Impact of updating the MALDI‐TOF MS database on the identification of nontuberculous mycobacteria

Abstract

Conventional identification of mycobacteria species is slow, laborious and has low discriminatory power. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has proved highly effective for identifying conventional bacteria, and it may also be useful for identifying mycobacteria. The aim of this study was to evaluate and compare MALDI-TOF MS with currently recommended molecular methods for the identification of nontuberculous mycobacteria (NTM), applying Mycobacteria Libraries v3.0 (ML3.0) and v2.0 (ML2.0). A total of 240 clinical isolates of 41 NTM species grown on solid media were analysed: 132 isolates of slow-growing mycobacteria and 108 of rapid-growing mycobacteria. MALDI-TOF MS, using ML3.0, identified 192 (80%) NTM isolates with a score ≥1.7, encompassing 35 (85.4%) different species, that is, 17 (7.1%; p = 0.0863) isolates and 15 (36.6%; p = 0.0339) species more than currently recommended molecular techniques (polymerase chain reaction reverse hybridization). All these isolates were correctly identified according to molecular identification methods. The application of ML3.0 also identified 15 (6.2%) NTM isolates more than ML2.0 (p < 0.01). The scores obtained with MALDI-TOF MS using ML3.0 (mean score: 1.960) were higher in 147 (61.2%) isolates than when using ML2.0 (mean score: 1.797; p < 0.01). Three of the species analysed were not included in either database, so they were not recognized by this system. In conclusion, MALDI-TOF MS identified more isolates and species than the recommended polymerase chain reaction reverse hybridization assays. Although the new ML3.0 is not the definitive database, it yielded better results than ML2.0. This shows that the updating of the MALDI-TOF MS database plays an essential role in mycobacterial identification. Copyright © 2017 John Wiley & Sons, Ltd.

Evaluation of Two Protein Extraction Protocols Based on Freezing and Mechanical Disruption for Identifying Nontuberculous Mycobacteria by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry from Liquid and Solid Cultures

“…Therefore, at the end of the process, the protein concentration will have been too low for detection by mass spectrometry. Another reason is that some species are not included in the current Mycobacteria Library database, such as M. madagascariense, M. paraterrae, and M. yongonense, which precluded identification by MALDI-TOF MS (26). In addition, some species have only one reference or a small number of references in the database, which may have led to low scores when analyzed.…”

How to: identify non-tuberculous Mycobacterium species using MALDI-TOF mass spectrometry

“…In the last decade we have witnessed how MALDI-TOF MS has become a reliable tool for NTM identification [13e24] because of (i) the development of several extraction methods that enhance the amount of bacterial proteins available for MALDI-TOF MS identification, and (ii) the increasing number of mycobacterial spectra in commercial databases. On the Bruker Daltonics platform (Bremen, Germany), the database version 3.0 has been a great advance (regarding its predecessor) and it included as many as 853 spectra from 149 different Mycobacterium species [21,23]. The latest released version (Mycobacteria Library v5.0) represents a further slight improvement with a total of 912 spectra from 159 Mycobacterium species.…”

Evaluation of MALDI Biotyper Interpretation Criteria for Accurate Identification of Nontuberculous Mycobacteria

“…Second, only one reference spectrum for M. setense is included in the current database. As mentioned above, the addition of several new reference spectra to a database can greatly improve the reliability of identification for those species (11). Finally, one isolate of M. kansasii was identified as M. gastri with a score of 1.64, in another case of strong phylogenetic closeness.…”

“…In the case of mycobacterial identification, the application of mass spectrometry has had to overcome several critical challenges in order to demonstrate its validity. The main challenges were the optimization of the protein extraction protocol (5)(6)(7)(8)(9) and the updating of the database in order to cover the maximum number of species of clinical importance (10,11). However, more studies are needed to reduce the diagnostic delay entailed by the analysis of liquid culture media (12,13) and to establish suitable criteria for interpreting the results of MALDI-TOF MS for the reliable identification of several mycobacterial species (14).…”