Urine Bacterial Culture and Identification

Ten microliters of each uncentrifuged urine sample was cultured on UriSelect chromogenic agar (Bio-Rad, Berkeley, CA, USA), blood agar (bioMérieux, Marcy-l’Étoile, Lyon, France) and eosin-methylene blue agar (EMB; Bio-Rad, Berkeley, CA, USA) plates with a calibrated loop, according to the manufacturer’s instructions; the plates were incubated at 37 °C for 24–48 h, aerobically [39 (link)]. In the first part of the study period (2008–2012), presumptive, biochemical reaction-based methods and VITEK 2 Compact ID/AST (bioMérieux, Marcy-l’Étoile, France) were used for bacterial identification. Starting from 2013, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was introduced to the workflow of the Institute of Clinical Microbiology. Mass spectrometry was performed by the microFlex LT MALDI Biotyper (Bruker Daltonics, Bremen, Germany) instrument, using the MALDI Biotyper RTC 3.1 software (Bruker Daltonics, Bremen, Germany) and MALDI Biotyper Library 3.1 for the spectrum analysis. The sample preparation procedure, methodology, and the technical details of the MALDI-TOF MS measurements were described elsewhere [39 (link)].