1
|
Jiang C, Zhao Z, Grossart HP, Ju F, Zhao Y, Gadd GM, Korzeniewska E, Yang Y. Health risk ranking of antibiotic resistance genes in the Yangtze River. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 21:100388. [PMID: 38351955 PMCID: PMC10862502 DOI: 10.1016/j.ese.2024.100388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 02/16/2024]
Abstract
Antibiotic resistance is an escalating global health concern, exacerbated by the pervasive presence of antibiotic resistance genes (ARGs) in natural environments. The Yangtze River, the world's third-longest river, traversing areas with intense human activities, presents a unique ecosystem for studying the impact of these genes on human health. Here, we explored ARGs in the Yangtze River, examining 204 samples from six distinct habitats of approximately 6000 km of the river, including free-living and particle-associated settings, surface and bottom sediments, and surface and bottom bank soils. Employing shotgun sequencing, we generated an average of 13.69 Gb reads per sample. Our findings revealed a significantly higher abundance and diversity of ARGs in water-borne bacteria compared to other habitats. A notable pattern of resistome coalescence was observed within similar habitat types. In addition, we developed a framework for ranking the risk of ARG and a corresponding method for calculating the risk index. Applying them, we identified water-borne bacteria as the highest contributors to health risks, and noted an increase in ARG risks in particle-associated bacteria correlating with heightened anthropogenic activities. Further analysis using a weighted ARG risk index pinpointed the Chengdu-Chongqing and Yangtze River Delta urban agglomerations as regions of elevated health risk. These insights provide a critical new perspective on ARG health risk assessment, highlighting the urgent need for strategies to mitigate the impact of ARGs on human health and to preserve the ecological and economic sustainability of the Yangtze River for future human use.
Collapse
Affiliation(s)
- Chunxia Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China
| | - Zelong Zhao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, China
| | - Hans-Peter Grossart
- Leibniz-Institute for Freshwater Ecology and Inland Fisheries (IGB), Neuglobsow, 16775, Germany
- Institute for Biochemistry and Biology, Potsdam University, Potsdam, 14469, Germany
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310030, China
| | - Yi Zhao
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum, Beijing, 102249, China
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Olsztyn, 10-720, Poland
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China
| |
Collapse
|
2
|
Zhang Y, Wang M, Zhou X, Cheng W, Ren J, Wan T, Liu X. Transmission mechanism of antibiotic resistance genes and their differences between water and sediment in the Weihe River Basin. ENVIRONMENTAL RESEARCH 2024; 252:119057. [PMID: 38705450 DOI: 10.1016/j.envres.2024.119057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/12/2024] [Accepted: 04/30/2024] [Indexed: 05/07/2024]
Abstract
Antibiotic resistance genes (ARGs) are emerging microbial pollutants that are regulated by many factors and pose potential threats to aquatic environments. In this study, we used network analysis, correlation analysis, and constructed models based on metagenomic sequencing results to explore the spatial patterns, impact mechanisms, transmission risks and differences in ARGs in the water and sediment of the Weihe River Basin. The findings revealed notable disparities in ARGs, mobile genetic elements (MGEs), and bacterial communities. In the sediment, the abundance of ARGs was considerably greater than that in water. Moreover, the percentage of ARGs shared by the two components reached a value of 85.8%. Through network analysis, it was determined that the presence of 16 MGEs and 20 bacterial phyla was strongly associated with ARGs (R2 > 0.7, P < 0.05). The Mantel test showed that abiotic factors including DO, pH, nutrients, and heavy metals played important roles in the distribution of ARGs (P < 0.05). A structural equation model revealed that the key factors influencing the distribution of ARGs in water were bacterial diversity and environmental parameters (standardized effects of -0.730 and -0.667), and those in sediment were bacterial diversity and MGEs (standardized effects of -0.751 and 0.851). Neutral modeling indicated that deterministic processes played an important role in the assembly of ARGs in the water of the Weihe River Basin, and stochastic processes were dominant in the sediment. There was a highly significant positive linear correlation between ARGs and pathogens, and there was more complex co-occurrence in the water than in the sediment (R2 > 0.9, P < 0.05), with stronger migration and transmission occurring. Exploring ARGs in large-scale watersheds is immensely important for elucidating their traits and transmission mechanisms and consequently paving the way for the formulation of efficient strategies to mitigate resistance threats.
Collapse
Affiliation(s)
- Yutong Zhang
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China; Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
| | - Min Wang
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China; Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China.
| | - Xiaoping Zhou
- Power China Northwest Engineering Corporation Limited, Xi'an, Shaanxi, China
| | - Wen Cheng
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China; Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China.
| | - Jiehui Ren
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China; Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
| | - Tian Wan
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China; Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
| | - Xiaoyan Liu
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China; Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
| |
Collapse
|
3
|
Wang S, Fang L, Sun X, Lu W. Occurrence and distribution of antibiotic resistance genes in urban rivers with black-odor water of Harbin, China. ENVIRONMENTAL RESEARCH 2024; 259:119497. [PMID: 38944102 DOI: 10.1016/j.envres.2024.119497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/04/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
Antibiotic resistance gene contamination in polluted rivers remains a widely acknowledged environmental issue. This study focused on investigating the contamination conditions of antibiotic resistance genes (ARGs) in Harbin's urban black-odor rivers, specifically Dongfeng Ditch and Hejia Ditch. The research employed a SmartChip Real-Time PCR System to explore the types, abundance, and distribution of ARGs in diverse habitats, such as surface water and sediment. Additionally, the study examined the correlation of ARGs with mobile genetic elements (MGEs) and various environmental factors. It was found that antibiotic resistance genes were prevalent in both water and sediment within the black-odor ditches. The dominant types of ARGs identified included aminoglycoside, sulfonamide, multidrug-resistant, and β-lactam ARGs. Notably, the top four ARGs, in terms of relative abundance, were sul1, fox5, qacEdelta1-01 and aadA1. Most categories of ARGs have significant positive connections with MGEs, indicating that the enrichment and spreading of ARGs in rivers are closely related to MGEs. Based on the correlation analysis, it is found that environmental factors such as dissolved oxygen (DO), ammonia nitrogen (NH4-N), and phosphate (PO4-P) played a substantial role in influencing the variations observed in ARGs. By employing a risk assessment framework based on the human association, host pathogenicity, and mobility of ARGs, the identification of seven high-risk ARGs was achieved. In addition, it is important to assess the environmental risk of ARGs from multiple perspectives (abundance,detection rateand mobility). This study provides a significant reference regarding the presence of ARGs contamination in urban inland black-odor rivers, essential for assessing the health risks associated with ARGs and devising strategies to mitigate the threat of antibiotic resistance.
