Identification and validation of two peptide markers for the recognition of Clostridioides difficile MLST-1 and MLST-11 by MALDI-MS

J Corver; J Sen; B V H Hornung; B J Mertens; E K L Berssenbrugge; C Harmanus; I M J G Sanders; N Kumar; T D Lawley; E J Kuijper; P J Hensbergen; S Nicolardi

doi:10.1016/j.cmi.2018.10.008

Identification and validation of two peptide markers for the recognition of Clostridioides difficile MLST-1 and MLST-11 by MALDI-MS

Clin Microbiol Infect. 2019 Jul;25(7):904.e1-904.e7. doi: 10.1016/j.cmi.2018.10.008. Epub 2018 Oct 26.

Authors

J Corver¹, J Sen², B V H Hornung¹, B J Mertens³, E K L Berssenbrugge⁴, C Harmanus⁴, I M J G Sanders⁴, N Kumar⁵, T D Lawley⁵, E J Kuijper¹, P J Hensbergen⁶, S Nicolardi⁷

Affiliations

¹ Leiden University Medical Centre, Centre of Infectious Diseases, Department Medical Microbiology, Section Experimental Bacteriology, Leiden, the Netherlands; Centre for Microbiota Analysis and Therapeutics, Department Medical Microbiology, Leiden University, Leiden, the Netherlands.
² Leiden University Medical Centre, Centre for Proteomics and Metabolomics, Leiden, the Netherlands.
³ Leiden University Medical Centre, Department of Medical Statistics and Bioinformatics, Leiden, the Netherlands.
⁴ Leiden University Medical Centre, Centre of Infectious Diseases, Department Medical Microbiology, Section Experimental Bacteriology, Leiden, the Netherlands.
⁵ Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
⁶ Leiden University Medical Centre, Centre for Proteomics and Metabolomics, Leiden, the Netherlands. Electronic address: P.J.Hensbergen@lumc.nl.
⁷ Leiden University Medical Centre, Centre for Proteomics and Metabolomics, Leiden, the Netherlands. Electronic address: s.nicolardi@lumc.nl.

PMID: 31130255
DOI: 10.1016/j.cmi.2018.10.008

Abstract

Objectives: Clostridioides difficile infection (CDI) has become the main cause of nosocomial infective diarrhoea. To survey and control the spread of different C. difficile strains, there is a need for suitable rapid tests. The aim of this study was to identify peptide/protein markers for the rapid recognition of C. difficile strains by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS).

Methods: We analysed 44 well-characterized strains, belonging to eight different multi-locus sequence types (MLST), using ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) MS. The amino acid sequence of two peptide markers specific for MLST-1 and MLST-11 strains was elucidated by MALDI-TOF-MS/MS. The investigation of 2689 C. difficile genomes allowed the determination of the sensitivity and specificity of these markers. C18-solid-phased extraction was used to enrich the MLST-1 marker.

Results: Two peptide markers (m/z 4927.81 and m/z 5001.84) were identified and characterized for MLST-1 and MLST-11 strains, respectively. The MLST-1 marker was found in 786 genomes of which three did not belong to MLST-1. The MLST-11 marker was found in 319 genomes, of which 14 did not belong to MLST-11. Importantly, all MLST-1 and MLST-11 genomes were positive for their respective marker. Furthermore, a peptide marker (m/z 5015.86) specific for MLST-15 was found in 59 genomes. We translated our findings into a fast and simple method that allowed the unambiguous identification of the MLST-1 marker on a MALDI-TOF-MS platform.

Conclusions: MALDI-FTICR MS-based peptide profiling resulted in the identification of peptide markers for C. difficile MLST-1 and MLST-11.

Keywords: Clostridioides difficile; Matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance; Matrix-assisted laser desorption/ionization time-of-flight; Multilocus sequence typing; Peptide marker; Typing.

Publication types

Validation Study

MeSH terms

Bacterial Typing Techniques
Biomarkers / analysis
Clostridioides difficile / classification*
Clostridium Infections / diagnosis
Clostridium Infections / microbiology
Genome, Bacterial
Humans
Multilocus Sequence Typing*
Peptides / genetics*
Sensitivity and Specificity
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

Substances

Biomarkers
Peptides