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Prospective examination of the changes in the urinary microbiome induced by transrectal biopsy of the prostate using 16S rRNA gene analysis

Prostate Cancer and Prostatic Diseases volume 22, pages 446–452 (2019)Cite this article

Subjects

Abstract

Objectives

To prospectively examine the changes in microbiota within the urinary tract after transrectal prostate biopsy.

Materials and methods

Data, urine, and fecal samples prospectively collected from 30 patients before and after transrectal biopsy of the prostate. DNA was extracted from urine collected after a prostate massage before and after prostate biopsy, and from fecal samples collected before the biopsy. We sequenced DNA using the bacterial 16S rRNA high-throughput next-generation sequencing and analyzed changes in microbial profiles for taxonomy comparison between samples.

Results

Pre-biopsy urinary microbial profiles contained Lactobacillus and Staphylococcus bacteria. Post-biopsy urinary microbial profiles included lower levels of Lactobacillus and higher levels of Prevotella bacteria. Bacteroides bacteria were predominant in fecal samples. We identified two clustering patterns containing both pre- and post-biopsy urine samples. Cluster 1 had a urine cluster pattern that was distinct from fecal, whereas cluster 2 was similar to fecal. We observed two different modes of microbial changes, 11 patients had both of their urine (pre and post) samples associated with a particular cluster group, whereas others (n = 15) had movement between clusters 1 and 2 following the biopsy procedure. Four patient’s post-biopsy urine microbial profiles clustered very tightly to the fecal microbial profile.

Conclusions

We describe two models of change in the urinary tract microbiota after prostate biopsy using 16S RNA gene analysis. Further research to determine what controls changes in the urinary microbiota after prostate biopsy can help us understand why some patients are more susceptible to develop post-biopsy infections.

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References

  1. Liss MA, Chang A, Santos R, Nakama-Peeples A, Peterson EM, Osann K, et al. Prevalence and significance of fluoroquinolone resistant Escherichia coli in patients undergoing transrectal ultrasound guided prostate needle biopsy. J Urol. 2011;185:1283–8.

    Article  Google Scholar 

  2. Zani EL, Clark OA, Rodrigues Netto N, Jr. Antibiotic prophylaxis for transrectal prostate biopsy. Cochrane Database Syst Rev. 2011;CD006576.

  3. Nam RK, Saskin R, Lee Y, Liu Y, Law C, Klotz LH, et al. Increasing hospital admission rates for urological complications after transrectal ultrasound guided prostate biopsy. J Urol. 2010;183:963–8.

    Article  Google Scholar 

  4. Wolfe AJ, Toh E, Shibata N, Rong R, Kenton K, Fitzgerald M, et al. Evidence of uncultivated bacteria in the adult female bladder. J Clin Microbiol. 2012;50:1376–83.

    Article  Google Scholar 

  5. Brubaker L, Nager CW, Richter HE, Visco A, Nygaard I, Barber MD, et al. Urinary bacteria in adult women with urgency urinary incontinence. Int Urogynecol J. 2014;25:1179–84.

    Article  Google Scholar 

  6. Hilt EE, McKinley K, Pearce MM, Rosenfeld AB, Zilliox MJ, Mueller ER, 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;52:871–6.

    Article  Google Scholar 

  7. Khasriya R, Sathiananthamoorthy S, Ismail S, Kelsey M, Wilson M, Rohn JL, et al. Spectrum of bacterial colonization associated with urothelial cells from patients with chronic lower urinary tract symptoms. J Clin Microbiol. 2013;51:2054–62.

    Article  Google Scholar 

  8. Riesenfeld CS, Schloss PD, Handelsman J. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet. 2004;38:525–52.

    Article  CAS  Google Scholar 

  9. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334:105–8.

    Article  CAS  Google Scholar 

  10. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.

    Article  CAS  Google Scholar 

  11. Shrestha E, White JR, Yu SH, Kulac I, Ertunc O, De Marzo AM, et al. Profiling the urinary microbiome in men with positive versus negative biopsies for prostate cancer. J Urol. 2017;199:161–71.

    Article  Google Scholar 

  12. Mohanty NK, Jolly BB. Incidence of anaerobic bacterial infection following transurethral instrumentation. Indian J Pathol Microbiol. 1996;39:33–6.

    CAS  PubMed  Google Scholar 

  13. Shivde SR, Cooke RP, O’Neill WA, Cowie AG, Lawrence WT, Watson GM. Trimethoprim versus gentamicin for the prevention of bacteriuria following transrectal biopsy of the prostate–do patients need additional anaerobic cover? Urol Int. 2002;69:106–10.

    Article  CAS  Google Scholar 

  14. Duplessis CA, Bavaro M, Simons MP, Marguet C, Santomauro M, Auge B, et al. Rectal cultures before transrectal ultrasound-guided prostate biopsy reduce post-prostatic biopsy infection rates. Urology. 2012;79:556–61.

    Article  Google Scholar 

  15. Evaldson G, Heimdahl A, Kager L, Nord CE. The normal human anaerobic microflora. Scand J Infect Dis Suppl. 1982;35:9–15.

    CAS  PubMed  Google Scholar 

  16. Lloyd AL, Smith SN, Eaton KA, Mobley HL. Uropathogenic Escherichia coli suppresses the host inflammatory response via pathogenicity island genes sisA and sisB. Infect Immun. 2009;77:5322–33.

    Article  CAS  Google Scholar 

  17. Gorvitovskaia A, Holmes SP, Huse SM. Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle. Microbiome. 2016;4:15.

    Article  Google Scholar 

  18. Yu H, Meng H, Zhou F, Ni X, Shen S, Das UN. Urinary microbiota in patients with prostate cancer and benign prostatic hyperplasia. Arch Med Sci. 2015;11:385–94.

    Article  Google Scholar 

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Acknowledgements

This work was supported by Southern Illinois University research grant.

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Authors and Affiliations

  1. Vattikuti Urology Institute, Henry Ford Health System, Detroit, MI, USA

    Shaheen Alanee

  2. Division of Urology, Department of Surgery, Southern Illinois University School of Medicine, Springfield, IL, USA

    Ahmed El-Zawahry, Danuta Dynda & Kevin McVary

  3. Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL, USA

    Mallory Karr & Andrea Braundmeier-Fleming

Authors
  1. Shaheen Alanee
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  2. Ahmed El-Zawahry
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  3. Danuta Dynda
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  4. Kevin McVary
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  5. Mallory Karr
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  6. Andrea Braundmeier-Fleming
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Contributions

SA: Study design, data collection and interpretation, manuscript writing, and supervision. Ahmed El-Zawahry MD, PhD: Study design, data collection and interpretation, manuscript writing. Danuta Dynda MD: Regulatory coordination and patient consenting, data collection and analysis. Kevin McVary MD: Data analysis, critical revision of the paper, and supervision. Mallory Karr: Data analysis and interpretation, manuscript writing. Andrea Braundmeier-Fleming PhD: Study design, data analysis and interpretation, manuscript writing, and supervision.

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Correspondence to Shaheen Alanee.

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Alanee, S., El-Zawahry, A., Dynda, D. et al. Prospective examination of the changes in the urinary microbiome induced by transrectal biopsy of the prostate using 16S rRNA gene analysis. Prostate Cancer Prostatic Dis 22, 446–452 (2019). https://doi.org/10.1038/s41391-018-0120-3

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