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Mass Spectrometry: An Undeniable Tool in Current Microbiology

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A special issue of Microorganisms (ISSN 2076-2607).

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 57278

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Special Issue Editors

Prof. Dr. Nelson Lima

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Guest Editor

CEB—Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4700-057 Braga, Portugal
Interests: food and environmental mycology; fungal polyphasic identification; fungi ex situ preservation; fungal culture collections; science and environmental education
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Cledir Santos

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Guest Editor

Department of Chemical Science and Natural Resources, Universidad de La Frontera, Av. Francisco Salazar 01145, Temuco 4811-230, Chile
Interests: biofungicides and "One Health" agricultural systems; study of fungal resistance to fungicides; chemotaxonomy of filamentous fungi, mycotoxins and climate change; new techniques for long-term fungal preservation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Mass spectrometry (MS) is an analytical tool in chemistry with a long history of constant technological progress regarding the mass resolution, accuracy, and acquisition speed of instruments and the software that makes them operational. In the last two decades, MS has also become indispensable in the study of microorganisms. Among the MS techniques, MALDI-TOF MS offers a reliable and cost-effective method for microbial identification. Fingerprints obtained from ribosomal proteins and other small molecules, in the range of 2–20 kDa, are nowadays used to identify microorganisms in many laboratories all around the world.

Moreover, methods based on LC–MS, GC–MS, and other coupled MS techniques have been developed, and contribute decisively towards the expansion of microbial proteomics, metabolomics, and lipidomics knowledge. Developments have also been observed in the discovery of new microbial biomarkers which have allowed new promising applications in health and life sciences.

Overall, MS generates an unprecedented large volume of data in microbiology that has fostered the development of bioinformatics tools and their associated databases. However, several challenges need to be investigated and performed, such as common protocols and databases for the exchange of information under standardized quality assurance and quality control (QA/QC).

Taking all this into consideration, we are interested in receiving papers which update on the progress made in the last five years, not only in solving problems in the QA/QC of microbial identification using MS techniques but also new applications of MS towards generating information about microbial traits and the deployment of data. We encourage authors to submit original research, opinion pieces, and reviews to this Special Issue and demonstrate that MS in current microbiology is an essential tool.

Prof. Dr. Nelson Lima
Prof. Dr. Cledir Santos
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. 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.

Published Papers (14 papers)

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Research

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11 pages, 1476 KiB

Open AccessArticle

Network Analysis Based on Unique Spectral Features Enables an Efficient Selection of Genomically Diverse Operational Isolation Units

by Charles Dumolin, Charlotte Peeters, Evelien De Canck, Nico Boon and Peter Vandamme

Microorganisms 2021, 9(2), 416; https://doi.org/10.3390/microorganisms9020416 - 17 Feb 2021

Cited by 3 | Viewed by 2938

Abstract

Culturomics-based bacterial diversity studies benefit from the implementation of MALDI-TOF MS to remove genomically redundant isolates from isolate collections. We previously introduced SPeDE, a novel tool designed to dereplicate spectral datasets at an infraspecific level into operational isolation units (OIUs) based on unique spectral features. However, biological and technical variation may result in methodology-induced differences in MALDI-TOF mass spectra and hence provoke the detection of genomically redundant OIUs. In the present study, we used three datasets to analyze to which extent hierarchical clustering and network analysis allowed to eliminate redundant OIUs obtained through biological and technical sample variation and to describe the diversity within a set of spectra obtained from 134 unknown soil isolates. Overall, network analysis based on unique spectral features in MALDI-TOF mass spectra enabled a superior selection of genomically diverse OIUs compared to hierarchical clustering analysis and provided a better understanding of the inter-OIU relationships. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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11 pages, 1079 KiB

Open AccessArticle

Identification of Adult Fasciola spp. Using Matrix-Assisted Laser/Desorption Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry

by Issa Sy, Lena Margardt, Emmanuel O. Ngbede, Mohammed I. Adah, Saheed T. Yusuf, Jennifer Keiser, Jacqueline Rehner, Jürg Utzinger, Sven Poppert and Sören L. Becker

