INTRODUCTION: Human urine microbiota (UM) research has uncovered associations between composition of microbial communities of the lower urinary tract and various disease states including several reports on the putative link between UM and bladder cancer (BC). The aim of this study was to investigate male UM in patients with BC and controls using catheterised urine specimens unlike in previous studies. METHODS: Urine samples were obtained in theatre after surgical prepping and draping using aseptic catheterisation. DNA was extracted and hypervariable region V4 of the 16S rRNA gene was amplified using 515F and 806R primers. Sequencing was performed on Illumina MiSeq platform. Sequencing data were processed using appropriate software tools. Alpha diversity measures were calculated and compared between groups. Prevalence Interval for Microbiome Evaluation was used to test differences in beta diversity. RESULTS: A total of 63 samples were included in the analysis. Mean age of study subjects was 65.1 years (SD 12.5). Thirty-four men had bladder cancer and 29 participants were undergoing interventions for benign conditions (benign prostate hyperplasia or upper urinary tract stone disease). BC patients had lower UM richness and diversity than controls (83 vs. 139 operational taxonomic units, P = 0.015; Shannon index: 2.46 vs. 2.94, P = 0.049). There were specific taxa enriched in cancer (Veillonella, Varibaculum, Methylobacterium-Methylorubrum) and control groups (Pasteurella, Corynebacterium, Acinetobacter), respectively. CONCLUSION: BC patients had lower bladder microbiota richness and diversity than controls. Specific genera were enriched in cancer and control groups, respectively. These results corroborate some of previous reports while contradicting others. Future microbiota research would benefit from parallel transcriptomic/metabolomic analysis.
After a decade of human urinary microbiota research, little is known about the composition of the urinary virome and its association with health and disease. This study aimed to investigate the presence of 10 common DNA viruses in human urine and their putative association with bladder cancer (BC). Catheterized urine samples were collected from patients undergoing endoscopic urological procedures under anesthesia. After DNA extraction from the samples, viral DNA sequences were detected using real-time PCR. Viruria rates were compared between BC patients and controls. A total of 106 patients (89 males and 17 females) were included in the study. Fifty-seven (53.8%) were BC patients and 49 (46.2%) had upper urinary tract stones or bladder outlet obstruction. The viruses detected in the urine were human cytomegalovirus (2.0%), Epstein-Barr virus (6.0%), human herpesvirus-6 (12.5%), human papillomavirus (15.2%), BK polyomavirus (15.5%), torque teno virus (44.2%), and JC polyomavirus (47.6%), while no adenoviruses, herpes simplex virus 1 and 2, or parvoviruses were found. There were statistically significant differences in HPV viruria rates between cancer patients and controls (24.5% vs. 4.3%, p=0.032 after adjustment for age and gender). Viruria rates increased from benign to non-muscle-invasive and muscle-invasive tumors. Patients with a history of BC have higher HPV viruria rates than controls. Whether this relationship is a causal one remains to be established by further research.
Hrbáček J, Hanáček V, Tláskal V, Saláková M, Čermák P, Tachezy R, Zachoval R. Detekce mikrobiomu horních močových cest u pacientů s urolitiázou: studie proveditelnosti. Cíl: Zjistit, zda existuje mikrobiální osídlení horních močových cest (HMC) a pokud ano, tak liší-li se od mikrobiomu dolních močových cest (DMC). Materiál a metoda: Soubor tvoří pacienti podstupující endoskopický operační zákrok v anestezii pro litiázu HMC. Moč z močového měchýře byla odebrána aseptickou katetrizací, z HMC cystoskopicky zavedeným ureterálním katétrem. Po izolaci DNA byla bakteriální 16S rDNA sekvenována na platformě Illumina MiSeq a získaná data zpracována příslušnými bioinformatickými nástroji. Část izolované DNA byla využita k detekci virových nukleových kyselin pomocí kvantitativní polymerázové řetězové reakce (qPCR). Párové vzorky vždy z HMC a DMC byly porovnány z hlediska struktury bakteriálního společenstva a přítomnosti vybraných DNA virů. Výsledky: Zařazeno bylo devět pacientů (8 mužů a 1 žena) průměrného věku 49,7 let, z nichž u osmi byla provedena sekvenace bakteriálních nukleových kyselin a u sedmi qPCR na přítomnost sedmi běžných DNA virů. Bohatost a diverzita mikrobiomu (alfa diverzita) HMC a DMC nebyla statisticky významně odlišná. Struktura mikrobiálních komunit z HMC a DMC (beta diverzita) vykázala větší podobnost v rámci jednoho pacienta, než byla podobnost všech vzorků HMC, resp. všech vzorků DMC. Virová DNA byla detekována jak v HMC, tak v DMC. Závěr: Výsledky naší pilotní studie poukazují na přítomnost bakteriálního a virového osídlení horních močových cest u pacientů s urolitiázou.
