Characteristics of Antibiotic Resistance Genes and Antibiotic-Resistant Bacteria in Full-Scale Drinking Water Treatment System Using Metagenomics and Culturing

Abstract

The contamination of antibiotic resistance genes (ARGs) may directly threaten human health. This study used a metagenomic approach to investigate the ARG profile in a drinking water treatment system (DWTS) in south China. In total, 317 ARG subtypes were detected; specifically, genes encoding bacitracin, multidrug, and sulfonamide were widely detected in the DWTS. Putative ARG hosts included Acidovorax (6.0%), Polynucleobacter (4.3%), Pseudomonas (3.4%), Escherichia (1.7%), and Klebsiella (1.5%) as the enriched biomarkers in the DWTS, which mainly carried bacitracin, beta-lactam, and aminoglycoside ARGs. From a further analysis of ARG-carrying contigs (ACCs), Stenotrophomonas maltophilia and Pseudomonas aeruginosa were the most common pathogens among the 49 ACC pathogens in the DWTS. The metagenomic binning results demonstrated that 33 high-quality metagenome-assembled genomes (MAGs) were discovered in the DWTS; particularly, the MAG identified as S. maltophilia-like (bin.195) harbored the greatest number of ARG subtypes (n = 8), namely, multidrug (n = 6; smeD, semE, multidrug_transporter, mexE, semB, and smeC), beta-lactam (n = 1; metallo-beta-lactamase), and aminoglycoside [n = 1; aph(3’)-IIb]. The strong positive correlation between MGEs and ARG subtypes revealed a high ARG dissemination risk in the DWTS. Based on the pure-culture method, 93 isolates that belong to 30 genera were recovered from the DWTS. Specifically, multidrug-resistant pathogens and opportunistic pathogens such as P. aeruginosa, Bacillus cereus, and S. maltophilia were detected in the DWTS. These insights into the DWTS’s antibiotic resistome indicated the need for more comprehensive ARG monitoring and management in the DWTS. Furthermore, more effective disinfection methods need to be developed to remove ARGs in DWTSs, and these findings could assist governing bodies in the surveillance of antibiotic resistance in DWTSs.

Sensitivity and consistency of long- and short-read metagenomics and epicPCR for the detection of antibiotic resistance genes and their bacterial hosts in wastewater

“…Proteobacteria was the dominant host phylum for ARGs across the entire wastewater treatment process (Fig. 2d), which is consistent with previous studies [70][71][72] . Our results indicate that the shift in the microbial community, and specifically the growth and decay of certain phyla drove changes in the resistome across the WWTP (Fig.…”

New drinking water genome catalog identifies a globally distributed bacterial genus adapted to disinfected drinking water systems

“…This could suggest disinfection-mediated selection for UBA4765_DW1549 in disinfected DWDSs. Indeed, we observed significant increase in the relative abundance of UBA4765_DW1549 post-disinfection in multiple datasets [85][86][87][88][89][90][91] .…”

The occurrence of antimicrobial residues and antimicrobial resistance genes in urban drinking water and sewage in Southern Brazil

“…Moreover, the effect of wastewater treatment on the dispersion of AR and ARGs in the environment should be clarified. Metagenomic approach to investigating the ARG profile in water bodies and analysis of plasmid types present in this environment can contribute to a better understanding of the dispersion of resistance [40] .…”