Development of a Web Tool for Escherichia coli Subtyping Based on fimH Alleles

Abstract

The aim of this study was to construct a valid publicly available method for in silico fimH subtyping of Escherichia coli particularly suitable for differentiation of fine-resolution subgroups within clonal groups defined by standard multilocus sequence typing (MLST). FimTyper was constructed as a FASTA database containing all currently known fimH alleles. The software source code is publicly available at https://bitbucket.org/genomicepidemiology/fimtyper, the database is freely available at https://bitbucket.org/genomicepidemiology/fimtyper_db, and a service implementing the software is available at https://cge.cbs.dtu.dk/services/FimTyper. FimTyper was validated on three data sets: one containing Sanger sequences of fimH alleles of 42 E. coli isolates generated prior to the current study (data set 1), one containing whole-genome sequence (WGS) data of 243 third-generation-cephalosporin-resistant E. coli isolates (data set 2), and one containing a randomly chosen subset of 40 E. coli isolates from data set 2 that were subjected to conventional fimH subtyping (data set 3). The combination of the three data sets enabled an evaluation and comparison of FimTyper on both Sanger sequences and WGS data. FimTyper correctly predicted all 42 fimH subtypes from the Sanger sequences from data set 1 and successfully analyzed all 243 draft genomes from data set 2. FimTyper subtyping of the Sanger sequences and WGS data from data set 3 were in complete agreement. Additionally, fimH subtyping was evaluated on a phylogenetic network of 122 sequence type 131 (ST131) E. coli isolates. There was perfect concordance between the typology and fimH-based subclones within ST131, with accurate identification of the pandemic multidrug-resistant clonal subgroup ST131-H30. FimTyper provides a standardized tool, as a rapid alternative to conventional fimH subtyping, highly suitable for surveillance and outbreak detection. KEYWORDS fimH, Escherichia coli, typing, whole-genome sequencing analysisT he fimH gene is part of the fim operon, which encodes a surface organelle named type 1 fimbriae found in most Escherichia coli strains (1). The FimH protein is located at the tip of the fimbrial structure and serves as a D-mannose-specific adhesin, which aids in immobilizing the bacterium on both biotic and abiotic surfaces (2, 3). Studies have shown only minor sequence variation within the fimH genes, which renders the fimH alleles feasible for use in high-resolution subtyping of multilocus sequence typing (MLST)-based E. coli clonal groups. The applicability of fimH subtyping has been shown to be particularly relevant within the highly virulent sequence type 131 (ST131) clonal group, where the resistant and multiresistant H30 subgroups carrying the fimH30 allele have been identified (4, 5). As ST131 E. coli is the most dominant human-pathogenic clonal group being reported in relation to bloodstream infections, the need to perform fimH subtyping is undisputed. Traditionally, typing of fimH alleles has been obtained

Comprehensive Molecular Characterization of Escherichia coli Isolates from Urine Samples of Hospitalized Patients in Rio de Janeiro, Brazil

“…The ST was identified by uploading the assembled genomes in fasta format to the Center for Genomic Epidemiology (CGE) MLST finder website (version 1.7) (Larsen et al, 2012 ). Presence of antibiotic resistant genes was determined by uploading assembled genomes in fasta format to ResFinder 2.1 (Zankari et al, 2012 ), the serotyping by using the SerotypeFinder tool (Joensen et al, 2015 ), and the fimH type by uploading the genomes to FimTyper (version 1.0) (Roer et al, 2017 ) all present through the CGE website.…”

High frequency of hybrid Escherichia coli strains with combined Intestinal Pathogenic Escherichia coli (IPEC) and Extraintestinal Pathogenic Escherichia coli (ExPEC) virulence factors isolated from human faecal samples

“…The fimH90 subtype was also an interesting finding as it appears to be rare among E. coli strains and was not found among 243 draft genomes of E. coli isolates in a study using the CGE FimTyper Web tool [ 42 ]. However, BLAST searches found an identical fimH gene in a sequence scaffold from a human aEPEC strain (702898_aEPEC) isolated in Pakistan (GenBank: CYBW01000017.1).…”

Escherichia coli Sequence Type 410 Is Causing New International High-Risk Clones

“…fimH subtypes were identified with FimTyper 1.0 ( https://cge.cbs.dtu.dk/services/FimTyper/ ) ( 39 ).…”