Microorganisms 2021, 9(1), 82; https://doi.org/10.3390/microorganisms9010082 - 31 Dec 2020

Cited by 15 | Viewed by 3609

Abstract

Fascioliasis is a neglected trematode infection caused by Fasciola gigantica and Fasciola hepatica. Routine diagnosis of fascioliasis relies on macroscopic identification of adult worms in liver tissue of slaughtered animals, and microscopic detection of eggs in fecal samples of animals and humans. However, the diagnostic accuracy of morphological techniques and stool microscopy is low. Molecular diagnostics (e.g., polymerase chain reaction (PCR)) are more reliable, but these techniques are not routinely available in clinical microbiology laboratories. Matrix-assisted laser/desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a widely-used technique for identification of bacteria and fungi; yet, standardized protocols and databases for parasite detection need to be developed. The purpose of this study was to develop and validate an in-house database for Fasciola species-specific identification. To achieve this goal, the posterior parts of seven adult F. gigantica and one adult F. hepatica were processed and subjected to MALDI-TOF MS to create main spectra profiles (MSPs). Repeatability and reproducibility tests were performed to develop the database. A principal component analysis revealed significant differences between the spectra of F. gigantica and F. hepatica. Subsequently, 78 Fasciola samples were analyzed by MALDI-TOF MS using the previously developed database, out of which 98.7% (n = 74) and 100% (n = 3) were correctly identified as F. gigantica and F. hepatica, respectively. Log score values ranged between 1.73 and 2.23, thus indicating a reliable identification. We conclude that MALDI-TOF MS can provide species-specific identification of medically relevant liver flukes. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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26 pages, 5153 KiB

Open AccessArticle

Global Proteomic Profiling of Piscirickettsia salmonis and Salmon Macrophage-Like Cells during Intracellular Infection

by Javiera Ortiz-Severín, Dante Travisany, Alejandro Maass, Verónica Cambiazo and Francisco P. Chávez

Microorganisms 2020, 8(12), 1845; https://doi.org/10.3390/microorganisms8121845 - 24 Nov 2020

Cited by 16 | Viewed by 3478

Abstract

Piscirickettsiasalmonis is an intracellular bacterial fish pathogen that causes piscirickettsiosis, a disease with numerous negative impacts in the Chilean salmon farming industry. Although transcriptomic studies of P. salmonis and its host have been performed, dual host–pathogen proteomic approaches during infection are still missing. Considering that gene expression does not always correspond with observed phenotype, and bacteriological culture studies inadequately reflect infection conditions, to improve the existing knowledge for the pathogenicity of P. salmonis, we present here a global proteomic profiling of Salmon salar macrophage-like cell cultures infected with P. salmonis LF-89. The proteomic analyses identified several P. salmonis proteins from two temporally different stages of macrophages infection, some of them related to key functions for bacterial survival in other intracellular pathogens. Metabolic differences were observed in early-stage infection bacteria, compared to late-stage infections. Virulence factors related to membrane, lipopolysaccharide (LPS) and surface component modifications, cell motility, toxins, and secretion systems also varied between the infection stages. Pilus proteins, beta-hemolysin, and the type VI secretion system (T6SS) were characteristic of the early-infection stage, while fimbria, upregulation of 10 toxins or effector proteins, and the Dot/Icm type IV secretion system (T4SS) were representative of the late-infection stage bacteria. Previously described virulence-related genes in P. salmonis plasmids were identified by proteomic assays during infection in SHK-1 cells, accompanied by an increase of mobile-related elements. By comparing the infected and un-infected proteome of SHK-1 cells, we observed changes in cellular and redox homeostasis; innate immune response; microtubules and actin cytoskeleton organization and dynamics; alteration in phagosome components, iron transport, and metabolism; and amino acids, nucleoside, and nucleotide metabolism, together with an overall energy and ATP production alteration. Our global proteomic profiling and the current knowledge of the P. salmonis infection process allowed us to propose a model of the macrophage–P. salmonis interaction. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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15 pages, 989 KiB