Collapse
Affiliation(s)
- Shuangshuang Wang
- School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Lanjin Fang
- School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Xingbin Sun
- School of Forestry, Northeast Forestry University, Harbin, 150040, China.
| | - Weimin Lu
- Heilongjiang Province Light Industrial Science Research Institute, Harbin, Heilongjiang, 150010, China
| |
Collapse
|
4
|
Masuda Y, Mise K, Xu Z, Zhang Z, Shiratori Y, Senoo K, Itoh H. Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome. MICROBIOME 2024; 12:95. [PMID: 38790049 PMCID: PMC11127431 DOI: 10.1186/s40168-024-01812-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 04/09/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome. RESULTS After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments). CONCLUSION Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.
Collapse
Affiliation(s)
- Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Kazumori Mise
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Zhengcheng Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, 857 Nagakura-machi, Nagaoka, Niigata, 940-0826, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hideomi Itoh
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
| |
Collapse
|
5
|
Li Z, Yuan D, Kou Y, Li X, Du C. Metagenome sequencing to unveil the occurrence and distribution of antibiotic resistome and in a wastewater treatment plant. ENVIRONMENTAL TECHNOLOGY 2024; 45:1933-1942. [PMID: 36812908 DOI: 10.1080/09593330.2022.2158758] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 12/03/2022] [Indexed: 06/18/2023]
Abstract
The emergence and persistence of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs) has aroused growing public concern for its risk to human health and ecological safety. Moreover, heavy metals concentrated in sewage and sludge could potentially favour co-selection of ARGs and heavy metal resistance genes (HMRGs). In this study, the profile and abundance of antibiotic and metal resistance genes in influent, sludge and effluent were characterized based on the Structured ARG Datebase (SARG) and Antibacterial Biocide and Metal Resistance Gene Datebase (BacMet) by metagenomic analysis. Sequences were aligning against the INTEGRALL, ISFinder, ICEberg and NCBI RefSeq databases to obtain the diversity and abundance of mobile genetic elements (MGEs, e.g.plasmid and transposon). Among them, 20 types of ARGs and 16 types of HMRG were detected in all samples, the influent metagenomes contained many more resistance genes (both ARGs and HMRGs) than the sludge and the influent sample, large reductions in the relatively abundance and diversity of ARG were achieved by biological treatment. ARGs and HMRGs cannot be completely eliminated during the oxidation ditch. A total of 32 species of the potential pathogens were detected, relative abundances of pathogens had no obvious changes. It is suggested that more specific treatments are required to limit their proliferation in the environment. This study can be helpful for further understanding the removal of antibiotic resistance genes in the sewage treatment process via metagenomic sequencing.
Collapse
Affiliation(s)
- Zhonghong Li
- Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Donghai Yuan
- Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Yingying Kou
- Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Xiaoguang Li
- State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, People's Republic of China
| | - Caili Du
- State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, People's Republic of China
| |
Collapse
|
6
|
Gao FZ, He LY, Liu YS, Zhao JL, Zhang T, Ying GG. Integrating global microbiome data into antibiotic resistance assessment in large rivers. WATER RESEARCH 2024; 250:121030. [PMID: 38113599 DOI: 10.1016/j.watres.2023.121030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/13/2023] [Accepted: 12/16/2023] [Indexed: 12/21/2023]
Abstract
Rivers are important in spreading antimicrobial resistance (AMR). Assessing AMR risk in large rivers is challenged by large spatial scale and numerous contamination sources. Integrating river resistome data into a global framework may help addressing this difficulty. Here, we conducted an omics-based assessment of AMR in a large river (i.e. the Pearl River in China) with global microbiome data. Results showed that antibiotic resistome in river water and sediment was more diversified than that in other rivers, with contamination levels in some river reaches higher than global baselines. Discharge of WWTP effluent and landfill waste drove AMR prevalence in the river, and the resistome level was highly associated with human and animal sources. Detection of 54 risk rank I ARGs and emerging mobilizable mcr and tet(X) highlighted AMR risk in the river reaches with high human population density and livestock pollution. Florfenicol-resistant floR therein deserved priority concerns due to its high detection frequency, dissimilar phylogenetic distance, mobilizable potential, and presence in multiple pathogens. Co-sharing of ARGs across taxonomic ranks implied their transfer potentials in the community. By comparing with global genomic data, we found that Burkholderiaceae, Enterobacteriaceae, Moraxellaceae and Pseudomonadaceae were important potential ARG-carrying bacteria in the river, and WHO priority carbapenem-resistant Enterobacteriaceae, A. baumannii and P. aeruginosa should be included in future surveillance. Collectively, the findings from this study provide an omics-benchmarked assessment strategy for public risk associated with AMR in large rivers.
Collapse
Affiliation(s)
- Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Jian-Liang Zhao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China.
| |
Collapse
|
7
|
Patel V, Patil K, Patel D, Kikani B, Madamwar D, Desai C. Distribution of bacterial community structures and spread of antibiotic resistome at industrially polluted sites of Mini River, Vadodara, Gujarat, India. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:208. [PMID: 38279971 DOI: 10.1007/s10661-024-12380-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/17/2024] [Indexed: 01/29/2024]
Abstract
The influence of anthropogenic pollution on the distribution of bacterial diversity, antibiotic-resistant bacteria (ARBs), and antibiotic resistance genes (ARGs) was mapped at various geo-tagged sites of Mini River, Vadodara, Gujarat, India. The high-throughput 16S rRNA gene amplicon sequencing analysis revealed a higher relative abundance of Planctomycetota at the polluted sites, compared to the pristine site. Moreover, the relative abundance of Actinobacteriota increased, whereas Chloroflexi decreased in the water samples of polluted sites than the pristine site. The annotation of functional genes in the metagenome samples of Mini River sites indicated the presence of genes involved in the defence mechanisms against bacitracin, aminoglycosides, cephalosporins, chloramphenicol, streptogramin, streptomycin, methicillin, and colicin. The analysis of antibiotic resistome at the polluted sites of Mini River revealed the abundance of sulfonamide, beta-lactam, and aminoglycoside resistance. The presence of pathogens and ARB was significantly higher in water and sediment samples of polluted sites compared to the pristine site. The highest resistance of bacterial populations in the Mini River was recorded against sulfonamide (≥ 7.943 × 103 CFU/mL) and ampicillin (≥ 8.128 × 103 CFU/mL). The real-time PCR-based quantification of ARGs revealed the highest abundance of sulfonamide resistance genes sul1 and sul2 at the polluted sites of the Mini River. Additionally, the antimicrobial resistance genes aac(6')-Ib-Cr and blaTEM were also found abundantly at polluted sites of the Mini River. The findings provide insights into how anthropogenic pollution drives the ARG and ARB distribution in the riverine ecosystem, which may help with the development of antimicrobial resistance mitigation strategies.
Collapse
Affiliation(s)
- Vandan Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India
| | - Kishor Patil
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India
| | - Dishant Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India
| | - Bhavtosh Kikani
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India
| | - Datta Madamwar
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, 388 421, Anand, Gujarat, India.
| | - Chirayu Desai
- Department of Environmental Biotechnology, Gujarat Biotechnology University (GBU), Near Gujarat International Finance Tec (GIFT)-City, Gandhinagar, 382355, Gujarat, India.
| |
Collapse
|
8
|
Rao C, Liu X, Xue L, Xiang D, Xian B, Chu F, Fang F, Tang W, Bao S, Fang T. Determining the spatiotemporal variation, sources, and ecological processes of antibiotic resistance genes in a typical lake of the middle reaches of the Yangtze River. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167779. [PMID: 37844640 DOI: 10.1016/j.scitotenv.2023.167779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
Antibiotic resistance genes (ARGs) are emerging environmental pollutants, influenced by complex regulatory factors. River-lake systems act as natural reservoirs for ARGs and provide an ideal model for studying their regulatory mechanisms. This study employed high-throughput quantitative PCR, high-throughput sequencing, correlation analyses, and model predictions to investigate the dynamics of ARGs and their influencing factors in Liangzi Lake, located in the mid-reaches of the Yangtze River. The research specifically centered on three environmental components: lake water, sediment, and river water. Results indicated that the ARGs from eight major antibiotic classes, displaying distinct seasonal distribution patterns. In comparison to the sediment, the water phase demonstrated a higher diversity of ARGs, with the highest level of ARGs sharing observed between lake and river waters (approximately 83.7 %). Furthermore, seasonal variations significantly influenced the distributions of both ARGs and bacterial communities. The diversity of ARGs was highest during the summer and autumn, and specific bacterial species exhibited robust correlations with ARGs (including matA/mel, aac (6')-Ib-03, and blaROB). It is worth noting that environmental attributes and bacterial diversity had the most substantial impact on the dynamic changes in ARGs. Lastly, source tracking analysis pinpointed that sediment as the primary source of ARGs in lake water, constituting 45 % to 48 % of the total ARGs. Our study provides a comprehensive analysis of ARGs and their influencing factors in the river-lake system of the middle reaches of the Yangtze River, with Liangzi Lake as a representative case.
Collapse
Affiliation(s)
- Chenyang Rao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiaying Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Lu Xue
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Dongfang Xiang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Bo Xian
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fuhao Chu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fang Fang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Wei Tang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Shaopan Bao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Tao Fang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| |
Collapse
|
9
|
Liu C, Shan X, Chen J, Zhang Y, Wang J, Chen H. Fate, risk and sources of antibiotic resistome and its attenuation dynamics in the river water-sediment system: Field and microcosm study. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122853. [PMID: 37925010 DOI: 10.1016/j.envpol.2023.122853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023]
Abstract
Antibiotic resistance genes (ARGs) in rivers have received widespread attentions. Deciphering the fate and spread mechanisms of ARGs in river system can contribute to the design of effective strategies for reducing resistome risk in the environment. Although some studies have reported the prevalence and distribution of ARGs in rivers worldwide, few have systematically explored their fates, sources and risks in river water-sediment system. Also, the role of natural sunlight on the attenuation and fate of ARGs in river remains to be demonstrated. To fill the gaps, field investigation and microcosm experiment have been conducted in this study to reveal the fate, risk, source-sink relationship and attenuation dynamics of ARGs in an urban river water-sediment system, by utilizing high-throughput sequencing-based metagenomic assembly analysis and machine-learning-based source tracking tool. In all, 527 unique ARGs belonging to 29 antimicrobial classes were identified in the river. Relatively, the level of ARGs in the sediments were significantly higher (p < 0.05) than that in the waters. Variance partitioning analysis indicated the biotic and abiotic factors co-governed the riverine resistome, totally explaining 76% and 83% variations of ARGs in the waters and sediments, respectively. Microcosm experiment under natural light and dark condition showed that light induced the decay of ARGs in the waters and might promote their transfers from waters to sediments, which were also confirmed by the attenuation dynamics of bacteria in the experimental water-sediment system. Notably, the co-occurrences of ARGs with MGEs and VFs on the same contigs suggested resistome risk in the river, and relatively, the risk scores in the sediments were significantly higher (p < 0.05) than those in the waters. Source apportionment with metagenomic resistome signatures showed the Wenyu River was the most dominant contributor of ARGs in the downstream, with average contributions of 44.5% and 40.8% in the waters and sediments, respectively.
Collapse
Affiliation(s)
- Chang Liu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Xin Shan
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Jinping Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Yuxin Zhang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Jinsheng Wang
- Advanced Institute of Natural Science, Beijing Normal University at Zhuhai, 519087, China
| | - Haiyang Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China.
| |
Collapse
|
10
|
Liu C, Shan X, Zhang Y, Song L, Chen H. Microcosm experiments revealed resistome coalescence of sewage treatment plant effluents in river environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122661. [PMID: 37778491 DOI: 10.1016/j.envpol.2023.122661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/01/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Sewage treatment plant (STP) effluents are important contributors of antibiotic resistance (AR) pollution in rivers. Effluent discharging into rivers causes resistome coalescence. However, their mechanisms and dynamic processes are poorly understood, especially for the effects of dilution, diffusion, and sunlight-induced attenuation on coalescence. In this study, we have constructed microcosmic experiments based on in-situ investigation to explore these issues. The first batch experiment revealed the effects of dilution and diffusion. The coverage of water coalesced resistomes ranged 66.26∼152.18 × /Gb and was positively correlated with effluent volume (Mann-Kendall test, p < 0.01). Principal coordinate analysis (PCoA) and source tracking analysis demonstrated that dilution and diffusion stepwise reduced AR pollution. The second batch experiment explored the temporal dynamics and sunlight attenuation on coalesced resistomes. Under natural light, the coverage and diversity of water resistomes posed decreasing trends, primarily attributed to drastic erasure of effluent traces. The proportion of effluent-specific ARGs in coalesced resistomes significantly declined over time (Spearman's r = -0.83 and -0.94 in coverage and richness). While under dark condition, the coverage and diversity increased. Sunlight radiation intensified the interactions between water and sediment resistomes, as evidenced by more shared ARGs and less dissimilarities across niches. Network analysis, metagenome-assembled genome (MAG) analysis and variation partitioning analysis (VPA) showed that microbiome controlled resistome coalescence, explaining 56.5% and 58.4% of resistomes in water and sediment, respectively. Biotic and abiotic factors synergistically explained 40% of water resistomes. This study offers a comprehensive understanding of AR transmission and provides theoretical bases for grasping AR pollution and developing effective suppression strategies.
Collapse
Affiliation(s)
- Chang Liu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Xin Shan
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Yuxin Zhang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Liuting Song
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Haiyang Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China.
| |
Collapse
|
11
|
Wan R, Ge L, Chen B, Tang JM, Tan E, Zou W, Tian L, Li M, Liu Z, Hou L, Yin G, Kao SJ. Permeability decides the effect of antibiotics on sedimentary nitrogen removal in Jiulong River Estuary. WATER RESEARCH 2023; 243:120400. [PMID: 37523923 DOI: 10.1016/j.watres.2023.120400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023]
Abstract
Sedimentary denitrification takes place beneath the oxic layer at the sediment-water interface, where nitrate and antibiotics need to diffuse through the overlying water. However, the antibiotics' effect on sedimentary N removal and associated N2O production has not been adequately investigated under in situ conditions. Here, isotope pairing techniques, including slurry incubations (potential) and intact core incubations (in situ), combined with metagenomic analysis were applied to investigate the impacts of two protein-inhibiting antibiotics (oxytetracycline and thiamphenicol) on sediment nitrogen removal in a subtropical estuary. Slurry incubations showed that the two antibiotics significantly inhibited denitrification (67-98%) and anammox (49-99%), while intact core incubations presented no antibiotic effect at upstream but significant inhibition (23%-52%) at downstream. Meanwhile, N2O yields were stimulated up to 20 folds in slurry incubations yet showing insignificant response in intact cores. Such contrasting results between up- and down-stream and between slurry and intact core incubations strongly indicated that permeability, which determines diffusion of antibiotics to microbes, is the key to exert the effect of antibiotics on in situ sedimentary nitrogen removal processes regardless the existence of antibiotics resistance genes. This diffusive obstruction may mitigate the toxic effect of antibiotics on nitrogen removal related microbes in natural environments.
Collapse
Affiliation(s)
- Ru Wan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lianghao Ge
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Bin Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jin-Ming Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ehui Tan
- State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Science and Engineering, Hainan University, Haikou, Hainan, China.
| | - Wenbin Zou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Li Tian
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Zongbao Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Guoyu Yin
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Science and Engineering, Hainan University, Haikou, Hainan, China.
| |
Collapse
|
12
|
Khatiebi S, Kiprotich K, Onyando Z, Wekesa C, Chi CN, Mulambalah C, Okoth P. Shotgun Metagenomic Analyses of Microbial Assemblages in the Aquatic Ecosystem of Winam Gulf of Lake Victoria, Kenya Reveals Multiclass Pollution. BIOMED RESEARCH INTERNATIONAL 2023; 2023:3724531. [PMID: 37521121 PMCID: PMC10382247 DOI: 10.1155/2023/3724531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023]
Abstract
Lake Victoria, the second-largest freshwater lake in the world, provides an important source of food and income, particularly fish for both domestic consumption and for export market. In recent years, Lake Victoria has suffered massive pollution from both industrial and wastewater discharge. Microplastic biomes, pharmaceutical residues, drugs of abuse, heavy metals, agrochemicals, and personal care products are ubiquitous in the aquatic ecosystem of Winam Gulf. These pollutants are known to alter microbial assemblages in aquatic ecosystems with far-reaching ramification including a calamitous consequence to human health. Indeed, some of these pollutants have been associated with human cancers and antimicrobial resistance. There is a paucity of data on the microbial profiles of this important but heavily polluted aquatic ecosystem. The current study sought to investigate the metagenomic profiles of microbial assemblages in the Winam Gulf ecosystem. Water and sediment samples were collected from several locations within the study sites. Total genomic DNA pooled from all sampling sites was extracted and analyzed by whole-genome shotgun sequencing. Analyses revealed three major kingdoms: bacteria, archaea and eukaryotes belonging to 3 phyla, 13 classes, 14 families, 9 orders, 14 genera, and 10 species. Proteobacteria, Betaproteobacteria, Comamonadaceae, Burkholdariales, and Arcobacter were the dominated phyla, class, family, order, genera, and species, respectively. The Kyoto Encyclopedia of Genes and Genomes indicated the highest number of genes involved in metabolism. The presence of carbohydrate metabolism genes and enzymes was used to infer organic pollutions from sewage and agricultural runoffs. Similarly, the presence of xylene and nutrotoluene degradation genes and enzyme was used to infer industrial pollution into the lake. Drug metabolism genes lend credence to the possibility of pharmaceutical pollutants in water. Taken together, there is a clear indication of massive pollution. In addition, carbohydrate-active enzymes were the most abundant and included genes in glycoside hydrolases. Shotgun metagenomic analyses conveyed an understanding of the microbial communities of the massively polluted aquatic ecosystem of Winam Gulf, Lake Vicoria, Kenya. The current study documents the presence of multiclass pollutants in Lake Victoria and reveals information that might be useful for a potential bioremediation strategy using the native microbial communities.
