# In Silico Prediction of Secreted Proteins in Shiga Toxin-Producing Escherichia coli: Identification of a Hydrolase as a Robust Genomic Marker

## TL;DR

Researchers identified a hydrolase gene in harmful E. coli strains that could help improve detection and control of these dangerous bacteria.

## Contribution

A hydrolase-encoding gene was identified as a novel genomic marker associated with pathogenic STEC strains.

## Key findings

- A hydrolase gene was found in 81.6% of STEC genomes but only 15.8% of non-STEC genomes.
- The hydrolase is predicted to be secreted and may contribute to STEC virulence.
- The gene could complement existing genetic screening methods for STEC.

## Abstract

Shiga toxin-producing Escherichia coli is a foodborne bacterium that can cause severe illness in humans. Identifying harmful strains remains challenging due to their high genetic and biological diversity. In this study, we analyzed more than thirty-five thousand Escherichia coli genomes from public databases using computer-based methods to identify disease-associated factors. We focused on proteins secreted outside the bacterial cell as potential markers. One hundred fifty-five candidate genes were identified, and a hydrolase-encoding gene showed a strong association with pathogenic strains. This hydrolase could complement existing screening methods and support the development of improved strategies for detection and control.

Shiga toxin-producing Escherichia coli (STEC) are major foodborne pathogens that can cause severe human disease. Identifying molecular markers associated with pathogenicity is essential to improve detection and to better understand virulence mechanisms. In this study, 35,828 E. coli genomes available in a public database were analyzed with the purpose of identifying STEC genes encoding proteins secreted to the outer membrane or into the extracellular space. The strains belong to six different sequence types (STs): ST442, ST297, ST1131, ST2217, ST2387, and ST2520. Comparative genomics allowed identification of 155 genes that were initially evaluated as potential virulence-associated candidates. Among these, a hydrolase-encoding gene showed a wide distribution and a significant association with STEC genomes versus non-STEC genomes (81.6% in the STEC group and 15.8% in the non-STEC group). The protein product is predicted to be released into the extracellular space and, according to examples in other bacterial pathogens, may contribute to STEC virulence. Altogether, our findings highlight this hydrolase as a relevant molecular marker that could complement current genetic screening schemes and support the design of novel control strategies against STEC infections.