lytA-based identification methods can misidentify Streptococcus pneumoniae

Area of Science:

• Microbiology
• Molecular Diagnostics
• Bacterial Identification

Background:

• Accurate identification of Streptococcus pneumoniae is crucial for epidemiological surveillance and clinical management.
• Widely accepted phenotypic and genotypic methods are used for pneumococcal identification.
• Surveillance studies identified isolates with conflicting results using standard methods.

Purpose of the Study:

• To investigate the genetic basis for unexpected results from lytA-BsaAI-RFLP.
• To evaluate the accuracy of the WHO-recommended lytA real-time PCR assay for classifying challenging isolates.

Main Methods:

• Phenotypic characterization (optochin susceptibility, bile solubility).
• Genotypic characterization (lytA-BsaAI-RFLP, MLST).
• Real-time PCR targeting the lytA gene.

Main Results:

• Three novel lytA-BsaAI-RFLP signatures were identified in *S. pneumoniae* and *S. mitis*.
• Misidentification occurred for one *S. pneumoniae* and two *S. pseudopneumoniae* isolates using lytA-based methods.
• The lytA real-time PCR assay misclassified three of the eleven challenging isolates.

Conclusions:

• Identification of *S. pneumoniae* using lytA-based methodologies, including real-time PCR, can lead to false results.
• The findings have significant implications for colonization studies relying on culture-independent methods.
• Re-evaluation of diagnostic strategies for pneumococcal identification is warranted.