SSP

SSP performs serotyping of Salmonella by analyzing protein sequences involved in O-antigen biosynthesis and H-antigen filament formation to identify O-, H1-, and H2-antigens across over 2,500 known serovars.

Key Features:

• O-Antigen Serotyping: Utilizes initializing transferases WbaP, WecA, and GNE, plus Wzx and Wzy, and additional transferases RfbE, Orf17.4, WecB, WbbE, WbbF, Wzm, and Wzt where required to distinguish O-antigen types based on biosynthetic protein sequences.
• H-Antigen Serotyping: Analyzes flagellin proteins FliC and FljB using 302 reference datasets to identify unique sequence patterns for H1- and H2-typing.
• Whole Proteome Analysis and Validation: Evaluated on 2,136 whole proteome sequences representing 740 Salmonella serovars (including newly identified species) and achieved 99.72% accuracy in serotype prediction.
• Independent O/H1/H2 Prediction and Integration: Generates independent predictions for O-, H1-, and H2-antigens and integrates these predictions into composite serovar assignments.

Scientific Applications:

• Public health surveillance: Enables rapid molecular identification of Salmonella serovars for epidemiological monitoring.
• Quality control of genomic annotation: Detects misannotated strains by comparing predicted antigenic profiles with existing annotations.
• Discovery of emerging species: Identifies novel or emerging Salmonella species through discordant or novel antigenic signatures.
• Outbreak investigation and evolutionary analysis: Supports outbreak tracking and studies of antigenic and evolutionary dynamics of Salmonella populations.

Methodology:

Performs protein-sequence analysis of O-antigen biosynthesis proteins (WbaP, WecA, GNE, Wzx, Wzy, RfbE, Orf17.4, WecB, WbbE, WbbF, Wzm, Wzt) and of flagellins FliC and FljB using 302 reference datasets to identify discriminatory sequence patterns; generates independent O-, H1-, and H2-antigen predictions and validates performance on 2,136 whole proteome sequences representing 740 serovars (99.72% accuracy).