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Microorganisms
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Application of MALDI-TOF MS in Microbiology
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Application of MALDI-TOF MS in Microbiology

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 14141

Special Issue Editor

Dr. Jae-Seok Kim

E-Mail Website
Guest Editor
Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
Interests: MALDI-TOF MS; clinical microbiology; staphylococcus; NGS application on bacteria
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The introduction of MALDI-TOF MS in the microbiology laboratory for the identification of bacteria and mycobacterium has revolutionized routine laboratory work on microorganisms. This Special Issue deals with the use of identification of microorganisms as well as the new application of MALDI-TOF MS in microbiology. This issue covers laboratory diagnosis of microorganisms, epidemiological applications, biomarker discovery of microorganisms, improvement of common procedures, and novel applications of MALDI-TOF MS for microorganisms isolated from human, animal, and environment. With the advances and novel approaches of the application of MALDI-TOF MS being documented and disseminated in this Special Issue, more improvements and benefits could be achieved in microbiology. As a Guest Editor of this Special Issue, we look forward to publishing your work related to this topic.

Dr. Jae-Seok Kim
Guest Editor

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. Microorganisms is an international peer-reviewed open access monthly 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 2700 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
  • mass spectrometry
  • bacteria
  • mycobacteria
  • epidemiology
  • antibiotic resistance

Related Special Issue

Published Papers (7 papers)

