Modern concepts of the urinary tract microbiome in children

Мұқаба

Дәйексөз келтіру

Толық мәтін

Ашық рұқсат Ашық рұқсат
Рұқсат жабық Рұқсат берілді
Рұқсат жабық Рұқсат ақылы немесе тек жазылушылар үшін

Аннотация

Introduction. The second most common reason for prescribing antibiotics in children is urinary tract infection (UTI). Since antimicrobial stewardship is a priority in the further development of strategies of the treatment of children with UTIs, the need to form an optimal model for its diagnosis and treatment is relevant in pediatric urology.

Aim. To analyze domestic and foreign publications devoted to the study of the urinary tract microbiome in children.

Results. Cultivation or culturing methods continue to be considered the “gold standard” in many countries for the diagnosis of bacterial infections, although more sensitive and specific technologies are available. A urine sample was previously considered sterile if uropathogens did not grow using standard techniques. It remains unclear whether standard microbial culturing methods are adequate to determine species diversity and identify all microorganisms capable of causing UTIs.

A study of the bladder microbiome and maintenance of its homeostasis to prevent inflammatory lower urinary tract diseases is an emerging area of research. It is known that the bladder of a healthy person contains non-uropathogenic bacteria, such as Lactobacillus, which are believed to function as an immune system and protect against the effects of uropathogens.

Толық мәтін

Рұқсат жабық

Авторлар туралы

Filipp Turov

GBUZ V.F. Voyno-Yasenetsky Scientific and Practical Center of Specialized Medical Care for Children of the Moscow Health Department

Email: TurovFO@zdrav.mos.ru
ORCID iD: 0000-0002-9301-7586

Ph.D., leading researcher, pediatric urologist and andrologist

Ресей, 119620, Moscow, Aviatorov St., Building 38

Sergey Yatsyk

FGBOU DPO RMANPO

Email: makadamia@yandex.ru
ORCID iD: 0000-0001-6966-1040

Corresponding Member of the RAS, Ph.D., MD, Professor, Professor of the Department of Pediatric Surgery 

Ресей, 125993, Moscow, Barrikadnaya St., 2/1, Building 1

Aleksey Krapivkin

GBUZ V.F. Voyno-Yasenetsky Scientific and Practical Center of Specialized Medical Care for Children of the Moscow Health Department; N.I. Pirogov Russian National Research Medical University of the Ministry of Health of the Russian Federation

Email: npcmpd@zdrav.mos.ru
ORCID iD: 0000-0002-4653-9867

Ph.D., MD, Director, professor at the Department of Hospital Pediatrics

Ресей, 119620, Moscow, Aviatorov St., Building 38

Granitovich Vrublevsky

GBUZ V.F. Voyno-Yasenetsky Scientific and Practical Center of Specialized Medical Care for Children of the Moscow Health Department; N.I. Pirogov Russian National Research Medical University of the Ministry of Health of the Russian Federation

Email: VrublevskijSG@zdrav.mos.ru
ORCID iD: 0000-0001-9400-7673

Ph.D., MD, Deputy Chief for Surgery, professor at the Department of Pediatric Surgery, Chief pediatric urologist and andrologist at the Moscow Health Department

Ресей, 119620, Moscow, Aviatorov St., Building 38

Ilgar Mamedov

GBUZ V.F. Voyno-Yasenetsky Scientific and Practical Center of Specialized Medical Care for Children of the Moscow Health Department

Email: is_mamedov@mail.ru
ORCID iD: 0000-0003-0783-2873

Ph.D., leading researcher 

Ресей, 119620, Moscow, Aviatorov St., Building 38

Oleg Perevezentsev

GBUZ V.F. Voyno-Yasenetsky Scientific and Practical Center of Specialized Medical Care for Children of the Moscow Health Department

