SeroBA(v2.0)

SeroBA(v2.0) identifies pneumococcal serotypes from genome sequencing data using a curated library of known serotypes.

Key Features:

• Comprehensive Serotype Coverage: Accurately identifies 102 of 107 known pneumococcal serotypes and 18 genetic subtypes within serotypes 6A, 6B, 11A, 19A, 19F and 33F.
• Community-Contribution System: Enables global submission of putative novel serotypes through GitHub for curation based on cps region genetic sequence, capsular structure and serological profile.
• High Concordance Validation: Achieved 88.9% concordance at the serotype level and 91.9% at the serogroup level with phenotypic serotypes determined by Quellung or latex agglutination.
• SeroBAnk Atlas Integration: Built upon a comprehensive curated library encompassing all known pneumococcal serotypes with genetic locus, capsular structure, vaccine formulation and licensure history.

Scientific Applications:

• Pneumococcal Epidemiology: Supports understanding of global distribution, evolution and bacterial population response to vaccination through accurate and timely serotyping of isolates.
• Novel Serotype Discovery: Reliably detects recently discovered serotypes from whole genome sequencing data, validated on 26,306 genomes from the Global Pneumococcal Sequencing project and reference isolates.
• Vaccine Development Research: Provides genetic and structural data on capsular polysaccharide biosynthetic (cps) locus diversity to inform basic research and pneumococcal conjugate vaccine development.
• In Silico Serotyping: Replaces or supplements phenotypic methods such as Quellung and latex agglutination with genome-based inference for clinical and public health laboratories.

Methodology:

SeroBA(v2.0) uses a curated library of cps locus genetic sequences for serotype identification. Validation was performed on 26,306 genomes from the Global Pneumococcal Sequencing project, reference isolates, and simulated reads derived from reference cps locus genetic sequences.