New and developing diagnostic technologies for urinary tract infections

Key Points

  • UTIs are increasingly caused by multidrug-resistant organisms as a result of the overuse of empirical, broad-spectrum antibiotic therapy

  • Antimicrobial susceptibility, determined by the phenotypic response to antibiotic exposure, is key for clinical decision making for treating the wide variety of uropathogens and identifying resistance markers

  • Existing technologies (such as PCR, fluorescence in situ hybridization, and mass spectrometry) and new technologies (such as droplet microfluidic and biosensor platforms) need to focus on direct urine testing to expedite objective diagnoses

  • Integrated biosensor–microfluidic platforms have the most potential for point-of-care testing, as they facilitate direct urine analysis and can encompass all assay steps in a compact device

  • New technologies are a key step towards improved antimicrobial stewardship

Abstract

Timely and accurate identification and determination of the antimicrobial susceptibility of uropathogens is central to the management of UTIs. Urine dipsticks are fast and amenable to point-of-care testing, but do not have adequate diagnostic accuracy or provide microbiological diagnosis. Urine culture with antimicrobial susceptibility testing takes 2–3 days and requires a clinical laboratory. The common use of empirical antibiotics has contributed to the rise of multidrug-resistant organisms, reducing treatment options and increasing costs. In addition to improved antimicrobial stewardship and the development of new antimicrobials, novel diagnostics are needed for timely microbial identification and determination of antimicrobial susceptibilities. New diagnostic platforms, including nucleic acid tests and mass spectrometry, have been approved for clinical use and have improved the speed and accuracy of pathogen identification from primary cultures. Optimization for direct urine testing would reduce the time to diagnosis, yet these technologies do not provide comprehensive information on antimicrobial susceptibility. Emerging technologies including biosensors, microfluidics, and other integrated platforms could improve UTI diagnosis via direct pathogen detection from urine samples, rapid antimicrobial susceptibility testing, and point-of-care testing. Successful development and implementation of these technologies has the potential to usher in an era of precision medicine to improve patient care and public health.

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Figure 1: Overview of the clinical workflow of existing and future diagnostic technologies for UTI.
Figure 2: Biosensor-based diagnosis of UTI.
Figure 3: Single-cell analysis of antimicrobial susceptibility.

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Acknowledgements

We thank members of the Liao and Wang Laboratories for helpful discussions. Research is supported in part by National Institutes of Health (NIH)/National Institute of Allergy and Infectious Diseases grant R01 AI117032 (J.C.L. and T.W.) and U01 AI082457 (J.C.L.).

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All authors made substantial contributions to discussions of content and reviewed and edited the article before submission. M.D., K.E.M., N.B., T.-H.W. and J.C.L. researched data for the article and M.D., K.E.M., T.-H.W. and J.C.L. wrote the manuscript.

Corresponding author

Correspondence to Joseph C. Liao.

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The authors declare no competing financial interests.

PowerPoint slides

Glossary

Antimicrobial susceptibility

Antimicrobial susceptibility refers to phenotypic response of the bacteria in the presence of antimicrobial agents.

Multidrug-resistant pathogens

Bacterial pathogens that have developed resistance to multiple antimicrobials. Common multidrug resistant uropathogens include Enterobacteriaceae that produce AmpC β-lactamase, extended-spectrum β-lactamase and carbapenamase.

Antimicrobial resistance

Antimicrobial resistance refers to the inherent or acquired genetic mechanisms by which bacteria withstand antimicrobial agents.

Antimicrobial stewardship

Coordinated interventions to improve the appropriate use of antimicrobials by reducing the administration of unnecessary antimicrobials and promoting the selection of the optimal antimicrobial drug, dose, duration of therapy, and route of administration when needed. The major goals of antimicrobial stewardship include achieving optimal clinical outcomes at the same time minimizing toxicity and adverse events, limiting the selection pressure on bacterial populations that drives the emergence of antimicrobial-resistant strains, and reducing excessive costs related to suboptimal antimicrobial use.

Sample preparation

Multistep assay preparation that includes pipetting (such as reagent transfer and mixing), centrifugation (separation and concentration), and washing.

Lateral flow assays

A single-use, point-of-care diagnostic tool based on liquid transport driven by capillary action without the requirement of external support. The major advantages of these test strips include simplicity, portability, and cost-effectiveness. Examples include urinalysis test strips.

Mass spectrometry

A technique in which charged molecules are created by ionization and their identity determined based on the mass:charge ratio. Matrix-assisted laser desorption ionization–time of flight (MALDI–TOF) mass spectrometry can be used for the identification of large biological molecules enabling its use in pathogen identification. In the current clinical application of MALD–TOF mass spectrometry for pathogen identification, the sample (such as urine) is first cultured to isolate the bacteria and a colony from the culture plate is analysed by MALDI–TOF mass spectrometry.

System integration

Integration of the functional building blocks of microfluidic components including pumps, mixers, concentrators, and valves to create an automated system capable of 'sample-in, answer-out' for the end users. System integration is a major hurdle in translating microfluidic devices into practical applications. Key factors include throughput, cost, multiplexity, diversity of components, accuracy, and programmability.

Fluorescence in situ hybridization

(FISH). A cytogenetic technique that uses fluorescent probes that bind to complementary sequences in target cells (such as bacterial pathogens).

Matrix

Components present in biological samples can affect the detection of the analyte of interest. Urinary constituents that can cause matrix effects in diagnostics include somatic cells, electrolytes, organic molecules, proteins, and crystals. Matrix effects can affect assay sensitivity and reproducibility.

Minimum inhibitory concentration

(MIC). The lowest dose of antimicrobial to which a bacterial strain is sensitive.

Biosensors

A molecular sensing device composed of a recognition element that binds specifically to a target analyte and generates a measurable signal via a transducer. For quantitative detection, the magnitude of the signal is proportional to the analyte concentration.

Microfluidics

A multidisciplinary field based on the manipulation of small amounts of fluids at the micron scale. Microfluidics-based platforms commonly integrate reagent transfer, target isolation, and sample-mixing steps in a multilayered cartridge containing channels, valves, and reagent reservoirs. Such 'lab-on-a-chip' platforms offer the potential advantages of microfluidics including low fluid volumes (reduced reagent use and cost), short assay time, low power consumption, rapid generation of small liquid compartments, and a high degree of parallelization.

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Davenport, M., Mach, K., Shortliffe, L. et al. New and developing diagnostic technologies for urinary tract infections. Nat Rev Urol 14, 296–310 (2017). https://doi.org/10.1038/nrurol.2017.20

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