Journal: Frontiers in Microbiology

Article Title: Evaluation of whole and core genome multilocus sequence typing allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA

doi: 10.3389/fmicb.2023.1254777

Figure Lengend Snippet: Range of hqSNP, cgMLST, and wgMLST allele differences between strains for the outbreaks included in this study.

Article Snippet: Clustering concordance of allele-based methods [cgMLST vs. wgMLST (chrom)] when compared to one another was measured with a Baker’s gamma index (BGI) between 0.90 and 1.00, indicating statistically similar clustering between trees.

Techniques: Plasmid Preparation

Journal: Frontiers in Microbiology

Article Title: Evaluation of whole and core genome multilocus sequence typing allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA

doi: 10.3389/fmicb.2023.1254777

Figure Lengend Snippet: Scatterplot of Lyve-SET hqSNP differences against cgMLST (A) and wgMLST (chrom) (B) pairwise allele differences and wgMLST (chrom) against cgMLST pairwise allele differences (C) . Regression equations, R 2 values, and Pearson’s correlation coefficients are displayed on plots.

Article Snippet: Clustering concordance of allele-based methods [cgMLST vs. wgMLST (chrom)] when compared to one another was measured with a Baker’s gamma index (BGI) between 0.90 and 1.00, indicating statistically similar clustering between trees.

Techniques:

Journal: Frontiers in Microbiology

Article Title: Evaluation of whole and core genome multilocus sequence typing allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA

doi: 10.3389/fmicb.2023.1254777

Figure Lengend Snippet: K-means analysis results for one representative outbreak (outbreak 03) using cgMLST, wgMLST (chrom), and hqSNP pairwise genomic differences. Top row: hierarchical clustering results of the dataset show partitioning of outbreak (blue) isolate sequences and sporadic (orange) isolate sequences. Bottom row: elliptical cluster plots show outbreak (blue) and sporadic (orange) isolates plotted separately on a two-dimensional plane, with ellipses fit to the points in the two clusters. On elliptical plots, the sum of values on the x and y -axis scales indicate that a principle component analysis accounts for 93.0% (cgMLST), 89.8% [wgMLST(chrom)], and 92.1% (hqSNP) of variation.

Article Snippet: Clustering concordance of allele-based methods [cgMLST vs. wgMLST (chrom)] when compared to one another was measured with a Baker’s gamma index (BGI) between 0.90 and 1.00, indicating statistically similar clustering between trees.

Techniques:

Journal: Frontiers in Microbiology

Article Title: Evaluation of whole and core genome multilocus sequence typing allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA

doi: 10.3389/fmicb.2023.1254777

Figure Lengend Snippet: Summary table of metrics obtained in study.

Article Snippet: Clustering concordance of allele-based methods [cgMLST vs. wgMLST (chrom)] when compared to one another was measured with a Baker’s gamma index (BGI) between 0.90 and 1.00, indicating statistically similar clustering between trees.

Techniques: