Genomic Characterization of Extended-Spectrum β-Lactamase (ESBL) Producing E. coli Harboring blaOXA−1-catB3-arr-3 Genes Isolated From Dairy Farm Environment in China

Abstract

Anthropogenic activities in the environment affect the ecosystem and can play an important role in selecting and spreading antibiotic-resistant bacteria (ARB) and genes (ARGs). The dairy farm environment may serve as a hotspot and reservoir for exchanging and spreading ARGs, but studies are scarce. Here, we investigated and characterized the extended-spectrum β-lactamase producing Escherichia coli strains recovered from the dairy farm environment co-harboring bla_OXA−1, catB3, and arr-3 genes. The isolates were identified and characterized by PCR, antimicrobial susceptibility testing, conjugation assay, whole genome sequencing (WGS), and multiple bioinformatics tools. Seven E. coli strains co-harboring bla_OXA−1, catB3, and arr-3 genes were identified which belonged to distinct sequence types (STs) and carried diverse plasmid replicon types. The conjugation assay revealed a successful transfer of bla_OXA−1, catB3, and arr-3 genes into the recipient E. coli J53 with a co-conjugation frequency ranging from (2.25 ± 0.3) × 10⁻⁴ to (3.85 ± 0.3) × 10⁻³. Bioinformatics analysis of WGS revealed the diversity of acquired ARGs, conferring resistance to aminoglycosides, beta-lactams, quinolones, tetracyclines, macrolides, trimethoprim–sulfamethoxazole, phosphonic, phenicol, and rifamycin. The genetic environment analysis showed that aac(6^′)-Ib-cr-bla_OXA−1-catB3-arr-3-qacE1-sul1 was the common genetic backbone among the seven E. coli strains. Among the mobile genetic elements, insertion sequences were the predominant elements as compared to transposons. The phylogenetic analysis demonstrated a close relationship between the E. coli of this study and other strains of human–animal-environment origin retrieved from the NCBI database. This study presented the whole genome-based characterization of E. coli strains carrying the bla_OXA−1-catB3-arr-3 genes. It provided evidence that the dairy environment may harbor a variety of ARGs and act as a potential reservoir for their spread in the ecosystem. The results recommend the routine surveillance of ARGs carrying bacteria in dairy environments and the need for additional studies to understand the dissemination mechanism within One Health perspective to prevent their further spread.