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Diagnostics
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What’s up with MALDI-TOF Mass Spectrometry in Microbiology?
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What’s up with MALDI-TOF Mass Spectrometry in Microbiology?

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Diagnostic Microbiology and Infectious Disease".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 9084

Special Issue Editors

Dr. Belén Rodríguez-Sánchez

E-Mail Website
Guest Editor
Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Doctor Esquerdo, 46, 28007 Madrid, Spain
Interests: microorganism identification; machine learning; bacterial subtyping
Dr. David Rodríguez Temporal

E-Mail Website
Assistant Guest Editor
Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Doctor Esquerdo, 46, 28007 Madrid, Spain
Interests: MALDI-TOF MS; mycobacteria; tuberculosis; nontuberculous mycobacteria
Dr. James O Connor

E-Mail Website
Assistant Guest Editor
Department of Clinical Microbiology, Mercy University Hospital, Cork, Ireland
Interests: MALDI-TOF MS; mycobacteria; nontuberculosis mycobacteria; molecular diagnostics
Dr. Maureen Feucherolles

E-Mail Website
Assistant Guest Editor
Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
Interests: MALDI-TOF MS; One Health; antimicrobial resistance; subtyping

Special Issue Information

Dear Colleagues,

For decades, the microbiology field has experienced an incredible revolution at every stage, with the development of fast and new molecular technologies for the quick identification of microorganisms. Among those techniques, MALDI-TOF mass spectrometry has been implemented in most routine diagnostics laboratories and is the reference method for the swift, reliable, and cost-effective identification of bacteria and fungi. The research community is extremely active in regard to the development of new MALDI-TOF mass spectrometry applications: antimicrobial resistances and mass COVID-19 screening, rapid typing, and identification of microorganisms, such as viruses, helminths and ectoparasites. A large volume of data is generated everyday by mass spectrometry, requiring ever more new approaches to investigate it. For the few past years, a combination of MALDI-TOF mass spectrometry and machine learning has shown promising results for clinical big data problems, such as fast antimicrobial resistance screening.

In the context of the last mass spectrometry symposium (https://www.list.lu/en/event/online-conference-whats-up-with-maldi-tof-mass-spectrometry-in-microbiology/), we are interested in receiving original and review papers from all fields in order to offer, through this Special Issue, an opportunity to share recent advances in MALDI-TOF mass spectrometry in every field of microbiology.

Dr. Belén Rodríguez-Sánchez
Guest Editor
Dr. David Rodríguez Temporal
Dr. James O Connor
Dr. Maureen Feucherolles
Assistant Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diagnostics is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • MALDI-TOF MS
  • Diagnostics
  • Microorganism identification
  • Machine learning
  • Antimicrobial resistances
  • Subtyping
  • Phenomics

Published Papers (4 papers)

