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

Huang, Bin; Zhang, Lei; Zhang, Weizheng; Liao, Kang; Zhang, Shihong; Zhang, Zhiquan; Ma, Xingyan; Chen, Jialong; Zhang, Xiuhong; Qu, Pinghua; Wu, Shangwei; Cha, Chen; Tang, Yi‐Wei

doi:10.1128/jcm.02549-16

Cited by 29 publications

(17 citation statements)

References 20 publications

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“…on the identification performance of the Biotyper system, and the remaining three studies [24][25][26] reported on the identification performance of the Vitek MS system.…”

Section: Discussionmentioning

confidence: 99%

“…And to obtain sufficient spectra for MALDI-TOF MS detecting, the sample must be concentrated. The included studies used various concentration procedures to facilitate identification, including a centrifugation (low and high speed)/wash protocol that yields pure microbial pellets and added formic acid and acetonitrile to destroy the cell wall more fully [18][19][20][21][22][23]26]. Ferreira et.al [19] compared the ICM with PEM and showed that the intact cell method (ICM) provided excellent results for urine.…”

Section: Discussionmentioning

confidence: 99%

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Diagnostic accuracy of MALDI-TOF mass spectrometry for the direct identification of clinical pathogens from urine

et al. 2020

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AbstractMatrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) has become one of the most popular methods for the rapid and cost-effective detection of clinical pathogenic microorganisms. This study aimed to evaluate and compare the diagnostic performance of MALDI-TOF MS with that of conventional approaches for the direct identification of pathogens from urine samples. A systematic review was conducted based on a literature search of relevant databases. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and area under the summary receiver operating characteristic (SROC) curve of the combined studies were estimated. Nine studies with a total of 3920 subjects were considered eligible and included in the meta-analysis. The pooled sensitivity was 0.85 (95% CI 0.79-0.90), and the pooled specificity was 0.93 (95% CI 0.82-0.97). The PLR and NLR were 11.51 (95% CI 4.53-29.26) and 0.16 (95% CI 0.11-0.24), respectively. The area under the SROC curve was 0.93 (95% CI 0.91-0.95). Sensitivity analysis showed that the results of this meta-analysis were stable. MALDI-TOF MS could directly identify microorganisms from urine samples with high sensitivity and specificity.

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“…on the identification performance of the Biotyper system, and the remaining three studies [24][25][26] reported on the identification performance of the Vitek MS system.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Diagnostic accuracy of MALDI-TOF mass spectrometry for the direct identification of clinical pathogens from urine

et al. 2020

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“…For the proteomic analysis, a minimum concentration of 10 5 CFU/mL and a volume of 5 mL of fresh urine sample or urine stored in the refrigerator up to 4 weeks. In this preliminary study, we Previous studies had considered the impact of ultrasonication on microorganisms to improve sample preparation [51,32,52]. In our research protein extraction using B-PER worked for both gram-negative and gram-positive bacteria, so there was no need for additional mechanical methods of cell rupture.…”

Section: Sample Preparationmentioning

confidence: 99%

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

Starčević

Oros

Ceprnja

et al. 2020

Preprint

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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 10 5 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. Keywords: urine, sample preparation, pathogen identification, proteomics, MALDI-TOF/TOF, 16S rRNA sequencing

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“…Recent studies have demonstrated that MALDI-TOF MS has great potential to be part of a direct identification protocol performed on urine (6)(7)(8)(9)(10). However, we noted that the majority of the direct analysis protocols developed require a large volume of urine sample and a minimum of 10 5 CFU/ml in order to correctly identify the pathogen.…”

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confidence: 90%

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

Cited by 29 publications

References 20 publications

Diagnostic accuracy of MALDI-TOF mass spectrometry for the direct identification of clinical pathogens from urine

Diagnostic accuracy of MALDI-TOF mass spectrometry for the direct identification of clinical pathogens from urine

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

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

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