Identification of urinary tract pathogens after 3-hours urine culture by MALDI-TOF mass spectrometry

Haiko, Johanna; Savolainen, Laura; Hilla, Risto; Pätäri-Sampo, Anu

doi:10.1016/j.mimet.2016.08.006

Cited by 26 publications

(17 citation statements)

References 19 publications

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“…Direct analysis of clinical samples further increased the usefulness of this method by eliminating the time required for microorganism growth and isolation. Several studies have applied the technique to detect and identify microbial pathogens directly from urine (10)(11)(12)(13) and have revealed that clinicians would receive therapeutically helpful information for 96.1% of samples in less than 1 h (10,14).…”

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confidence: 99%

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Direct Detection and Identification of Bacterial Pathogens from Urine with Optimized Specimen Processing and Enhanced Testing Algorithm

Huang

Zhang

et al. 2017

J Clin Microbiol

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Rapid and accurate detection and identification of microbial pathogens causing urinary tract infections allow prompt and specific treatment. We optimized specimen processing to maximize the limit of detection (LOD) by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and evaluated the capacity of combination of MALDI-TOF MS and urine analysis (UA) for direct detection and identification of bacterial pathogens from urine samples. The optimal volumes of processed urine, formic acid/acetonitrile, and supernatant spotted onto the target plate were 15 ml, 3 l, and 3 l, respectively, yielding a LOD of 1.0 ϫ 10 5 CFU/ml. Among a total of 1,167 urine specimens collected from three hospital centers, 612 (52.4%) and 351 (30.1%) were, respectively, positive by UA and urine culture. Compared with a reference method comprised of urine culture and 16S rRNA gene sequencing, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of MALDI-TOF MS alone and MALDI-TOF MS coupled with UA were 86.6% versus 93.4% ( 2 ϭ 8.93; P Ͻ 0.01), 91.5% versus 96.3% ( 2 ϭ 7.06; P Ͻ 0.01), 81.5% versus 96.4% ( 2 ϭ 37.32; P Ͻ 0.01), and 94.1% versus 93.1% ( 2 ϭ 0.40; P Ͼ 0.05), respectively. No significant performance differences were revealed among the three sites, while specificity and NPV of MALDI-TOF MS for males were significantly higher than those for females (specificity, 94.3% versus 77.3%, 2 ϭ 44.90, P Ͻ 0.01; NPV, 95.5% versus 86.1%, 2 ϭ 18.85, P Ͻ 0.01). Our results indicated that the optimization of specimen processing significantly enhanced analytical sensitivity and that the combination of UA and MALDI-TOF MS provided an accurate and rapid detection and identification of bacterial pathogens directly from urine.KEYWORDS identification, urine, pathogen, MALDI-TOF MS, urine analysis U rinary tract infections (UTIs) are among the most common bacterial infections seen in women. The initial treatment of UTI is mostly empirical, and immediately initiating therapy avoids serious complications and shortens the time of patient discomfort (1, 2). Diagnosis of UTI is currently based on the following three criteria: (i) clinical symptoms, (ii) detection of signs of infection in the urine, and (iii) detection and

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confidence: 99%

“…Much effort has been spent to improve urine processing and to enhance the identification capability of MALDI-TOF MS by coupling it with rapid urine analysis (4,10,12,(14)(15)(16). This study aimed to establish and optimize a urine processing method to improve the analytical sensitivity and specificity of MALDI-TOF MS.…”

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confidence: 99%

Direct Detection and Identification of Bacterial Pathogens from Urine with Optimized Specimen Processing and Enhanced Testing Algorithm

Huang

Zhang

et al. 2017

J Clin Microbiol

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“…This choice proved to be more relevant since the identification scores obtained were significantly improved with use of the Urinf database. Some of the recently published protocols require tedious prehandling, such as a preincubation step (15,16), dual filtration (16), or diafiltration (17), that would be difficult to implement in a clinical laboratory because of the substantial amount of incoming samples. It was estimated that only 40 to 60 min was necessary to carry out our entire procedure on up to 20 samples and to perform bacterial identification.…”

