis K. Price
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
- Present address: Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Birte Wolff
- Department of Obstetrics and Gynecology, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Urology, Loyola University Medical Center, Maywood, IL 60153, USA
- Present address: Swedish Hospital, NorthShore University, Suite 605, 5140 N California Avenue, Chicago, IL 60625, USA
| | - Thomas Halverson
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Roberto Limeira
- Loyola Genomics Facility, Loyola University Chicago, Maywood, IL 60153, USA
| | - Linda Brubaker
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth R. Mueller
- Department of Obstetrics and Gynecology, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Urology, Loyola University Medical Center, Maywood, IL 60153, USA
| | - Catherine Putonti
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
- 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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17
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Jiang S, Lu S, Chen X, Li F, Zhu C, Zheng Y, Wang X, Xu S. Dysbiosis of urine microbiota in obstructive urinary retention patients revealed by next-generation sequencing. Ann Clin Microbiol Antimicrob 2021; 20:2. [PMID: 33407528 PMCID: PMC7789751 DOI: 10.1186/s12941-020-00408-5] [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: 09/11/2020] [Accepted: 12/08/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Urinary retention (UR) is a common urinary system disease can be caused by urinary tract obstruction with numerous reasons, however, the role of urine microbes in these disorders is still poorly understood. The aim of this study was to identify the urine microbial features of two common types of obstructive UR, caused by urinary stones or urinary tract tumors, with comparison to healthy controls. METHODS Urine samples were collected from a cohort of 32 individuals with stone UR, 25 subjects with tumor UR and 25 healthy controls. The urine microbiome of all samples was analyzed using high-throughput 16S rRNA (16S ribosomal RNA) gene sequencing. RESULTS We observed dramatically increased urine microbial richness and diversity in both obstructive UR groups compared to healthy controls. Despite different origins of UR, bacteria such as Pseudomonas, Acinetobacter and Sphingomonas were enriched, while Lactobacillus, Streptococcus, Gardnerella, Prevotella and Atopobium were decreased in both UR groups in comparison with healthy controls, exhibited an approximate urine microbial community and functional characteristics of two types of obstructive UR. Furthermore, disease classifiers were constructed using specific enriched genera in UR, which can distinguish stone UR or tumor UR patients from healthy controls with an accuracy of 92.29% and 97.96%, respectively. CONCLUSION We presented comprehensive microbial landscapes of two common types of obstructive urinary retention and demonstrated that urine microbial features of these patients are significantly different from that of healthy people. The urine microbial signatures would shed light on the pathogenesis of these types of urinary retention and might be used as potential classification tools in the future.
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Affiliation(s)
- Shan Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Saisai Lu
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaomin Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Fengxia Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Chengwei Zhu
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuancai Zheng
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaobing Wang
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
| | - Shihao Xu
- Department of Ultrasonography, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
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18
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Advances in Understanding the Human Urinary Microbiome and Its Potential Role in Urinary Tract Infection. mBio 2020; 11:mBio.00218-20. [PMID: 32345639 PMCID: PMC7188990 DOI: 10.1128/mbio.00218-20] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent advances in the analysis of microbial communities colonizing the human body have identified a resident microbial community in the human urinary tract (UT). Compared to many other microbial niches, the human UT harbors a relatively low biomass. Studies have identified many genera and species that may constitute a core urinary microbiome. However, the contribution of the UT microbiome to urinary tract infection (UTI) and recurrent UTI (rUTI) pathobiology is not yet clearly understood. Evidence suggests that commensal species within the UT and urogenital tract (UGT) microbiomes, such as Lactobacillus crispatus, may act to protect against colonization with uropathogens. However, the mechanisms and fundamental biology of the urinary microbiome-host relationship are not understood. The ability to measure and characterize the urinary microbiome has been enabled through the development of next-generation sequencing and bioinformatic platforms that allow for the unbiased detection of resident microbial DNA. Translating technological advances into clinical insight will require further study of the microbial and genomic ecology of the urinary microbiome in both health and disease. Future diagnostic, prognostic, and therapeutic options for the management of UTI may soon incorporate efforts to measure, restore, and/or preserve the native, healthy ecology of the urinary microbiomes.
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19
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Urinary microbiome in uncomplicated and interstitial cystitis: is there any similarity? World J Urol 2020; 38:2721-2731. [PMID: 32006175 DOI: 10.1007/s00345-020-03099-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/19/2020] [Indexed: 01/12/2023] Open
Abstract
PURPOSE Acute/uncomplicated cystitis is the most common bacterial infection causing inflammation in the bladder tissues and predominantly diagnosed in women. Interstitial cystitis may too, cause inflammation in the bladder but its etiology has been elusive. Even though the site and symptoms of both diseases are largely shared, state of the urinary microbiome in these disorders have not been comparatively evaluated before. The purpose of this review is to assess and qualitatively compare structure and composition of the urinary microbiome in acute/uncomplicated cystitis and interstitial cystitis. METHODS AND RESULTS The available literature in MEDLINE are extensively searched using keywords and screened. Pertinent evidence is carefully assessed and synthesized. We included the original studies with a cohort of medically stable, non-pregnant women with otherwise functionally normal urinary tract and excluded the original articles if the infection in a patient's cohort is accompanied by urinary syndromes such as incontinence and overactive bladder syndrome. A total of six original papers reporting on the urinary microbiome in acute cystitis and nine papers on the interstitial cystitis met the selection criteria. CONCLUSION The evidence we have gleaned from the literature on the urinary microbiome associated with the acute and interstitial cystitis does not point to convergence of microbiome similarities between the two diseases. More studies with direct sampling of the bladder tissues besides sampling bladder surfaces are warranted for accurate comparison of microbiome similarity between the two conditions. The future research on interstitial cystitis microbiome should include stratified cohorts with prospective design.
