SerotypeFinder

SerotypeFinder performs in silico serotyping of Escherichia coli from whole-genome sequencing (WGS) data to determine O and H antigen types.

Key Features:

• WGS integration: Processes WGS data from complete and partial genome sequences to identify serotype determinants.
• Serotype gene database: Uses a curated FASTA database of genes associated with O-antigen processing (wzx, wzy, wzm, wzt) and flagellin genes (fliC, flkA, fllA, flmA, flnA) for type assignment.
• Detection of gene presence and variation: Identifies presence and sequence variations of serotype-specific genes to distinguish O and H types.
• Validation and accuracy: Evaluated on 682 E. coli genomes, including 108 newly sequenced isolates, correctly predicting 560 of 569 O types and 504 of 508 H types compared to conventional serotyping.

Scientific Applications:

• Surveillance and outbreak detection: Enables rapid serotype determination to support epidemiological surveillance and outbreak investigations.
• Routine typing: Provides an in silico alternative for routine serotyping of E. coli isolates in clinical and research contexts.
• Integration with genomic analyses: Can be combined with other WGS-based typing tools to contribute to comprehensive genomic characterization of strains.

Methodology:

Compares WGS data against a curated FASTA database of serotype-specific genes to detect gene presence and sequence variation and assign O and H types.