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Research

8 pages, 790 KiB  
Communication
Improved MALDI-TOF MS Identification of Mycobacterium tuberculosis by Use of an Enhanced Cell Disruption Protocol
by Gisele Bacanelli, Flabio Ribeiro Araujo and Newton Valerio Verbisck
Microorganisms 2023, 11(7), 1692; https://doi.org/10.3390/microorganisms11071692 - 29 Jun 2023
Cited by 1 | Viewed by 1563
Abstract
Mycobacterium tuberculosis is the microorganism that causes tuberculosis, a disease affecting millions of people worldwide. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast, reliable, and cost-effective method for microorganism identification which has been used for the identification of Mycobacterium [...] Read more.
Mycobacterium tuberculosis is the microorganism that causes tuberculosis, a disease affecting millions of people worldwide. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast, reliable, and cost-effective method for microorganism identification which has been used for the identification of Mycobacterium spp. isolates. However, the mycobacteria cell wall is rich in lipids, which makes it difficult to obtain proteins for MALDI-TOF MS analysis. In this study, two cell preparation protocols were compared: the MycoEx, recommended by MALDI-TOF instrument manufacturer Bruker Daltonics, and the MycoLyser protocol described herein, which used the MagNA Lyser instrument to enhance cell disruption with ethanol. Cell disruption and protein extraction steps with the two protocols were performed using the Mycobacterium tuberculosis H37Rv strain, and the MALDI-TOF MS results were compared. The MycoLyser protocol allowed for improved Biotyper identification of M. tuberculosis since the log(score) values obtained with this protocol were mostly ≥ 1.800 and significantly higher than that underwent MycoEx processing. The identification reliability was increased as well, considering the Bruker criteria. In view of these results, it is concluded that the MycoLyser protocol for mycobacterial cell disruption and protein extraction improves the MALDI-TOF MS method’s efficacy for M. tuberculosis identification. Full article
(This article belongs to the Special Issue Application of MALDI-TOF MS in Microbiology)
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15 pages, 18868 KiB  
Article
Monitoring of an Applied Beneficial Trichoderma Strain in Root-Associated Soil of Field-Grown Maize by MALDI-TOF MS
by Thomas Edison E. dela Cruz, Jan Helge Behr, Joerg Geistlinger, Rita Grosch and Katja Witzel
Microorganisms 2023, 11(7), 1655; https://doi.org/10.3390/microorganisms11071655 - 25 Jun 2023
Cited by 3 | Viewed by 1399
Abstract
The persistence of beneficial microorganisms in the rhizosphere or surrounding soil following their application is a prerequisite for the effective interaction with the plant or indigenous microbial communities in the respective habitats. The goal of the study was to analyze the establishment and [...] Read more.
The persistence of beneficial microorganisms in the rhizosphere or surrounding soil following their application is a prerequisite for the effective interaction with the plant or indigenous microbial communities in the respective habitats. The goal of the study was to analyze the establishment and persistence of the applied beneficial Trichoderma harzianum (OMG16) strain in the maize root-associated soil depending on agricultural practice (soil management practice, N-fertilizer intensity) in a field experiment. A rapid identification of the inoculated strain OMG16 is essential for its monitoring. We used a culture-based approach coupled to matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis for the rapid identification of the inoculated Trichoderma strain as part of the beneficial microbe consortium (BMc). We isolated 428 fungal isolates from eight treatments of the field experiment. Forty eight percent of the isolated fungi equivalent to 205 fungal isolates were identified as Trichoderma, of which 87% (=179 isolates) were obtained from the fields inoculated with BMc. Gene sequence analysis showed a high similarity of the MALDI-TOF MS-identified Trichoderma, with that of the inoculated Trichoderma harzianum OMG16 confirming the re-isolation of the added beneficial fungus. This study highlighted the use of MALDI-TOF MS analysis as a quick, cost-effective detection and efficient monitoring tool for microbial-based bioinoculants in the field. Full article
(This article belongs to the Special Issue Application of MALDI-TOF MS in Microbiology)
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9 pages, 921 KiB  
Article
Evaluation of Two Different Preparation Protocols for MALDI-TOF MS Nontuberculous Mycobacteria Identification from Liquid and Solid Media
by Lisa Pastrone, Antonio Curtoni, Giulia Criscione, Francesca Scaiola, Paolo Bottino, Luisa Guarrasi, Marco Iannaccone, Markus Timke, Cristina Costa and Rossana Cavallo
Microorganisms 2023, 11(1), 120; https://doi.org/10.3390/microorganisms11010120 - 03 Jan 2023
Cited by 4 | Viewed by 2090
Abstract
Nontuberculous mycobacteria (NTM) identification is essential for establishing the relevance of the isolate and for appropriate antimicrobial therapy. Traditionally, NTM identification is performed by using Line Probe Assays (LPA), a costly and time-consuming technique requiring trained personnel. MALDI-TOF MS is a promising tool [...] Read more.