Collapse
Affiliation(s)
- Sandra Khatiebi
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
| | - Kelvin Kiprotich
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
| | - Zedekiah Onyando
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
| | - Clabe Wekesa
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
| | - Celestine N. Chi
- Department of Medical Biochemistry and Microbiology, University of Uppsala, P.O. Box 582, 75123 Uppsala, Sweden
| | - Chrispinus Mulambalah
- Department of Medical Microbiology & Parasitology, School of Medicine, Moi University, P.O. Box 4606, 30100 Eldoret, Kenya
| | - Patrick Okoth
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
| |
Collapse
|
13
|
Yang H, Xu M, Wang L, Wang X, Jeppesen E, Zhang W. Metagenomic analysis to determine the characteristics of antibiotic resistance genes in typical antibiotic-contaminated sediments. J Environ Sci (China) 2023; 128:12-25. [PMID: 36801028 DOI: 10.1016/j.jes.2022.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/09/2022] [Accepted: 08/09/2022] [Indexed: 06/18/2023]
Abstract
Comprehensive studies of the effects of various physical and chemical variables (including heavy metals), antibiotics, and microorganisms in the environment on antibiotic resistance genes are rare. We collected sediment samples from the Shatian Lake aquaculture area and surrounding lakes and rivers located in Shanghai, China. The spatial distribution of sediment ARGs was assessed by metagenomic analysis that revealed 26 ARG types (510 subtypes), dominated by Multidrug, β-lactam, Aminoglycoside, Glycopeptides, Fluoroquinolone, and Tetracyline. Redundancy discriminant analysis indicated that antibiotics (SAs and MLs) in the aqueous environment and sediment along with water TN and TP were the key variables affecting the abundance distribution of total ARGs. However, the main environmental drivers and key influences differed among the different ARGs. For total ARGs, the environmental subtypes affecting their structural composition and distribution characteristics were mainly antibiotic residues. Procrustes analysis showed a significant correlation between ARGs and microbial communities in the sediment in the survey area. Network analysis revealed that most of the target ARGs were significantly and positively correlated with microorganisms, and a small number of ARGs (e.g., rpoB, mdtC, and efpA) were highly significantly and positively correlated with microorganisms (e.g., Knoellia, Tetrasphaera, and Gemmatirosa). Potential hosts for the major ARGs included Actinobacteria, Proteobacteria, and Gemmatimonadetes. Our study provides new insight and a comprehensive assessment of the distribution and abundance of ARGs and the drivers of ARG occurrence and transmission.
Collapse
Affiliation(s)
- Han Yang
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Centre for Research on Environmental Ecology and Fish Nutrient of the Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Mu Xu
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Centre for Research on Environmental Ecology and Fish Nutrient of the Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Liqing Wang
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Centre for Research on Environmental Ecology and Fish Nutrient of the Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China
| | - Xianyun Wang
- Shanghai National Engineering Research Center for Urban Water Resources Co., Ltd., Shanghai 200082, China
| | - Erik Jeppesen
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé 3, 8000 Aarhus C, Denmark; Sino-Danish Centre for Education and Research (SDC), University of Chinese Academy of Sciences, Beijing 100190, China; Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara 06800, Turkey; Institute of Marine Sciences, Middle East Technical University, 33731 Mersin, Turkey
| | - Wei Zhang
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Centre for Research on Environmental Ecology and Fish Nutrient of the Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China.
| |
Collapse
|
14
|
Ji B, Qin J, Ma Y, Liu X, Wang T, Liu G, Li B, Wang G, Gao P. Metagenomic analysis reveals patterns and hosts of antibiotic resistance in different pig farms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:52087-52106. [PMID: 36826766 DOI: 10.1007/s11356-023-25962-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
In actual production environments, antibiotic-resistant genes (ARGs) are abundant in pig manure, which can form transmission chains through animals, the environment, and humans, thereby threatening human health. Therefore, based on metagenomic analysis methods, ARGs and mobile genetic elements (MGEs) were annotated in pig manure samples from 6 pig farms in 3 regions of Shanxi Province, and the potential hosts of ARGs were analyzed. The results showed that a total of 14 ARG types were detected, including 182 ARG subtypes, among which tetracycline, phenol, aminoglycoside, and macrolide resistance genes were the main ones. ARG profiles, MGE composition, and microbial communities were significantly different in different regions as well as between different pig farms. In addition, Anaerobutyricum, Butyrivibrio, and Turicibacter were significantly associated with multiple ARGs, and bacteria such as Prevotella, Bacteroides, and the family Oscillospiraceae carried multiple ARGs, suggesting that these bacteria are potential ARG hosts in pig manure. Procrustes analysis showed that bacterial communities and MGEs were significantly correlated with ARG profiles. Variation partitioning analysis results indicated that the combined effect of MGEs and bacterial communities accounted for 64.08% of resistance variation and played an important role in ARG profiles. These findings contribute to our understanding of the dissemination and persistence of ARGs in actual production settings, and offer some guidance for the prevention and control of ARGs contamination.
