Filling the gaps in clinical proteomics: a do-it-yourself guide for the identification of the emerging pathogen Arcobacter by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Abstract

Arcobacters are considered emerging gastrointestinal pathogens. Rapid, reliable and species-specific identification of these bacteria is important. Biochemical tests commonly yield negative or variable results. Molecular methods prove more reliable but are time consuming and lack specificity. Matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a fast, cheap and robust technique that has revolutionized genus and species identification in clinical microbiology.The performance of an in vitro diagnostic (RUO) spectral database of MALDI-TOF MS for the identification of human clinically relevant Arcobacter isolates was validated and compared to an in house created Reference Spectral database (RS) containing a representative set of deposited Arcobacter strains of zoonotic interest. A challenge panel of clinical, human and veterinary, unique Campylobacteraceae strains was used to test accuracy.Using direct colony transfer, sensitivity with RS was significantly better than with RUO for A. butzleri and A. cryaerophilus identification (100% and 92% versus 74% and 16%). For A. skirrowii, sensitivity remained low (21% versus 0%). Reanalysis using formic acid overlay (on-target extraction) augmented sensitivity for the latter species to 64%. Specificity of RS database remained excellent without any misidentifications of human clinical strains including Campylobacter fetus and C. jejuni/coli.The use of an enriched database for MALDI-TOF MS identification of Arcobacter spp. of human interest produced high-confidence identifications to species level resulting in a significantly improved sensitivity with conservation of excellent specificity. Misidentifications, which can have therapeutic and public health consequences, were not encountered.