Dairy farm waste: A potential reservoir of diverse antibiotic resistance and virulence genes in aminoglycoside- and beta-lactam-resistant Escherichia coli in Gansu Province, China

Abstract

Aminoglycosides (AGs) and beta-lactams are the most commonly used antimicrobials in animal settings, particularly on dairy farms. Dairy farm waste is an important reservoir of antibiotic resistance genes (ARGs) and virulence genes (VGs) in environmental Escherichia coli, which is an important indicator of environmental contamination and foodborne pathogen that potentially threaten human and animal health. In the present study, we aimed to characterize the ARGs and VGs in AG- and beta-lactam-resistant E. coli from dairy farm waste in Gansu Province, China. The dairy farm waste consisted of fecal (n = 265) and sewage (n = 54) samples processed using standard microbiological techniques and the Clinical & Laboratory Standards Institute guidelines. The total DNA of AG- and beta-lactam-resistant E. coli was extracted, and whole-genome sequencing (WGS) was performed using the Illumina NovaSeq platform and analyzed using various bioinformatics tools. In this study, among 84.3% (269/319) of the E. coli strains, 23.8% (64/269) were identified as AG- and beta-lactam-resistant E. coli. WGS analysis revealed a large pool of ARGs belonging to multiple classes such as AGs, beta-lactams, aminocoumarins, fluoroquinolones, macrolides, phenicol, tetracyclines, phosphonic acid, disinfecting and antiseptic agents, elfamycin, rifamycin, and multidrug resistance genes. Furthermore, virulome analysis of 64 E. coli strains revealed clinically important virulence factors associated with adherence, biofilm, invasion, auto-transportation, siderophores, secretion systems, toxins, anti-phagocytosis, quorum sensing, regulation, metabolism, and motility. We identified dairy farm feces and sewage waste as important reservoirs of antimicrobial resistance and virulence determinants in E. coli in Gansu, China, which can threaten human and animal health through ecological exposure and contamination of food and water. We recommend continuous large-scale surveillance in dairy farm settings to formulate protective guidelines for public health safety.