The risk assessment of the acquisition of ambient Antibiotic Resistance Genes (ARGs) by pathogenetic populations during treatment is attracting more and more attention in Wastewater Treatment Facilities (WWTPs), which serve as the interface between human society and the natural environment. However, due to a lack of reliable Resistome profiling techniques, genotype and resistance phenotype are still insufficiently associated in human pathogens found in sewage samples. The resistance genes of Multiple Antibiotic Resistant (MAR) coliform bacteria, a frequent indicator of human enteric pathogens in sewage samples, were quantified here using Minion sequencing. Within 30 hours of collecting the samples, our pipeline could produce the results, and the Resistome quantification was accurate and comparable to that based on the Illumina platform. Long Nano pore reads also facilitated the genome reconstruction of a representative MAR strain, from which we identified an instance of chromosomal integration of an environmental resistance gene acquired through plasmid exchange with a porcine pathogen. This allowed for the simultaneous identification of the carrier populations of ARGs detected. This study showed how to use minion sequencing to quickly monitor and simultaneously track evolutionary changes in environmental ARGs to address any potential health risks.gap.