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20
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Chen MF, Chang CH, Chiang-Ni C, Hsieh PH, Shih HN, Ueng SWN, Chang Y. Rapid analysis of bacterial composition in prosthetic joint infection by 16S rRNA metagenomic sequencing. Bone Joint Res 2019; 8:367-377. [PMID: 31537994 PMCID: PMC6719533 DOI: 10.1302/2046-3758.88.bjr-2019-0003.r2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Objectives Prosthetic joint infection (PJI) is the most common cause of arthroplasty failure. However, infection is often difficult to detect by conventional bacterial cultures, for which false-negative rates are 23% to 35%. In contrast, 16S rRNA metagenomics has been shown to quantitatively detect unculturable, unsuspected, and unviable pathogens. In this study, we investigated the use of 16S rRNA metagenomics for detection of bacterial pathogens in synovial fluid (SF) from patients with hip or knee PJI. Methods We analyzed the bacterial composition of 22 SF samples collected from 11 patients with PJIs (first- and second-stage surgery). The V3 and V4 region of bacteria was assessed by comparing the taxonomic distribution of the 16S rDNA amplicons with microbiome sequencing analysis. We also compared the results of bacterial detection from different methods including 16S metagenomics, traditional cultures, and targeted Sanger sequencing. Results Polymicrobial infections were not only detected, but also characterized at different timepoints corresponding to first- and second-stage exchange arthroplasty. Similar taxonomic distributions were obtained by matching sequence data against SILVA, Greengenes, and The National Center for Biotechnology Information (NCBI). All bacteria isolated from the traditional culture could be further identified by 16S metagenomics and targeted Sanger sequencing. Conclusion The data highlight 16S rRNA metagenomics as a suitable and promising method to detect and identify infecting bacteria, most of which may be uncultivable. Importantly, the method dramatically reduces turnaround time to two days rather than approximately one week for conventional cultures. Cite this article: M-F. Chen, C-H. Chang, C. Chiang-Ni, P-H. Hsieh, H-N. Shih, S. W. N. Ueng, Y. Chang. Rapid analysis of bacterial composition in prosthetic joint infection by 16S rRNA metagenomic sequencing. Bone Joint Res 2019;8:367–377. DOI: 10.1302/2046-3758.88.BJR-2019-0003.R2.
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Affiliation(s)
- Mei-Feng Chen
- Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chih-Hsiang Chang
- Bone and Joint Research Center, Chang Gung Memorial Hospital; Department of Orthopaedic Surgery, Chang Gung Memorial Hospital; Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University. Taoyuan, Taiwan
| | - Chuan Chiang-Ni
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital. Taoyuan, Taiwan
| | - Pang-Hsin Hsieh
- Bone and Joint Research Center, Chang Gung Memorial Hospital; Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hsin-Nung Shih
- Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Steve W N Ueng
- Bone and Joint Research Center, Chang Gung Memorial Hospital; Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yuhan Chang
- Bone and Joint Research Center, Chang Gung Memorial Hospital; Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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21
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Massari F, Mollica V, Di Nunno V, Gatto L, Santoni M, Scarpelli M, Cimadamore A, Lopez-Beltran A, Cheng L, Battelli N, Montironi R, Brandi G. The Human Microbiota and Prostate Cancer: Friend or Foe? Cancers (Basel) 2019; 11:E459. [PMID: 30935126 PMCID: PMC6521295 DOI: 10.3390/cancers11040459] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/21/2019] [Accepted: 03/26/2019] [Indexed: 02/06/2023] Open
Abstract
The human microbiome is gaining increasing attention in the medical community, as knowledge on its role not only in health but also in disease development and response to therapies is expanding. Furthermore, the connection between the microbiota and cancer, especially the link between the gut microbiota and gastrointestinal tumors, is becoming clearer. The interaction between the microbiota and the response to chemotherapies and, more recently, to immunotherapy has been widely studied, and a connection between a peculiar type of microbiota and a better response to these therapies and a different incidence in toxicities has been hypothesized. As knowledge on the gut microbiota increases, interest in the residing microbial population in other systems of our body is also increasing. Consequently, the urinary microbiota is under evaluation for its possible implications in genitourinary diseases, including cancer. Prostate cancer is the most common cancer in the male population; thus, research regarding its etiology and possible factors correlated to disease progression or the response to specific therapies is thriving. This review has the purpose to recollect the current knowledge on the relationship between the human microbiota and prostate cancer.
