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Streptococcus pneumoniae serotype 12F rarely colonizes the nasopharynx but commonly causes invasive pneumococcal disease. Here, we report the complete genome sequence of a sequence type 4846 (ST4846) S. pneumoniae serotype 12F strain isolated from a cluster of invasive pneumococcal disease patients in Japan.

Complete Genome Sequence of a Sequence Type 4846 Streptococcus pneumoniae Serotype 12F Strain Isolated from a Meningitis Case in Japan