Distinct ARG profiles associated with class 1 integrons in municipal and industrial wastewater treatment plants

Class 1 integrons facilitate horizontal gene transfer, significantly influencing antibiotic resistance gene (ARG) dissemination within microbial communities. Wastewater treatment plants (WWTPs) are critical reservoirs of ARGs and integrons, yet the integron-mediated dynamics of ARG transfer across different WWTP types remain poorly understood. Here we show distinct ARG profiles associated with class 1 integrons in municipal and industrial WWTPs using a novel approach combining nested-like high-throughput qPCR and PacBio sequencing. Although industrial WWTPs contained higher absolute integron abundances, their relative ARG content was lower (1.27 × 10⁷-9.59 × 10⁷ copies/ng integron) compared to municipal WWTPs (3.72 × 10⁷-1.98 × 10⁸ copies/ng integron). Of the 132,084 coding sequences detected from integrons, 56.8 % encoded antibiotic resistance, with industrial plants showing lower ARG proportions, reduced ARG array diversity, and greater incorporation of non-ARG sequences. These findings suggest industrial WWTP integrons integrate a broader array of exogenous genes, reflecting adaptation to complex wastewater compositions. This work enhances our understanding of integron-driven ARG dynamics in wastewater and offers a robust strategy for environmental integron analysis.