FimTyper

FimTyper subtypes Escherichia coli by assigning fimH alleles to provide high-resolution subtyping for epidemiological and phylogenetic analyses.

Key Features:

• fimH allele FASTA database: A comprehensive FASTA reference containing all currently known fimH alleles underpinning subtype assignment.
• Input data support: Accepts Sanger sequences and draft whole-genome sequencing (WGS) assemblies as input for fimH allele assignment.
• High-resolution discrimination: Differentiates fine-resolution subgroups within multilocus sequence typing (MLST)-defined clonal groups using fimH variation.
• Phylogenetic concordance: Resolves subclones in phylogenetic network analyses, including identification of ST131-H30.

Scientific Applications:

• Sanger sequence validation: Predicted all fimH subtypes for a dataset of 42 E. coli isolates with Sanger sequences.
• Whole-genome sequencing analysis: Accurately analyzed draft genomes from 243 third-generation-cephalosporin-resistant E. coli isolates.
• Conventional subtyping comparison: Achieved complete agreement with conventional fimH subtyping for a subset of 40 isolates.
• Phylogenetic network analysis (ST131): Demonstrated perfect concordance in identifying subclones within a phylogenetic network of 122 ST131 isolates, including the pandemic multidrug-resistant subgroup ST131-H30.

Methodology:

Uses a comprehensive fimH allele FASTA database to assign fimH subtypes from Sanger and WGS sequence data via an in silico standardized subtyping approach.