Comparison of Saramis 4.12 and IVD 3.0 Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identification of Mycobacteria from Solid and Liquid Culture Media

摘要

The genus Mycobacterium consists of 177 species whose taxonomy has constantly been evolving over the past few decades. The major causes of morbidity and mortality are due to mycobacteria belonging to the Mycobacterium tuberculosis complex (MTC), with 9.6 million people newly infected and 1.5 million people dying from tuberculosis every year (1). Nontuberculous mycobacteria (NTM) comprise a large group of organisms widely present in the environment and considered opportunistic pathogens causing pulmonary, soft tissue, lymphatic, and disseminated infections (2). Species such as M. abcsessus, M. xenopi, and M. chimaera have also been involved in nosocomial outbreaks (3–6). An accurate identification (ID) of NTM is, then, important for epidemiological and public health and for therapeutic reasons. Species identification is especially essential in diagnosis of M. avium complex (MAC) lung disease to differentiate transient colonization by different species from chronic pulmonary infection (2). Identification of mycobacterial isolates has traditionally been based on phenotypic characteristics and conventional biochemical tests, which were complex and required long incubation times. More recently, molecular methods such as DNA sequencing and DNA hybridization have become the new “gold standards” for mycobacterial identification. Although these techniques are fast and specific ways of identifying main Mycobacterium spp., they remain expensive, are available for only a limited number of common species, and require a high level of technical expertise. The limitations encountered with currently available methods led several investigators to suggest the use of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) as an alternative strategy. MALDI-TOF MS is now predominant in an increasing number of clinical laboratories (7). This technique is quite simple and cost-effective (8) and allows rapid identification of organisms on the basis of spectral fingerprints produced by extracted proteins. It was initially evaluated with mycobacterial intact cells (9–12), but several investigators worked on improving inactivation and protein extraction (13–20). Most published studies assessed the performance of MALDI-TOF BioTyper (Bruker Daltonics, Bremen, Germany) (15, 17, 19–31). Few of them evaluated Vitek MS (bioMérieux, Marcy l'Etoile, France) (16, 17, 20, 24, 25, 32). Performances ranged widely, from 0% (24) to 94.4% (17) correct identifications depending on database versions, algorithms, and media (liquid or solid) used. We aimed to assess identification of Mycobacterium spp. from both liquid and solid media through two distinct databases: the Saramis v4.12 Vitek MS-Plus RUO (research use only) open database and the v3.0 CE-marked In Vitro Diagnostic (IVD). To our knowledge, IVD v3.0 has been evaluated only for mycobacteria growing from solid media (20). We aimed to establish the performance of this technique in the routine clinical microbiology laboratory and to highlight its limits.