Automated web-based typing of Clostridioides difficile ribotypes via MALDI-TOF MS.

Background: Clostridioides difficile is a major cause of hospital-acquired diarrhea and a driver of nosocomial outbreaks, yet rapid, accurate ribotype identification remains challenging. We sought to develop a MALDI-TOF MS-based workflow coupled with machine learning to distinguish epidemic toxigenic ribotypes (RT027 and RT181) from other strains in real time.

Results: We analyzed MALDI-TOF spectra from 379 clinical isolates collected across ten Spanish hospitals and identified seven discriminant biomarker peaks.

Current Performance of MALDI-TOF Mass Spectrometry Databases for the Identification of Dermatophyte Species.

The identification of filamentous fungi by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) represents a challenge due to their complex taxonomy and the lack of comprehensive databases. The aim of this study was to evaluate the current status of available MALDI-TOF MS databases for the identification of dermatophytes, including commercial, in-house, and web-based databases. We collected 289 dermatophyte strains from different centers and analyzed them using four databases and a combination of them.

Analysis of high-molecular-weight proteins using MALDI-TOF MS and machine learning for the differentiation of clinically relevant Clostridioides difficile ribotypes.

Purpose: Clostridioides difficile is the main cause of antibiotic related diarrhea and some ribotypes (RT), such as RT027, RT181 or RT078, are considered high risk clones. A fast and reliable approach for C. difficile ribotyping is needed for a correct clinical approach.

Multicenter evaluation of Fourier transform infrared (FTIR) spectroscopy as a first-line typing tool for carbapenemase-producing in clinical settings.

Early use of infection control methods is critical for preventing the spread of antimicrobial resistance. Whole-genome sequencing (WGS) is considered the gold standard for investigating outbreaks; however, the turnaround time is usually too long for clinical decision-making and the method is also costly. The aim of this study was to evaluate the performance of Fourier transform infrared (FTIR) and artificial intelligence tools as a first-line typing tool for typing carbapenemase-producing (CPK) in the hospital setting.

Characterization of an outbreak caused by Elizabethkingia miricola using Fourier-transform infrared (FTIR) spectroscopy.

Fourier-transform infrared (FTIR) spectroscopy has the potential to be used for bacterial typing and outbreak characterization. We evaluated FTIR for the characterization of an outbreak caused by Elizabethkingia miricola. During the 2020-2021 period, 26 isolates (23 clinical and 3 environmental) were collected and analyzed by FTIR (IR Biotyper) and core-genome MLST (cgMLST), in addition to antimicrobial susceptibility testing.

Rapid Discrimination of ST175 Isolates Involved in a Nosocomial Outbreak Using MALDI-TOF Mass Spectrometry and FTIR Spectroscopy Coupled with Machine Learning.

The goal of this study was to evaluate matrix-assisted laser desorption ionization-iime of flight mass spectrometry (MALDI-TOF MS) and Fourier-transform infrared spectroscopy (FTIR-S) as diagnostic alternatives to DNA-based methods for the detection of sequence type (ST) 175 isolates involved in a hospital outbreak. For this purpose, 27 isolates from an outbreak detected in the Hematology department of our hospital were analyzed by the above-mentioned methodologies. Previously, these isolates had been characterized by pulse-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS).

Validation of an expanded, in-house library and an optimized preparation method for the identification of fungal isolates using MALDI-TOF mass spectrometry.

The goal of this study was to validate an optimized sample preparation method for filamentous fungal isolates coupled with the use of an in-house library for the identification of moulds using Matrix Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) in a multicenter context. For that purpose, three Spanish microbiology laboratories participated in the identification of 97 fungal isolates using MALDI-TOF MS coupled with the Filamentous Fungi library 3.0 (Bruker Daltonics) and an in-house library containing 314 unique fungal references.

Automatic Discrimination of Species within the Enterobacter cloacae Complex Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry and Supervised Algorithms.

The Enterobacter cloacae complex (ECC) encompasses heterogeneous clusters of species that have been associated with nosocomial outbreaks. These species may have different acquired antimicrobial resistance and virulence mechanisms, and their identification is challenging. This study aims to develop predictive models based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) profiles and machine learning for species-level identification.

Determination of the ability of matrix-assisted laser desorption ionization time-of-flight mass spectrometry to identify high-biofilm-producing strains.

