Evaluation of pneumococcal serotyping in nasopharyngeal carriage isolates by latex agglutination, whole genome sequencing (PneumoCaT) and DNA microarray in a high pneumococcal carriage prevalence population in Malawi

Background: Accurate assessment of the serotype distribution associated with pneumococcal colonization and disease is essential for the evaluation and formulation of pneumococcal vaccines and informing vaccine policy. Methods: We evaluated pneumococcal serotyping concordance between latex agglutination, PneumoCaT by whole genome sequencing (WGS) and DNA microarray using samples from community carriage surveillance in Blantyre, Malawi. Nasopharyngeal swabs were collected, following WHO recommendations, between 2015 and 2017, using stratified random sampling among study populations. Participants included healthy children 3-6 years old (PCV13 vaccinated as part of EPI), healthy children 5-0 years (age-ineligible for PCV13), and HIV-infected adults (18-40yrs) on ART. For phenotypic serotyping we used a 13-valent latex kit (SSI, Denmark). For genomic serotyping we applied PneumoCaT pipeline to whole genome sequence libraries. For molecular serotyping by microarray we used the BUGS Bioscience DNA microarray. Results: 1347 samples were analysed. Concordance was 90.7% (95% CI: 89.0-92.2) between latex and PneumoCaT; 95.2% (93.9-96.3) between latex and microarray; and 96.6% (95.5-97.5) between microarray and PneumoCaT. By detecting carried vaccine serotype (VT) pneumococcus in low relative abundance (median 8%), microarray increased VT detection by 31.5% compared to latex serotyping. Conclusion: All three serotyping methods were highly concordant in identifying dominant serotypes. Latex serotyping is accurate in identifying vaccine-serotypes and requires the least expertise and resources for field-implementation and analysis. However, WGS, which adds population structure, and microarray, which adds multiple-serotype carriage, should be considered at regional reference laboratories while investigating the importance of VT in low relative abundance in transmission and disease.