An international research team with the participation of Justus Liebig University Giessen (JLU), the German Center for Infection Research (DZIF) and partners from Norway and Denmark has developed a fast, precise and cost-effective method for diagnosing complicated urinary tract infections. The method combines direct metagenomic sequencing of the entire DNA from patient samples with real-time data analysis and provides reliable information about the pathogen and its antibiotic sensitivity within about four hours. The results were published in Nature Communications.

Urinary tract infections are one of the most common bacterial infections worldwide, affecting around 405 million people annually. Conventional microbiological diagnostics usually require two to four days, as a bacterial culture must be created. During this time, patients are often given broad-spectrum antibiotics, which promotes the development of resistance and places unnecessary strain on therapy.

The new method completely dispenses with culture and sequences all DNA material directly from urine samples. “This so-called metagenomic sequencing enables precise pathogen and antibiotic resistance profiling in complicated urinary tract infections in about four hours,” explains PD Dr. Torsten Hain, acting head (research and teaching) of the Institute of Medical Microbiology at JLU. “The method is also extremely reliable: it detects the disease-causing bacterium in 99 percent of cases.”

PD Dr. Can Imirzalioglu, Acting Director of the Institute (Diagnostics/Clinical Microbiology) at JLU, emphasizes: “The common practice is that large quantities of broad-spectrum antibiotics are used while doctors wait for the results of the laboratory diagnostic confirmation of the pathogen and its sensitivity. We can prove that our method can replace this practice and has several advantages: It means better treatment for patients by optimising the use of antibiotics and avoiding unnecessary treatments. Last but not least, the risk of resistance development is reduced.”

Antibiotic susceptibility can be predicted with an accuracy of 90 percent. This is crucial as multidrug-resistant germs are on the rise worldwide and threaten the effectiveness of many standard antibiotics. A targeted, reduced administration of antibiotics is therefore essential.

In addition, the method is up to 30 percent more cost-effective than conventional alternatives.

The study thus underlines the potential of metagenomic approaches for rapid, targeted therapy in urinary tract infections and contributes to the fight against global antibiotic resistance.

Original Paper:

Bellankimath AB et al.: Metagenomic sequencing enables accurate pathogen and antimicrobial susceptibility profiling in complicated UTIs in approximately four hours. Nature Communications, 2025; DOI: 10.1038/s41467-025-66865-8

Metagenomic sequencing enables accurate pathogen and antimicrobial susceptibility profiling in complicated UTIs in approximately four hours – PubMed

Editor: X-Press Journalistenbüro GbR

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