engleski

Identification of pathogens from urine samples by MALDI-TOF/TOF

Fast and reliable microbial pathogen identification procedure in human urine samples is a crucial diagnostics step for all clinical microbiology laboratories, especially due to a growing antibiotic resistance concern. Currently used identification methods in a clinical set-up are often lengthy and may lead to prescription of unnecessary or inadequate antibiotic therapy. Therefore, we developed a new and robust MALDI-TOF/TOF mass spectrometry- based method coupled to bioinformatics analysis for identification of microorganisms and quantification of peptides from urine samples, readily transferable into a clinical environment. Bioinformatics analysis relied on database peptide matching and species identification by use of newly, in-house developed software based on natural language processing. In the presented study we evaluated this newly developed protocol for analysis of 40 human urine samples previously screened in the clinical microbiology laboratory as pathogen-positive and with concentrations higher than 10000 c.f.u. 1/ml. As a reference for bacterial diversity, seven randomly selected urine samples were determined using 16S rRNA gene sequencing. Our results show that MALDI-TOF/TOF MS proved useful for determination of bacteria in urine samples and that obtained result highly depend on the sample preparation method, starting material properties and number of MS spectra used for the MSMS analysis.

Urine culture; MALDI-TOF/TOF; pathogen identification; proteomics

Rijeka within the project “Research Infrastructure for Campus-based Laboratories at University of Rijeka”, financed by European Regional Development Fund (ERDF).