Development of a tool for the control of multidrug resistant and pathogenic Esherichia coli in pigs and poultry using whole genome sequencing

The overall aim of this project is to set up and validate genomic tools for rapid detection and identification of pathogenic and antimicrobial resistant E. coli in intensive production animals and interface with a user-friendly web platform. The processes to be developed are firstly ColipathID, a tool using whole genome sequencing (WGS), for identification of pathogenic and antimicrobial resistant E. coli isolates and phylogenetic analysis of highly pathogenic E. coli clones in intensive production animals, that is, pigs and poultry, and interfaced with a userfriendly web platform; and secondly, ColipathDetect, a tool using WGS and based on markers identified by ColipathID, for rapid detection and quantification of pathogenic and antimicrobial resistant E. coli in fecal samples or the E. coli community enriched from samples in intensive production animals.

In the current process, which is costly, time consuming and lacks resolution, E. coli isolates from clinically sick animals in Quebec are examined by conventional techniques. Results and relevant demographic and geographic data are entered in a database developed by EcL and reported on a publically accessible web platform and in quarterly reports to the Ministère de l'Agriculture, des Pêcheries et de l'Alimentation (MAPAQ). MAPAQ uses these data to identify emerging pathogenic antimicrobial resistant clones and take the appropriate steps with veterinarians and producers. ColipathID consists of replacing the currently used techniques with WGS of E. coli isolates. Virulence and antimicrobial resistance gene sequences and whole genome phylogenetic typing will be rapidly extracted and analysed using algorithms developed for already accessible databases for pathogenic E. coli and will be linked with the APZEC database. The platform will be validated using OIE guidelines. Markers for pathogenic clones and antimicrobial resistance will be identified for use in the ColipathDetect tool for rapid detection of pathogenic and antimicrobial resistant E. coli. Quantitative evaluation of samples is currently tedious and will be replaced with a metagenomics approach based on sequencing of the genome of the E. coli community in the primary E. coli culture (ColipathDetect). The presence and quantification of genes or markers will permit a rapid and inexpensive estimation of sample prevalence for use in large scale studies such as monitoring of antibiotic-free farms. The tools will be validated using reference E. coli strains, and samples both from MAPAQ and collected in field projects with various industry partners. Thus, ColipathDetect will allow initial detection of pathogenic E. coli whereas ColipathID will be used for routine surveillance and specific tracking of outbreaks.