LAUSR

Urinary tract infections (UTIs) are the most common infectious diseases in both communities and hospitals. With non-anatomical or functional abnormalities, UTIs are usually self-limiting, though women suffer more reinfections throughout their lives. Certainly, antibiotic treatment leads to a more rapid resolution of symptoms, but also it selects resistant uropathogens and adversely affects the gut and vaginal microbiota. As uropathogens are increasingly becoming resistant to currently available antibiotics, it could be time to explore alternative strategies for managing UTIs. Rapid identification and antimicrobial susceptibility testing (AST) allow fast and precise treatment. The objective of this study was to shorten the time of diagnosis of UTIs by combining pathogen screening through flow cytometry, microbial identification by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS), and the VITEK 2 system for the direct analysis of urine samples. First, we selected positive urine samples by flow cytometry using UF5000, establishing the cut-off for positive at 150 bacteria/mL. After confirming the identification using MALDI-TOF MS and filtering the urine samples for Escherichia coli, we directly tested the AST N388 card using VITEK 2. We tested a total of 211 E. coli from urine samples. Cefoxitin, ertapenem, imipenem, gentamicin, nalidixic acid, ciprofloxacin, fosfomycin, and nitrofurantoin had no major important errors (MIE), and ampicillin, cefuroxime, and tobramycin showed higher MIEs. Cefepime, imipenem, and tobramycin had no major errors (ME). Fosfomycin was the antibiotic with the most MEs. The antibiotic with the most minor errors (mE) was ceftazidime. The total categorical agreement (CA) was 97.4% with a 95% CI of (96.8–97.9)95%. The direct AST from the urine samples proposed here was shorter by one day, without significant loss of sensibility regarding the standard diagnosis. Therefore, we hypothesize that this method is more realistic and better suited to human antibiotic concentrations.