VirulenceFinder

VirulenceFinder identifies virulence genes from whole-genome sequencing (WGS) data to characterize ExPEC-associated virulence profiles in Escherichia coli.

Key Features:

• Database Expansion: 38 ExPEC-associated virulence genes were added, resulting in a database of 139 genes (44 specifically ExPEC-related) comprising 2,826 alleles after removal of redundant sequences and verification of open reading frames (ORFs).
• Allele Identification: The updated database contains 1,890 distinct alleles after validation, including cross-referencing with 27 primer pairs, identification of serotype-specific papA alleles for P fimbriae, and confirmation of etsC, iucC, kpsE, neuC, sitA, tcpC, and terC by BLASTn.
• Validation and Concordance: Evaluation with nine control strains and 288 human-source E. coli strains classified by PCR showed an average concordance of 93.4% between PCR and WGS results, with WGS detecting additional alleles.
• Sequencing Platform Compatibility: Accepts data from Illumina, Ion Torrent, Roche 454, SOLiD, Oxford Nanopore, and PacBio sequencing platforms.
• Read Mapping Algorithm: Uses KMA (K-mer based Mapping Algorithm) to map raw sequencing reads.

Scientific Applications:

• Virulence gene detection: Extraction and identification of virulence-related genes from WGS data for genotyping of E. coli isolates.
• Genetic diversity and evolutionary analysis: Detailed genotyping to study genetic diversity and evolutionary dynamics of E. coli virulence factors.
• Clinical diagnostics and surveillance: Support for classification of ExPEC versus non-ExPEC isolates and comparison of WGS-based profiles with PCR results.

Methodology:

KMA is used to map raw sequencing reads; BLASTn was used to confirm specific genes; database curation included removal of redundant sequences and verification of ORFs; allele validation included cross-referencing with 27 primer pairs and comparison to PCR-classified strains.