Escherichia coli Genome sequencing and assembly. Escherichia coli

The goal of this study was to provide a genomic and metagenomic context for the determinant ESBL genes of E. coli isolated from various wastewater treatment utilities in Oregon, USA. We resolved the genome of ESBL-producing E. coli isolates collected from wastewater utilities in Oregon whose AMR genotypes and phenotypes were previously characterized in our lab. Using a hybrid sequencing and assembly strategy (short- and long-read sequencing), we identified ARGs and virulence factors harbored on plasmids and chromosomes. We further characterized incompatibility types and the co-occurrences of virulence factors and ARGs on plasmids. We investigated the transferability of these plasmid-mediated ESBLs via conjugation. Finally, using shotgun metagenomic analysis of the E. coli-originated wastewater samples, we described the microbial community, the resistome composition, and the potential associations with plasmid-mediated ESBL genes as well as other ARGs.