Хат алмасуға жауапты Автор.
Email: PZPO@mail.ru
ORCID iD: 0000-0002-7070-3209

Ph.D., laboratory geneticist

Ресей, 119620, Moscow, Aviatorov St., Building 38

Әдебиет тізімі

  1. Sender R, Fuchs S., Milo R. Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans. Cell. 2016;164:337–340.
  2. Amon P., Sanderson, I. What is the microbiome? Arch. Dis. Child. Educ. Pract. Ed. 2017;102:258–261.
  3. Locey K.J., Lennon J.T. Scaling laws predict global microbial diversity. Proc. Natl. Acad. Sci. U. S. A. 2016;113:5970–5975.
  4. Frank D.N. et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. U. S. A. 2007;104:13780–13785.
  5. Naboka Yu.L., Kotieva V.M., Kogan M.I. The role of infectious complications in the overall structure of complications in urethroplasty, treatment and antibiotic prophylaxis: a systematic review. Bulletin of Urology. 2023;11(4):141–150. doi: 10.21886/2308-6424-2023-11-4-141-150.
  6. Naboka Yu.L., Alkina A.K., Kogan M.I. et al. Monitoring of urine microbiota and antibiotic resistance of uropathogens in one urology hospital. Bulletin of Urology. 2020;8(3):47–57. doi: 10.21886/2308-6424-2020-8-3-47-57.
  7. Cho I., Blaser M.J. The human microbiome: At the interface of health and disease. Nat. Rev. Genet. 2012;13:260–270.
  8. Metchnikoff E. In: Mitchell PC. editor. The Prolongation of Life. Optimistic Studies. New York: G P Putnam’s Sons; 1910. 96 p.
  9. Podolsky S.H. Metchnikoff and the microbiome. Lancet. 2012;380:1810–11 doi: 10.1016/S0140-6736(12)62018-2.
  10. Thomas-White K. et al. The bladder is not sterile: history and current discoveries on the urinary microbiome. Current bladder dysfunction reports. 2016;11:18–24.
  11. Xu R. et al. A new gold rush: a review of current and developing diagnostic tools for urinary tract infections. Diagnostics. 2021;11(3):479.
  12. KASS E.H. Bacteriuria and the diagnosis of infections of the urinary tract; with observations on the use of methionine as a urinary antiseptic. A.M.A. archives of internal medicine. 1957;100(5):709–714.
  13. Stamm W.E., Counts G.W., Running Katherine R., W.H.C.S. Diagnosis of Coliform Infection in Acutely Dysuric Women N Engl J Med. 1982;307:463–468.
  14. Latham R.H. et al. Laboratory diagnosis of urinary tract infection in ambulatory women. JAMA. 1985;254(23):3333–36.
  15. Wolfe A.J., Brubaker Linda. «Sterile Urine» and the Presence of Bacteria. Eur Urology. 2015;68(2):173–74. doi: 10.1016/j.eururo.2015.02.041
  16. Hilt Evann E. et al. Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. J Clin Microbiol 2014;52(3): 871–876.
  17. Perez-Carrasco V., Soriano-Lerma A., Soriano M., Gutiérrez-Fernández J., Garcia-Salcedo J.A. Urinary Microbiome: Yin and Yang of the Urinary Tract. Front. Cell. Infect. Microbiol. 2021;11:421.
  18. Karstens L. et al. Does the urinary microbiome play a role in urgency urinary incontinence and its severity? Frontiers in cellular and infection microbiology. 2016;6 :78.
  19. Pearce M.M., Hilt E.E., Rosenfeld A.B., Zilliox M.J., Thomas-White K., Fok C., Kliethermes S., Schreckenberger P.C., Brubaker L., Gai X., Wolfe A.J. The female urinary microbiome: a comparison of women with and without urgency urinary incontinence. mBio. 2014 Jul 8;5(4):e01283-14. doi: 10.1128/mBio.01283-14. PMID: 25006228; PMCID: PMC4161260.
  20. Van der Zee, Anneke et al. Molecular Diagnosis of Urinary Tract Infections by Semi-Quantitative Detection of Uropathogens in a Routine Clinical Hospital Setting. PloS One 2016;11(3):e0150755. doi: 10.1371/journal.pone.0150755
  21. Neugent M.L. et al. Advances in understanding the human urinary microbiome and its potential role in urinary tract infection. MBio. 2020;11(2).
  22. Hilt E.E., McKinley K., Pearce M.M., Rosenfeld A.B., Zilliox M.J., Mueller E.R., Brubaker L., Gai X., Wolfe A.J., Schreckenberger PC2014. Urine Is Not Sterile: Use of Enhanced Urine Culture Techniques To Detect Resident Bacterial Flora in the Adult Female Bladder. J Clin Microbiol 52.
