Speciation of the Mycobacterium tuberculosis complex using mass spectrometry: a proof-of-concept

Mycobacteria that form the Mycobacterium tuberculosis complex are responsible for deadly tuberculosis in animals and patients. Identification of these pathogens at the species level is of primary importance for treatment and source tracing, and currently relies on DNA analysis, including whole genome sequencing (WGS), which takes a whole day. In this study, we report on the unprecedented identification of the M. tuberculosis complex species using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), with WGS as the comparative gold standard. In a first step, an optimised peptide extraction applied to 24 isolates otherwise identified in three of the 11 M. tuberculosis complex species by WGS, yielded 94 MALDI-TOF spectra which clustered according to WGS identification. In a second step, 70/74 (95%) other isolates were correctly identified at the species level by this clustering method. This study is the first to report a MALDI-TOF-MS method of identification of M. tuberculosis complex mycobacteria at the species level and is easily implantable in clinical microbiology laboratories.