Emergence of bacterial infections resistant to last resort antibiotics, such as beta-lactams, is an increasing human health concern. Extended-spectrum beta-lactamases (ESBLs) are mostly encoded on plasmids (i.e., mobile genetic elements) and can easily spread via horizontal gene transfer. Wastewater treatment plants are reservoirs and sources of antibiotic resistant bacteria and their determinant genes, facilitating spread into the environment. This study characterizes the resistome (i.e., entire ecology of resistance determinants) of 13 ESBL-producing Escherichia coli isolates collected from 9 wastewater treatment facilities across Oregon. These ESBL-producing E. coli isolates were collected from wastewater influent (n = 3), secondary effluent (i.e., after biological treatment and before disinfection; n = 2), treated effluent (i.e., after disinfection; n = 4), and treated biosolids (n = 4) over winter and summer between 2019 and 2020. All isolates contained multi-drug resistance phenotypes (i.e., resistance to three or more classes of antibiotics), including seven demonstrating resistance to six classes of antibiotics. Of these antibiotics, cephalosporin was found to be the most common (n = 13), followed by ampicillin (n = 11), tetracycline (n = 11), ciprofloxacin (n = 9), sulfamethoxazole/trimethoprim (n = 9), and streptomycin (n = 8). The collected ESBL-producing E. coli isolates were sequenced using an Illumina MiSeq system. The most common ESBL-associated genes identified were CTX-M-14 and CTX-M-15, which are the most reported genes associated with ESBL production globally. These ESBL genes also had high sequence conservation despite geographical differences as well as plasmid-associated DNA and conserved synteny of transposons, providing more evidence on plasmid-mediated transfer of these genes. Further analysis identified associated plasmids and other mobility agents, most abundant antibiotic resistance, and virulence genes. Moreover, multi-locus sequence typing was performed to examine associations between genotypes of resistance.