Open AccessArticle

MALDI-TOF MS and 16S RNA Identification of Culturable Gastric Microbiota: Variability Associated with the Presence of Helicobacter pylori

by Claudia Troncoso, Monica Pavez, Alvaro Cerda, Marcelo Oporto, Daniel Villarroel, Edmundo Hofmann, Eddy Rios, Armando Sierralta, Luis Copelli and Leticia Barrientos

Microorganisms 2020, 8(11), 1763; https://doi.org/10.3390/microorganisms8111763 - 10 Nov 2020

Cited by 8 | Viewed by 3044

Abstract

Helicobacter pylori is the main bacteria associated with gastroduodenal diseases. Recent studies have reported that gastric microbiota might be modified by the H. pylori colonization, favoring gastric lesions′ development. In Chile, the region of La Araucanía concentrates a high risk of gastric cancer associated with Helicobacter pylori colonization, rurality, poverty, and Mapuche ethnicity. Hence, we aimed to identify the culturable gastric microbiota and characterize its variability at different stages of epithelial injury, based on its H. pylori colonization in dyspeptic patients from this Chilean region. Microaerophilic bacteria strains were isolated from antrum biopsies of 155 dyspeptic patients′ biopsies and identified using MALDI-TOF MS or 16sRNA gene sequencing for non-pylori species identification, and UreC gene amplification for H. pylori confirmation. We found 48 species from 18 families, mainly belonging to Neisseriaceae (21.3%), Streptococcaceae (20.0%), Actynomicetaceae (9.0%), Enterobacteriaceae, and Lactobacillaceae (4.5%); however, Streptococcaceae and Actinomycetaceae families showed a significant reduction in samples infected with H. pylori, along with a considerably lower diversity of species. Our results revealed a microbiota modification due to H. pylori colonization associated with the gastric epithelial state, suggesting a potential microbiota role for developing and progressing gastric diseases. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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13 pages, 986 KiB

Open AccessArticle

Development and Validation of an In-House Library for Filamentous Fungi Identification by MALDI-TOF MS in a Clinical Laboratory in Medellin (Colombia)

by Juan C. Gómez-Velásquez, Natalia Loaiza-Díaz, Gilma Norela Hernández, Nelson Lima and Ana C. Mesa-Arango

Microorganisms 2020, 8(9), 1362; https://doi.org/10.3390/microorganisms8091362 - 06 Sep 2020

Cited by 10 | Viewed by 2771

Abstract

Identification of filamentous fungi by conventional phenotypic methods are time-consuming, and a correct identification at the species level is prone to errors. Therefore, a more accurate and faster time-to-results, and cost-effective technique, is required, such as the Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). In this study, we describe the development of an in-house spectra library for the identification of filamentous fungi frequently isolated from patients with infections. An in-house spectra library was constructed using 14 reference strains grown in solid medium. Clinical isolates were identified either by the in-house spectra library or the Biotyper commercial library from Bruker Daltonics. Fungal identification was carried following the Biotyper’s established scores: ≤1.699: not reliably identified (NRI); 1.700–1.999: genus-level; ≥2.000: species-level. Clinical isolates were identified, with the in-house library, at species- and genus-level at 88.70% (55) and 3.22% (2), respectively. While 4.80% (3) was NRI and 3.22% (2) was discrepant concerning sequencing. On the contrary, identification up to species and genus-level with the commercial library was 44.44% (16) and 22.22% (8), respectively. NRI and the discrepancy was 30.55% (11) and 2.77% (1), respectively. For the reaming 26 isolates, 16 from Neoscytalidium dimidiatum and 10 from Sporothrix spp., respectively, the absence of spectrum and the specific spectra within the Sporothrix complex in the commercial library resulted in the inability to obtain an identification. In conclusion, the current results advocate the importance that each clinical microbiological laboratory needs to develop an ad hoc library associated with the MALDI-TOF MS fungal identification to overcome the limitations of the available commercial libraries. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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9 pages, 1339 KiB

Open AccessArticle

Emergence of Staphylococcus lugdunensis as a Cause of Urinary Tract Infection: Results of the Routine Use of MALDI-TOF MS

by Kelvin H. Y. Chiu, Rex P. K. Lam, Elaine Chan, Susanna K. P. Lau and Patrick C. Y. Woo

