Table 1.
Clinical identity, identification technique, and source of all the clinical isolates used in this study.
Fig 1.
Bacterial identification by clinical microbiology laboratory techniques.
Typical temporal workflow of clinical microbiological laboratory to identify microbes from clinical samples based on phenotypic, biochemical, and culture-based techniques.
Fig 2.
16S rRNA percent identity within and between genera.
Distributions (shown as violin plots) of 16S rRNA percent identity (y-axis of each figure) of pairs of training set sequences belonging to the same (gray) and different genera. 95% identity, the traditional genus level cutoff, has been marked for reference. The genus Mycobacterium has been categorized as a gram-positive in the figure. For all of the genera, sequence variability between sequences from the same genera was significantly higher than between those from different genera for all comparisons (Wilcoxon test one-sided p-value<0.0001).
Fig 3.
16S rRNA percent identity within and between species (gram-positive bacteria).
Distributions (shown as violin plots) of 16S rRNA percent identity (y-axis of each figure) of pairs of training set sequences belonging to the same (gray) and different species for select gram-positive bacteria. 97% identity, the traditional species level cutoff, has been marked for reference. Species for which sequence variability between sequences from the same species was significantly higher than between those from different species are marked with a * (Wilcoxon test one-sided p-value<0.0001).
Fig 4.
16S rRNA percent identity within and between species (gram-negative bacteria).
Distributions (shown as violin plots) of 16S rRNA percent identity (y-axis of each figure) of pairs of training set sequences belonging to the same (gray) and different species for select gram-negative bacteria. 97% identity, the traditional species level cutoff, has been marked for reference. Species for which sequence variability between sequences from the same species was significantly higher than between those from different species are marked with a * (Wilcoxon test one-sided p-value<0.0001).
Table 2.
Concordance rates between clinical and 16S rRNA based identification.
Table 3.
Concordance rates between 16S rRNA based and clinical identification for isolates clinically identified by culture-based or non-16S based molecular methods.
Fig 5.
16S rRNA based genus and species level isolate identities with the Naïve Bayes classifier.
Each isolate was assigned to one of 12 categories (A-H, a-d) based on the agreement between clinical and 16S rRNA based genus and species classifications and the confidence scores.