Despite
the high removal efficiency for chemical pollutants by
tertiary wastewater treatment processes (TWTPs), there is no definite
conclusion in terms of microbial risk mitigation yet. This study utilized
metagenomic approaches to reveal the alterations of antibiotic resistance
genes (ARGs), virulence factor genes (VFGs), their co-occurrence,
and potential hosts during multiple TWTPs. Results showed that the
TWTPs reduced chemical pollutants in wastewater, but the denitrifying
biofilter (DB) significantly increased the absolute abundances of
selected antibiotic-resistant bacteria and ARGs, and simultaneously
elevated the relative abundances of ARGs and VFGs through the enrichment
of multidrug resistance and offensive genes, respectively. Moreover,
the co-occurrence of ARGs and VFGs (e.g., bacA–tapW, mexF–adeG)
was only identified after the DB treatment and all carried by Pseudomonas. Then, the ultraviolet and constructed wetland
treatment showed good complementarity for microbial risk reduction
through mitigating antibiotic resistance and pathogenicity. Network
and binning analyses showed that the shift of key operational taxonomic
units affiliating to Pseudomonas and Acinetobacter may contribute to the dynamic changes of ARGs and VFGs during the
TWTPs. Overall, this study sheds new light on how the TWTPs affect
the antibiotic resistome and VFG profiles and what TWTPs should be
selected for microbial risk mitigation.