Metagenomics in diagnosis and improved targeted treatment of UTI

  • Matthew Dixon
  • Maria Stefil
  • Michael McDonald
  • Truls Erik Bjerklund-Johansen
  • Kurt Naber
  • Florian Wagenlehner
  • Vladimir MouravievEmail author
Topic Paper



The genomic revolution has transformed our understanding of urinary tract infection. There has been a paradigm shift from the dogmatic statement that urine is sterile in healthy people, as we are becoming forever more familiar with the knowledge that bacterial communities exist within the urinary tracts of healthy people. Metagenomics can investigate the broad populations of microbial communities, analysing all the DNA present within a sample, providing comprehensive data regarding the state of the microenvironment of a patient’s urinary tract. This permits medical practitioners to more accurately target organisms that may be responsible for disease—a form of ‘precision medicine’.

Methods and Results

This paper is derived from an extensive review and analysis of the available literature on the topic of metagenomic sequencing in urological science, using the PubMed search engine. The search yielded a total of 406 results, and manual selection of appropriate papers was subsequently performed. Only one randomised clinical trial comparing metagenomic sequencing to standard culture and sensitivity in the arena of urinary tract infection was found.


Out of this process, this paper explores the limitations of traditional methods of culture and sensitivity and delves into the recent studies involving new high-throughput genomic technologies in urological basic and clinical research, demonstrating the advances made in the urinary microbiome in its entire spectrum of pathogens and the first attempts of clinical implementation in several areas of urology. Finally, this paper discusses the challenges that must be overcome for such technology to become widely used in clinical practice.


Metagenomics Next-generation sequencing Urinary tract infection Precision medicine Targeted treatment Infectious urology 



The authors would like to thank Jennifer White, M.S., MB(ASCP)cm for her excellent technical assistance and thorough description of metagenomics and Next Generation Sequence technologies.

Authors’ contributions

M Dixon: manuscript writing/editing. M Stefil: manuscript writing/editing. M McDonald: principal investigator of clinical trial; interpretation of NGS results; manuscript writing/editing. TE Bjerklund Johansen: diagnostic results analysis; manuscript writing/editing. K Naber: diagnostic results analysis; manuscript writing/editing. F Wagenlehner: diagnostic results analysis; manuscript writing/editing. V Mouraviev: project development; interpretation of NGS results; manuscript writing/editing.

Compliance with ethical standards

Conflicts of interest

Dr Mouraviev is a consultant for MicroGenDX.

Informed consent

Informed consent was obtained from all individual participants included in the study.


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Norwich Medical SchoolUniversity of East AngliaNorwichUK
  2. 2.Florida Hospital Celebration HealthCelebrationUSA
  3. 3.University of Central FloridaOrlandoUSA
  4. 4.Department of UrologyOslo University HospitalOsloNorway
  5. 5.Department of UrologyTechnical University of MunichMunichGermany
  6. 6.Department of Urology, Pediatric Urology and AndrologyJustus–Liebig UniversityGiessenGermany
  7. 7.Central Florida Cancer InstituteDavenportUSA

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