Use of MALDI-TOF mass spectrometry in the battle against bacterial infectious diseases: recent achievements and future perspectives

Psaroulaki, Anna; Chochlakis, Dimosthenis

doi:10.1080/14789450.2018.1499469

Cited by 21 publications

(7 citation statements)

References 19 publications

(20 reference statements)

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“…Other approaches, such as MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry may complementarily provide fast and reliable identification of clinically-relevant microorganisms (36). Yet, MALDI-TOF may also suffer from sub-optimal identification due to limitations, including insufficient representation of reference species profiles in available commercial databases, absence of newly discovered species, and the existence of several commercial systems (37)(38)(39).…”

Section: Discussionmentioning

confidence: 99%

A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing

et al. 2020

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Amplicon sequencing of the 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations, with the most significant being the inability to resolve mixed amplicons when closely related species are coamplified from a mixed culture. This often leads to either increased turnaround time or absence of usable sequence data. Short-read next-generation sequencing (NGS) technologies could solve the mixed amplicon issue but would lack both cost efficiency at low throughput and fast turnaround times. Nanopore sequencing developed by Oxford Nanopore Technologies (ONT) could solve those issues by enabling a flexible number of samples per run and an adjustable sequencing time. Here, we report on the development of a standardized laboratory workflow combined with a fully automated analysis pipeline LORCAN (long read consensus analysis), which together provide a sample-to-report solution for amplicon sequencing and taxonomic identification of the resulting consensus sequences. Validation of the approach was conducted on a panel of reference strains and on clinical samples consisting of single or mixed rRNA amplicons associated with various bacterial genera by direct comparison to the corresponding Sanger sequences. Additionally, simulated read and amplicon mixtures were used to assess LORCAN’s behavior when dealing with samples with known cross-contamination levels. We demonstrate that by combining ONT amplicon sequencing results with LORCAN, the accuracy of Sanger sequencing can be closely matched (>99.6% sequence identity) and that mixed samples can be resolved at the single-base resolution level. The presented approach has the potential to significantly improve the flexibility, reliability, and availability of amplicon sequencing in diagnostic settings.

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Section: Discussionmentioning

confidence: 99%

A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing

et al. 2020

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“…An essential feature of the MS innovation will be the possibility of its application to the quick discovery of microbes triggering hospital infection [ 107 ]. If combined with proper fast and delicate modern technologies for the medical diagnosis of avoidable diseases, MS can also influence quality control of sterile blood items and food security [ 108 ]. Assimilation of molecular and computational strategies with MS needs to generate analysis assays for wide, regular public health and medical practice applications.…”

Section: Future Perspectivesmentioning

confidence: 99%

MALDI-TOF Mass Spectroscopy Applications in Clinical Microbiology

Alizadeh

Yousefi

Pakdel

et al. 2021

Advances in Pharmacological and Pharmaceutical Sciences

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There is a range of proteomics methods to spot and analyze bacterial protein contents such as liquid chromatography-mass spectrometry (LC-MS), two-dimensional gel electrophoresis, and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS), which give comprehensive information about the microorganisms that may be helpful within the diagnosis and coverings of infections. Microorganism identification by mass spectrometry is predicted on identifying a characteristic spectrum of every species so matched with an outsized database within the instrument. MALDI-TOF MS is one of the diagnostic methods, which is a straightforward, quick, and precise technique, and is employed in microbial diagnostic laboratories these days and may replace other diagnostic methods. This method identifies various microorganisms such as bacteria, fungi, parasites, and viruses, which supply comprehensive information. One of the MALDI-TOF MS’s crucial applications is bacteriology, which helps identify bacterial species, identify toxins, and study bacterial antibiotic resistance. By knowing these cases, we will act more effectively against bacterial infections.

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“…Базы данных масс-спектров протеинового состава клеток микромицетов постоянно пополняются, что облегчает и ускоряет диагностику возбудителей микозов [16]. Помимо идентификации, метод MALDI-TOF MS позволяет в короткие сроки определить профиль резистентности выделенного штамма, что имеет основополагающее значение для обеспечения быстрой и эффективной антимикробной терапии, особенно в случаях развития диссеминированных форм микозов [17].…”

Section: этапы проведения Maldi-tof Ms при идентификации возбудителей...unclassified

The use of MALDI-TOF massspectrometry for the identification of fungal pathogens

Surkova¹,

Sharov²,

Polovets³

et al. 2021

Immunopathol Allergol Infectol

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Here we review modern data on the advantages and disadvantages of identifying mycoses pathogens using the MALDI-TOF mass spectrometry method. The advantages of this method are the high accuracy of the results obtained, the simplicity of the analysis, and the ability to determine the indicators of sensitivity to antifungal drugs. Limitations in using the method are associated with the lack of reference mass spectra of many micromycetes in the databases and standardized protocols for preparing micromycete cultures for MALDI-TOF mass spectrometry. Additional difficulties arise in the identification of pathogens of especially dangerous mycoses due to the limited representation of reference mass spectra in databases. When developing unified protocols for sample preparation, it is also necessary to take into account the growth phase of dimorphic micromycetes.

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Use of MALDI-TOF mass spectrometry in the battle against bacterial infectious diseases: recent achievements and future perspectives

Cited by 21 publications

References 19 publications

A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing

A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing

MALDI-TOF Mass Spectroscopy Applications in Clinical Microbiology

The use of MALDI-TOF massspectrometry for the identification of fungal pathogens

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Use of MALDI-TOF mass spectrometry in the battle against bacterial infectious diseases: recent achievements and future perspectives

Cited by 21 publications

References 19 publications

A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing

A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing

MALDI-TOF Mass Spectroscopy Applications in Clinical Microbiology

The use of MALDI­-TOF mass­spectrometry for the identification of fungal pathogens

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The use of MALDI-TOF massspectrometry for the identification of fungal pathogens