Four-hour turnaround for diagnosing complex UTIs using nanopore sequencing | LC 25

Biography

Rafi Ahmad is a professor at the University of Inland Norway and the University of Southampton. With six years of experience in the life sciences industry, he has worked with AstraZeneca, Dassault Systèmes, and Medivir. Rafi has led drug discovery projects focused on developing new antibiotics. Currently, he is concentrating on rapid diagnostic solutions for bacterial infections and AMR. He oversees multiple projects that utilise nanopore technology, which are undergoing clinical testing at various hospitals both nationally and internationally.

Abstract

Urinary tract infections (UTIs) affect approximately 405 million people globally. Current diagnostic methods rely on culture, making them time-consuming and in need of improvement. Processing patient urine samples is challenging due to numerous host cells, low bacterial counts, and impurities. Eleven techniques were evaluated, consisting of eight proprietary and three commercial methods for host depletion and selective DNA extraction, using 35 samples from clinical UTI patients, followed by nanopore sequencing. The results were compared to routine clinical microbiology data from MALDI-TOF and antibiotic susceptibility tests. Additionally, human and bacterial cell count information from flow cytometry was used for validation. The metagenomic results were highly consistent with culture-based clinical routines. The selected in-house developed method demonstrated a mean accuracy score of 89% for pathogen identification and 91% for antimicrobial susceptibility profiling. The method's robustness is highlighted by accurately identifying the pathogen with only 33 bacterial cells, a low bacterial-to-leukocyte ratio limit of 0.04, and a low read coverage of 6%. This method has a detection limit of 103 CFU/ml, which agrees with the clinical definition of UTI. Moreover, 12 samples (35%) tested had polymicrobial infections, with 50% containing three or more pathogens, underscoring the complexity of the tested patient samples. This research highlights rapid UTI diagnosis using a cost-effective DNA extraction method in urological settings. Reducing diagnosis time from four days to four hours could save 1.62 billion doses of broad-spectrum antibiotics annually before starting tailored therapy, promoting antimicrobial resistance (AMR) stewardship, and improving UTI management.