Hrbáček J, Hanáček V, Tláskal V, Saláková M, Čermák P, Tachezy R, Zachoval R. Profiling upper urinary tract microbiota: a feasibility study in patients with urinary stone disease. Aim: To investigate the putative existence of upper urinary tract microbiota and if present, to compare the microbial communities from the kidney with those in the urinary bladder. Patients and Methods: Patients were undergoing endoscopic procedures under anesthesia for upper urinary tract stones. Bladder urine was obtained by aseptic catheterisation, renal urine samples were collected via ureteric catheter inserted into the renal pelvis under cystoscopic and radiographic guidance. Pairwise comparison of urine samples from the same individual were made with regard to their bacteriome and virome. Results: A total of nine patients (8 males, 1 female) provided both samples for analysis. Next-generation sequencing of the V4 hypervariable region of the 16S rDNA using primers 515F and 806R was performed on eight of them and quantitative polymerase chain reaction for the presence of viral nucleic acids of seven common DNA viruses was performed on seven of them. There were no significant differences in alpha diversity measures (number of OTUs, iChao1, ACE, Shannon and Simpson indices) of samples from the kidney and bladder from the same individual. Likewise, microbial communities from the upper and lower urinary tract within the same individual were more similar to each other than samples within the respective group (e.g. all kidney samples). Viral nucleic acids were detected in the upper as well as lower urinary tract. Conclusion: Upper urinary tracts seem to be inhabited by microbial communities whose composition resembles that of the lower urinary tract.
- Klíčová slova
- Human microbiome, upper urinary tract, virome, kidney, urinary bladder, Lidský mikrobiom, horní močový trakt, virom, ledvina, močový měchýř,
- MeSH
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mikrobiologické techniky MeSH
- mikrobiota * MeSH
- močové ústrojí * mikrobiologie MeSH
- pilotní projekty MeSH
- polymerázová řetězová reakce MeSH
- sekvenční analýza MeSH
- studie proveditelnosti MeSH
- urolitiáza mikrobiologie MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
BACKGROUND: Since the discovery of the human urinary microbiota (UM), alterations in microbial community composition have been associated with various genitourinary conditions. The aim of this exploratory study was to examine possible associations of UM with clinical conditions beyond the urinary tract and to test some of the conclusions from previous studies on UM. METHODS: Catheterised urine samples from 87 men were collected prior to endoscopic urological interventions under anaesthesia. The composition of the bacterial community in urine was characterized using the hypervariable V4 region of the 16S rRNA gene. Samples from 58 patients yielded a sufficient amount of bacterial DNA for analysis. Alpha diversity measures (number of operational taxonomic units, ACE, iChao2, Shannon and Simpson indices) were compared with the Kruskal-Wallis test. Beta diversity (differences in microbial community composition) was assessed using non-metric dimensional scaling in combination with the Prevalence in Microbiome Analysis algorithm. RESULTS: Differences in bacterial richness and diversity were observed for the following variables: age, diabetes mellitus, dyslipidemia, smoking status and single-dose preoperative antibiotics. Differences in microbial community composition were observed in the presence of chronic kidney disease, lower urinary tract symptoms and antibiotic prophylaxis. CONCLUSIONS: UM appears to be associated with certain clinical conditions, including those unrelated to the urinary tract. Further investigation is needed before conclusions can be drawn for diagnostics and treatment.
