High-resolution two-locus clonal typing of extraintestinal pathogenic Escherichia coli

Area of Science:

• Bacteriology
• Molecular Epidemiology
• Genotyping

Background:

• Multilocus sequence typing (MLST) is a standard method for bacterial population structure analysis.
• Identical MLST profiles (sequence types, STs) can mask distinct genotypes and lifestyles within bacterial strains.
• Improved genotyping is needed for detailed molecular epidemiology.

Purpose of the Study:

• To develop and evaluate a more discriminating and economical typing scheme for Escherichia coli.
• To compare the discriminatory power of a novel two-locus scheme with standard MLST.
• To assess the correlation between the novel scheme and existing MLST-based groupings.

Main Methods:

• Developed a two-locus typing scheme (CH typing) using internal fragments of fimH and fumC genes.
• Sequenced fimH and fumC loci from 191 model and 853 clinical E. coli isolates.
• Compared haplotype diversity and clonal subgrouping with standard 7-locus MLST.

Main Results:

• CH typing consistently yielded more haplotypes than standard 7-locus MLST.
• The two-locus scheme effectively split large STs into distinct clonal subgroups.
• Specific CH profiles accurately predicted MLST-based profiles (STs/ST complexes) with 95% accuracy.

Conclusions:

• CH (fumC/fimH) typing provides superior clonal discrimination for E. coli compared to standard MLST.
• This two-locus method is a cost-effective genotyping tool for molecular epidemiology.
• CH typing offers a valuable alternative for detailed analysis of E. coli population structure.