<sec><title>Objectives</title><p>An atypical <italic>Shigella flexneri</italic> strain with a plural agglutination pattern [i.e., reacting not only with serum samples containing type antigen II but also with serum samples containing group antigens (3)4 and 7(8)] was selected for genome sequencing, with the aim of obtaining additional comparative information about such strains.</p></sec><sec><title>Methods</title><p>The genomic DNA of atypical <italic>S. flexneri</italic> strain NCCP 15744 was sequenced using an Ion Torrent PGM sequencing machine (Life Technologies, USA). The raw sequence data were preprocessed and reference-assembled in the CLC Assembly Cell software (version 4.0.6; CLC bio, USA).</p></sec><sec><title>Results</title><p>Ion Torrent sequencing produced 1,450,025 single reads with an average length of 144 bp, totaling ~209 Mbp. The NCCP 15744 genome is composed of one chromosome and four plasmids and contains a <italic>gtrX</italic> gene. Among the published genome sequences of <italic>S. flexneri</italic> strains, including 2457T, Sf301, and 2002017, strain NCCP 15744 showed high similarity with strain 2002017. The differences between NCCP 15744 and 2002017 are as follows: i) NCCP 15744 carries four plasmids whereas 2002017 carries five; ii) 19 genes (including <italic>CI</italic>, <italic>CII</italic>, and <italic>cro</italic>) were lost in the <italic>SHI-O</italic> genomic island of NCCP 15744 and six genes were gained as compared with strain 2002017.</p></sec><sec><title>Conclusion</title><p>Strain NCCP 15744 is genetically similar to 2002017, but these two strains have different multilocus sequence types and serotypes. The exact reason is unclear, but the 19 lost genes may be responsible for the atypical seroconversion of strain NCCP 15744.</p></sec>