Nontuberculous mycobacteria (NTM) identification is essential for establishing the relevance of the isolate and for appropriate antimicrobial therapy. Traditionally, NTM identification is performed by using Line Probe Assays (LPA), a costly and time-consuming technique requiring trained personnel. MALDI-TOF MS is a promising tool for NTM identification, and its use is rapidly growing. We evaluated the newly introduced MBT Mycobacteria kit (MBT) and the MycoEx preparation protocol (Bruker Daltonics, Germany) for NTM MALDI-TOF MS identification using LPA results as a reference. Fifty NTM grown on 7H11 agar and MGIT broth were analyzed with both protocols using the Bruker Microflex® LT MALDI-TOF MS (Bruker Daltonics) instrument. MBT and MycoEx provided identification results in 97.0% and 95.0% of the cases, respectively. With both protocols, 100% of the provided results agreed with LPA with no registered mismatch. MBT achieved an elevated number of highly probable identifications (88.0% vs. 83.0%) and a higher reproducibility rate of correct results (86.6% vs. 75.8%) in comparison to MycoEx. This study provides results about MBT performance for liquid and solid media, underlining the strengths and weakness under different conditions. Our results suggest that MALDI-TOF MS could provide a great advantage for timely and cost-saving NTM identification with potential implications for patient outcome. Full article
(This article belongs to the Special Issue Application of MALDI-TOF MS in Microbiology)
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11 pages, 875 KiB  
Article
Direct MALDI-TOF MS and Antimicrobial Susceptibility Testing of Positive Blood Cultures Using the FASTTM System and FAST-PBC Prep Cartridges—Performance Evaluation in a Clinical Microbiology Laboratory Serving High-Risk Patients
by Khay Ugaban, Pil Pak and Rosemary C. She
Microorganisms 2022, 10(10), 2076; https://doi.org/10.3390/microorganisms10102076 - 20 Oct 2022
Cited by 4 | Viewed by 1949
Abstract
Bloodstream infections are a leading cause of morbidity and mortality. The rapid diagnostic testing of positive blood cultures (PBCs) shortens times to effective therapy and the de-escalation of broad-spectrum empiric therapy. This is the first study examining the Qvella FASTTM System for [...] Read more.
Bloodstream infections are a leading cause of morbidity and mortality. The rapid diagnostic testing of positive blood cultures (PBCs) shortens times to effective therapy and the de-escalation of broad-spectrum empiric therapy. This is the first study examining the Qvella FASTTM System for the rapid (~20 min) purification of microorganisms directly from PBCs using BacT/Alert® FA/FAN bottles in the bioMérieux Virtuo instrument. We compared the performance of the FASTTM System Liquid ColonyTM (LC), for immediate downstream ID and phenotypic AST, to standard workflow involving colonies obtained by overnight subculture. The LC yielded a concordant species ID by VITEK MS in 121/138 (87.7%) samples, identifying 32 different Gram-positive and Gram-negative species with 3/123 (2.6%) discordances. Compared to standard workflow, direct AST of the LC using VITEK® 2 yielded 98.4% categorical agreement and 98.0% essential agreement. Very major error, major error, and minor error rates were 1.0%, 0.0%, and 1.8%, respectively, for Gram-negative organisms; and 1.9%, 0.2%, and 1.2%, respectively, for Gram-positive organisms. The median times from positive blood culture flag to results by FASTTM System for ID and AST were 7.8 h and 15.7 h, respectively, versus 22.4 h and 36.6 h for standard workflow, respectively. In conclusion, the FASTTM System provides reliable results for direct ID and AST from PBCs with significantly decreased turnaround times. Full article
(This article belongs to the Special Issue Application of MALDI-TOF MS in Microbiology)
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7 pages, 235 KiB  
Communication
Performance of MALDI-TOF Mass Spectrometry (VITEK MS) in the Identification of Salmonella Species
by Gyu Ri Kim, Si Hyun Kim, Eun-Young Kim, Eun Hee Park, In Yeong Hwang, Seok Hoon Jeong, Hyun Soo Kim, Young Ah Kim, Young Uh, Kyeong Seob Shin, Young Ree Kim, Namhee Ryoo, Jong Hee Shin and Jeong Hwan Shin
Microorganisms 2022, 10(10), 1974; https://doi.org/10.3390/microorganisms10101974 - 05 Oct 2022
Cited by 3 | Viewed by 2288
Abstract
Salmonella is a major pathogen causing foodborne infections in humans. Salmonella isolates are identified using biochemical and serological tests, including automated systems such as the VITEK2 system. However, there are few reports on Salmonella identification using VITEK MS. Therefore, we aimed to evaluate [...] Read more.
