Discovery of IS1515 transposition into the Spn9802 fragment of Streptococcus pneumoniae and its implications for PCR-based diagnostic assays

This study investigates a diagnostic challenge in detecting Streptococcus pneumoniae using a Spn9802-targeted PCR assay. Four S. pneumoniae isolates tested lytA-positive but Spn9802-negative due to an insertion sequence (IS15151515) within Spn9802, which was confirmed by whole-genome sequencing. This insertion may lead to false-negative results, posing concerns for PCR-based diagnostics.