Increased dissemination and parallel evolution of antimicrobial resistance in Salmonella enterica serovar Paratyphi B variant Java in poultry from Europe and Latin America

Previous reports from Latin American countries have identified S. Paratyphi B var. Java as prevalent in poultry and poultry products. In a previous report from Colombia, all analyzed isolates of S. Paratyphi B var. Java from poultry belonged to ST28. Comparisons between strains of S. Paratyphi B var. Java ST28 from Colombia and Europe, showed a phylogenomic separation between Colombian and European isolates. In the present study the evolutionary separation between S. Paratyphi B var. Java from Europe and Latin America using Whole Genome Sequencing (WGS)-based phylogenomic and temporal analysis was investigated. A selection of S. Paratyphi B var. Java ST28 isolates from Colombia, Guatemala, Costa Rica and the Netherlands was sequenced. This was complemented with existing publicly available genomes. Phylogenetic time trees and effective population sizes (Ne) were determined. In addition, Principal Component Analyses (PCA) were performed on core-, non-core genomes and plasmid content.