Microorganisms 2020, 8(3), 381; https://doi.org/10.3390/microorganisms8030381 - 09 Mar 2020

Cited by 5 | Viewed by 4860

Abstract

We analyzed the incidence and the clinical and laboratory characteristics of Staphylococcus lugdunensis urinary tract infections (UTIs) during a 10-year period (2009–2018) and compared them with those of Staphylococcus saprophyticus UTIs. A total of 38 and 162 episodes of S. lugdunensis and S. saprophyticus UTIs were observed. The number of S. saprophyticus UTIs was stable throughout the 10 years, whereas there was an obvious surge in the apparent number of S. lugdunensis UTIs since 2014, coinciding with the commencement of a routine use of MALDI-TOF MS. Univariate analysis showed that male sex (p < 0.001), advanced age (p < 0.001), hospital-acquired infections, (p < 0.001), upper UTI (p < 0.005), polymicrobial infections (p < 0.05), hypertension (p < 0.001), solid-organ malignancies (p < 0.001), renal stones (p < 0.001), urinary stricture (p < 0.05), vesicoureteral reflux (p < 0.001), and presence of a urinary catheter (p < 0.001) were significantly associated with S. lugdunensis UTI. Multivariable analysis revealed that S. lugdunensis UTI was associated with male sex (OR = 6.08, p < 0.05), solid-organ malignancies (OR = 12.27, p < 0.01), and urological system abnormalities (OR = 7.44, p < 0.05). There were significant differences in the patient population affected and predisposing factors between S. lugdunensis and S. saprophyticus UTIs. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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13 pages, 3492 KiB

Open AccessArticle

Rapid Detection of Echinocandins Resistance by MALDI-TOF MS in Candida parapsilosis Complex

by Ana Emília M. Roberto, Danilo E. Xavier, Esteban E. Vidal, Cláudia Fernanda de L. Vidal, Rejane P. Neves and Reginaldo G. de Lima-Neto

Microorganisms 2020, 8(1), 109; https://doi.org/10.3390/microorganisms8010109 - 13 Jan 2020

Cited by 17 | Viewed by 3225

Abstract

Mass spectrometry by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) was used to identify and differentiate the pattern of susceptibility of clinical isolates of Candida parapsilosis complex. 17 C. parapsilosis sensu stricto, 2 C. orthopsilosis, and 1 C. metapsilosis strains were obtained from blood cultures, and three different inocula (10³, 10⁵, and 10⁷ CFU/mL) were evaluated against three echinocandins at concentrations ranging from 0.03 to 16 µg/mL after incubation of 1 h, 2 h, and 3 h. Drug-free control was used. The spectra obtained at these concentrations were applied to generate composite correlation index (CCI) matrices for each yeast individually. After cross correlations and autocorrelations of each spectra with null (zero) and maximal (16) concentrations, the CCI was used as separation parameter among spectra. Incubation time and inoculum were critical factors to reach higher precision and reliability of this trial. With an incubation time of 3 h and inoculum of 10⁷ CFU/mL, it was possible to determine the breakpoint of the clinical yeasts by MALDI-TOF that presented high agreement with the clinical laboratory standard institute (CLSI) reference method. Herein, we show that mass spectrometry using the MALDI-TOF technique is powerful when it exploits antifungal susceptibility testing assays. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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14 pages, 2023 KiB

Open AccessArticle

First Comprehensive Report of Clinical Fusarium Strains Isolated in the State of Sao Paulo (Brazil) and Identified by MALDI-TOF MS and Molecular Biology

by Mario Henrique Paziani, Ludmilla Tonani Carvalho, Marcia de Souza Carvalho Melhem, Margarete Teresa Gottardo de Almeida, Maria Emilia Nadaletto Bonifácio da Silva, Roberto Martinez, Cledir Santos and Marcia Regina von Zeska Kress

Microorganisms 2020, 8(1), 66; https://doi.org/10.3390/microorganisms8010066 - 31 Dec 2019

