Environmental acquisition of antimicrobial resistance is global threat to public health where wastewater treatment plants (WWTP) serve as a hub of carrying diverse range of antimicrobial resistant organism and provide suitable conditions for nonvertical transmission of genetic determinants of antimicrobial resistance. Despite of the advancement in wastewater treatment techniques, certain bacteria and antimicrobial resistant genes (ARGs) persist in the final effluent and are disseminated into the environment. We aimed at characterizing the core resistome of two WWTP influent and final effluent in a four-year longitudinal metagenomic study. We adapted read based approach to calculate the absolute abundance of ARGs and contig based approach to identify the host of the core ARGs. Moreover, we find the human fecal pollution in the both influent and effluent samples and calculated the metagenomic risk score.

We find a diversity of ARGs from 151 to maximum of 654 ARGs per site and the abundance ranges from 1.2 X 10^-1 to 2.4 copies of ARGs per copy of 16S rRNA gene. Of the total 1100 ARGs found in all sites, 73 ARGs in SeoNam WWTP and 75 in JungRang WWTP were found to be persistent in all four years. CrAssphage abundance and metagenomic risk score was higher in influent samples. ARGs diversity was negatively correlated to the core resistome while it was positively correlated with the crAssphage abundance (p<0.05). Abundance of some of the core ARGs got increased in effluent (p<0.01). Pseudomonas, Acinetobacter, Aeromonas and Mycobacterium were the major genera carrying core ARGs both in influent and effluent. The results of our study indicate that core resistome is sharing more than half of the total ARGs abundance and the presence of these ARGs on plasmid make them an environmental hazard. As core ARGs are not correlated to the either plasmids, chromosome or crAssphage, but their constant release in the environment can cause critical public health problems and needs to be addressed carefully.