E. coli May Look Identical, but ‘Genetic Fingerprints’ Reveal Pathogenicity

The Rural Development Administration has developed a new genotyping technology that precisely identifies Escherichia coli with different levels of risk despite their similar appearance, using “genetic fingerprints.”

The Rural Development Administration said on the 30th that it had developed a technology to identify the precise lineages of E. coli strains by analyzing their distinctive genetic arrangement patterns. The study was conducted in response to strengthening global trends in agricultural product safety management, including the U.S. Food Safety Modernization Act (FSMA) and European Union (EU) hygiene regulations.

Existing pathogenicity gene tests (PCR) can determine only whether pathogenicity is present and have difficulty identifying variation between strains. Standard genotyping analysis (MLST) also has limitations in finely distinguishing genetically similar strains.

The researchers analyzed 83 publicly available E. coli genomes and precisely classified the strains into 14 types based on their genetic characteristics. The technology can identify even subtle regions of bacterial variation that existing testing methods miss.

The new analytical technology had a Simpson’s diversity index of 0.726, indicating its ability to differentiate strains, and showed a level of precision equivalent to or better than that of the existing standard analytical method (MLST, 0.723).

In particular, the technology can predict E. coli pathogenicity and antibiotic resistance characteristics using only genetic fingerprint analysis. The researchers found a tendency for longer genetic fingerprint patterns to be associated with more virulence genes, while shorter patterns tended to be associated with more antibiotic resistance genes.

The findings were published in the international journal BMC Genomics. The Rural Development Administration plans to distribute the technology to agricultural product safety management agencies and relevant testing sites after conducting additional validation of its field applicability.

“Just as each person has a different fingerprint, E. coli also has a unique genetic fingerprint,” said Han Sang-hyun, director of the Agricultural Microbiology Division at the National Institute of Agricultural Sciences under the Rural Development Administration. “We established a practical research framework that overcomes the limitations of existing analytical methods and clearly distinguishes the subtle genetic diversity of E. coli.”