Implementation of a New Protocol for Direct Identification from Urine in the Routine Microbiological Diagnosis

Area of Science:

• Clinical microbiology
• Infectious diseases
• Diagnostic technology

Background:

• Early identification of uropathogens and antimicrobial resistance is crucial for effective empirical treatment.
• Current methods can delay timely adjustments to antimicrobial therapy.
• Developing rapid diagnostic tools is essential for improving patient outcomes.

Purpose of the Study:

• To evaluate a protocol for direct identification of uropathogens from urine samples.
• To assess the rapid detection of extended-spectrum beta-lactamase (ESBL) and carbapenemase-producing strains.
• To determine the reliability and utility of this combined approach for clinical application.

Main Methods:

• Analysis of 298 urine samples processed between June and December 2020.
• Utilized flow cytometry for sample selection (>5000 bacteria/µL).
• Employed MALDI-TOF mass spectrometry for direct pathogen identification and lateral flow assays for rapid resistance detection (ESBL, carbapenemases).

Main Results:

• A positive predictive value of 96.4% for direct identification in samples meeting flow cytometry criteria.
• Reliable direct identification achieved in 51.8% of urinary source bacteraemias.
• 100% agreement observed between lateral flow assays and antibiograms for ESBL and carbapenemase detection.

Conclusions:

• The developed protocol offers a reliable and useful method for direct uropathogen identification from urine.
• Rapid detection of ESBL and carbapenemase-producing strains is feasible and accurate.
• This approach facilitates timely and appropriate antimicrobial treatment adjustments.