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A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia

Asare, P. T. and Lee, C. H. and Hürlimann, V. and Teo, Y. and Cuénod, A. and Akduman, N. and Gekeler, C. and Afrizal, A. and Corthesy, M. and Kohout, C. and Thomas, V. and de Wouters, T. and Greub, G. and Clavel, T. and Pamer, E. G. and Egli, A. and Maier, L. and Vonäsch, P.. (2023) A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia. Front Microbiol, 14. p. 1104707.

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Abstract

INTRODUCTION: Microbial isolates from culture can be identified using 16S or whole-genome sequencing which generates substantial costs and requires time and expertise. Protein fingerprinting via Matrix-assisted Laser Desorption Ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used for rapid bacterial identification in routine diagnostics but shows a poor performance and resolution on commensal bacteria due to currently limited database entries. The aim of this study was to develop a MALDI-TOF MS plugin database (CLOSTRI-TOF) allowing for rapid identification of non-pathogenic human commensal gastrointestinal bacteria. METHODS: We constructed a database containing mass spectral profiles (MSP) from 142 bacterial strains representing 47 species and 21 genera within the class Clostridia. Each strain-specific MSP was constructed using >20 raw spectra measured on a microflex Biotyper system (Bruker-Daltonics) from two independent cultures. RESULTS: For validation, we used 58 sequence-confirmed strains and the CLOSTRI-TOF database successfully identified 98 and 93% of the strains, respectively, in two independent laboratories. Next, we applied the database to 326 isolates from stool of healthy Swiss volunteers and identified 264 (82%) of all isolates (compared to 170 (52.1%) with the Bruker-Daltonics library alone), thus classifying 60% of the formerly unknown isolates. DISCUSSION: We describe a new open-source MSP database for fast and accurate identification of the Clostridia class from the human gut microbiota. CLOSTRI-TOF expands the number of species which can be rapidly identified by MALDI-TOF MS.
Faculties and Departments:09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH)
09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Medical Parasitology and Infection Biology (MPI) > Malaria Gene Regulation (Voss)
09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Epidemiology and Public Health (EPH) > Human and Animal Health > One Health (Zinsstag)
UniBasel Contributors:Asare, Paul Tetteh and Lee, Chi-Hsien and Vonäsch, Pascale
Item Type:Article, refereed
Article Subtype:Research Article
ISSN:1664-302X (Print)1664-302X (Electronic)1664-302X (Linking)
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
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Last Modified:09 May 2023 07:54
Deposited On:09 May 2023 07:54

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