Phylogenetic distribution of persistent Shigella. Phylogenetic trees (codon trees) for (A) S. sonnei and (B) S. flexneri were constructed by using complete reference genomes of known serotypes (available in BV-BRC, https://www.bv-brc.org/), draft genome sequences of isolates associated with persistent carriage in humans [29], and the isolates used in this study (sequenced with nanopore technology). Red (labeled with diamond symbols ◆), strains associated with persistent carriage in humans; orange (labeled with star symbols ★), strains that established persistent infection in zebrafish; black (labeled with square symbols ■), strains that did not establish persistent infection in zebrafish; blue (unlabeled), other strains available in the BV-BRC database and utilized to construct the phylogenetic trees. For the S. sonnei tree, lineages II and III and sublineages 3.6 and 3.7 are highlighted. For the S. flexneri tree, the 3 main clusters encompassing the serotypes investigated in this study (2a, 3, and 5) are highlighted, and the serotype of each strain is reported in parentheses after the strain name. BV-BRC, Bacterial and Viral Bioinformatics Resource Centre.
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