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Identification of pathogens from native urine samples by MALDI-TOF/TOF tandem mass spectrometry

Oros, Damir; Ceprnja, Marina; Žučko, Jurica; Cindrić, Mario; Hozić, Amela; Škrlin, Jasenka; Barišić, Karmela; Melvan, Ena; Uroić, Ksenija; Kos, Blaženka; Starčević, Antonio (2020) Identification of pathogens from native urine samples by MALDI-TOF/TOF tandem mass spectrometry. Clinical Proteomics, 17 (1). ISSN 1559-0275

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Background: Reliable high-throughput microbial pathogen identification in human urine samples is crucial for patients with cystitis symptoms. Currently employed methods are time-consuming and could lead to unnecessary or inadequate antibiotic treatment. Purpose of this study was to assess the potential of mass spectrometry for uropathogen identification from a native urine sample. Methods: In total, 16 urine samples having more than 105 CFU/mL were collected from clinical outpatients. These samples were analysed using standard urine culture methods, followed by 16S rRNA gene sequencing serving as control and here described culture-independent MALDI-TOF/TOF MS method being tested. Results: Here we present advantages and disadvantages of bottom-up proteomics, using MALDI-TOF/TOF tandem mass spectrometry, for culture-independent identification of uropathogens (e.g. directly from urine samples). The direct approach provided reliable identification of bacteria at the genus level in monobacterial samples. Taxonomic identifications obtained by proteomics were compared both to standard urine culture test used in clinics and genomic test based on 16S rRNA sequencing. Conclusions: Our findings indicate that mass spectrometry has great potential as a reliable high-throughput tool for microbial pathogen identification in human urine samples. In this case, the MALDI-TOF/TOF, was used as an analytical tool for the determination of bacteria in urine samples, and the results obtained emphasize high importance of storage conditions and sample preparation method impacting reliability of MS2 data analysis. The proposed method is simple enough to be utilized in existing clinical settings and is highly suitable for suspected single organism infectious etiologies. Further research is required in order to identify pathogens in polymicrobial urine samples.

Item Type: Article
Uncontrolled Keywords: Urine ; Sample preparation ; Pathogen identification ; Proteomics ; MALDI-TOF/TOF ; 16S rRNA sequencing
Subjects: NATURAL SCIENCES > Biology > Biochemistry and Molecular Biology
Divisions: Division of Molecular Medicine
Project titleProject leaderProject codeProject type
Istraživanje ravnoteže mikrobioma debelog crijevaStarčević, AntonioIP-2016-06-3509HRZZ
Depositing User: Mario Cindrić
Date Deposited: 14 Feb 2022 15:19
DOI: 10.1186/s12014-020-09289-4

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