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

Journal: Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2019;25(7):904.e1-904.e7

PMID: 31130255

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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.

Address: 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.; Leiden University Medical Centre, Centre for Proteomics and Metabolomics, Leiden, the Netherlands.; Leiden University Medical Centre, Department of Medical Statistics and Bioinformatics, Leiden, the Netherlands.; Leiden University Medical Centre, Centre of Infectious Diseases, Department Medical Microbiology, Section Experimental Bacteriology, Leiden, the Netherlands.; Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.; Leiden University Medical Centre, Centre for Proteomics and Metabolomics, Leiden, the Netherlands. Electronic address: [email protected].; Leiden University Medical Centre, Centre for Proteomics and Metabolomics, Leiden, the Netherlands. Electronic address: [email protected].

DOI: 10.1016/j.cmi.2018.10.008

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MeSH Terms: Bacterial Typing Techniques, Biomarkers, Clostridioides difficile, Clostridium Infections, Genome, Bacterial, Humans, Multilocus Sequence Typing, Peptides, Sensitivity and Specificity, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization