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Human sewage pollution is a major threat to public health because sewage always comes with pathogens. Human sewage is usually received and treated by wastewater treatment plants (WWTPs) to control pathogenic risks and ameliorate environmental health. However, untreated sewage that flows into water environments may cause serious waterborne diseases, as reported in India and Bangladesh. To examine the fate of the human sewage microbiome in a local municipal WWTP of Hong Kong, we used massively parallel sequencing of 16S rRNA gene to systematically profile microbial communities in samples from three sections (i.e., influent, activated sludge, and effluent) obtained monthly throughout 1 year. The results indicated that: (1) influent sewage bacterial profile reflected the human microbiome; (2) human gut bacterial community was the dominant force shaping influent sewage bacterial profile; (3) most human sewage bacteria could be effectively removed by the WWTP; (4) a total of 75 genera were profiled as potentially pathogenic bacteria, most of which were still present in the effluent although at a very low level; (5) a grouped pattern of bacterial community was observed among the same section samples but a dispersed pattern was found among the different section samples; and (6) activated sludge was less affected by the influent sewage bacteria, but it showed a significant impact on the effluent bacteria. All of these findings provide novel insights toward a mechanistic understanding of the fate of human sewage microbiome in the WWTP. [ABSTRACT FROM AUTHOR]

• High-resolution temporal profile of a broad-spectrum of ARGs in AS was obtained. • Both abundance and composition of ARGs changed significantly every two-three years. • The core resistome were found disseminated broadly in other ecotypes. • Structural linkages of AS resistomes and the contributing factors were built. • The HGT potential between AS bacteria was higher than that in soil. The spread of antibiotic resistance genes (ARGs) is a growing global problem. Activated sludge (AS) in wastewater treatment plants (WWTPs) has been proposed as a hotspot for ARGs. However, few studies have been conducted to uncover the temporal dynamics of the resistome of AS in WWTPs by long-term longitudinal sampling. In this study, we quantified ARGs and identified their host microbiome in a Hong Kong WWTP in 97 monthly AS samples spanning 9 years. Throughout this analysis, we demonstrated that both the abundance and structures of the resistome changed significantly every two to three years, implying that there was a successive selection of resistomes in the AS system over the study period. The detection of genes of antibiotic-resistant pathogens that are emerging major threats to public health in the AS samples, including mcr , CRE (carbapenem-resistant Enterobacteriaceae) and MRSA (methicillin-resistant Staphylococcus aureus)-related genes, highlight the role of WWTPs as reservoirs of ARGs. In addition, the core resistome (abundant and persistent genes) in AS were found to overlap with those in other ecosystems such as urban sewage, livestock feces, and fishpond sediments, revealing the broad dissemination of ARGs in WWTPs and other environments. Annual variation of resistomes were explained via structural equation modeling (SEM), which deciphered the structural linkages of determining factors such as the operational parameters, microbial community composition and horizontal gene transfer (HGT). Specifically, potentially relevant antibiotic resistance bacteria (ARBs) were explored and discussed based on assembly-based analyses and network correlations. Moreover, consistent with the clear relationship between resistomes and mobile genetic elements (MGEs), it was found that there was a relatively high potential for gene exchange in AS in comparison with soil genomes, which could be explained by the engineering features of WWTPs. Based on these findings, longitudinal monitoring of WWTPs is warranted for risk assessment to reveal emerging ARGs, resistome evolution, correlations with ARBs, and the potential for spread in downstream environments and concomitant exposure risks for humans. [ABSTRACT FROM AUTHOR]