Cited by 8 | Viewed by 2861

Abstract

The aim of this study was to compare the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), phenotypic and molecular methods for the identification of Fusarium species complexes isolated from clinical cases in the State of Sao Paulo (Brazil) between the years 2001 and 2017. Sequencing of ITS region of ribosomal DNA and elongation factor 1 alpha gene (ET1α) were used as reference method in the analysis of a total of 108 Fusarium spp. clinical strains isolated from human hosts with superficial and systemic infections. Agreement between MALDI-TOF-MS and molecular data was observed for 97 out of 108 clinical isolates (89.8%), whereas five (4.6%) and six (5.5%) clinical isolates were misidentified and were not identified by MALDI-TOF MS, respectively. ITS region sequences and MALDI-TOF MS mass spectra identified and grouped correctly most of Fusarium clinical isolates at species complex level. This investigation highlights the potential of MALDI-TOF MS technique as a fast and cost-efficient alternative for clinical Fusarium identification. However, MALDI-TOF MS requires a more accurate and larger database. This work is the first comprehensive report for Fusarium population, based on phenotypic analyses, proteomic profile by MALDI-TOF and phylogenetic analyses of Fusarium species complexes isolated from clinical cases in the State of Sao Paulo, Brazil. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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10 pages, 1885 KiB

Open AccessArticle

ITS rDNA Gene Analysis Versus MALDI-TOF MS For Identification of Neoscytalidium dimidiatum Isolated from Onychomycosis and Dermatomycosis Cases in Medellin (Colombia)

by Sindy V. Flórez-Muñoz, Juan C. Gómez-Velásquez, Natalia Loaiza-Díaz, Célia Soares, Carla Santos, Nelson Lima and Ana C. Mesa-Arango

Microorganisms 2019, 7(9), 306; https://doi.org/10.3390/microorganisms7090306 - 01 Sep 2019

Cited by 11 | Viewed by 2656

Abstract

Within the Neoscytalidium genus, N. dimidiatum, N. oculus, N. orchidacearum, and N. novaehollandiae have been recognized. Although these species are frequently found in soil, N. dimidiatum has been identified as an etiologic agent of onychomycosis or dermatomycosis, and N. oculus has been identified as an etiologic agent of an ocular lesion. All these species can be cultured in vitro, but their morphological identification by macroscopic and microscopic traits is difficult and imprecise due to their similarity. In this study, 34 isolates of Neoscytalidium spp. from 32 onychomycosis and two dermatomycosis cases in Medellin (Colombia) were identified at the species level using sequencing of the ITS1+5.8S+ITS2 nuclear rDNA region and MALDI-TOF mass spectrometry (MS). Neoscytalidium dimidiatum strain MUM 17.21 was used to construct the reference spectrum in the in-house library to identify the clinical isolates by MALDI-TOF MS. Additionally, N. dimidiatum PPC-216 and PLAB-055 strains were used to validate the in-house constructed reference spectra. Although four groups were observed in the dendrogram obtained from the proteins of each isolate profile, MALDI-TOF MS and sequencing results are in accordance, since all isolates were identified as N. dimidiatum. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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17 pages, 2629 KiB

Open AccessArticle

Polyphasic, Including MALDI-TOF MS, Evaluation of Freeze-Drying Long-Term Preservation on Aspergillus (Section Nigri) Strains

by Rodrigo Rodriguez, Carla Santos, Marta F. Simões, Célia Soares, Cledir Santos and Nelson Lima

Microorganisms 2019, 7(9), 291; https://doi.org/10.3390/microorganisms7090291 - 25 Aug 2019

