Matrix-assisted laser desorption/ionization time-of-flight MS for the accurate identification of complex and in the clinical microbiology laboratory.

complex (Bcc) bacteria, currently consisting of 23 closely related species, and , can cause serious and difficult-to-treat infections in people with cystic fibrosis. Identifying bacteria to the species level is considered important for understanding epidemiology and infection control, and predicting clinical outcomes. Matrix-assisted laser desorption/ionization time-of-flight MS (MALDI-TOF) is a rapid method recently introduced in clinical laboratories for bacterial species-level identification. However, reports on the ability of MALDI-TOF to accurately identify Bcc to the species level are mixed. The aim of this project was to evaluate the accuracy of MALDI-TOF using the Biotyper and VITEK MS systems in identifying isolates from 22 different Bcc species and compared to gene sequencing, which is considered the current gold standard for Bcc. To capture maximum intra-species variation, phylogenetic trees were constructed from concatenated multi-locus sequence typing alleles and clustered with a novel k-medoids approach. One hundred isolates representing 22 Bcc species, plus , were assessed for bacterial identifications using the two MALDI-TOF systems. At the genus level, 100 and 97.0 % of isolates were confidently identified as by the Biotyper and VITEK MS systems, respectively; moreover, 26.0 and 67.0 % of the isolates were correctly identified to the species level, respectively. In many, but not all, cases of species misidentification or failed identification, a representative library for that species was lacking. Currently available MALDI-TOF systems frequently do not accurately identify Bcc bacteria to the species level.