title: 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.
authors.affiliation: Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil.
authors.forename: Rubens C S
authors.initials: RC
authors.lastname: Dias
authors.forename: Beatriz M
authors.initials: BM
authors.lastname: Moreira
authors.forename: Lee W
authors.initials: LW
authors.lastname: Riley
mesh_terms: D018830:Adhesins, Escherichia coli / Q000235:genetics*; D015373:Bacterial Typing Techniques / Q000379:methods*; D016000:Cluster Analysis; D016172:DNA Fingerprinting / Q000379:methods*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004926:Escherichia coli / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D004927:Escherichia coli Infections / Q000453:epidemiology* / Q000382:microbiology; D005260:Female; D036781:Fimbriae Proteins / Q000235:genetics*; D005838:Genotype; D006801:Humans; D008297:Male; D017720:Molecular Epidemiology / Q000379:methods; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D018830:Adhesins, Escherichia coli; D004269:DNA, Bacterial; C058769:fimH protein, E coli; D036781:Fimbriae Proteins