ECTyper

ECTyper predicts serotypes and performs species-level identification for Escherichia coli and Shigella from whole-genome sequencing (WGS) data.

Key Features:

• In silico serotype prediction: Predicts O-antigen and H-antigen serotypes from whole-genome sequencing (WGS) data.
• Speciation: Distinguishes Escherichia coli and Shigella at the species level.
• Input formats: Accepts fasta and fastq file formats.
• Quality control reporting: Provides quality control information for input sequence data.
• Result output: Generates interpretable serotype and speciation results.
• Benchmarking and concordance: Evaluated against SRST2, SerotypeFinder, and EToKi EBEis; on 185 newly sequenced isolates concordance was 92–97% for O-antigens and 98–100% for H-antigens, and on 6,954 publicly available E. coli genomes concordance was 75–91% for O-antigens and 62–90% for H-antigens.

Scientific Applications:

• Surveillance and outbreak detection: Provides serotype and speciation data used in detection and investigation of Escherichia coli outbreaks.
• Public health and food safety: Supports pathogen characterization in public health and food safety laboratory contexts.
• Method validation and comparison: Enables comparative benchmarking of WGS-based serotyping methods.

Methodology:

Performs in silico serotype prediction from whole-genome sequencing (WGS) data.