Resolved Genomes of Wastewater ESBL-ProducingEscherichia coliand Metagenomic Analysis of Source Wastewater Samples

Abstract

ABSTRACTExtended-spectrum beta-lactamase (ESBL) producingEscherichia colipose 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 ofE. coliisolated from various wastewater treatment utilities 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 (sulfonamides and aminoglycosides) along with insertional elements. ESBL genes such asblaCTX-M,blaTEM, andblaSHV were also detected on conjugable plasmids of IncF and IncI incompatibility types. One novel IncF plasmid (pSHV2A_ESBLF) was identified in which carried a multi-drug resistance genotype (blaSHV-2A,aadA22, aac(3), aph(6),tetA, andsul1) in addition to amer(mercury resistance) operon, colicin, and aerobactin genes. Shotgun metagenomic analysis of theE. coli-originating wastewater samples showed the presence of class A beta-lactamases; however, the ESBL genes identified in theE. coligenomes were below the detection limits. Other ESBL-associated genes (i.e.,blaOXA.11,blaFOX.7, andblaGES.17) were identified in the wastewater samples and their occurrences were correlated with the core microbial genera (e.g.,Paraprevotella). In both theE. coligenomes 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.