Optimization of matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis for bacterial identification

Abstract

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a relatively new addition to the clinical microbiology laboratory. The performance of the MALDI Biotyper system (Bruker Daltonics) was compared to those of phenotypic and genotypic identification methods for 690 routine and referred clinical isolates representing 102 genera and 225 unique species. We systematically compared direct-smear and extraction methods on a taxonomically diverse collection of isolates. The optimal score thresholds for bacterial identification were determined, and an approach to address multiple divergent results above these thresholds was evaluated. Analysis of identification scores revealed optimal species- and genus-level identification thresholds of 1.9 and 1.7, with 91.9% and 97.0% of isolates correctly identified to species and genus levels, respectively. Not surprisingly, routinely encountered isolates showed higher concordance than did uncommon isolates. The extraction method yielded higher scores than the direct-smear method for 78.3% of isolates. Incorrect species were reported in the top 10 results for 19.4% of isolates, and although there was no obvious cutoff to eliminate all of these ambiguities, a 10% score differential between the top match and additional species may be useful to limit the need for additional testing to reach single-species-level identifications.

Fig 1

Cumulative proportion of isolates above a chosen MALDI-TOF MS threshold (1 to 2.6) reaching species (diamonds), reaching genus only (squares), or showing no agreement (triangles) between results of MALDI-TOF MS and standard methods.

Fig 2

Cumulative proportion of the 568 core isolates with a significant species or genus mismatch among the top 10 MALDI-TOF MS results that scored within cutoff values ranging from 1 to 35% below the top match score. (A) Proportion of mismatches within each Biotyper consistency category (A, 427 isolates; B, 69 isolates; C, 72 isolates). (B) Proportion of mismatches within major organism categories. GPC, Gram-positive cocci (n = 132); GPR, Gram-positive rods (n = 99); GNC, Gram-negative cocci (n = 23); Enteric, enteric Gram-negative rods (n = 160); NF, nonfermenting Gram-negative rods (n = 77); Fastidious, fastidious Gram-negative rods (n = 57).

Fig 3

Box and whisker plot showing the median (solid horizontal lines), upper and lower quartiles (boxes), upper and lower 1.5 interquartile ranges (whiskers), and outliers (open circles) of the percentage differences from the top-scoring match for all significant mismatches by species. In parentheses are the numbers of all significant mismatches followed by the number of isolates contributing to those mismatches. The area below the dashed horizontal line illustrates the relative proportion of isolates that would include mismatches using the 10% cutoff rule.