Collapse
Affiliation(s)
- Bingzhen Ji
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Junjun Qin
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yijia Ma
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Xin Liu
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, 100097, China
| | - Tian Wang
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, 100097, China
| | - Guiming Liu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Guoliang Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Pengfei Gao
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
| |
Collapse
|
15
|
Wang Y, Li H, Li Y, Guo H, Zhou J, Wang T. Metagenomic analysis revealed sources, transmission, and health risk of antibiotic resistance genes in confluence of Fenhe, Weihe, and Yellow Rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159913. [PMID: 36343807 DOI: 10.1016/j.scitotenv.2022.159913] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/18/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Rivers are important vectors and reservoirs of antibiotics resistance genes (ARGs). Information regarding transmission and health risk of ARGs in river confluence is still lacking. In this study, metagenomics was used to distinguish contributions of human activities on ARGs and human pathogenic bacteria (HPB) in confluence of Fenhe, Weihe, and Yellow Rivers. Bacitracin resistance gene and bacA were the highest in all rivers, with 1.86 × 10-2-7.26 × 10-2 and 1.79 × 10-2-9.12 × 10-2 copies/16S rRNA copies, respectively. River confluence significantly increased the abundance of ARGs, especially at the confluence of three rivers with the highest 1.53 × 10-1 copies/16S rRNA copies. Antibiotic efflux and antibiotic target alteration were the dominant resistant mechanisms in three rivers. ARGs profiles were influenced by multiple factors, with the contributions of various factors ranked as microbial communities > physicochemical factors > human activities > mobile genetic elements (MGEs). Notably, human activities and animal feces were important potential contributors of ARGs in the Weihe River and Yellow River. Transposons, as the main MGEs in three rivers, played important roles in ARGs transfer. The confluence of three rivers had the highest abundance of MGEs with the greatest transfer potentials, and therefore exhibiting the largest exposure risk of ARGs with 232.4 copies/cap·d. Furthermore, correlations of ARGs, MGEs, and HPB in different rivers were constructed via co-occurrence modes to systematically illustrate the health risks of ARGs. This study firstly unveiled the transmission and health risk of ARGs in river confluence, providing supports for ARGs control in watershed.
Collapse
Affiliation(s)
- Yangyang Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Hu Li
- Breeding Base for State Key Lab. of Land Degradation and Ecological Restoration in northwestern, China; Key Lab. of Restoration and Reconstruction of Degraded Ecosystems in northwestern China of Ministry of Education, China; School of Ecology and Environment, Ningxia University, Yinchuan 750021, China
| | - Yingwei Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - He Guo
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Jian Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Tiecheng Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China.
| |
Collapse
|
16
|
Liu B, Zhang D, Pan X. Nodules of wild legumes as unique natural hotspots of antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156036. [PMID: 35597353 DOI: 10.1016/j.scitotenv.2022.156036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 06/15/2023]
Abstract
Root nodules (RN) of legumes have distinct microenvironment from their symbiotic roots and surrounding soils. The rhizobia can withstand the host-produced phytoalexins and antimicrobial compounds. We thus hypothesize that the wild legume RN may develop unique natural resistome and be antibiotic resistance gene (ARG) hotspots. In this study, in comparison with rhizosphere soil (RS) and bulk soil (BS), we characterized the feature of antibiotic resistance in the RN of two wild legumes, Medicago polymorpha and Astragalus sinicus, by metagenomics. It was shown that the total relative abundance of ARGs followed the order of RN > RS > BS for both legumes. ARGs encoding antibiotic efflux pump predominated in all samples with increased proportion from BS to RN samples for both legumes. Totally 275 ARG subtypes were detected, and diversity of ARGs in RN was significantly lower than in BS samples for both legumes. 32 and 25 unique ARGs subtypes were detected in RN of both legumes. Bacterial community played a key role in shaping nodule-associated resistome because both ARG profiles and bacterial community differed greatly among BS, RS and RN. Rhizobia potentially hosted 10 and 15 ARGs subtypes for both legumes. The number and proportion of plasmid- and ARG-carrying contigs (ACCs) were higher in RN than in BS. Host tracking analysis of plasmid-ACCs suggests that proportion of rhizobial bacteria identified as their hosts decreased from BS to RN samples. No plasmid-ACCs with multiple ARGs were observed in BS samples, whereas they were detected in RN samples of both legumes. Our study showed that even wild legume nodules are unique natural ARG hotspots and enough attention should be paid to the dissemination risk of ARGs posed by globally produced legume crops.
Collapse
Affiliation(s)
- Bingshen Liu
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiangliang Pan
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| |
Collapse
|
17
|
Song W, Chen H, Xue N, Wang S, Yang Y. Metagenomic binning and assembled genome analysis revealed the distinct composition of resistome and mobilome in the Ili River. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113886. [PMID: 35868179 DOI: 10.1016/j.ecoenv.2022.113886] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/08/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Rivers play an important role in receiving and transporting the resistome among different environmental compartments. However, the difference in resistome and mobilome between the water and sediment and their underlying mechanisms were still poorly understood. In this study, the Ili River, an important water source in the arid area of Central Asia, was selected as the studied target. The comprehensive profile of resistome and mobilome and their host in water and sediment were studied based on metagenomic binning and assembled genome (MAG) analysis. The relative abundance of resistome and mobilome in sediment were 28.0 - 67.8 × /Gb and 46.5 - 121.1 × /Gb, respectively, which were significantly higher than those in water (23.1 - 52.8 ×/Gb and 25.3 - 67.7 ×/Gb). Multidrug and macrolides-lincosamides-streptogramin (MLS) resistance genes were the main ARG types in both water and sediment from relative abundance. Transposases dominated the relative abundance of mobilome, followed by insert elements and integrases. Strong correlations were found between the relative abundance of resistome and mobilome (r > 0.6 and p < 0.01) in both water and sediment, indicating the mobilome played an important role in the propagation of resistome in the Ili River. The main hosts for multidrug resistance genes via MAG analysis differed in water (Alphaproteobacteria and Gammaproteobacteria) and sediment (Gammaproteobacteria). Distinct compositions of resistome and mobilome existed between water and sediment in the Ili River. Specificity-occupancy analysis of the differential resistome and mobilome showed that occurrence frequencies and habitat selections of the differential ARGs shaped the resistome of water and sediment. In contrast, habitat was the main driver that shaped the mobilome in the Ili River.