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Affiliation(s)
- Francesco Massari
- Division of Oncology, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy.
| | - Veronica Mollica
- Division of Oncology, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy.
| | - Vincenzo Di Nunno
- Division of Oncology, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy.
| | - Lidia Gatto
- Division of Oncology, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy.
| | | | - Marina Scarpelli
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, 60126 Ancona, Italy.
| | - Alessia Cimadamore
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, 60126 Ancona, Italy.
| | | | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | | | - Rodolfo Montironi
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, 60126 Ancona, Italy.
| | - Giovanni Brandi
- Oncology Unit, Department of Experimental, Diagnostic and Specialty Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy.
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22
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Reassessment of Routine Midstream Culture in Diagnosis of Urinary Tract Infection. J Clin Microbiol 2019; 57:JCM.01452-18. [PMID: 30541935 PMCID: PMC6425166 DOI: 10.1128/jcm.01452-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/05/2018] [Indexed: 12/11/2022] Open
Abstract
Midstream urine (MSU) culture remains the gold standard diagnostic test for confirming urinary tract infection (UTI). We previously showed that patients with chronic lower urinary tract symptoms (LUTS) below the diagnostic cutoff on MSU culture may still harbor bacterial infection and that their antibiotic treatment was associated with symptom resolution. Here, we evaluated the results of the United Kingdom's MSU culture in symptomatic patients and controls. Next, we compared the bacterial enrichment capabilities of the MSU culture with those of a 50-µl uncentrifuged culture, a 30-ml centrifuged sediment culture, and 16S rRNA gene sequencing. This study was conducted on urine specimens from 33 LUTS patients attending their first clinical appointment (mean age, 48.7 years; standard deviation [SD], 16.5 years), 30 LUTS patients on treatment (mean age, 47.8 years; SD, 16.5 years) whose symptoms had relapsed, and 29 asymptomatic controls (mean age, 40.7 years, SD, 15.7 years). We showed that the routine MSU culture, adopting the UK interpretation criteria tailored to acute UTI, failed to detect a variety of bacterial species, including recognized uropathogens. Moreover, the diagnostic MSU culture was unable to discriminate between patients and controls. In contrast, genomic analysis of urine enriched by centrifugation discriminated between the groups, generating a more accurate understanding of species richness. In conclusion, the United Kingdom's MSU protocol misses a significant proportion of bacteria, which include recognized uropathogens, and may be unsuitable for excluding UTI in patients with LUTS.
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Liu F, Lv L, Jiang H, Yan R, Dong S, Chen L, Wang W, Chen YQ. Alterations in the Urinary Microbiota Are Associated With Cesarean Delivery. Front Microbiol 2018; 9:2193. [PMID: 30258432 PMCID: PMC6143726 DOI: 10.3389/fmicb.2018.02193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 08/27/2018] [Indexed: 12/20/2022] Open
Abstract
Similar to the gut, the bladder contains urinary microbiota, and its bacterial composition and structure are determined by the individual’s health status. Cesarean section is a traumatic event for women and it is correlated with postpartum complications. To better understand the urinary microbiota alterations caused by cesarean section, 16S rDNA sequencing was used to assess urine specimens collected by transurethral catheterization from 30 healthy women undergoing cesarean section pre-delivery (PreD) and post-delivery (PostD). A significant increase in bacterial diversity and more detectable bacteria at the phylum, family, and genus levels was observed in the PostD group compared to the PreD group, indicating that cesarean delivery (a process that includes surgery and delivery) altered the bacterial community. Specifically, the phylum Firmicutes and its affiliated family Lactobacillaceae and genus Lactobacillus dramatically decreased in the PostD group, suggesting that beneficial bacteria decreased after cesarean section, and clinicians should be aware that this might increase the risk of complications. Concurrently, the phylum Proteobacteria and its affiliated bacteria Pseudomonadaceae and Pseudomonas increased in the PostD group compared to the PreD group. This indicates that pathogen growth increases after cesarean section, making it important for clinicians to combat these changes to protect women from infectious diseases. Interestingly, several metabolic pathways, such as metabolism of energy, cofactors and vitamins were strengthened in the PostD group, whereas membrane transport was lessened in this group. This suggests that women’s metabolic disorders might be cured by balancing urinary microbiota. In conclusion, the altered urinary microbiota between the PreD and PostD periods appears to provide insight into how to prevent postpartum metabolic disorders.
