Maximizing the Taxonomic Resolution of MALDI-TOF-MS-Based Approaches to Bacterial Characterization: From Culture Conditions Through Data Analysis

Zhang, Lin; Sandrin, Todd R.

doi:10.1007/978-3-319-26070-9_6

Cited by 5 publications

(4 citation statements)

References 180 publications

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“…With regard to the strain-level characterization, BioTyper has been suggested to be useful in characterizing bacteria at the strain level, but typically with the assistance of additional software, such as Clin-ProTools™. 5 Analysis of the entire spectrum with rigorous analytical tools is often required to obtain reliable strain identification. The ClinProTools™ provides a Principal component analysis (PCA) that also can differentiate between closely related samples, recalibrate to generate the necessary alignment, normalize each peak, and then can contribute equally to model generation.…”

Section: Analysis Of Mass Spectrometry Datamentioning

confidence: 99%

“…Several methods have been developed to be a rapid and effective tool to profile bacteria at the genus and species level with high reproducibility such as more recently the matrixassisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). 5 MALDI-TOF MS with library-based and/or bioinformatics-enabled methods has been successfully applied in many areas. For example, in clinical microbiology, MALDI-TOF MS has been used to identify pathogens, which can be rapidly reported by comparing spectra to a database and this technique has been used to accurately identify various microorganisms including S. aureus.…”

Section: S Rrna Gene Sequencementioning

confidence: 99%

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Evaluation of conventional methods for species identification of Staphylococcus aureus using MALDI-TOF MS, protein identification and quantification

Arsheewa¹,

Samosornsuk²,

Khattiyawech³

et al. 2023

JAMS

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Objectives: This study aimed to evaluate conventional methods for species identification of Staphylococcus aureus by MALDI-TOF MS. Additionally, the representatives of different species were used to analyze protein expression. Materials and methods: A total of 185 non-duplicated clinical S. aureus identified using the conventional method (colony morphology, Gram’s stain, slide coagulase test, tube coagulase test, catalase test, and mannitol fermentation) was confirmed the identification by MALDI-TOF MS and analyzed by Mass spectral profiling (MSP) and Principal component analysis (PCA). The representatives of different species reported by both methods were confirmed using 16SrRNA sequence and analyzed proteins expression by timsTOF MS. Results: All S. aureus suspected isolates could discriminate among species by MALDI-TOF MS including S. aureus (N=151, 81.6%), S. argenteus (N=32, 17.3%), S. hominis (N=1, 0.5%), and S. haemolyticus (N=1, 0.5%). Using 16S rRNA genebased analysis, S. aureus and S. argenteus could not differentiate from each other. Protein expression of S. aureus was similar to S. argenteus. These genes including rpsT, Huti, pyrF, atpD.1, cpfC, SAUA300_0786, atl.1, and MW2416 showed higher expression in S. aureus (MS076) than S. argenteus (MS060), S. haemolyticus (MS095) and S. hominis (MS060). Conclusion: MALDI-TOF MS provides an excellent tool for accurately species identification of staphylococci. S. aureus expressed protein analyzed higher than the other 3 species. The highest protein expression in S. aureus implies the most virulence of this strain.

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Section: Analysis Of Mass Spectrometry Datamentioning

confidence: 99%

Section: S Rrna Gene Sequencementioning

confidence: 99%

Evaluation of conventional methods for species identification of Staphylococcus aureus using MALDI-TOF MS, protein identification and quantification

Arsheewa¹,

Samosornsuk²,

Khattiyawech³

et al. 2023

JAMS

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“…The development of lean but highly diverse microbe libraries permits efficient industrial exploitation [ 3 ]. In addition, the description and differentiation of both species and strains within a species are of equal importance to environmental monitoring, clinical microbiology, as well as water quality and food safety [ 4 , 5 ]. However, long-term maintenance of large culture collections and processing of genomically redundant isolates result in an exponential increase in analysis costs.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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.

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“…Regardless of the particular MS technology used to characterize microorganisms, there is clear consensus in the literature that MS‐based approaches are highly effective at characterizing pure cultures of diverse microorganisms in both clinical/medical and environmental settings . Clinical microbiology labs often employ workflows, in particular isolation and monomicrobial cultivation of target microorganisms, to facilitate MS‐based characterization of microorganisms.…”

Section: Introductionmentioning

confidence: 99%

Characterization of microbial mixtures by mass spectrometry

Sandrin

Demirev

2017

Mass Spectrometry Reviews

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MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.

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Maximizing the Taxonomic Resolution of MALDI-TOF-MS-Based Approaches to Bacterial Characterization: From Culture Conditions Through Data Analysis

Cited by 5 publications

References 180 publications

Evaluation of conventional methods for species identification of Staphylococcus aureus using MALDI-TOF MS, protein identification and quantification

Evaluation of conventional methods for species identification of Staphylococcus aureus using MALDI-TOF MS, protein identification and quantification

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

Characterization of microbial mixtures by mass spectrometry

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