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Research

13 pages, 3242 KiB  
Article
Rapid and Reproducible MALDI-TOF-Based Method for the Detection of Vancomycin-Resistant Enterococcus faecium Using Classifying Algorithms
by Ana Candela, Manuel J. Arroyo, Ángela Sánchez-Molleda, Gema Méndez, Lidia Quiroga, Adrián Ruiz, Emilia Cercenado, Mercedes Marín, Patricia Muñoz, Luis Mancera, David Rodríguez-Temporal and Belén Rodríguez-Sánchez
Diagnostics 2022, 12(2), 328; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics12020328 - 27 Jan 2022
Cited by 6 | Viewed by 2385
Abstract
Vancomycin-resistant Enterococcus faecium represents a health threat due to its ability to spread and cause outbreaks. MALDI-TOF MS has demonstrated its usefulness for E. faecium identification, but its implementation for antimicrobial resistance detection is still under evaluation. This study assesses the repeatability of [...] Read more.
Vancomycin-resistant Enterococcus faecium represents a health threat due to its ability to spread and cause outbreaks. MALDI-TOF MS has demonstrated its usefulness for E. faecium 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). The study was carried out on protein spectra from 178 E. faecium unique clinical isolates—92 VSE, 31 VanA VRE, 55 VanB VRE-, processed with Clover MS Data Analysis software. Technical and biological repeatability were assayed. Unsupervised (principal component analysis, (PCA)) and supervised algorithms (support vector machine (SVM), random forest (RF) and partial least squares–discriminant analysis (PLS-DA)) were applied. The repeatability assay was performed with 18 peaks common to VSE and VRE with intensities above 1.0% of the maximum peak intensity. It showed lower variability for normalized data and for the peaks within the 3000–9000 m/z range. It was found that 80.9%, 79.2% and 77.5% VSE vs. VRE discrimination was achieved by applying SVM, RF and PLS-DA, respectively. Correct internal differentiation of VanA from VanB VRE isolates was obtained by SVM in 86.6% cases. The implementation of MALDI-TOF MS and peak analysis could represent a rapid and effective tool for VRE screening. However, further improvements are needed to increase the accuracy of this approach. Full article
(This article belongs to the Special Issue What’s up with MALDI-TOF Mass Spectrometry in Microbiology?)
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13 pages, 1388 KiB  
Article
Multicenter Evaluation of Rapid BACpro® II for the Accurate Identification of Microorganisms Directly from Blood Cultures Using MALDI-TOF MS
by Marina Oviaño, André Ingebretsen, Anne K. Steffensen, Antony Croxatto, Guy Prod’hom, Lidia Quiroga, Germán Bou, Gilbert Greub, David Rodríguez-Temporal and Belén Rodríguez-Sánchez
Diagnostics 2021, 11(12), 2251; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11122251 - 01 Dec 2021
Cited by 2 | Viewed by 1794
Abstract
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 (n [...] Read more.
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 (n = 801) were processed using a rapid BACpro® II kit and then compared with the routine gold standard. A subset of monomicrobial BCs (n = 560) were analyzed in parallel with a Sepsityper® Kit (Bruker Daltonics, Bremen, Germany) and compared with the rapid BACpro® II kit. In addition, this kit was also compared with two different in-house methods. Overall, 80.0% of the monomicrobial isolates (609/761; 95% CI 71.5–88.5) were correctly identified by the rapid BACpro® II kit at the species level (92.3% of the Gram negative and 72.4% of the Gram positive bacteria). The comparison with the Sepsityper® Kit showed that the rapid BACpro® II kit generated higher rates of correct species-level identification for all categories (p > 0.0001), except for yeasts identified with score values > 1.7. It also proved superior to the ammonium chloride method (p > 0.0001), but the differential centrifugation method allowed for higher rates of correct identification for Gram negative bacteria (p > 0.1). The percentage of accurate species-level identification of Gram positive bacteria was particularly noteworthy in comparison with other commercial and in-house methods. Full article
(This article belongs to the Special Issue What’s up with MALDI-TOF Mass Spectrometry in Microbiology?)
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17 pages, 2141 KiB  
Article
Investigation of MALDI-TOF Mass Spectrometry for Assessing the Molecular Diversity of Campylobacter jejuni and Comparison with MLST and cgMLST: A Luxembourg One-Health Study
by Maureen Feucherolles, Morgane Nennig, Sören L. Becker, Delphine Martiny, Serge Losch, Christian Penny, Henry-Michel Cauchie and Catherine Ragimbeau
Diagnostics 2021, 11(11), 1949; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11111949 - 20 Oct 2021
Cited by 10 | Viewed by 2082
Abstract
There is a need for active molecular surveillance of human and veterinary Campylobacter infections. However, sequencing of all isolates is associated with high costs and a considerable workload. Thus, there is a need for a straightforward complementary tool to prioritize isolates to sequence. [...] Read more.
There is a need for active molecular surveillance of human and veterinary Campylobacter infections. However, sequencing of all isolates is associated with high costs and a considerable workload. Thus, there is a need for a straightforward complementary tool to prioritize isolates to sequence. In this study, we proposed to investigate the ability of MALDI-TOF MS to pre-screen C. jejuni genetic diversity in comparison to MLST and cgMLST. A panel of 126 isolates, with 10 clonal complexes (CC), 21 sequence types (ST) and 42 different complex types (CT) determined by the SeqSphere+ cgMLST, were analysed by a MALDI Biotyper, resulting into one average spectra per isolate. Concordance and discriminating ability were evaluated based on protein profiles and different cut-offs. A random forest algorithm was trained to predict STs. With a 94% similarity cut-off, an AWC of 1.000, 0.933 and 0.851 was obtained for MLSTCC, MLSTST and cgMLST profile, respectively. The random forest classifier showed a sensitivity and specificity up to 97.5% to predict four different STs. Protein profiles allowed to predict C. jejuni CCs, STs and CTs at 100%, 93% and 85%, respectively. Machine learning and MALDI-TOF MS could be a fast and inexpensive complementary tool to give an early signal of recurrent C. jejuni on a routine basis. Full article
(This article belongs to the Special Issue What’s up with MALDI-TOF Mass Spectrometry in Microbiology?)
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8 pages, 582 KiB  
Article
Rapid Simultaneous Testing of Multiple Antibiotics by the MALDI-TOF MS Direct-on-Target Microdroplet Growth Assay
by Evgeny A. Idelevich, Ilka D. Nix, Janika A. Busch, Katrin Sparbier, Oliver Drews, Markus Kostrzewa and Karsten Becker
Diagnostics 2021, 11(10), 1803; https://0-doi-org.brum.beds.ac.uk/10.3390/diagnostics11101803 - 29 Sep 2021
Cited by 7 | Viewed by 1875
Abstract
Accelerating antimicrobial susceptibility testing (AST) is a priority in the development of novel microbiological methods. The MALDI-TOF MS-based direct-on-target microdroplet growth assay (DOT-MGA) has recently been described as a rapid phenotypic AST method. In this proof-of-principle study, we expanded this method to simultaneously [...] Read more.
Accelerating antimicrobial susceptibility testing (AST) is a priority in the development of novel microbiological methods. The MALDI-TOF MS-based direct-on-target microdroplet growth assay (DOT-MGA) has recently been described as a rapid phenotypic AST method. In this proof-of-principle study, we expanded this method to simultaneously test 24 antimicrobials. An Enterobacterales panel was designed and evaluated using 24 clinical isolates. Either one or two (only for antimicrobials with the EUCAST “I” category) breakpoint concentrations were tested. Microdroplets containing bacterial suspensions with antimicrobials and growth controls were incubated directly on the spots of a disposable MALDI target inside a humidity chamber for 6, 8 or 18 h. Broth microdilution was used as the standard method. After 6 and 8 h of incubation, the testing was valid (i.e., growth control was successfully detected) for all isolates and the overall categorical agreement was 92.0% and 92.7%, respectively. Although the overall assay performance applying short incubation times is promising, the lower performance with some antimicrobials and when using the standard incubation time of 18 h indicates the need for thorough standardization of assay conditions. While using “homebrew” utensils and provisional evaluation algorithms here, technical solutions such as dedicated incubation chambers, tools for broth removal and improved software analyses are needed. Full article
(This article belongs to the Special Issue What’s up with MALDI-TOF Mass Spectrometry in Microbiology?)
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