Collapse
Affiliation(s)
- Wenjuan Song
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Haiyang Chen
- College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China; Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, Beijing 100875, China
| | - Nana Xue
- College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi 830052, China
| | - Shuzhi Wang
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China.
| |
Collapse
|
18
|
Lu L, He Y, Peng C, Wen X, Ye Y, Ren D, Tang Y, Zhu D. Dispersal of antibiotic resistance genes in an agricultural influenced multi-branch river network. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154739. [PMID: 35331763 DOI: 10.1016/j.scitotenv.2022.154739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Rivers in agricultural regions serve as an important sink for livestock and poultry farm runoff, fertilizer runoff, and country living sewage, which could bring antibiotic resistance genes (ARGs) contaminations. However, the diversity and distribution of ARGs has not been well documented in the agricultural influenced river. Here, the diversity of ARGs, and their relationship with biochemical factors were determined in the surface water in an agricultural region of the Jialing River and its five rural branches. The 218 unique ARGs encoding resistance to eight major antibiotic classes have been detected using high-throughput quantitative PCR. The branches of the river had a remarkably higher abundance of ARGs than the mainstream. The aminoglycoside, beta_Lactamase, MLSB, and Multidrug resistance genes were significantly enriched in the branches compared to the mainstream. Compared with the mainstream, the ARGs profiles in the branches showed obvious higher spatial variability. Significant correlation between ARGs profiles and bacterial community structures were observed, and network analysis further showed that the ARGs were associated with their potential hosts, such as Ottowia and Novosphingobium. Redundancy discrimination analysis revealed that Cu content has a significant contribution to the increase of ARGs in the river. The microbial diversity index was negatively correlated with the abundance of the ARGs. These results provide evidence for the enrichment of ARGs in the agricultural influenced river and branches due to the joint influence of chemical and microbial variables.
Collapse
Affiliation(s)
- Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yan He
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Chao Peng
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Xingyue Wen
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yuqiu Ye
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Dong Ren
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Yun Tang
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Dong Zhu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China; Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| |
Collapse
|
19
|
Deshpande AS, Fahrenfeld NL. Abundance, diversity, and host assignment of total, intracellular, and extracellular antibiotic resistance genes in riverbed sediments. WATER RESEARCH 2022; 217:118363. [PMID: 35390554 DOI: 10.1016/j.watres.2022.118363] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Human health risk assessment for environmental antibiotic resistant microbes requires not only quantifying the abundance of antibiotic resistance genes (ARGs) in environmental matrices, but also understanding their hosts and genetic context. Further, differentiating ARGs in intracellular and extracellular DNA (iDNA and eDNA) fractions may help refine our understanding of ARG transferability. The objectives of this study were to understand the (O1) abundance and diversity of extracellular, intracellular, and total ARGs along a land use gradient and (O2) impact of bioinformatics pipeline on the assignment of putative hosts for the ARGs observed in the different DNA fractions. Sediment samples were collected along a land use gradient in the Raritan River, New Jersey, USA. DNA was extracted to separate eDNA and iDNA and qPCR was performed for select ARGs and the 16S rRNA gene. Shotgun metagenomic sequencing was performed on DNA extracts for the different DNA fractions. ARG hosts were assigned via two different bioinformatic pipelines: network analysis of raw reads versus assembly. Results of the two pipelines were compared to evaluate their performance in terms of number and diversity of linkages and accuracy of in silico matrix spike host assignments. No differences were observed in the 16S rRNA gene normalized sul1 concentrations between the DNA fractions. The overall microbial community structure was more similar for iDNA and total DNA compared to eDNA and generally clustered by sampling site. ARGs associated with mobile genetic elements increased in iDNA for the downstream sites. Regarding host assignment, the raw reads pipeline via network analysis identified 247 ARG hosts as compared to 53 hosts identified by assembly pipeline. Other comparisons between the pipelines were made including ARG assignment to taxa containing waterborne pathogens and practical considerations regarding processing time.
Collapse
Affiliation(s)
- A S Deshpande
- Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - N L Fahrenfeld
- Civil and Environmental Engineering, Rutgers University, 500 Bartholomew Rd., Piscataway, NJ 08854, USA.
| |
Collapse
|
20
|
Du C, Yang F, Li X, Liao H, Li Z, Gao J, Zhang L. Metagenomic analysis of microbial community structure and distribution of resistance genes in Daihai Lake, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 302:119065. [PMID: 35227842 DOI: 10.1016/j.envpol.2022.119065] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
Abstract
The emergence of resistance genes is a global phenomenon that poses a significant threat to both animals and humans. Lakes are important reservoirs of genes that confer resistant to antibiotics and metals. In this study, we investigated the distribution and diversity of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in the sediment of Daihai Lake using high-throughput sequencing and metagenomic analysis. The results indicated that all sampling sites had similar bacterial community structures, with Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes being the most abundant. A total of 16 ARG types containing 111 ARG subtypes were deposited in the sediment. Among the resistance genes to bacitracin, multidrug, macrolide-lincosamide-streptogramin (MLS), tetracycline, beta-lactam, and sulfonamide were the dominant ARG types, accounting for 89.9-94.3% of the total ARGs. Additionally, 15 MRG types consisting of 146 MRG subtypes were identified. In all samples, MRGs of the same type presented resistance to Pb, Ni, Hg, W, Zn, Ag, Cr, Fe, As, Cu, and multimetals. Overall, the distribution and diversity of antibiotic and metal resistance genes showed no significant differences in the samples. Plasmids (91.03-91.82%) were the most dominant mobile genetic elements in the sediments of Daihai Lake. Network analysis indicated that the target ARGs and MRGs were significantly positively correlated with the microorganisms. Potential hosts for various ARGs and MRGs include Proteobacteria, Euryarchaeota, Actinobacteria, Chloroflexi, and Bacteroidetes.