Salmonella is a major pathogen causing foodborne infections in humans. Salmonella isolates are identified using biochemical and serological tests, including automated systems such as the VITEK2 system. However, there are few reports on Salmonella identification using VITEK MS. Therefore, we aimed to evaluate the usefulness of MALDI-TOF VITEK MS for Salmonella identification. A total of 1389 Salmonella isolates were identified using VITEK MS ver3.0 or ver3.2. All Salmonella isolates were confirmed by serotyping using the Kauffmann-White scheme, and the results were compared with the VITEK MS results. A total of 1389 Salmonella isolates, including 66 serotypes, were correctly identified at the genus level by VITEK MS. However, these systems failed to correctly identify typhoidal Salmonella. Among the five Salmonella enterica ssp. diarizonae isolates, only one was correctly identified, whereas one and three isolates were partially identified and misidentified, respectively. On the other hand, the VITEK2 system successfully identified all typhoidal Salmonella (Typhi and Paratyphi A) and Salmonella enterica ssp. diarizonae isolates. VITEK MS was useful for identifying Salmonella species isolated from clinical specimens; however, additional biochemical tests, such as the VITEK2 System, should be considered to accurately identify Salmonella ser. Typhi, and Salmonella ser. Paratyphi A. Full article
(This article belongs to the Special Issue Application of MALDI-TOF MS in Microbiology)
11 pages, 1311 KiB  
Article
Performance of a Machine Learning-Based Methicillin Resistance of Staphylococcus aureus Identification System Using MALDI-TOF MS and Comparison of the Accuracy according to SCCmec Types
by Kibum Jeon, Jung-Min Kim, Kyoohyoung Rho, Seung Hee Jung, Hyung Soon Park and Jae-Seok Kim
Microorganisms 2022, 10(10), 1903; https://doi.org/10.3390/microorganisms10101903 - 25 Sep 2022
Cited by 5 | Viewed by 1684
Abstract
The prompt presumptive identification of methicillin-resistant Staphylococcus aureus (MRSA) using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) can aid in early clinical management and infection control during routine bacterial identification procedures. This study applied a machine learning approach to MALDI-TOF peaks [...] Read more.
The prompt presumptive identification of methicillin-resistant Staphylococcus aureus (MRSA) using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) can aid in early clinical management and infection control during routine bacterial identification procedures. This study applied a machine learning approach to MALDI-TOF peaks for the presumptive identification of MRSA and compared the accuracy according to staphylococcal cassette chromosome mec (SCCmec) types. We analyzed 194 S. aureus clinical isolates to evaluate the machine learning-based identification system (AMRQuest software, v.2.1, ASTA: Suwon, Korea), which was constructed with 359 S. aureus clinical isolates for the learning dataset. This system showed a sensitivity of 91.8%, specificity of 83.3%, and accuracy of 87.6% in distinguishing MRSA. For SCCmec II and IVA types, common MRSA types in a hospital context, the accuracy was 95.4% and 96.1%, respectively, while for the SCCmec IV type, it was 21.4%. The accuracy was 90.9% for methicillin-susceptible S. aureus. This presumptive MRSA identification system may be helpful for the management of patients before the performance of routine antimicrobial resistance testing. Further optimization of the machine learning model with more datasets could help achieve rapid identification of MRSA with less effort in routine clinical procedures using MALDI-TOF MS as an identification method. Full article
(This article belongs to the Special Issue Application of MALDI-TOF MS in Microbiology)
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10 pages, 274 KiB  
Article
Comparative Study of Different Diagnostic Routine Methods for the Identification of Acinetobacter radioresistens
by Richard Bigge, Boyke Bunk, Wolfram W. Rudolph, Florian Gunzer, Sina M. Coldewey, Thomas Riedel and Percy Schröttner
Microorganisms 2022, 10(9), 1767; https://doi.org/10.3390/microorganisms10091767 - 31 Aug 2022
Cited by 1 | Viewed by 2107
Abstract
Recent publications indicate that A. radioresistens can cause infections in humans, even though it is rarely reported in routine diagnostics. However, the fact that it is infrequently detected may be explained by the misidentification of the species by conventional methods. It is also [...] Read more.
Recent publications indicate that A. radioresistens can cause infections in humans, even though it is rarely reported in routine diagnostics. However, the fact that it is infrequently detected may be explained by the misidentification of the species by conventional methods. It is also likely that A. radioresistens is not considered clinically relevant and therefore not consistently included in diagnostic results. To elucidate the medical significance of this probably clinically underestimated bacterial species, we created a well-documented reference strain collection of 21 strains collected in routine diagnostics. For further analysis of A. radioresistens, it is essential to know which methods can be used to achieve a trustworthy identification. We, therefore, compared three methods widely used in routine diagnostics (MALDI-TOF MS, VITEK 2, and sequencing of housekeeping genes) in terms of secure and reliable identification of A. radioresistens. As reference methods, whole genome-based approaches were applied. VITEK 2 led to misidentification for four strains. However, MALDI-TOF MS and sequencing of housekeeping genes led to reliable and robust identifications. Full article
(This article belongs to the Special Issue Application of MALDI-TOF MS in Microbiology)
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