Genome wide association study (GWAS) in E. coli: an approach to the search for genetic markers of the Shiga toxin-producing pathotype (STEC)

Due to genetic changes, certain strains of E. coli have moved from commensals to pathogens. According to the pathogenic mechanisms involved, different pathotypes are recognized, one of them is STEC, a pathotype that produces Shiga toxins (Stxs). STEC infections occur at any age but in children under five years of age can produce severe processes such as hemorrhagic colitis (CH) or hemolytic uremic syndrome (HUS), which can be fatal in the acute stage or leave long-term sequelae. There is no specific treatment for STEC infection in humans and even the use of some antibiotics during the diarrheal phase can increase the chances of developing severe complications such as HUS or PPT. Thus, the most effective strategy so far is the prevention of the infection. On the other hand, the detection of STEC in raw meat for export is an important cause of alerts and has generated a block the import of products with very significant economic losses. In both cases, the diagnosis of the presence of this pathogen is essential. In currently used methods, whether in the clinic, in food and in livestock, the presence of stx and eae genes must be ensured in order to establish the pathogenic capacity of the strain. However, recently, stx positive and eae negative strains that have pathogenic capacity have begun to be identified worldwide, therefore thinking only about these genes when carrying out a screening has clear disadvantages to evaluate the potential pathogenic capacity of the crops involved. This project proposes a strategy based on in-silico analysis for the detection of genetic markers associated with the STEC pathotype. The GWAS technique will be implemented on freely available genomes, looking for kamers that are associated with: 1) the STEC pathotype and 2) the invasive STEC phenotype. The approach proposed in this project also includes the identification of non-coding markers such as regulatory regions, small RNAs, which despite being relevant for pathogenicity and virulence in bacterial pathogens are not well understood. Finally, using a bank of local strains and by sequencing complete genomes and / or amplification/sequencing of identified regions, we will proceed to validate the predictions in strains isolated from Uruguay.

CSIC I+D-2018, Code: ID-404.

Funding Source: CSIC-UDELAR, Uruguay.

Research Associates: Gustavo Varela, Sylvia Vazquez, Cecilia Quiroga, Francisco Peñagaricano