Escobase

Compiling the Escobase (EScherichia COli dataBASE) was part of Lucile Martin's Internship for her MSc-1 at the University of Clermont-Auvergne, who PS supervised from May-August 2023. The E. coli genomes were downloaded or assembled with SPADES (when only reads were present), and after examination of the metadata to select only the genomes of isolates from cattle, the Escobase was put together. We compared the predicted ORFs (identified with Prodigal) of all genomes to the virulence factor database (VFdb), the ResFinder AMR database, and a custom-made database using genes which have been shown to contribute to bacterial acid resistance (AcR_AA_nr_latest30Dec2024.faa ).