Evaluation of Metagenomic-Enabled Antibiotic Resistance Surveillance at a Conventional Wastewater Treatment Plant

Abstract

Wastewater treatment plants (WWTPs) receive a confluence of sewage containing antimicrobials, antibiotic resistant bacteria, antibiotic resistance genes (ARGs), and pathogens and thus are a key point of interest for antibiotic resistance surveillance. WWTP monitoring has the potential to inform with respect to the antibiotic resistance status of the community served as well as the potential for ARGs to escape treatment. However, there is lack of agreement regarding suitable sampling frequencies and monitoring targets to facilitate comparison within and among individual WWTPs. The objective of this study was to comprehensively evaluate patterns in metagenomic-derived indicators of antibiotic resistance through various stages of treatment at a conventional WWTP for the purpose of informing local monitoring approaches that are also informative for global comparison. Relative abundance of total ARGs decreased by ∼50% from the influent to the effluent, with each sampling location defined by a unique resistome (i.e., total ARG) composition. However, 90% of the ARGs found in the effluent were also detected in the influent, while the effluent ARG-pathogen taxonomic linkage patterns identified in assembled metagenomes were more similar to patterns in regional clinical surveillance data than the patterns identified in the influent. Analysis of core and discriminatory resistomes and general ARG trends across the eight sampling events (i.e., tendency to be removed, increase, decrease, or be found in the effluent only), along with quantification of ARGs of clinical concern, aided in identifying candidate ARGs for surveillance. Relative resistome risk characterization further provided a comprehensive metric for predicting the relative mobility of ARGs and likelihood of being carried in pathogens and can help to prioritize where to focus future monitoring and mitigation. Most antibiotics that were subject to regional resistance testing were also found in the WWTP, with the total antibiotic load decreasing by ∼40–50%, but no strong correlations were found between antibiotics and corresponding ARGs. Overall, this study provides insight into how metagenomic data can be collected and analyzed for surveillance of antibiotic resistance at WWTPs, suggesting that effluent is a beneficial monitoring point with relevance both to the local clinical condition and for assessing efficacy of wastewater treatment in reducing risk of disseminating antibiotic resistance.

Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant

“…4 ). This suggests that UV disinfection was able to reduce bacterial abundance although not as effectively as other studies that demonstrate 16S rRNA log-fold reductions after secondary clarification and UV disinfection [ 75 ] as well as chlorine disinfection [ 20 ]. The cold temperatures during the sampling events (ranging from -18.6 °C to 2.8 °C) and grab temperatures around 13.6 °C (Table 1 ) may have reduced the efficacy of UV disinfection although also reducing potential reactivation of UV irradiated cells [ 76 , 77 ].…”

Metagenomic Analysis of Antibiotic Resistance Genes in Untreated Wastewater From Three Different Hospitals

“…Currently, most wastewaters are treated with sewage processing techniques before discharging into the urban sewage, which can remove some antibiotics resistance bacteria ( Huang et al, 2012 ; Majeed et al, 2021 ). Yet, it still contains higher ARGs than natural water, and one of the main sources of ARGs is hospital effluent ( Verlicchi et al, 2010 ).…”

“…As Firmicutes live in an anaerobic environment and also are associated with high antibiotic and pollutant levels (Li et al, 2011;Bäumlisberger et al, 2015), monitoring the condition of wastewater may control the abundance of bacteria of this phylum. Currently, most wastewaters are treated with sewage processing techniques before discharging into the urban sewage, which can remove some antibiotics resistance bacteria (Huang et al, 2012;Majeed et al, 2021). Yet, it still contains higher ARGs than natural water, and one of the main sources of ARGs is hospital effluent (Verlicchi et al, 2010).…”

Metagenomic Community Composition and Resistome Analysis in a Full-scale Cold Climate Wastewater Treatment Plant

“…4). This suggests that UV disinfection was able to reduce bacterial abundance although not as effectively as other studies that demonstrate 16S rRNA log-fold reductions after secondary clarification and UV disinfection [75] as well as chlorine disinfection [20]. The cold temperatures during the sampling events (ranging from -18.6 °C to 2.8 °C) and grab temperatures around 13.6 °C (Table 1) may have reduced the efficacy of UV disinfection although also reducing potential reactivation of UV irradiated cells [76,77].…”

“…These strategies include both clinical and environmental considerations to curtail ARG dissemination. Recent advancements along with the reduction in cost of high-throughput culture-independent methods such as next-generation sequencing have improved our ability to monitor ARG dissemination [19][20][21].…”