  23. Harding C. et al. How can we improve investigation, prevention and treatment for recurrent urinary tract infections–ICI‐RS 2018. Neurourology and Urodynamics. 2019;38:S90-S97.
  24. Price T.K. et al. The clinical urine culture: enhanced techniques improve detection of clinically relevant microorganisms. Journal of clinical microbiology. 2016;54(5):1216–1222.
  25. Thapaliya J., Khadka P., Thapa S., Gongal C. Enhanced quantitative urine culture technique, a slight modification, in detecting under-diagnosed pediatric urinary tract infection. BMC Res Notes. 2020;13(5):5. doi: 10.1186/s13104-019-4875-y
  26. Hochstedler B.R., Burnett L., Price T.K., Jung C., Wolfe A.J., Brubaker L. Urinary microbiota of women with recurrent urinary tract infection: collection and culture methods. Int Urogynecol J. 2021;33(3):563–70. doi: 10.1007/s00192-021-04780-4
  27. Atay Nursel, Arife Uslu Gökceoğlu. Evaluation of urinalysis and urine culture in children with first-time urinary tract infection. Turkish J Urol. 2021;47(3):242–247. doi: 10.5152/tud.2020.20387.
  28. Hoffman C, Siddiqui NY, Fields I, Gregory WT, Simon HM, Mooney MA, Wolfe AJ, Karstens L. Species-Level Resolution of Female Bladder Microbiota from 16S rRNA Amplicon Sequencing. mSystems. 2021 Oct 26;6(5):e0051821. doi: 10.1128/mSystems.00518-21. Epub 2021 Sep 14. PMID: 34519534; PMCID: PMC8547459.
  29. Zheng J., Wittouck S., Salvetti E., Franz C.M.A.P., Harris H.M.B., Mattarelli P. et al. A taxonomic note on the genus Lactobacillus: description of 23 novel genera, emended description of the genus Lactobacillus beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol. 2020;70(4):2782–858. doi: 10.1099/ijsem.0.004107
  30. Shevchenko S.G., Radey M., Tchesnokova V., Kisiela D., Sokurenko E.V. Escherichia coli clonobiome: assessing the strain diversity in feces and urine by deep amplicon sequencing. Applied and Environmental Microbiology. 2019;85(23):e01866-19.
  31. Lewis Debbie A. et al. The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults. Frontiers in cellular and infection microbiology. 2013;3:41.
  32. Siddiqui Huma et al. Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC microbiology. 2011;11:1–12.
  33. Jones-Freeman B. et al. The microbiome and host mucosal interactions in urinary tract diseases. Mucosal immunology. 2021;14(4):779–792. doi: 10.1038/s41385-020-00372-5
  34. Mulder M.D. Radjabzadeh R.J. et al. The effect of antimicrobial drug use on the composition of the genitourinary microbiota in an elderly population. BMC microbiology. 2019;19:1–7.
  35. Hasman Henrik et al. Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol. 2014;52(1):139–46. doi: 10.1128/JCM.02452-13
  36. Barraud O., Ravry C., François B., Daix T., Ploy M.C., Vignon P. Shotgun metagenomics for microbiome and resistome detection in septic patients with urinary tract infection. International journal of antimicrobial agents. 2019;54(6):803–808.
  37. Moustafa A. et al. Microbial metagenome of urinary tract infection. Scientific reports. 2018;8(1):4333.
  38. Karstens L. et al. Community profiling of the urinary microbiota: considerations for low-biomass samples. Nature Reviews Urology. 2018;15(12):735–749.
  39. Brubaker L., Gourdine J.-.P, Siddiqui N.Y., Holland A., Halverson T., Limeria R., et al. Forming consensus to advance urobiome research. Msystems. 2021;6(4):e01371–20. doi: 10.1128/msystems.01371-20
  40. Mulcrone A.E., Parikh M., Ahmad F. . Reducing infant catheterization in the emergency department through clean-catch urine collection. Journal of the American College of Emergency Physicians Open. 2020;1(6):1533–1541.
  41. Herreros M.L. et al. Urine collection methods for infants under 3 months of age in clinical practice. Pediatric Nephrology. 2021;36(12):3899–3904.
  42. Bundgaard-Nielsen C. et al. Voided urinary microbiota is stable over time but impacted by post void storage. Frontiers in Cellular and Infection Microbiology. 2020;10:435.
