Antibiotic Resistance from Wastewater to Agricultural Soils and Food Crops

Extended-spectrum beta-lactamase (ESBL) producing Escherichia coli are a serious threat to human health because of their resistance to the most commonly prescribed antibiotics: penicillins and cephalosporins. In this study, we provide a genomic and metagenomic context for the determinant ESBL genes of E. coli isolated from various wastewater treatment plants in Oregon, USA. Class A beta-lactamase genes on chromosomes (blaCTX-M, blaTEM) were clustered with antibiotic resistance genes associated with other classes of antibiotics (i.e., sulfonamides and aminoglycosides) along with insertional elements such as IS26. ESBL genes such as blaCTX-M, blaTEM and blaSHV were also detected on conjugable plasmids of IncF and IncI incompatibility types. One IncF plasmid novel to this study carried a multi-drug resistance genotype in addition to a mer mercury resistance operon and colicin and aerobactin virulence factors. Class A beta-lactamases were present in the wastewater samples from which the E. coli isolates were collected, however, the specific ESBL genes in the E. coli genomes were below the detection limit in the samples. Other ESBL-associated genes blaOXA.11, blaFOX.7, and blaGES.17 were correlated with core microbial genera such as Paraprevotella. In both the E. coli genomes and the wastewater samples, tetracycline, aminoglycoside, and beta-lactam resistance determinants frequently co-occurred. The unique combination of whole-genome and metagenomic analysis provides a holistic description of ESBL-producing organisms and genes in the Oregonian wastewater system.