- Publikační typ
- časopisecké články MeSH
Considerable variation exists in the methodology of urinary microbiota studies published so far including the cornerstone of any biomedical analysis: sample collection. The aim of this study was to compare the urinary microbiota of first-catch voided urine (FCU), mid-stream voided urine (MSU) and aseptically catheterised urine in men and define the most suitable urine sampling method. Forty-nine men (mean age 71.3 years) undergoing endoscopic urological procedures were enrolled in the study. Each of them contributed three samples: first-catch urine (FCU), mid-stream urine (MSU) and a catheterised urine sample. The samples were subjected to next-generation sequencing (NGS, n = 35) and expanded quantitative urine culture (EQUC, n = 31). Using NGS, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla in our population. The most abundant genera (in order of relative abundance) included: Prevotella, Veillonella, Streptococcus, Porphyromonas, Campylobacter, Pseudomonas, Staphylococcus, Ezakiella, Escherichia and Dialister. Eighty-two of 105 samples were dominated by a single genus. FCU, MSU and catheterised urine samples differed significantly in three of five alpha-diversity measures (ANOVA, p < 0.05): estimated number of operational taxonomic units, Chao1 and abundance-based coverage estimators. Beta-diversity comparisons using the PIME method (Prevalence Interval for Microbiome Evaluation) resulted in clustering of urine samples according to the mode of sampling. EQUC detected cultivable bacteria in 30/31 (97%) FCU and 27/31 (87%) MSU samples. Only 4/31 (13%) of catheterised urine samples showed bacterial growth. Urine samples obtained by transurethral catheterisation under aseptic conditions seem to differ from spontaneously voided urine samples. Whether the added value of a more exact reflection of the bladder microbiota free from urethral contamination outweighs the invasiveness of urethral catheterisation remains to be determined.
- MeSH
- analýza moči MeSH
- biodiverzita * MeSH
- komorbidita MeSH
- lidé středního věku MeSH
- lidé MeSH
- metagenomika metody MeSH
- mikrobiota * MeSH
- močové ústrojí mikrobiologie MeSH
- senioři MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Předpoklad sterility zdravé moči byl v posledních letech vyvrácen průkazem existence močového mikrobiomu (MM). Rozšířená kvantitativní močová kultivace poskytuje inokulu delší čas k inkubaci za rozličných růstových podmínek a dokazuje přítomnost bakterií ve vzorcích hodnocených standardní kultivací jako negativní. Masivní paralelní sekvenování (NGS) s vysokou citlivostí detekuje bakteriální gen pro ribozomální 16S RNA a podle variabilních sekvencí tohoto genu lze daný mikroorganismus taxonomicky zařadit. Lidský MM tvoří převážně taxony spadající do kmenů Proteobacteria, Firmicutes, Bacteroidetes a Actinobacteria. U žen dominuje rod Lactobacillus, u mužů není rozdělení urotypů zatím zcela objasněno. Změny ve složení MM jsou dle dosavadních poznatků spojovány s funkčními poruchami urogenitálního traktu (symptomy dolních močových cest, urgentní inkontinence, neurogenní měchýř, chronická renální insuficience), syndromem chronické pánevní bolesti, intersticiální cystitidou a dokonce s nádory močového měchýře. MM může potenciálně plnit řadu úloh, které bude teprve třeba objasnit, a předpokládá se jeho diagnostické i terapeutické využití.
The assumption of healthy urine being sterile has been contradicted recently when the existence of urinary microbiota (UM) was revealed. Extended quantitative urine culture is based on longer incubation times in a wide selection of diverse growth conditions; bacteria are detected even in samples reported as negative by the standard urine culture protocol. Next‑generation sequencing helps with taxonomic assignment of prokaryotic DNA fragments according to the sequence in hypervariable regions of the 16S rRNA gene. Human UM is composed of the phyla Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria. Female UM is dominated by the genus Lactobacillus, male urotypes have not been assigned with certainty to date. Changes in UM have been associated with functional disorders of the genitourinary tract (lower urinary tract symptoms, urge urinary incontinence, neurogenic bladder dysfunction, chronic kidney disease), chronic pelvic pain syndrome, interstitial cystitis and even with urinary bladder cancer. UM may potentially play many a role; what they are is a matter of ongoing research. UM might be a useful tool in the diagnostics and therapy of disease.
