Development of a multiplex taqMan real-time PCR assay for typing of Mycoplasma pneumoniae based on type-specific indels identified through whole genome sequencing

•We developed a multiplex real-time PCR assay for detecting and typing M. pneumoniae.•Typing was based on the presence of short type-specific indels for P1 typing.•This assay was 100% specific compared to existing methods.

We developed a multiplex real-time PCR assay for simultaneously detecting M. pneumoniae and typing into historically-defined P1 types. Typing was achieved based on the presence of short type-specific indels identified through whole genome sequencing. This assay was 100% specific compared to existing methods and may be useful during epidemiologic investigations.