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Affiliation(s)
- Fengping Liu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Longxian Lv
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huiyong Jiang
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ren Yan
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shurong Dong
- Key Laboratory of Advanced Micro/Nano Electronic Devices and Smart Systems of Zhejiang, College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou, China
| | - Liping Chen
- Intensive Unit, Affiliated Yancheng Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Wei Wang
- Department of Urology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yong Q Chen
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
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The urinary microbiome in patients with refractory urge incontinence and recurrent urinary tract infection. Int Urogynecol J 2018; 29:1775-1782. [PMID: 29946828 PMCID: PMC6244753 DOI: 10.1007/s00192-018-3679-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/28/2018] [Indexed: 12/19/2022]
Abstract
INTRODUCTION AND HYPOTHESIS Urinary urge incontinence is a chronic, debilitating condition that is difficult to treat. Patients refractory to standard antimuscarinic therapy often experience recurrent urinary tract infections (rUTIs). The microbiota of these refractory patients with rUTI remains unexplored. METHODS A midstream urine (MSU) sample was collected from patients with refractory urge incontinence and coexistent rUTI during acute symptomatic episodes. Culture-based diagnosis was performed using routine microbiological methods. Culture-independent profiling was performed using bacterial 16S RNA profiling. E. coli strain typing was performed by amplicon pyrosequencing of the fimH gene. RESULTS Over 2 years, 39 patients with refractory urge incontinence and coexistent rUTI were studied, yielding 9 severely affected cases. These 9 patients were carefully monitored for a further 2 years, resulting in the collection of 102 MSU samples, 70 of which were diagnosed as UTI (median of 8 UTIs/woman). Culture-independent analysis of 38 of these samples revealed the existence of a diverse urinary microbiota. Strain typing of E. coli identified instances of rUTI caused by the same persisting strain and by new infecting strains. CONCLUSIONS Patients with refractory urge incontinence and coexistent rUTI possess a diverse urinary microbiota, suggesting that persistent bladder colonisation might augment the pathology of their chronic condition.
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Abstract
Urine culture and microscopy techniques are used to profile the bacterial species present in urinary tract infections. To gain insight into the urinary flora, we analyzed clinical laboratory features and the microbial metagenome of 121 clean-catch urine samples. 16S rDNA gene signatures were successfully obtained for 116 participants, while metagenome sequencing data was successfully generated for samples from 49 participants. Although 16S rDNA sequencing was more sensitive, metagenome sequencing allowed for a more comprehensive and unbiased representation of the microbial flora, including eukarya and viral pathogens, and of bacterial virulence factors. Urine samples positive by metagenome sequencing contained a plethora of bacterial (median 41 genera/sample), eukarya (median 2 species/sample) and viral sequences (median 3 viruses/sample). Genomic analyses suggested cases of infection with potential pathogens that are often missed during routine urine culture due to species specific growth requirements. While conventional microbiological methods are inadequate to identify a large diversity of microbial species that are present in urine, genomic approaches appear to more comprehensively and quantitatively describe the urinary microbiome.
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Dysbiosis of urinary microbiota is positively correlated with type 2 diabetes mellitus. Oncotarget 2018; 8:3798-3810. [PMID: 28008148 PMCID: PMC5354796 DOI: 10.18632/oncotarget.14028] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/13/2016] [Indexed: 12/13/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) may be associated with altered urinary microbiota in female patients. We investigated alterations of urinary microbiota in Chinese female T2DM patients, and explored the associations between urinary microbiota and a patient's fasting blood glucose (FBG), urine glucose (UGLU), age, menstrual status, and body mass index (BMI). Midstream urine was collected from 70 female T2DM patients and 70 healthy females. Microbial diversity and composition were analyzed using the Illumina MiSeq sequencing platform by targeting the hypervariable V3-V4 regions of the 16S rRNA gene. We found that bacterial diversity was decreased in T2DM patients. Increased Actinobacteria phylum was positively correlated with FBG, UGLU, and BMI; Lactobacillus abundance decreased with age and menopause; and increased Lactobacillus correlated positively with FBG and UGLU. Decreased Akkermansia muciniphila was associated with FBG and UGLU. Escherichia coli abundance did not differ between the two cohorts. Carbohydrate and amino acid metabolism was reduced in T2DM patients, which were associated with bacterial richness indices such as Chao1 and ACE. Detailed microbiota analysis of well-characterized T2DM patients and healthy controls indicate that Chinese T2DM female patients exhibit dysbiosis of urinary microbiota.
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Miao J, Han N, Qiang Y, Zhang T, Li X, Zhang W. 16SPIP: a comprehensive analysis pipeline for rapid pathogen detection in clinical samples based on 16S metagenomic sequencing. BMC Bioinformatics 2017; 18:568. [PMID: 29297318 PMCID: PMC5751400 DOI: 10.1186/s12859-017-1975-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Pathogen detection in clinical samples based on 16S metagenomic sequencing technology in microbiology laboratories is an important strategy for clinical diagnosis, public health surveillance, and investigations of outbreaks. However, the implementation of the technology is limited by its accuracy and the time required for bioinformatics analysis. Therefore, a simple, standardized, and rapid analysis pipeline from the receipt of clinical samples to the generation of a test report is needed to increase the use of metagenomic analyses in clinical settings. RESULTS We developed a comprehensive bioinformatics analysis pipeline for the identification of pathogens in clinical samples based on 16S metagenomic sequencing data, named 16SPIP. This pipeline offers two analysis modes (fast and sensitive mode) for the rapid conversion of clinical 16S metagenomic data to test reports for pathogen detection. The pipeline includes tools for data conversion, quality control, merging of paired-end reads, alignment, and pathogen identification. We validated the feasibility and accuracy of the pipeline using a combination of culture and whole-genome shotgun (WGS) metagenomic analyses. CONCLUSIONS 16SPIP may be effective for the analysis of 16S metagenomic sequencing data for real-time, rapid, and unbiased pathogen detection in clinical samples.
