STECFinder

STECFinder performs clustering and serotyping of Shiga toxin-producing Escherichia coli using genomic cluster-specific markers to support epidemiological, food-safety, and population-genetics analyses.

Key Features:

• Phylogenetic Analysis: Leverages phylogenetic analysis of nearly 41,000 publicly available STEC genomes representing 460 serotypes and identifies 19 major and 229 minor STEC clusters.
• Cluster-Specific Gene Markers: Identifies cluster-specific gene markers by comparative genomic analysis with reported accuracy of 99.54% and specificity greater than 97.25% against large collections of STEC and non-STEC E. coli genomes.
• Serotype-Specific Gene Markers: Pinpoints serotype-specific gene markers for the top 10 most frequent non-O157:H7 STEC serotypes.
• In Silico Serotyping Pipeline: Integrates cluster and serotype gene markers with established E. coli serotype-specific O and H antigen genes and stx genes to assign identification, cluster, and serotype with assignment accuracies of 99.85% for assembled genomes and 99.83% for Illumina reads.
• Detection of stx Subtypes: Predicts stx subtypes concurrently with STEC serotype assignment.
• Metagenomic Sequencing Compatibility: Detects spiked STEC serotypes in shotgun metagenomic sequencing reads from food samples, demonstrating culture-independent typing capability.

Scientific Applications:

• Epidemiological Surveillance: Enables rapid and accurate typing of STEC strains to support epidemiological investigations.
• Food Safety and Outbreak Investigation: Supports detection and serotyping of STEC in food samples, including culture-independent shotgun metagenomics for outbreak response.
• Public Health Surveillance: Assists public health monitoring by providing cluster determination and serotype assignments for STEC isolates.
• Population Genetics and Diversity Studies: Facilitates analysis of genetic diversity within STEC populations through phylogenetic and comparative genomic marker data.

Methodology:

Performed phylogenetic analysis of ~41,000 STEC genomes and comparative genomic analysis to identify cluster- and serotype-specific gene markers; integrated these markers with established E. coli O and H antigen genes and stx genes for in silico serotyping; validated marker performance against collections of STEC and non-STEC E. coli genomes and on assembled genomes, Illumina reads, and shotgun metagenomic reads.