Integrase Variants Drive the Aquisition of Antibiotic Resistance and Phage Defense Gene Cassettes in Antibiotic-Contaminated Environments

A total of eighteen soil samples, including five from soils outside the manufacturing facilities (hereafter referred to as “outside samples”) and thirteen from inside the manufacturing facilities (hereafter referred to as “inside samples”), as well as three influent samples (INF), four process water (PW) samples, four effluent (EFF) samples, and five surface water samples were collected from three typical antibiotic pharmaceutical factories.

The daily wastewater discharge of these factories ranged from 400 to 1200 tons. Two pig farms (each with a rearing capacity >10,000 pigs) and one chicken farm (housing more than 100,000 chickens) were selected, from which fifteen soil samples (including ten outside and five inside samples), four surface water samples, and four wastewater samples were collected.Total genomic DNA from soil samples and filter membranes was extracted using the DNeasy PowerSoil Pro Kit (QIAGEN, Germany) following the manufacturer’s protocol.