Resolved Genomes of Wastewater ESBL-Producing Escherichia coli and Metagenomic Analysis of Source Wastewater Samples

Extended-spectrum beta-lactamase (ESBL) producing Escherichia coli pose 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 utilities in Oregon, USA. Class A beta-lactamase genes on chromosomes ( bla CTX-M, bla TEM ) were clustered with antibiotic resistance genes associated with other classes of antibiotics (sulfonamides and aminoglycosides) along with insertional elements. ESBL genes such as bla CTX-M, bla TEM, and bla SHV 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 ( bla SHV-2A, aadA22, aac(3), aph(6) , tetA , and sul1 ) in addition to a mer (mercury resistance) operon, colicin, and aerobactin genes. Shotgun metagenomic analysis of the E. coli -originating wastewater samples showed the presence of class A beta-lactamases; however, the ESBL genes identified in the E. coli genomes were below the detection limits. Other ESBL-associated genes ( i.e. , bla OXA.11, bla FOX.7, and bla GES.17) were identified in the wastewater samples and their occurrences were correlated with the core microbial genera (e.g., 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.