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Affiliation(s)
- Jiaojiao Miao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206 China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003 China
| | - Na Han
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206 China
| | - Yujun Qiang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206 China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003 China
| | - Tingting Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206 China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003 China
| | - Xiuwen Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206 China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003 China
| | - Wen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206 China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003 China
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Liu F, Ling Z, Xiao Y, Yang Q, Zheng L, Jiang P, Li L, Wang W. Characterization of the urinary microbiota of elderly women and the effects of type 2 diabetes and urinary tract infections on the microbiota. Oncotarget 2017; 8:100678-100690. [PMID: 29246012 PMCID: PMC5725054 DOI: 10.18632/oncotarget.21126] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 09/05/2017] [Indexed: 12/21/2022] Open
Abstract
Evidence shows that urine has complex bacterial profiles with considerable variation between individuals. Aging and age-related conditions can lead to the changes to the composition of urine, which means that the available nutrition for bacteria in the bladder changes with age. We explored the characteristics of the urinary microbiota of elderly women and whether these are associated with age-related conditions such as diabetes and urinary tract infections. An elderly and a non-elderly cohort of women were included. Magnetic beads were used to isolate bacterial genomic DNA, which was analyzed based on the V3-V4 hypervariable region of the 16S rRNA gene. There were significant differences between the elderly and non-elderly regarding thirteen genera of bacteria. For example, the relative abundance of Lactobacillus was dramatically reduced in the elderly compared with the non-elderly; it also decreased with age in the elderly cohort and it was not correlated with urine pH. The relative abundance of Peptococcus increased with age in the elderly while the abundance of Bifidobacteria decreased with age. The abundance of Escherichia coli was the same in the two cohorts, and it increased with water intake and was not associated with urinary tract infection events. Higher levels of Lactobacillus (including Lactobacillus iners) in the elderly were associated with diabetes, and lower levels of Peptoniphilus and Dialister were correlated with asymptomatic bacteriuria. The urinary microbiota of women is affected by ageing, type 2 diabetes mellitus and asymtomatic bacteriuria.
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Affiliation(s)
- Fengping Liu
- Department of Urology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
- Nursing Department, Jiangsu Vocational College of Medicine, Yancheng, Jiangsu, 224005, China
| | - Zongxin Ling
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Qing Yang
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Li Zheng
- Department of Urology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Ping Jiang
- Department of Urology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Wei Wang
- Department of Urology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
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The microbiome in urogenital schistosomiasis and induced bladder pathologies. PLoS Negl Trop Dis 2017; 11:e0005826. [PMID: 28793309 PMCID: PMC5565189 DOI: 10.1371/journal.pntd.0005826] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 08/21/2017] [Accepted: 07/21/2017] [Indexed: 02/01/2023] Open
Abstract
Background Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. Research on the molecular mechanisms influencing the outcomes of bladder infection by Schistosoma haematobium is urgently needed to develop new diagnostics, therapeutics and infection prevention strategies. The objective of the research study was to determine the microbiome features and changes in urine during urogenital schistosomiasis and induced bladder pathologies. Methodology Seventy participants from Eggua, southwestern Nigeria provided morning urine samples and were screened for urogenital schistosomiasis infection and bladder pathologies in a cross-sectional study. Highthroughput NGS sequencing was carried out, targeting the 16S V3 region. Filtered reads were processed and analyzed in a bioinformatics pipeline. Principal findings The study participants (36 males and 34 females, between ages 15 and 65) were categorized into four groups according to status of schistosomiasis infection and bladder pathology. Data analytics of the next-generation sequencing reads revealed that Proteobacteria and Firmicutes dominated and had influence on microbiome structure of both non-infected persons and persons with urogenital schistosomiasis. Furthermore, gender and age influenced taxa abundance independent of infection or bladder pathology. Several taxa distinguished urogenital schistosomiasis induced bladder pathologies from urogenital schistosomiasis infection alone and from healthy persons, including known immune-stimulatory taxa such as Fusobacterium, Sphingobacterium and Enterococcus. Some of these significant taxa, especially Sphingobacterium were projected as markers of infection, while several genera including potentially beneficial taxa such as Trabulsiella and Weissella, were markers of the non-infected. Finally, expected changes in protein functional categories were observed to relate to cellular maintenance and lipid metabolism. Conclusion The urinary microbiome is a factor to be considered in developing biomarkers, diagnostic tools, and new treatment for urogenital schistosomiasis and induced bladder pathologies. The human microbiome comprises bacteria (plus viruses, fungi and archeae) inhabiting different sites of the body. They do not specifically cause diseases, but their presence, absence or population influence body functions. We therefore examined such organisms found along the urinary tract, in persons living in a rural community in Nigeria who considered themselves healthy, were infected with the parasite Schistosoma haematobium or had developed bladder complications along with the parasite infection. We found that these groups shared a large portion of the microbiome, but there were microbial species unique to infected persons and those with bladder complication. Some of these were capable of inducing inflammation and could offer less protection to the host. We also predicted pathways that are affected by the difference in the microbiome.
