The impact of protein extraction protocols on the performance of currently available MALDI-TOF mass spectrometry for identification of mycobacterial clinical isolates cultured in liquid media

Protein extraction step is particularly important for identification of mycobacterial isolates by MALDI-TOF mass spectrometry (MS) because of its thick and solid cell wall. This study compared the performance of MALDI-TOF MS for identification of mycobacterial clinical isolates cultured in liquid media between heating-based protocol and non-heating protocol.Clinical mycobacterial isolates cultured in liquid media were prospectively analyzed. Reference identification was real-time PCR and restriction fragment length polymorphism. The specimens prepared by heating protocol and non-heating protocol were tested using MALDI Biotyper (Bruker Daltonics, Bremen, Germany) and Vitek MS (bioMérieux, Marcy l'Etoile, France), respectively.Among the 206 clinical specimens prepared by heating method, identification rates were 90.3% and 60.7% in MALDI Biotyper and Vitek MS, respectively. Identification accuracy of MALDI Biotyper and Vitek MS was 100% for the isolates of Mycobacterium tuberculosis complex (MTBC), Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium abscessus and Mycobacterium fortuitum. Among the 121 clinical specimens prepared by non-heating method, identification rate for MALDI Biotyper and Vitek MS were 61.2% and 69.4%, respectively. Identification accuracy of MALDI Biotyper/Vitek MS were 92.9%/94.1% for MTBC, 92.9%/100% for M. avium, 90%/100% for M. intracellulare, 100%/100% for M. abscessus and 100%/100% for M. fortuitum.The performance of MALDI-TOF MS for identification of mycobacterial clinical isolates is affected by protein extraction protocol. For best performance, protein extraction protocol should be chosen considering the MALDI-TOF MS system. In the present study, heating protocol with MALDI Biotyper system showed reliable identification results for mycobacterial clinical isolates.