Horizontal Gene Transfer Dynamics and Integron-Mediated Multi-Drug Resistance Dissemination in Enterobacteriaceae Isolated from Hospital and Agricultural Environments in Rivers State

Horizontal gene transfer mediated by integrons and mobile genetic elements is a central driver of multi-drug resistance (MDR) dissemination across ecological boundaries, and understanding these transfer dynamics in the complex hospital-agricultural interface of Rivers State offers critical One Health insights. This mechanistic genomics study characterized integron-mediated resistance gene dissemination in Enterobacteriaceae from clinical patients, hospital wastewater, aquaculture ponds, and rice paddy fields across Obio-Akpor and Eleme local government areas, Rivers State, in the South South geopolitical zone of Nigeria. A total of 200 Enterobacteriaceae isolates from four compartments underwent whole-genome sequencing. Integron detection, gene cassette characterization, and mobile genetic element (plasmid incompatibility groups, transposons, IS elements) annotation were performed by bioinformatics analysis. Conjugation efficiency assays measured inter-strain horizontal gene transfer rates. Class 1 integrons were detected in 64 percent of all isolates and were the primary carriers of aadA, dfrA, blaOXA, and qnr gene cassettes. Conjugal transfer frequency was highest between clinical and aquaculture-derived E. coli isolates sharing identical IncF plasmid backbones. Comparative genomics identified identical gene cassette arrays in human clinical and fish pond isolates, providing direct evidence of cross-compartment transfer. A phylogenetic transfer network model quantified hospital wastewater as the dominant ARG seeding source for agricultural water environments. These findings establish integron-mediated horizontal transfer as the primary MDR dissemination mechanism linking clinical and environmental resistance in Rivers State. Keywords: horizontal gene transfer, integrons, multi-drug resistance, Rivers State, One Health.