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Burton EN, Cohn LA, Reinero CN, Rindt H, Moore SG, Ericsson AC. Characterization of the urinary microbiome in healthy dogs. PLoS One 2017; 12:e0177783. [PMID: 28545071 PMCID: PMC5435306 DOI: 10.1371/journal.pone.0177783] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 05/03/2017] [Indexed: 12/31/2022] Open
Abstract
The urinary bladder in healthy dogs has dogmatically been considered free of bacteria. This study used culture independent techniques to characterize the healthy canine urinary microbiota. Urine samples collected by antepubic cystocentesis from dogs without urinary infection were used for DNA extraction. Genital tract and rectal samples were collected simultaneously from the same dogs. The V4 hypervariable region of the 16S rRNA bacterial gene was amplified and compared against Greengenes database for OTU assignment and relative abundance for urine, genital, and rectal samples. After excluding 4 dogs with cultivable bacteria, samples from 10 male (M; 1 intact) and 10 female (F) spayed dogs remained. All samples provided adequate genetic material for analysis. Four taxa (Pseudomonas sp., Acinetobacter sp., Sphingobium sp. and Bradyrhizobiaceae) dominated the urinary microbiota in all dogs of both sexes. These taxa were also detected in the genital swabs of both sexes, while the rectal microbiota differed substantially from the other sample sites. Principal component (PC) analysis of PC1 through PC3 showed overlap of urinary and genital microbiota and a clear separation of rectal swabs from the other sample sites along PC1, which explained 44.94% variation. Surprisingly, the urinary microbiota (mean # OTU 92.6 F, 90.2 M) was significantly richer than the genital (67.8 F, 66.6 M) or rectal microbiota (68.3 F, 71.2 M) (p < 0.0001), with no difference between sexes at any sample site. The canine urinary bladder is not a sterile environment and possesses its own unique and diverse microbiota compared to the rectal and genital microbiota. There was no difference between the sexes at any microbiota sample site (urine, genital, and rectal). The predominant bacterial genus for either sex in the urine and genital tracts was Pseudomonas sp.
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Affiliation(s)
- Erin N. Burton
- Department of Veterinary Pathobiology, University of Missouri College of Veterinary Medicine, Columbia, Missouri, United States of America
- * E-mail:
| | - Leah A. Cohn
- Department of Veterinary Medicine and Surgery, University of Missouri College of Veterinary Medicine, Columbia, Missouri, United States of America
| | - Carol N. Reinero
- Department of Veterinary Medicine and Surgery, University of Missouri College of Veterinary Medicine, Columbia, Missouri, United States of America
| | - Hans Rindt
- Department of Veterinary Medicine and Surgery, University of Missouri College of Veterinary Medicine, Columbia, Missouri, United States of America
| | - Stephen G. Moore
- Division of Animal Sciences, University of Missouri College of Agriculture, Food and Natural Resources, Columbia, Missouri, United States of America
| | - Aaron C. Ericsson
- Department of Veterinary Pathobiology, University of Missouri College of Veterinary Medicine, Columbia, Missouri, United States of America
- University of Missouri Metagenomics Center (MUMC), Columbia, Missouri, United States of America
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Pevsner-Fischer M, Tuganbaev T, Meijer M, Zhang SH, Zeng ZR, Chen MH, Elinav E. Role of the microbiome in non-gastrointestinal cancers. World J Clin Oncol 2016; 7:200-213. [PMID: 27081642 PMCID: PMC4826965 DOI: 10.5306/wjco.v7.i2.200] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 11/15/2015] [Accepted: 02/24/2016] [Indexed: 02/06/2023] Open
Abstract
“The forgotten organ”, the human microbiome, comprises a community of microorganisms that colonizes various sites of the human body. Through coevolution of bacteria, archaea and fungi with the human host over thousands of years, a complex host-microbiome relationship emerged in which many functions, including metabolism and immune responses, became codependent. This coupling becomes evident when disruption in the microbiome composition, termed dysbiosis, is mirrored by the development of pathologies in the host. Among the most serious consequences of dysbiosis, is the development of cancer. As many as 20% of total cancers worldwide are caused by a microbial agent. To date, a vast majority of microbiome-cancer studies focus solely on the microbiome of the large intestine and the development of gastrointestinal cancers. Here, we will review the available evidence implicating microbiome involvement in the development and progression of non-gastrointestinal cancers, while distinguishing between viral and bacterial drivers of cancer, as well as “local” and “systemic”, “cancer-stimulating” and “cancer-suppressing” effects of the microbiome. Developing a system-wide approach to cancer-microbiome studies will be crucial in understanding how microbiome influences carcinogenesis, and may enable to employ microbiome-targeting approaches as part of cancer treatment.
