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

Qihui Gu,Wei Chen,Youxiong Zhang,Rui Pang,Zhenjie Liu,Juan Wang,Tao Lin,Qingping Wu,Liang Xue,Xianhu Wei,Xiuhua Lin,Moutong Chen,Shi Wu,Ming Sun,Yu Ding,Shuhong Zhang,Ling Chen,Jumei Zhang

doi:10.3389/fmicb.2021.798442

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.

Highlights

Antibiotic resistance genes (ARGs) are emerging environmental pollutants (Pruden et al, 2006)
The results indicated that Proteobacteria, Acidobacteria, Bacteroidetes, and Firmicutes were the dominant phyla in the drinking water treatment system (DWTS) and shifted largely during the water treatment process
Gene-encoded bacitracin (0.3 × 10−2 to 0.40 copies/cell), multidrug (0.02– 0.23 copies/cell), and sulfonamide (0.2 × 10−3 to 0.7 × 10−1 copies/cell) were detected at the highest levels of abundance before chlorination, while the aminoglycoside, beta-lactam, and rifamycin antibiotic resistance genes (ARGs) were notably enriched after chlorination

Summary

Introduction

Antibiotic resistance genes (ARGs) are emerging environmental pollutants (Pruden et al, 2006). The excessive use and abuse of antibiotics in medicine and agriculture have promoted the emergence, spread, and accumulation of ARGs in various environmental matrices (Jia et al, 2019), including natural and man-impacted environments, such as soil (Fang et al, 2015), sediment (Jiang et al, 2018), surface water (Zhang et al, 2020b), wastewater (Wang et al, 2020), groundwater (Wu et al, 2020), drinking water (Wan et al, 2020), and tap water (Ma et al, 2019). Antibiotic-resistant bacteria (ARB) have become a serious threat to human health. There has been limited comprehensive research on the antibiotic resistance of different species of bacteria or multigroup-resistant bacteria in a drinking water treatment system (DWTS). A comprehensive risk identification of ARB in DWTSs has not been conducted

Methods

Results

Conclusion