Shigella flexneri serotype 2a2 bacteria are the most prevalent serotype that cause shigellosis in developing countries. Chemical modifications (eg. glucosylation and O-acetylation) of lipopolysaccharide (LPS) O antigen (O polysaccharides) contribute to a wide diversity of serotypes. The increase in new serotype strains due to serotype conversion and the rise of multi-antibiotic resistant Shigella have led to the re-emergence of interest in phage therapy as a therapeutic strategy. Bacteriophage Sf6 is a Shigella-specific phage that infects serotype Y and X strains by targeting and hydrolysing the LPS O antigen via its tailspike protein (TSP). This study determined the impact of the various O antigen acetylations and glucosylation on S. flexneri 2457T (2a2) LPS and their effect on pathogenesis and bacteriophage Sf6 sensitivity. We created a collection of isogenic mutants using S. flexneri 2457T as the parent strain and deleted O antigen modification genes in different combinations. Deletion of these genes converted serotype 2a2 to various 2a and Y sub-serotypes. These isogenic mutants were compared with respect to their LPS profiles, adherence and invasion efficiency on different cell lines, and sensitivity to Sf6 infection. We identified a novel serotype variant that was unexpectedly sensitive to Sf6 infection, suggesting that Shigella has acquired a specific O antigen modification gene that provides protection against this phage. In addition, we also provide the first molecular evidence that shows Sf6TSP is able to hydrolyse the LPS O antigen of serotype 2a2 and its sub-serotype in a dose-dependent manner.