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

The aim of this study was to construct a valid publicly available method for subtyping of 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 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 alleles of 42 isolates generated prior to the current study (data set 1), one containing whole-genome sequence (WGS) data of 243 third-generation-cephalosporin-resistant isolates (data set 2), and one containing a randomly chosen subset of 40 isolates from data set 2 that were subjected to conventional 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 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, subtyping was evaluated on a phylogenetic network of 122 sequence type 131 (ST131) isolates. There was perfect concordance between the typology and -based subclones within ST131, with accurate identification of the pandemic multidrug-resistant clonal subgroup ST131- 30. FimTyper provides a standardized tool, as a rapid alternative to conventional subtyping, highly suitable for surveillance and outbreak detection.