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Sahl JW, Schupp JM, Rasko DA, Colman RE, Foster JT, Keim P. Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data. Genome Med 2015; 7:52. [PMID: 26136847 PMCID: PMC4487561 DOI: 10.1186/s13073-015-0176-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/15/2015] [Indexed: 12/30/2022] Open
Abstract
We describe an approach for genotyping bacterial strains from low coverage genome datasets, including metagenomic data from complex samples. Sequence reads from unknown samples are aligned to a reference genome where the allele states of known SNPs are determined. The Whole Genome Focused Array SNP Typing (WG-FAST) pipeline can identify unknown strains with much less read data than is needed for genome assembly. To test WG-FAST, we resampled SNPs from real samples to understand the relationship between low coverage metagenomic data and accurate phylogenetic placement. WG-FAST can be downloaded from https://github.com/jasonsahl/wgfast.
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Affiliation(s)
- Jason W. Sahl
- />Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ USA
- />Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 USA
| | - James M. Schupp
- />Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ USA
| | - David A. Rasko
- />Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Rebecca E. Colman
- />Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ USA
| | - Jeffrey T. Foster
- />Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 USA
- />Current address: Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH USA
| | - Paul Keim
- />Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, AZ USA
- />Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011 USA
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Horwitz D, McCue T, Mapes AC, Ajami NJ, Petrosino JF, Ramig RF, Trautner BW. Decreased microbiota diversity associated with urinary tract infection in a trial of bacterial interference. J Infect 2015; 71:358-367. [PMID: 26048203 DOI: 10.1016/j.jinf.2015.05.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/19/2015] [Accepted: 05/26/2015] [Indexed: 01/22/2023]
Abstract
BACKGROUND Patients with long-term indwelling catheters are at high risk of catheter-associated urinary tract infection (CAUTI). We hypothesized that colonizing the bladder with a benign Escherichia coli strain (E. coli HU2117, a derivative of E. coli 83972) would prevent CAUTI in older, catheterized adults. MATERIALS AND METHODS Adults with chronic, indwelling urinary catheters received study catheters that had been pre-coated with E. coli HU2117. We monitored the cultivatable organisms in the bladder for 28 days or until loss of E. coli HU2117. Urine from 4 subjects was collected longitudinally for 16S rRNA gene profiling. RESULTS Eight of the ten subjects (average age 70.9 years) became colonized with E. coli HU2117, with a mean duration of 57.7 days (median: 28.5, range 0-266). All subjects also remained colonized by uropathogens. Five subjects suffered invasive UTI, 3 febrile UTI and 2 urosepsis/bacteremia, all associated with overgrowth of a urinary pathogen. Colonization with E. coli HU2117 did not impact bacterial bladder diversity, but subjects who developed infections had less diverse bladder microbiota. CONCLUSIONS Colonization with E. coli HU2117 did not prevent bladder colonization or subsequent invasive disease by uropathogens. Microbial diversity may play a protective role against invasive infection of the catheterized bladder. TRIAL REGISTRATION ClinicalTrials.gov, NCT00554996 http://clinicaltrials.gov/ct2/show/NCT00554996.
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Affiliation(s)
- Deborah Horwitz
- Section of Infectious Diseases, Departments of Medicine and Surgery, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Center for Innovations in Quality, Effectiveness, and Safety, Michael E. DeBakey Veterans Affairs Medical Center, 2002 Holcombe Blvd., Houston, TX, 77030, USA
| | - Tyler McCue
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Abigail C Mapes
- Section of Infectious Diseases, Departments of Medicine and Surgery, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Robert F Ramig
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Barbara W Trautner
- Section of Infectious Diseases, Departments of Medicine and Surgery, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Center for Innovations in Quality, Effectiveness, and Safety, Michael E. DeBakey Veterans Affairs Medical Center, 2002 Holcombe Blvd., Houston, TX, 77030, USA
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Mavromatis CH, Bokil NJ, Totsika M, Kakkanat A, Schaale K, Cannistraci CV, Ryu T, Beatson SA, Ulett GC, Schembri MA, Sweet MJ, Ravasi T. The co-transcriptome of uropathogenic Escherichia coli-infected mouse macrophages reveals new insights into host-pathogen interactions. Cell Microbiol 2015; 17:730-46. [PMID: 25410299 PMCID: PMC4950338 DOI: 10.1111/cmi.12397] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 11/01/2014] [Accepted: 11/11/2014] [Indexed: 12/26/2022]
Abstract
Urinary tract infections (UTI) are among the most common infections in humans. Uropathogenic Escherichia coli (UPEC) can invade and replicate within bladder epithelial cells, and some UPEC strains can also survive within macrophages. To understand the UPEC transcriptional programme associated with intramacrophage survival, we performed host–pathogen co‐transcriptome analyses using RNA sequencing. Mouse bone marrow‐derived macrophages (BMMs) were challenged over a 24 h time course with two UPEC reference strains that possess contrasting intramacrophage phenotypes: UTI89, which survives in BMMs, and 83972, which is killed by BMMs. Neither of these strains caused significant BMM cell death at the low multiplicity of infection that was used in this study. We developed an effective computational framework that simultaneously separated, annotated and quantified the mammalian and bacterial transcriptomes. Bone marrow‐derived macrophages responded to the two UPEC strains with a broadly similar gene expression programme. In contrast, the transcriptional responses of the UPEC strains diverged markedly from each other. We identified UTI89 genes up‐regulated at 24 h post‐infection, and hypothesized that some may contribute to intramacrophage survival. Indeed, we showed that deletion of one such gene (pspA) significantly reduced UTI89 survival within BMMs. Our study provides a technological framework for simultaneously capturing global changes at the transcriptional level in co‐cultures, and has generated new insights into the mechanisms that UPEC use to persist within the intramacrophage environment.
