2019-04-11

Outbreak Analysis Using 1928 - Salmonella enterica

cgMLST UPGMA-clustering of a Salmonella enterica outbreak using the 1928 platform

The tree is created using UPGMA and distances shown are computed based on pairwise allelic differences (hamming distance). Missing genes are not included in the count.

Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection.

A.J. Taylor, V. Lappi, W.J. Wolfgang, P. Lapierre, M.J. Palumbo, C. Medus, D. Boxrud

pmid: 26269623

The 1928D Salmonella enterica cgMLST schema is created from 600 reference genomes giving the scheme 2850 core genes. All genes included in the schema are present in at least 95% of reference genomes.