Fig. 2: Assessment of allele-based clustering at all possible threshold levels for L. monocytogenes and comparison with traditional MLST.

a Composition of the L. monocytogenes dataset used in this study in terms of ST in comparison with datasets of previous studies (Maury et al. 2016¹³⁹ and Moura et al. 2016⁶⁰), the LiSeq project¹⁴⁰ and the BIGSdb database, as of November 2021²³. A GrapeTree⁵⁹ visualization of the MST obtained with the INNUENDO-like pipeline is shown. Nodes (i.e., samples) are collapsed at the threshold with the highest congruence with CC (508 ADs for this pipeline) and colored according to the ST classification. b Number of partitions obtained by each pipeline at each possible distance threshold. c Clustering stability regions determined for each pipeline. To better distinguish each region (represented by separated rectangle blocks), the different blocks are vertically phased, starting in a different line. Distance thresholds (x axis) are presented in log2 scale. d Barplot (top) with the number of samples of the top represented STs (≥50 samples) in L. monocytogenes dataset, with a swarmplot (bottom) indicating the AD threshold at which each pipeline clusters together all samples of each ST. e Distribution of the AD thresholds at which each pipeline clusters together all samples of a given ST (n = 219). Boxplots show the interquartile range (25% to 75%) and median, and whiskers extend 1.5 times the range, with outliers (diamond symbol) plotted separately. The outlier STs are indicated above the respective symbol. Source data are provided as a Source Data file.