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

Paul Tetteh Asare; Chi-Hsien Lee; Vera Hürlimann; Youzheng Teo; Aline Cuénod; Nermin Akduman; Cordula Gekeler; Afrizal Afrizal; Myriam Corthesy; Claire Kohout; Vincent Thomas; Tomas de Wouters; Gilbert Greub; Thomas Clavel; Eric G Pamer; Adrian Egli; Lisa Maier; Pascale Vonaesch

doi:10.3389/fmicb.2023.1104707

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

Front Microbiol. 2023 Feb 21:14:1104707. doi: 10.3389/fmicb.2023.1104707. eCollection 2023.

Authors

Paul Tetteh Asare^{1

2

3

4}, Chi-Hsien Lee^{1

2

3}, Vera Hürlimann^{2

3}, Youzheng Teo¹, Aline Cuénod^{4

5}, Nermin Akduman^{6

7}, Cordula Gekeler^{6

7}, Afrizal Afrizal⁸, Myriam Corthesy⁹, Claire Kohout¹⁰, Vincent Thomas¹¹, Tomas de Wouters¹², Gilbert Greub⁹, Thomas Clavel⁸, Eric G Pamer¹⁰, Adrian Egli^{4

5}, Lisa Maier^{6

7}, Pascale Vonaesch^{1

2

3}

Affiliations

¹ Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
² Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.
³ University of Basel, Basel, Switzerland.
⁴ Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
⁵ Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland.
⁶ Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany.
⁷ Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany.
⁸ Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany.
⁹ Institute of Microbiology of the University of Lausanne, University Hospital Centre (CHUV), Lausanne, Switzerland.
¹⁰ Duchossois Family Institute, Division of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, United States.
¹¹ BioAster, Paris, France.
¹² PharmaBiome AG, Schlieren, Switzerland.

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.

Keywords: Clostridia; MALDI-TOF MS; anaerobic; bacterial identification; commensal bacteria; culturomics; human gut microbiota; next-generation probiotics.