Section: Discussionmentioning

confidence: 99%

Direct Identification of Pathogens in Urine by Use of a Specific Matrix-Assisted Laser Desorption Ionization–Time of Flight Spectrum Database

et al. 2019

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Urinary tract infections are among the most common reasons for antimicrobial treatment, and early diagnosis could have a significant impact by enabling rapid administration of the adapted antibiotic and preventing complications. The current delay between sample receipt and pathogen identification is about 24 to 48 h, which could be significantly shortened by use of an accurate direct method. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is already used for the identification of pathogens in clinical laboratories and constitutes a promising tool for direct diagnosis. A simple preparation protocol was established for the processing of urine samples prior to MS analysis. MALDI-TOF spectra collected directly from 1,000 infected urine samples were used to create a specific reference database (named Urinf). A prospective study was then carried out to evaluate the Urinf database and compare the results obtained with the standard database provided by Bruker on the Biotyper Real Time Classification software. Seven hundred eighty urine specimens were processed and analyzed according to our method. Among them, almost 90% of 500 infected monobacterial samples could be correctly diagnosed with the Urinf database, compared to 50% using the standard database. The identification of Enterobacteriaceae, Staphylococcus aureus, Staphylococcus saprophyticus, Pseudomonas aeruginosa, Enterococcus faecalis, and Enterococcus faecium was greatly improved but not for Staphylococcus epidermidis. The creation of a database adapted to a particular type of clinical sample has great potential to increase both the rate and rapidity of pathogen identification. Sensitivity still remains to be improved for bacterial species that exhibit few specific peaks on mass spectra.

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“…The confirmation of the identification of all isolates was performed by using MALDI-TOF MS as was previously described [19]. In brief, all isolates were activated in fresh Luria Bertani broth and grown overnight at 37° C. After that, isolates were grown on BHI agar 16 hours at 37º C and a sample of the growth was taken with a 1µL loop to the MALDI-TOF target plate.…”

Section: Maldi-tof-ms Based Identificationmentioning

confidence: 99%

Antibiotic resistance, virulence factors and genotyping of Pseudomonas aeruginosa in public hospitals of northeastern Mexico

González-Olvera

Pérez‐Morales

González‐Zamora

et al. 2019

J Infect Dev Ctries

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Introduction: Pseudomonas aeruginosa is the second most prevalent opportunistic pathogen causing nosocomial infections in Mexico. This study evaluated antibiotic resistance, production of virulence factors and clonal diversity of P. aeruginosa strains isolated from patients undergoing nosocomial infections in public hospitals of northeastern Mexico. Methodology: Ninety-two P. aeruginosa isolates from urine culture, Foley catheter, ear, wounds, respiratory tract secretions, scalp, blood culture, bronchoalveolar lavage, expectoration and cerebrospinal fluid causing nosocomial infections were analyzed. The isolates were identified by MALDI-TOF and antibiotic resistance profiles obtained by MicroScan®. The production of virulence factors was analyzed with spectrophotometric techniques and isolates genotyped by ERIC-PCR. Results: Out of the 92 isolates, 26 (28.2%) were found to be multidrug resistant (MDR); 21 (22.7%) were classified as extremely drug resistant (XDR). Highest resistance rate was found for gatifloxacin (42%) while ciprofloxacin accounted for the antibiotic with the lowest resistance rate (2%). Bronchoalveolar lavage isolates produced the highest amounts of virulence factors: biofilm (44.4% ± 2.7%), elastase (58.5% ± 4.3%), alkaline protease (60.1% ± 5.0%); except for pyocyanin production. The ERIC-PCR assay showed 83 genetic patterns (90% clonal diversity) and 13 isolates had 100% genetic similarity, forming 4 real clones, 3 of these clones were obtained from different anatomical site and/or hospital. Conclusions: Antibiotic resistance and virulence factors production was heterogeneous among samples analyzed. Genotyping of P. aeruginosa strains showed high genetic diversity in the studied isolates.

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Identification of urinary tract pathogens after 3-hours urine culture by MALDI-TOF mass spectrometry

Cited by 26 publications

References 19 publications

Direct Detection and Identification of Bacterial Pathogens from Urine with Optimized Specimen Processing and Enhanced Testing Algorithm

Direct Detection and Identification of Bacterial Pathogens from Urine with Optimized Specimen Processing and Enhanced Testing Algorithm

Direct Identification of Pathogens in Urine by Use of a Specific Matrix-Assisted Laser Desorption Ionization–Time of Flight Spectrum Database

Antibiotic resistance, virulence factors and genotyping of Pseudomonas aeruginosa in public hospitals of northeastern Mexico

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