Cited by 6 | Viewed by 3793

Abstract

This study aims to evaluate the effect of freeze-drying and long-term storage on the biotechnological potential of Aspergillus section Nigri strains. Twelve selected strains were freeze-dried and aged by accelerated storage, at 37 °C in the dark, for 2 and 4 weeks. To assess possible changes as a consequence of the ageing in the freeze-drying ampoules, morphological characteristics, mycotoxins and enzymes production, matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALTI-TOF MS) spectra, and M13 phage probe fingerprinting were used as part of a polyphasic approach. Phenotypical changes were observed; nevertheless, they did not substantially affect the potential biotechnological use of these strains. The activity of hydrolytic enzymes (protease, carboxymethylcellulase, xylanase, pectinase and mannanase) was maintained or increased after freeze-drying. MALDI-TOF MS data originated spectra that grouped, for the majority of samples, according to strain independently of preservation time point. M13 profiles revealed the presence of some genetic polymorphisms after preservation. However, the three studied times still clustered for more than 50% of strains. Our results show that the studied strains maintain their biotechnological potential after preservation, with minimal phenotypic alterations. These findings provide evidence that freeze-drying preservation is a suitable option to preserve biotechnologically relevant aspergilli strains from section Nigri, and one should consider that the observed effects might be species/strain-dependent. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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Review

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15 pages, 1988 KiB

Open AccessReview

COVID-19, Chikungunya, Dengue and Zika Diseases: An Analytical Platform Based on MALDI-TOF MS, IR Spectroscopy and RT-qPCR for Accurate Diagnosis and Accelerate Epidemics Control

by Jéssica Costa, Eugénio C. Ferreira and Cledir Santos

Microorganisms 2021, 9(4), 708; https://doi.org/10.3390/microorganisms9040708 - 30 Mar 2021

Cited by 8 | Viewed by 6525

Abstract

COVID-19 and arboviruses (ARBOD) epidemics co-occurrence is a great concern. In tropical and subtropical regions, ARBOD diseases such as chikungunya, dengue, and Zika are frequent. In both COVID-19 and ARBOD cases, an accurate diagnosis of infected patients is crucial to promote adequate treatment and isolation measures in COVID-19 cases. Overlap of clinical symptoms and laboratory parameters between COVID-19 and ARBOD present themselves as an extra challenge during diagnosis. COVID-19 diagnosis is mainly performed by quantitative reverse polymerase chain reaction (RT-qPCR), while ARBOD diagnosis is performed by serology, detection of antigen or antibody, and molecular diagnosis. In this review, the epidemiologic profile of arboviruses and SARS-CoV-2 is analyzed, and potential risks of symptom overlap is addressed. The implementation of an analytical platform based on infrared (IR) spectroscopy, MALDI-TOF mass spectrometry, and RT-qPCR is discussed as an efficient strategy for a fast, robust, reliable, and cost-effective diagnosis system even during the co-occurrence of virus outbreaks. The spectral data of IR spectroscopy and MALDI-TOF MS obtained from COVID-19 infected and recovered patients can be used to build up an integrated spectral database. This approach can enable us to determine quickly the groups that have been exposed and have recovered from COVID-19 or ARBOD, avoiding misdiagnoses. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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16 pages, 3280 KiB

Open AccessReview

MALDI-TOF Mass Spectrometry and Specific Biomarkers: Potential New Key for Swift Identification of Antimicrobial Resistance in Foodborne Pathogens

by Maureen Feucherolles, Henry-Michel Cauchie and Christian Penny

Microorganisms 2019, 7(12), 593; https://doi.org/10.3390/microorganisms7120593 - 21 Nov 2019

Cited by 22 | Viewed by 10188

Abstract

Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is today the reference method for direct identification of microorganisms in diagnostic laboratories, as it is notably time- and cost-efficient. In the context of increasing cases of enteric diseases with emerging multi-drug resistance patterns, there is an urgent need to adopt an efficient workflow to characterize antimicrobial resistance (AMR). Current approaches, such as antibiograms, are time-consuming and directly impact the “patient-physician” workflow. Through this mini-review, we summarize how the detection of specific patterns by MALDI-TOF MS, as well as bioinformatics, become more and more essential in research, and how these approaches will help diagnostics in the future. Along the same lines, the idea to export more precise biomarker identification steps by MALDI-TOF(/TOF) MS data towards AMR identification pipelines is discussed. The study also critically points out that there is currently still a lack of research data and knowledge on different foodborne pathogens as well as several antibiotics families such as macrolides and quinolones, and many questions are still remaining. Finally, the innovative combination of whole-genome sequencing and MALDI-TOF MS could be soon the future for diagnosis of antimicrobial resistance in foodborne pathogens. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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Other

