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

Abstract

The direct identification of uropathogens from urine samples, in combination with the rapid detection of resistance, would allow early adjustment of empirical antimicrobial treatment.Two hundred and ninety-eight urine samples processed between 1 June and 31 December 2020, selected with flow cytometry, with direct identification by MALDI-TOF mass spectrometry, and rapid detection of extended-spectrum beta-lactamase (ESBL) and carbapenemases-producing strains by lateral flow were analyzed.The positive predictive value of the direct identification of the 86 samples that met the flow cytometry criterion (>5000 bacteria/µL) was 96.4%. Reliable direct identification was obtained in 14 of the 27 (51.8%) urinary source bacteraemias. There was 100% agreement between the lateral flow and antibiogram in the detection of ESBL and carbapenemases.the protocol for the direct identification and rapid detection of ESBL and carbapenemases-producing strains from urine samples is a reliable and useful tool.