Use of fimH single-nucleotide polymorphisms for strain typing of clinical isolates of Escherichia coli for epidemiologic investigation

Abstract

Strain typing methods that compare electrophoresis banding patterns are commonly used but are difficult to standardize and poorly portable. Multilocus sequence typing (MLST) is a sequence-based alternative, but it is not practical for large-scale epidemiological studies. In the present study, the usefulness of fimH single-nucleotide polymorphisms (SNPs) for Escherichia coli typing was explored. fimH SNPs were determined for 345 E. coli clinical isolates (including 3 reference strains) and compared to PCR-based ECOR (E. coli reference collection) phylogrouping. The fimH gene could be amplified for 316 (92%) of the 345 isolates. fimH SNP analysis found 46 distinct terminal groups in the nucleotide sequence-based phylogenetic tree (fimH types). A subset of the E. coli isolates (162 clinical isolates and the 3 reference strains) were compared by fimH type, PCR phylogroup, and MLST. These isolates fell into 27 fimH types and 18 MLST clonal complexes (CCs) that contained 2 to 28 isolates per complex. The combination of PCR phylogroup and fimH type corresponded to a single CC for 113 (68%) isolates and 2 or 3 CCs for the other 52 (32%) isolates. We propose that the combination of PCR phylogrouping and fimH SNP analysis may be a useful method to type a large collection of clinical E. coli isolates for epidemiologic studies.

FIG. 1.

Phylogenetic tree derived from 46 partial fimH sequence variants found in 342 clinical E. coli isolates and E. coli reference strains K-12 (fimH type f-1), CFT073, and ATCC BAA-457 (CgA), determined by the neighbor-joining distance method using the Kimura 2-parameter model. fimH sequences were analyzed by comparison with the sequence of E. coli K-12. Boxes contain amino acid changes that resulted in 17 FimH protein variants deduced from the analysis of the nucleotide sequences. Replacements of the same amino acid in the same position independently acquired are distinguished by lowercase letters to the left of boxes.

FIG. 2.

Phylogenetic tree of 166 E. coli isolates (including reference strains K-12, CFT073, and ATCC BAA-457 [CgA]) derived from concatenated sequences of the seven standard MLST genes (described in the text), determined by the neighbor-joining distance method using the Kimura 2-parameter model. Duplicate concatenated sequences were removed from the input sample. B2, A, B1, and D are PCR phylogenetic groups. Numbers within the tree indicate the occurrence (%) of the branching order in 500 bootstrapped trees. Only values above 50 are shown. Roman numerals indicate clonal complexes.