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12 pages, 2570 KiB

Open AccessCase Report

Identification by MALDI-TOF MS of Sporothrix brasiliensis Isolated from a Subconjunctival Infiltrative Lesion in an Immunocompetent Patient

by Aline M. F. Matos, Lucas M. Moreira, Bianca F. Barczewski, Lucas X. de Matos, Jordane B. V. de Oliveira, Maria Ines F. Pimentel, Rodrigo Almeida-Paes, Murilo G. Oliveira, Tatiana C. A. Pinto, Nelson Lima, Magnum de O. Matos, Louise G. de M. e Costa, Cledir Santos and Manoel Marques Evangelista Oliveira

Microorganisms 2020, 8(1), 22; https://doi.org/10.3390/microorganisms8010022 - 21 Dec 2019

Cited by 17 | Viewed by 2947

Abstract

Sporotrichosis is a globally distributed subcutaneous fungal infection caused by dimorphic fungi belonging to the Sporothrix species complex that affects the skin of limbs predominantly, but not exclusively. A rare case of ocular sporotrichosis in an immunocompetent Brazilian patient from the countryside of Rio de Janeiro State is reported. A 68-year-old woman presented with a subconjunctival infiltrative lesion in the right eye with pre-auricular lymphadenopathy of onset 4 months ago that evolved to suppurative nodular lesions on the eyelids. Conjunctival secretion was evaluated by histopathological examination and inoculated on Sabouraud Dextrose Agar (SDA). Histopathology showed oval bodies within giant cells and other mononucleated histiocytes. Fungus grown on SDA was identified as Sporothrix sp. by morphological observations. The isolated strain was finally identified by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) associated with an in-house database enriched with reference Sporothrix complex spectra. The strain presented a MALDI spectrum with the ion peaks of the molecular mass profile of S. brasiliensis. The patient was adequately treated with amphotericin B subsequently replaced by itraconazole. Due to scars left by the suppurative process, the patient presented poor final visual acuity. The present work presents an overview of ocular sporotrichosis and discusses the diagnostic difficulty that can lead to visual sequelae in these cases. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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6 pages, 787 KiB

Open AccessBrief Report

Analysis of the Degradation of Broad-Spectrum Cephalosporins by OXA-48-Producing Enterobacteriaceae Using MALDI-TOF MS

by Marina Oviaño, María Rosario Rodicio, Jürgen J. Heinisch, Rosaura Rodicio, Germán Bou and Javier Fernández

Microorganisms 2019, 7(12), 614; https://doi.org/10.3390/microorganisms7120614 - 26 Nov 2019

Cited by 7 | Viewed by 3107

Abstract

The objective of the study was to evaluate the activity of OXA-48 against different broad-spectrum cephalosporins and to identify the reaction products by MALDI-TOF MS. The action of OXA-48 on cefotaxime, ceftazidime, and ceftriaxone was assessed by this method, using an Escherichia coli J53 transconjugant carrying only the ~62 Kb IncL plasmid containing the bla_OXA-48 gene, and the same strain without any plasmid was included as a negative control. In addition, a collection of 17 clinical OXA-48-producing Enterobacteriaceae, which were susceptible to broad-spectrum cephalosporins, was evaluated. MALDI-TOF MS-based analysis of the E. coli transconjugant carrying the bla_OXA-48-harboring plasmid, and also the clinical isolates, showed degradation of cefotaxime into two inactive compounds—decarboxylated and deacetylated cefotaxime (~370 Da) and deacetyl cefotaxime (~414 Da), both with the hydrolyzed beta-lactam ring. Reaction products were not obtained when the experiment was performed with ceftriaxone or ceftazidime. From a clinical point of view, our study supports the idea that the efficacy of cefotaxime against OXA-48-producing Enterobacteriaceae is doubtful, in contrast to ceftazidime and ceftriaxone which could be valid choices for treating infections caused by these bacteria. However, further clinical studies confirming this hypothesis are required. Full article

(This article belongs to the Special Issue Mass Spectrometry: An Undeniable Tool in Current Microbiology)

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