EcoliTyper

EcoliTyper integrates nine core genotyping analyses into a single automated workflow for comprehensive characterization and surveillance of Escherichia coli isolates.

Key Features:

• Species Confirmation: Verifies E. coli identity using fastANI.
• Assembly Quality Control: Assesses genome assembly quality as part of the automated workflow.
• Multi-Locus Sequence Typing (MLST): Performs MLST for strain characterization.
• Serotyping: Determines O and H antigen types.
• CH Typing: Profiles FumC and FimH alleles.
• Clermont Phylogrouping: Assigns isolates to phylogenetic groups using the Clermont method.
• Pathotype Classification: Classifies E. coli pathotypes.
• Antimicrobial Resistance (AMR) Screening: Detects AMR genes.
• Virulence Factor Profiling: Identifies virulence-associated genes.
• Plasmid Replicon Screening: Detects plasmid replicon types.
• Biocide and Heavy Metal Resistance Screening: Identifies markers for biocide and heavy metal resistance.
• Cross-Genome Pattern Discovery: Summarizes gene frequencies across analyzed genomes.
• Lineage Database Contextualization: Contextualizes results using a manually curated database of high-risk clones.
• Multi-Format Outputs: Generates interactive gene-centric HTML reports, TSV, JSON, and plain text files.

Scientific Applications:

• Clinical Microbiology: Enables rapid isolate characterization for diagnostic and surveillance purposes.
• Outbreak Investigation: Supports epidemiological tracking through integrated genotyping and high-risk clone identification.
• Genomic Research: Facilitates standardized E. coli genotyping for comparative and population genomic studies.
• Public Health Surveillance: Provides actionable intelligence for monitoring antimicrobial resistance and virulence trends.

Methodology:

EcoliTyper executes species confirmation via fastANI, assembly quality control, MLST, serotyping (O and H antigens), CH typing (FumC and FimH), Clermont phylogrouping, pathotype classification, and screening for AMR genes, virulence factors, plasmid replicons, biocide and heavy metal resistance markers. Cross-genome pattern discovery summarizes gene frequencies, and results are contextualized against a manually curated lineage database of high-risk clones.