Why This Matters:
- Streptococcus pneumoniae is a major global pathogen responsible for pneumonia, meningitis, and invasive diseases, especially among young children and the elderly, making accurate surveillance critical to public health.
- Pneumococcal serotype distribution directly informs vaccine design and effectiveness; shifts in serotype prevalence after conjugate vaccine implementation can undermine vaccine impact if not properly monitored.
- Conventional serotyping methods often fail to classify many isolates due to limited coverage, cross-reactivity, and inability to detect novel or underrepresented types, complicating public health tracking of vaccine escape and serotype replacement events.
- Nanopore Cas9-targeted sequencing offers rapid, scalable serotyping with the potential for broader global implementation and support of next-generation multivalent vaccine strategies.
Key Findings: The authors applied the nCATSerotyping platform to 276 clinical S. pneumoniae isolates from South Korea over the period of 2018-2020 and benchmarked performance against conventional serotyping methods.¹
- High serotyping success rate: The nCATSerotyping approach achieved a serotyping rate of 97.10% (268/276) across tested clinical isolates. Conventional monoclonal antibody and multiplex PCR methods identified only 76.45% (211/276) of isolates.
- Accurate species discrimination: Whole-genome sequencing of the remaining eight “non-typeable” isolates confirmed they were non-S. pneumoniae oral streptococci, validating nCATSerotyping’s species specificity (100% accuracy for true pneumococci).
- Emerging and underrepresented serotypes identified: The method successfully detected serotypes such as serotype 13 and strains belonging to null capsule clades that were missed by conventional technologies.
- Cas9 enrichment of cps locus: Targeted enrichment of the capsular polysaccharide synthesis (cps) locus using Cas9 ensured that long-read sequencing focused on the serotype-defining region, improving coverage and discrimination across diverse serotypes.
- Scalable and rapid: The platform enabled comprehensive serotype profiling of hundreds of isolates, highlighting feasibility for routine surveillance and possible field deployment.
- Data integration with bioinformatics: Long-read sequencing data were analyzed for complete locus reconstruction, enabling precise serotype calls and detection of divergent capsule types.
Bigger Picture: Accurate pneumococcal serotyping is foundational to disease surveillance, vaccine effectiveness monitoring, and outbreak investigation. In the post–conjugate vaccine era, shifts in circulating serotypes—driven by serotype replacement and emergence of non-vaccine types—have made comprehensive, high-resolution serotyping increasingly important for public health decision-making.
The nCATSerotyping approach addresses key limitations of conventional serotyping by combining targeted Cas9 enrichment of the capsular polysaccharide synthesis locus with long-read sequencing. This enables reliable discrimination of closely related serotypes, detection of emerging or underrepresented capsule types, and accurate exclusion of non-S. pneumoniae streptococci that can confound surveillance data.
From a policy and surveillance perspective, this method supports more precise estimation of serotype prevalence and dynamics, improving alignment between circulating strains and vaccine composition. Its scalability and resolution make it well suited for national reference laboratories, carriage studies, and genomic epidemiology programs where accurate serotype assignment directly informs vaccine strategy and public health response.
(Image Credit: iStock/quantic69)
References:
- Ji et al. 2025. Accurate Serotype Identification of Streptococcus pneumoniae Using Nanopore Cas9-Targeted Serotype Identification (nCATSerotyping). Journal of Clinical Microbiology.
