Classification Algorithm for Subspecies Identification within the Mycobacterium abscessus Species, Based on Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

Abstract

dMycobacterium abscessus, as a species, has been increasingly implicated in respiratory infections, notably in cystic fibrosis patients. The species comprises 3 subspecies, which can be difficult to identify. Since they differ in antibiotic susceptibility and clinical relevance, developing a routine diagnostic tool discriminating Mycobacterium abscessus at the subspecies level is a real challenge. Forty-three Mycobacterium abscessus species isolates, previously identified by multilocus sequence typing, were analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). A subspecies identification algorithm, based on five discriminating peaks, was drawn up and validated by blind identification of a further 49 strains, 94% of which (n ‫؍‬ 46) were correctly identified. Two M. abscessus subsp. massiliense strains were misidentified as M. abscessus subsp. abscessus, and for 1 other strain identification failed. Inter-and intralaboratory reproducibility tests were conclusive. This study presents, for the first time, a classification algorithm for MALDI-TOF MS identification of the 3 M. abscessus subspecies. MALDI-TOF MS proved effective in discriminating within the M. abscessus species and might be easily integrated into the workflow of microbiology labs.

Evaluation of Matrix-Assisted Laser Desorption Ionization−Time of Flight Mass Spectrometry for Identification of Mycobacterium abscessus Subspecies According to Whole-Genome Sequencing

“…massiliense to M. abscessus subsp. abscessus isolated was much lower in the United States and Europe (9,23,24,45), while the rate was much higher in Japan, South Korea, and Taiwan (5,14,(46)(47)(48). The results of the study presented herein show that 20.6% of M. abscessus identified in Shanghai, China, belonged to the massiliense subspecies.…”

“…massiliense from the other two subspecies (23)(24)(25)(26)(27). However, discrepancies in the specific peak signals of the three subspecies were reported.…”

“…massiliense (24). These hybrid allelic forms and associated proteomes displayed by several M. abscessus isolates were reported in previous studies (11,24,25,44). In addition, misidentification of the M. abscessus subsp.…”

“…However, improvements in MALDI-TOF MS are needed to identify very close taxa that include the M. abscessus subspecies (23). A number of studies used spectrum analysis to show that several peaks differentiated M. abscessus at the subspe-cies level; these findings, however, were inconsistent (23)(24)(25)(26)(27). Possibly, these inconsistencies in subspecies profiles were determined by geographic location and related to the horizontal transfer of genes during the evolution of M. abscessus worldwide.…”

“…Recently, this speculation was tested with a classification algorithm based upon 40 total strains composed of 24 M. abscessus subsp. abscessus, 10 M. abscessus massiliense subspecies, and 6 M, abscessus bolletii subspecies isolates and validated by 49 strains using the MALDI Biotyper (Bruker Daltonics, Bremen, Germany) (24). The improved algorithm reached 94% accuracy with 2% uncertainty and 4% error.…”