- MeSH
- kultivační techniky MeSH
- lidé MeSH
- mikrobiota * MeSH
- moč mikrobiologie MeSH
- urogenitální systém * mikrobiologie MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- přehledy MeSH
BACKGROUND: While the resistance rates of commonly detected uropathogens are well described, those of less frequent Gram-negative uropathogenic bacteria have seldom been reported. The aim of this study was to examine the resistance rates of less frequent uropathogenic Gram-negatives in a population of patients treated in a Department of Urology of a tertiary referral centre in Central Europe over a period of 9 years. METHODS: Data on all positive urine samples from urological in- and out-patients were extracted form the Department of Clinical Microbiology database from 2011 to 2019. Numbers of susceptible and resistant isolates per year were calculated for these uropathogens: Acinetobacter spp. (n = 74), Citrobacter spp. (n = 60), Enterobacter spp. (n = 250), Morganella morganii (n = 194), Providencia spp. (n = 53), Serratia spp. (n = 82) and Stenotrophomonas maltophilia (n = 27). Antimicrobial agents selected for the survey included: ampicillin, amoxicillin/clavulanic acid, piperacillin/tazobactam; cefuroxime, cefotaxime, ceftazidime and cefepime; ciprofloxacin and ofloxacin; gentamicin and amikacin; ertapenem, meropenem and imipenem; trimethoprim-sulfamethoxazole (co-trimoxazole), nitrofurantoin and colistin. RESULTS: Penicillin derivatives have generally poor effect except piperacillin/tazobactam. Cefuroxime is not efficient unlike cefotaxime (except against Acinetobacter spp. and S. maltophilia). Susceptibility to fluoroquinolones is limited. Amikacin is somewhat more efficient than gentamicine but susceptibilities for both safely exceed 80%. Nitrofurantoin shows virtually no efficiency. Cotrimoxazole acts well against Citrobacter spp., Serratia spp. and it is the treatment of choice for S. maltophilia UTIs. Among carbapenems, ertapenem was less efficient than meropenem and imipenem except for S. maltophilia whose isolates were mostly not suceptible to any carbapenems. CONCLUSIONS: Uropathogenic microorganisms covered in this report are noteworthy for their frequently multi-drug resistant phenotypes. Knowledge of resistance patterns helps clinicians choose the right empirical antibiotic treatment when the taxonomical assignment of the isolate is known but sensitivity results are pending.
- MeSH
- bakteriální léková rezistence * MeSH
- časové faktory MeSH
- centra terciární péče MeSH
- gramnegativní bakterie účinky léků izolace a purifikace MeSH
- infekce močového ústrojí mikrobiologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- nemocniční oddělení MeSH
- retrospektivní studie MeSH
- senioři MeSH
- urologie MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- pozorovací studie MeSH
- Geografické názvy
- Česká republika MeSH
Monitoring of pathogen resistance profiles is necessary to guide empirical antibiotic therapy before culture and sensitivity results become available. The aim of this study was to describe current antibiotic resistance patterns of five most frequent causative uropathogens in a Department of Urology of a tertiary referral centre in Central Europe over a period of nine years. The Hospital Department of Clinical Microbiology database was used to extract data on all positive urine samples from inpatients in the Department of Urology between 2011 and 2019. Numbers of susceptible and resistant isolates per year were calculated for five most frequent uropathogens: Escherichia coli, Enterococcus spp., Klebsiella spp., Pseudomonas aeruginosa, and Proteus spp. Antimicrobial agents selected for the survey included: ampicillin, amoxicillin/clavulanic acid, piperacillin/tazobactam; cefuroxime, cefotaxime, ceftazidime and cefepime; ciprofloxacin and ofloxacin; gentamicin and amikacin; ertapenem, meropenem and imipenem; trimethoprim-sulfamethoxazole (co-trimoxazole), nitrofurantoin, colistin, and vancomycin. High resistance rates of Gram-negative uropathogens were demonstrated to most common antimicrobials, with statistically significant increasing or decreasing trends in some cases. No carbapenem-resistant Enterobacteriaceae were isolated. Vancomycin-resistant Enterococcus spp. strains were rare in our population.
- Publikační typ
- časopisecké články MeSH
Gram negativní bakterie jsou nejčastější patogeny způsobující infekce močových cest Celosvětově dochází k nárůstu incidence rezistentních bakterií. Prevence a léčba infekcí způsobených rezistentními bakteriemi se stává závažným medicínským, sociálním a finančním problémem Jedním z největších problémů zůstávají nozokomiální infekce a infekce spojené s invazivními vstupy. Znalost mechanismu rezistence a lokální epidemiologické situace napomáhá ke správné volbě empirické antibiotické terapie v situaci, kdy nejsou k dispozici výsledky kultivačního vyšetření.
Gram-negative bacteria are the most common pathogens causing urinary tract infections. The incidence of bacterial resistance is increasing worldwide. Prevention and treatment of infections caused by resistant bacteria are becoming a vast medical, social and financial problem. The biggest problems are health care-associated infections and infections related to invasive lines. Knowledge of resistance mechanisms and local epidemiological situation help with effective initiation of empirical antibiotic therapy.
