Fig. 3.

Biotyper IR differentiates genetically distinct strains. A) Phylogenetic trees of strain genomes tested in the Biotyper IR analysis based on alignment of bacterial marker genes. Genetic distance is shown in a dendrogram; genomes used (generated in this study or obtained from public repositories) are in Table S1. B) Principal component analysis (PCA) plot showing clustering of strains for each species, with each color representing a unique isolate and each dot within that color representing the isolate’s replicate spectral measurements. Links to the dots showing the variance of the technical replicates; output from IR Biotyper interface. ##% in lower left corner indicate the sum of variance explained by the first two principal components. C) Dendrogram of isolates based on spectral measurements; output from IR Biotyper interface. Green and orange in dendrogram represent cluster purity as determined by the Bruker IR software, based on technical replicates of strain spectra: green (“GOOD”), orange (“BAD”). Cluster quality criterion (CQC) indicates how well replicate measurements of an isolate cluster with themselves as well as the purity or homogeneity of each cluster