# In Silico Detection of Virulence Genes in Whole-Genome Sequences of Extra-Intestinal Pathogenic Escherichia coli (ExPEC) Documented in Countries of the Andean Community

## TL;DR

This study used computer analysis to find virulence genes in E. coli from Andean countries, revealing high diversity and frequency in human and animal sources.

## Contribution

The study provides new insights into the virulence gene profiles of ExPEC in Andean countries using in silico analysis of whole-genome sequences.

## Key findings

- 30% of isolates were classified as ExPEC, with an average of 39 virulence genes per isolate.
- Human and animal isolates showed greater diversity in adhesin, secreted factors, and toxin genes compared to food and environmental samples.
- ST449 isolates had the highest average of 50 virulence genes, with equal representation of secreted factors and adhesins.

## Abstract

E. coli pathotypes, which cause extra-intestinal infections, pose significant public health challenges, emphasizing the need for virulence gene surveillance to understand their dynamics. Key virulence genes have been identified in E. coli from Andean community countries, predominantly linked to human and animal sources. However, detailed data on virulence profiles from environmental and food sources remain limited. This study utilized an in silico approach to analyze 2402 whole-genome sequences from EnteroBase, known for associations with antimicrobial resistance genes. Of the isolates, 30% were classified as ExPEC, averaging 39 virulence genes per isolate, with adhesin-related genes being the most predominant. These findings were consistent across human, environmental, animal, and food samples. Human and animal isolates exhibited greater diversity in adhesin, secreted factors, and toxin genes compared to other sources, whereas food samples contained the fewest factors. ST449 isolates exhibited an average of 50 virulence genes per genome, with secreted factors and adhesins equally represented, while ST131, ST38, and ST10 carried around 40 genes, predominantly adhesins. Overall, the diversity and frequency of virulence genes exceeded prior reports in the region, highlighting the importance of monitoring these traits to identify emerging patterns in pathogenic E. coli strains frequently subjected to antibiotic exposure.