Background: The traditional method for assessing the capacity of a microorganism to produce biofilm is generally a static model in a multi-well plate using the crystal violet (CV) binding assay, which takes 96 h. Furthermore, while the method is simple to perform, its reproducibility is poor.

Objective: We evaluated whether matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) could make it possible to differentiate between high-and low-biofilm-producing microorganisms on 24-h cultures of and .

Identification of Mycobacterium abscessus Subspecies by MALDI-TOF Mass Spectrometry and Machine Learning.

Mycobacterium abscessus is one of the most common and pathogenic nontuberculous mycobacteria (NTM) isolated in clinical laboratories. It consists of three subspecies: M. abscessus subsp.

Identification of Nocardia and non-tuberculous Mycobacterium species by MALDI-TOF MS using the VITEK MS coupled to IVD and RUO databases.

Identification of Nocardia and Mycobacterium species by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is still a challenging task that requires both suitable protein extraction procedures and extensive databases. This study aimed to evaluate the VITEK MS Plus system coupled with updated RUO (v4.17) and IVD (v3.

Evaluation of the Vitek Ms system for the identification of filamentous fungi.

Unlabelled: The implementation of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for the identification of fungal isolates remains challenging and has been limited to experienced laboratories in sample preparation and in-house libraries construction. However, the development of commercial kits for standardized fungal sample preparation and updated reference libraries can fill this gap. This study aimed to evaluate the performance of the commercial VITEK MS Mould Kit (bioMérieux, Marcy l'Etoile, France) and the VITEK MS system (bioMérieux) for identification using a panel of fungal species of clinical interest.

Rapid and Reproducible MALDI-TOF-Based Method for the Detection of Vancomycin-Resistant Using Classifying Algorithms.

Vancomycin-resistant represents a health threat due to its ability to spread and cause outbreaks. MALDI-TOF MS has demonstrated its usefulness for identification, but its implementation for antimicrobial resistance detection is still under evaluation. This study assesses the repeatability of MALDI-TOF MS for peak analysis and its performance in the discrimination of vancomycin-susceptible (VSE) from vancomycin-resistant isolates (VRE).

Multicentre study on the reproducibility of MALDI-TOF MS for nontuberculous mycobacteria identification.

The ability of MALDI-TOF for the identification of nontuberculous mycobacteria (NTM) has improved recently thanks to updated databases and optimized protein extraction procedures. Few multicentre studies on the reproducibility of MALDI-TOF have been performed so far, none on mycobacteria. The aim of this study was to evaluate the reproducibility of MALDI-TOF for the identification of NTM in 15 laboratories in 9 European countries.

Multicenter Evaluation of Rapid BACpro II for the Accurate Identification of Microorganisms Directly from Blood Cultures Using MALDI-TOF MS.

The identification of microorganisms directly from blood cultures using MALDI-TOF MS has been shown to be the most impacting application of this methodology. In this study, a novel commercial method was evaluated in four clinical microbiology laboratories. Positive blood culture samples ( = 801) were processed using a rapid BACpro II kit and then compared with the routine gold standard.

Evaluation of MALDI Biotyper Interpretation Criteria for Accurate Identification of Nontuberculous Mycobacteria.

Identification of mycobacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) requires not only a good protein extraction protocol but also an adequate cutoff score in order to provide reliable results. The aim of this study was to assess the cutoff scores proposed by the MALDI-TOF MS system for mycobacterial identification. A total of 693 clinical isolates from a liquid medium and 760 from a solid medium were analyzed, encompassing 67 different species of nontuberculous mycobacteria (NTM).

Evaluation of the Xpert MTB/RIF Ultra Assay for Direct Detection of Mycobacterium tuberculosis Complex in Smear-Negative Extrapulmonary Samples.

The rapid detection of complex (MTUBC) in clinical samples is essential for successful treatment. New techniques such as real-time PCR have been developed in order to facilitate rapid diagnosis, but their sensitivity is low in extrapulmonary specimens, due to the low bacillary load in such samples. A next-generation assay has recently been developed to try to overcome this limitation.

Evaluation of Two Protein Extraction Protocols Based on Freezing and Mechanical Disruption for Identifying Nontuberculous Mycobacteria by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry from Liquid and Solid Cultures.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has proved to be a useful diagnostic method for identifying conventional bacteria. In the case of mycobacteria, a good protein extraction protocol is essential in order to obtain reliable identification results. To date, no such protocol has been definitively established.