Metagenomics in diagnosis and improved targeted treatment of UTI

Abstract

The genomic revolution has transformed our understanding of urinary tract infection (UTI). 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 broad populations of microbial communities, analyzing 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'. 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 research, demonstrating the advances made in the role of urinary microbiome in a whole spectrum of pathologies from urinary tract infection, to prostate cancer. Finally, we discuss the challenges that must be overcome for such technology to become widely used in clinical practice.

A New Gold Rush: A Review of Current and Developing Diagnostic Tools for Urinary Tract Infections

“…While the presence of organisms are reported as a proportion relative to others, this does not definitively translate to identification of a causative organism. As stated by Dixon et al, future work is needed in order to identify prediction algorithms which would aid in NGS output analysis and targeted treatment [64]. This will also help to prevent overtreatment of organisms that may be part of the "normal" urinary microbiome.…”

“…In their current state, the databases are public in nature and can be annotated by anyone. Unfortunately, this leads to annotations of sequences and genomes that are incorrect [5,64]. Without accurate reference materials, it is difficult to trust the results of NGS outputs being used to make clinical decisions outside the context of a clinical trial.…”

Infections in urology: slow progress reflected in clinical practice

“…Based on the likelihood of these predictions, action can be taken to design targeted antibiotic management. This would indeed represent progress for individualized patient care [7].…”

Urogenital infections

“…Novel diagnostic techniques such as metagenomics are discussed by Dixon et al [5]. Their paper explores the limitations of traditional methods of culture and sensitivity and discusses 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.…”

“…Vladimir Mouraviev, who is the co-author of two papers in this topic issue [3,5], died of acute illness during the preparation of this topic issue. He was a highly valued member of the European Section of Infection in Urology of EAU, a dedicated scientist, investigating most modern technology, such as next generation sequencing in microbiological diagnosis, and a good friend to all of the authors.…”