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Affiliation(s)
- Charalampos Harris Mavromatis
- Division of Biological and Environmental Sciences and Engineering, Division of Computer, Electrical and Mathematical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia; Division of Medical Genetics, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
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Whiteside SA, Razvi H, Dave S, Reid G, Burton JP. The microbiome of the urinary tract--a role beyond infection. Nat Rev Urol 2015; 12:81-90. [PMID: 25600098 DOI: 10.1038/nrurol.2014.361] [Citation(s) in RCA: 370] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Urologists rarely need to consider bacteria beyond their role in infectious disease. However, emerging evidence shows that the microorganisms inhabiting many sites of the body, including the urinary tract--which has long been assumed sterile in healthy individuals--might have a role in maintaining urinary health. Studies of the urinary microbiota have identified remarkable differences between healthy populations and those with urologic diseases. Microorganisms at sites distal to the kidney, bladder and urethra are likely to have a profound effect on urologic health, both positive and negative, owing to their metabolic output and other contributions. Connections between the gut microbiota and renal stone formation have already been discovered. In addition, bacteria are also used in the prevention of bladder cancer recurrence. In the future, urologists will need to consider possible influences of the microbiome in diagnosis and treatment of certain urological conditions. New insights might provide an opportunity to predict the risk of developing certain urological diseases and could enable the development of innovative therapeutic strategies.
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Affiliation(s)
- Samantha A Whiteside
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Hassan Razvi
- Division of Urology, Department of Surgery, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Sumit Dave
- Division of Urology, Department of Surgery, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Gregor Reid
- Canadian Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, 268 Grosvenor Street, London, ON N6A 4V2, Canada
| | - Jeremy P Burton
- Division of Urology, Department of Surgery, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
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Kirkup BC. Bacterial Strain Diversity Within Wounds. Adv Wound Care (New Rochelle) 2015; 4:12-23. [PMID: 25566411 DOI: 10.1089/wound.2014.0560] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 06/23/2014] [Indexed: 12/17/2022] Open
Abstract
Significance: Rare bacterial taxa (taxa of low relative frequency) are numerous and ubiquitous in virtually any sample-including wound samples. In addition, even the high-frequency genera and species contain multiple strains. These strains, individually, are each only a small fraction of the total bacterial population. Against the view that wounds contain relatively few kinds of bacteria, this newly recognized diversity implies a relatively high rate of migration into the wound and the potential for diversification during infection. Understanding the biological and medical importance of these numerous taxa is an important new element of wound microbiology. Recent Advances: Only recently have these numerous strains been discovered; the technology to detect, identify, and characterize them is still in its infancy. Multiple strains of both gram-negative and gram-positive bacteria have been found in a single wound. In the few cases studied, the distribution of the bacteria suggests microhabitats and biological interactions. Critical Issues: The distribution of the strains, their phenotypic diversity, and their interactions are still largely uncharacterized. The technologies to investigate this level of genomic detail are still developing and have not been largely deployed to investigate wounds. Future Directions: As advanced metagenomics, single-cell genomics, and advanced microscopy develop, the study of wound microbiology will better address the complex interplay of numerous individually rare strains with both the host and each other.
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Affiliation(s)
- Benjamin C. Kirkup
- FE Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
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Host-specific induction of Escherichia coli fitness genes during human urinary tract infection. Proc Natl Acad Sci U S A 2014; 111:18327-32. [PMID: 25489107 DOI: 10.1073/pnas.1415959112] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the predominant etiological agent of uncomplicated urinary tract infection (UTI), manifested by inflammation of the urinary bladder, in humans and is a major global public health concern. Molecular pathogenesis of UPEC has been primarily examined using murine models of UTI. Translational research to develop novel therapeutics against this major pathogen, which is becoming increasingly antibiotic resistant, requires a thorough understanding of mechanisms involved in pathogenesis during human UTIs. Total RNA-sequencing (RNA-seq) and comparative transcriptional analysis of UTI samples to the UPEC isolates cultured in human urine and laboratory medium were used to identify novel fitness genes that were specifically expressed during human infection. Evidence for UPEC genes involved in ion transport, including copper efflux, nickel and potassium import systems, as key fitness factors in uropathogenesis were generated using an experimental model of UTI. Translational application of this study was investigated by targeting Cus, a bacterial copper efflux system. Copper supplementation in drinking water reduces E. coli colonization in the urinary bladder of mice. Additionally, our results suggest that anaerobic processes in UPEC are involved in promoting fitness during UTI in humans. In summary, RNA-seq was used to establish the transcriptional signature in UPEC during naturally occurring, community acquired UTI in women and multiple novel fitness genes used by UPEC during human infection were identified. The repertoire of UPEC genes involved in UTI presented here will facilitate further translational studies to develop innovative strategies against UTI caused by UPEC.
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