Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes

Abstract

Wastewater treatment plants (WWTPs) are implicated as hotspots for the dissemination of antibacterial resistance into the environment. However, the in situ processes governing removal, persistence, and evolution of resistance genes during wastewater treatment remain poorly understood. Here, we used quantitative metagenomic and metatranscriptomic approaches to achieve a broad-spectrum view of the flow and expression of genes related to antibacterial resistance to over 20 classes of antibiotics, 65 biocides, and 22 metals. All compartments of 12 WWTPs share persistent resistance genes with detectable transcriptional activities that were comparatively higher in the secondary effluent, where mobility genes also show higher relative abundance and expression ratios. The richness and abundance of resistance genes vary greatly across metagenomes from different treatment compartments, and their relative and absolute abundances correlate with bacterial community composition and biomass concentration. No strong drivers of resistome composition could be identified among the chemical stressors analyzed, although the sub-inhibitory concentration (hundreds of ng/L) of macrolide antibiotics in wastewater correlates with macrolide and vancomycin resistance genes. Contig-based analysis shows considerable colocalization between resistance and mobility genes and implies a history of substantial horizontal resistance transfer involving human bacterial pathogens. Based on these findings, we propose future inclusion of mobility incidence (M%) and host pathogenicity of antibiotic resistance genes in their quantitative health risk ranking models with an ultimate goal to assess the biological significance of wastewater resistomes with regard to disease control in humans or domestic livestock.

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome: bacteria, viruses and vesicles matter

“…The multidrug resistance category, as observed in prokaryotes, was the most abundant one. This category was also highly predominant in bacterial resistomes from different WWTPs (Ju et al ., ). In the 0.2 μm‐filtered fraction, the diaminopyrimidine category was also abundant, while it was undetectable in the bacterial resistomes (Fig.…”

“…In our experiments of polymyxin amendments at sub‐inhibitory concentrations, it was not observed a positive ARGs selection neither in prokaryotes nor viruses when employing two independent metagenomic ARGs search approaches based on machine learning and best hit score from unassembled and assembled resistomes (Forsberg et al ., ; Yang et al ., ; Zhu et al ., ; Li et al ., ; Pehrsson et al ., ; Ju et al ., ). Recently, a metagenomic study indicated that precisely polymyxin resistance, compared to other antibiotics, does not seem to be ‘highly mobilized’ among different WWTP compartments with low potential for horizontal dissemination (Ju et al ., ). Our study indicates that after spiking the microbiome with polymyxin sub‐inhibitory doses well above the natural concentration in effluent wastewater, ARGs and PRGs were not apparently selected in the microbiome, which indicates that the chance of dissemination from WWTPs to other ecosystems, in natural original conditions, is very low or insignificant.…”

“…Wastewater and wastewater treatment plants (WWTPs) are thus considered to be hotspots for dissemination of antibacterial resistance into the environment. In a recent prokaryotic metagenomic study of several WWTPs analysing 20 different antibiotics, authors found that the pool of antibiotic resistance genes (ARGs) in bacteria is persistent and shared among different WWTP compartments (Ju et al, 2018). Thus, these findings clearly underline the paramount role of WWTPs regarding disease control in humans and ARG spreading.…”

“…Globally, significant amounts of antibiotics used in domestic treatments, hospitals and cattle farming end up, directly or indirectly, in wastewater (Priyanka and Nandan, 2014). In municipal wastewater and even in natural streams and wells receiving water from agricultural areas dominated by animal-feeding operations, concentrations of different antibiotics remain very high (Loper et al, 2007;Hong et al, 2013;Ju et al, 2018). Wastewater and wastewater treatment plants (WWTPs) are thus considered to be hotspots for dissemination of antibacterial resistance into the environment.…”

On biological evolution and environmental solutions

“…For example, the emergence and amplification of antibiotic resistance genes is a global problem, caused by the widespread overuse of antibiotics (Palmer and Kishony, 2013). In wastewater treatment plants, the concentration of antibiotic resistance genes may be amplified by evolution prior to water discharge into natural aquatic environments (Ju et al, 2019) (Fig. 1).…”