Pitfalls in Using Matrix-assisted Laser Desorption Ionization-time of Flight Mass Spectrometry for the Identification of Mycobacterium

Background: Mycobacterial culture in solid or liquid medium remains one of the the gold standard methods for diagnosing mycobacterial infections. Identification of the correct species of mycobacteria is imperative for providing the appropriate treatment, as both tuberculous and nontuberculous mycobacteria can cause clinical infection. The current study was done to identify Mycobacterium species by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) from both solid and liquid media. Methods: In this cross-sectional pilot study, 50 isolates were included: 25 from liquid culture-mycobacterium growth indicator tubes (MGIT) and 25 from solid culture-Lowenstein Jensen (LJ) media, that were positive for the presence of acid-fast bacilli. The protein extraction was performed using VITEK MS Mycobacterium/Nocardia Kit (bioMerieux, France) extraction protocol and was further identified using VITEK MALDI-TOF MS (biomerieux, France) machine version 3.2. The results obtained were compared with GeneXpert results from the direct clinical specimen. Results: Among 25 MGIT isolates, only one was identified as Mycolicibacterium fortuitum (4%). Among the 25 LJ isolates, nine (36%) were identified to belong to the Genus Mycobacterium. Eight isolates were identified as Mycobacterium tuberculosis complex and one was identified as Mycobacterium kansasii. Conclusion: The study showed that even though MALDI-TOF MS has the advantage of being cost-effective, technically easier to perform and the ability to provide rapid results, the number of isolates giving identification from primary culture of clinical samples was found to be low (10/50, 2.5%). The purity of the culture has to be ensured, even while using the rigorous protein extraction process.