  43. Turov F.O., Zorkin S.N. et al. Do children with vesicoureteral reflux need antibiotic prophylaxis? Modern view of the big problem. Pediatria n.a. G.N. Speransky. 2020;99(5):265–271. doi: 10.24110/0031-403X-2020-99-5-265-271.
  44. Leung A.K.C. et al. Urinary Tract Infection in Children. Recent patents on inflammation & allergy drug discovery. 2019;13(1):2–18. doi: 10.2174/1872213X13666181228154940
  45. Nielsen K.L. et al. Whole-genome comparison of urinary pathogenic Escherichia coli and faecal isolates of UTI patients and healthy controls. International Journal of Medical Microbiology. 2017;307(8):497–507.
  46. Magruder Matthew et al. Gut uropathogen abundance is a risk factor for development of bacteriuria and urinary tract infection. Nature communications. 2019;10(1):5521.
  47. Thänert R. et al. Comparative genomics of antibiotic-resistant uropathogens implicates three routes for recurrence of urinary tract infections. MBio 2019;10(4):1110–1128.
  48. Thomas-White K. et al. Culturing of female bladder bacteria reveals an interconnected urogenital microbiota. Nature communications. 2018;9(1):1557.
  49. Kinneman L. et al. Assessment of the urinary microbiome in children younger than 48 months. The Pediatric infectious disease journal. 2020;39(7):565–570.
  50. Fredsgaard L. et al. Description of the voided urinary microbiota in asymptomatic prepubertal children – A pilot study. Journal of Pediatric Urology. 2021;17(4):545. e1-545. e8.
  51. Tett A., Pasolli E., Masetti G., Ercolini D., Segata N. Prevotella diversity, niches and interactions with the human host. Nat Rev Microbiol. 2021;19(9):585–99. doi: 10.1038/s41579-021-00559-y
  52. Palmer C., Bik E.M., DiGiulio D.B., Relman D.A., Brown P.O. Development of the human infant intestinal microbiota. PLoS Biol. 2007;5(7):e177. doi: 10.1371/journal.pbio.0050177
  53. Bučević Popović V. et al. The urinary microbiome associated with bladder cancer. Scientific reports. 2018;8(1):12157.
  54. Aragon I.M. et al. The urinary tract microbiome in health and disease. European urology focus. 2018;4(1):128–138.
  55. Magistro G., Stief C.G. The urinary tract microbiome: the answer to all our open questions? European Urology Focus. 2019;5(1):36–38.
  56. Gerber D., Forster C. S., Hsieh M. The role of the genitourinary microbiome in pediatric urology: a review. Current urology reports. 2018;19:1–8.
  57. Cole E., Shaikh N., Forster C.S. The pediatric urobiome in genitourinary conditions: A narrative review. Pediatric Nephrology. 2022. С. 1–10.
  58. Johnson C.L., Versalovic J. The human microbiome and its potential importance to pediatrics. Pediatrics. 2012;129(5):950–960.
  59. Brubaker L., Wolfe A.J. The new world of the urinary microbiota in women. American journal of obstetrics and gynecology. 2015;213(5):644–649.
  60. Gerber D., Forster C.S., Hsieh M. The role of the genitourinary microbiome in pediatric urology: a review. Current urology reports. 2018;19:1–8.
  61. Yang S. et al. Diagnosis and management of bladder bowel dysfunction in children with urinary tract infections: a position statement from the International Children’s Continence Society. Pediatric Nephrology. 2018;33:2207–2219.
  62. Shaikh N. et al. Recurrent urinary tract infections in children with bladder and bowel dysfunction. Pediatrics. 2016;137(1).
  63. Mulder M. et al. The effect of antimicrobial drug use on the composition of the genitourinary microbiota in an elderly population. BMC microbiology. 2019;19:1–7.
  64. Lev-Sagie A. et al. Vaginal microbiome transplantation in women with intractable bacterial vaginosis. Nature medicine. 2019;25(10):1500–1504.

Қосымша файлдар

Қосымша файлдар
Әрекет
1. JATS XML
Жүктеу
2. Figure. Scheme of methods of urine sampling and microbiome isolation (visual visualization)

Жүктеу (213KB)
Метадеректер

© Bionika Media, 2025