“Omic” Approaches to Bacteria and Antibiotic Resistance Identification

Janiszewska, Daria; Szultka‐Młyńska, Małgorzata; Pomastowski, Paweł; Buszewski, Bogusław

doi:10.3390/ijms23179601

Cited by 11 publications

(21 citation statements)

References 269 publications

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“…The computer software associated with the machine MALDI Biotyper (Bruker Daltonics GmbH, Bremen, Germany) uses this “score”; a score value of 2.0 is considered a reliable criterion of bacterial species identification, although the spectra obtained from a single strain are not identical in repeated runs because of a method-inherent noise. Score values between 1.7 and 2.0 are considered reliable for genus identification [ 22 , 23 , 24 , 25 , 27 , 28 , 29 , 30 , 31 , 32 ]. The machine MALDI VITEK MS (bio-Mérieux, Mercy L’Étoile, France) produces a confidence value, which can be reported as a percentage up to 99.9%.…”

Section: Maldi-tof Ms: Principles Of the Proceduresmentioning

confidence: 99%

MALDI-TOF MS: A Reliable Tool in the Real Life of the Clinical Microbiology Laboratory

Calderaro,

Chezzi

2024

Microorganisms

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Matrix-Assisted Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) in the last decade has revealed itself as a valid support in the workflow in the clinical microbiology laboratory for the identification of bacteria and fungi, demonstrating high reliability and effectiveness in this application. Its use has reduced, by 24 h, the time to obtain a microbiological diagnosis compared to conventional biochemical automatic systems. MALDI-TOF MS application to the detection of pathogens directly in clinical samples was proposed but requires a deeper investigation, whereas its application to positive blood cultures for the identification of microorganisms and the detection of antimicrobial resistance are now the most useful applications. Thanks to its rapidity, accuracy, and low price in reagents and consumables, MALDI-TOF MS has also been applied to different fields of clinical microbiology, such as the detection of antibiotic susceptibility/resistance biomarkers, the identification of aminoacidic sequences and the chemical structure of protein terminal groups, and as an emerging method in microbial typing. Some of these applications are waiting for an extensive evaluation before confirming a transfer to the routine. MALDI-TOF MS has not yet been used for the routine identification of parasites; nevertheless, studies have been reported in the last few years on its use in the identification of intestinal protozoa, Plasmodium falciparum, or ectoparasites. Innovative applications of MALDI-TOF MS to viruses’ identification were also reported, seeking further studies before adapting this tool to the virus’s diagnostic. This mini-review is focused on the MALDI-TOF MS application in the real life of the diagnostic microbiology laboratory.

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Section: Maldi-tof Ms: Principles Of the Proceduresmentioning

confidence: 99%

MALDI-TOF MS: A Reliable Tool in the Real Life of the Clinical Microbiology Laboratory

Calderaro,

Chezzi

2024

Microorganisms

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“…Proteomics and genomics were the first "OMICS" formed to date, and now there are lots of closely related scientific disciplines. Some of these disciplines gave birth to new scientific fields and covered narrower arrays of a specific scientific field [25].…”

Section: "Omics"mentioning

confidence: 99%

“…Consequently, analysis of PTMs is important for the study of cell biology and disease diagnostics and prevention. The worldwide studies of different PTMs and the proportion change of different proteins could provide new insights into the clinical approach [25].To highlight the relevance of MS in the analysis of PTM, statistics of each PTM experimentally and putatively detected have been compiled using proteome-wide information from the Swiss-Prot database [50]. Many physiological functions can be overviewed using MS-based quantitative strategies developed to quantify glycoprotein expression levels on a large scale [51].…”

Section: Ms-based Quantitative Strategies and Analysis Of Proteome Ge...mentioning

confidence: 99%

Mass Spectrometry-Based Techniques Towards OMICS 2.0

Šoša¹

2023

Preprint

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The literature was scoped to help place mass spectrometric (MS) platforms in the spotlight of the life sciences, as a tool of OMICS and OMICS 2.0 technologies. Moreover, today’s appliances are so handy, that they literally place a whole lab on a single chip. Methods of OMICS (and the most recently developed term OMICS 2.0) are tackled, having in mind their aptness for educational purposes, as well as their feasibility. This same topic was highlighted in many reviews that have been periodically published. The author’s initial interest was the forensic application of MS, but since these interests changed, terms such as “biosensors” were also examined, so the review included means of discovery of efficient biomarkers and clinical therapeutic targets. Aside from simply reviewing the research status and the future perspectives, this article tackles terms such as Society 5.0 and OMICS 2.0. However, within the framework of this review, physical chemistry, bioinformatics, or specific software solutions were not specifically studied. Since the topic of generating permanent collections of digital content for retrospective analysis was also reviewed, the need for loads of data – cloud storage was discussed in the context of MS. These large quantities of data are easier to operate with if generated by MS, rather than by any other commercially available assay. In this manner, the review has strengthened an in-depth understanding of the applications of MS.

show abstract

Section: "Omics"mentioning

confidence: 99%

“…Consequently, analysis of PTMs is important for the study of cell biology and disease diagnostics and prevention. The worldwide studies of different PTMs and the proportion change of different proteins could provide new insights into the clinical approach [24].To highlight the relevance of MS in the analysis of PTM, statistics of each PTM experimentally and putatively detected have been compiled using proteome-wide information from the Swiss-Prot database [49].…”

Section: Ms-based Quantitative Strategies and Analysis Of Proteome Ge...mentioning

confidence: 99%

Mass Spectrometry-Based Techniques Towards OMICS 2.0

Šoša¹

2022

Preprint

View full text Add to dashboard Cite

The literature was scoped to help place mass spectrometric (MS) platforms in the spotlight of the life sciences, as a tool of OMICS and OMICS 2.0 technologies. These methods were discussed, and their feasibility was highlighted in many reviews that have been periodically published, in addition to the most recently developed term OMICS 2.0. This author’s primary interest was the forensic application of MS, but since these interests got broadened, terms such as “biosensors” were also included. So, means of discovery of efficient biomarkers and clinical therapeutic targets were also reviewed. However, within the framework of this review, physical chemistry, bioinformatics, or specific software solutions were not specifically scoped. Aside from simply reviewing the research status and the future perspectives, this article tackles terms such as Society 5.0 and OMICS 2.0. Since the topic of generating permanent collections of digital content for retrospective analysis was reviewed, what requires loads of data – cloud storage is discussed in the context of MS. In this manner, the review has strengthened an in-depth understanding of the applications of MS. These large quantities of data are easier to operate with if generated by MS, rather than by any other commercially available assay.

show abstract

“Omic” Approaches to Bacteria and Antibiotic Resistance Identification

Cited by 11 publications

References 269 publications

MALDI-TOF MS: A Reliable Tool in the Real Life of the Clinical Microbiology Laboratory

MALDI-TOF MS: A Reliable Tool in the Real Life of the Clinical Microbiology Laboratory

Mass Spectrometry-Based Techniques Towards OMICS 2.0

Mass Spectrometry-Based Techniques Towards OMICS 2.0

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