Fig. 5

Results of streaming phylogenetic placement from the Oxford Nanopore MinION on a reference tree of Salmonella enterica serovar Enteritidis isolates collected by Public Health England during routine surveillance. The left-most panel demonstrates the confident placing of the outbreak isolate in the outbreak clade within 100 min, and the confident placing of the non-outbreak isolate into a clade containing multiple serotypes of Salmonella within 120 min. The red placements indicate the positions of the outbreak isolate and the blue placements indicate the positions of the non-outbreak isolate. The right-most panel shows a phylogenetic reconstruction of isolates from the outbreak and their source, set in context of a national outbreak of phage type 14b. Uncertainty in the phylogenetic placement technique is demonstrated early on in sequence data collection due to the low accuracy of the variant calls collected. As more data are collected, the number of possible phylogenetic placements reduces and the confidence values increase (not shown)