Collapse
Affiliation(s)
- Caili Du
- Chinese Research Academy of Environmental Science, Beijing 100012, China; College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Fang Yang
- Chinese Research Academy of Environmental Science, Beijing 100012, China.
| | - Xiaoguang Li
- Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Haiqing Liao
- Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Zhonghong Li
- Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Jiayue Gao
- School of Space and Environment, Beihang University, Beijing 100191 China
| | - Lieyu Zhang
- Chinese Research Academy of Environmental Science, Beijing 100012, China
| |
Collapse
|
21
|
Zou Y, Wu M, Liu J, Tu W, Xie F, Wang H. Deciphering the extracellular and intracellular antibiotic resistance genes in multiple environments reveals the persistence of extracellular ones. JOURNAL OF HAZARDOUS MATERIALS 2022; 429:128275. [PMID: 35093750 DOI: 10.1016/j.jhazmat.2022.128275] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/18/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
The extracellular and intracellular antibiotic resistance genes (eARGs and iARGs) together constitute the entire resistome in environments. However, the systematic analysis of eARGs and iARGs was still inadequate. Three kinds of environments, i.e., livestock manure, sewage sludge, and lake sediment, were analyzed to reveal the comprehensive characteristics of eARGs and iARGs. Based on the metagenomic data, the diversities, relative abundances, and compositions of eARGs and iARGs were similar. The extracellular and intracellular integrons and insertion sequences (ISs) also did not show any significant differences. However, the degree and significance of the correlation between total relative abundances of integrons/ISs and ARGs were lower outside than inside the cells. Gene cassettes carried by class 1 integron were amplified in manure and sludge samples, and sequencing results showed that the identified ARGs extracellularly and intracellularly were distinct. By analyzing the genetic contexts, most ARGs were found located on chromosomes. Nevertheless, the proportion of ARGs carried by plasmids increased extracellularly. qPCR was employed to quantify the absolute abundances of sul1, sul2, tetO, and tetW, and their extracellular proportions were found highest in sludge samples. These findings together raised the requirements of considering eARGs and iARGs separately in terms of risk evaluation and removal management.
Collapse
Affiliation(s)
- Yina Zou
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Menghan Wu
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiayu Liu
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Weiming Tu
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK
| | - Fengxing Xie
- Tianjin Institute of Agricultural Resources and Environment, Tianjin Academy of Agricultural Science, Tianjin 300384, China
| | - Hui Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
22
|
Zhang K, Li K, Xin R, Han Y, Guo Z, Zou W, Wei W, Cui X, Zhang Z, Zhang Y. Antibiotic resistomes in water supply reservoirs sediments of central China: main biotic drivers and distribution pattern. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:37712-37721. [PMID: 35066838 DOI: 10.1007/s11356-021-18095-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Water supply reservoirs form one of the critical drinking water resources. Their water quality directly affects human health. However, reservoir sediments have not received adequate attention in antibiotic resistance genes (ARGs) dissemination, though they reflect long-term ARGs contamination of water supply reservoirs. Moreover, the physicochemical parameters in water supply reservoir sediments are generally better than those in the other media. Thus, the main ARGs biotic drivers of the media would demonstrate their unique characteristics. In this study, sediment samples were collected from 10 water supply reservoirs in central China, and the antibiotic resistomes were determined with the metagenomic method. As revealed from the results, 174 ARGs (18 ARG types) were detected in the reservoir sediment. Besides, multidrug-, sulfonamide-, and vancomycin-ARGs were the dominant ARGs in the sediment samples. The macrolide-resistant Microcystis was prevalent (100% detection frequency with 0.35% average percentage) in reservoir sediments and posed potential risks to human health. Furthermore, the results of the Mantel test and VPA demonstrated that mobile genetic elements (MGEs) were the more essential biotic drivers in ARG contents of reservoir sediments rather than the bacteria community.
Collapse
Affiliation(s)
- Kai Zhang
- School of Geographic Sciences, Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, No.237, Nanhu Road, Shihe District, Xinyang, 464000, China.
| | - Kuangjia Li
- Development Research Center, Ministry of Water Resources of People's Republic of China, Beijing, 100032, China
| | - Rui Xin
- School of Marine Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Ya Han
- School of Geographic Sciences, Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, No.237, Nanhu Road, Shihe District, Xinyang, 464000, China
| | - Ziwei Guo
- School of Geographic Sciences, Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, No.237, Nanhu Road, Shihe District, Xinyang, 464000, China
| | - Wei Zou
- School of Environment, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory On Key Techniques in Water Treatment, Henan Normal University, Henan, 453007, China
| | - Wei Wei
- School of Geographic Sciences, Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, No.237, Nanhu Road, Shihe District, Xinyang, 464000, China
| | - Xiangchao Cui
- School of Geographic Sciences, Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, No.237, Nanhu Road, Shihe District, Xinyang, 464000, China
| | - Zhongshuai Zhang
- School of Geographic Sciences, Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, No.237, Nanhu Road, Shihe District, Xinyang, 464000, China
| | - Ying Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, No.38, Tongyan Road, Haihe Education Park, Tianjin, 300350, China.
| |
Collapse
|
23
|
Gu Q, Sun M, Lin T, Zhang Y, Wei X, Wu S, Zhang S, Pang R, Wang J, Ding Y, Liu Z, Chen L, Chen W, Lin X, Zhang J, Chen M, Xue L, Wu Q. Characteristics of Antibiotic Resistance Genes and Antibiotic-Resistant Bacteria in Full-Scale Drinking Water Treatment System Using Metagenomics and Culturing. Front Microbiol 2022; 12:798442. [PMID: 35273579 PMCID: PMC8902363 DOI: 10.3389/fmicb.2021.798442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/20/2021] [Indexed: 01/08/2023] Open
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.
Collapse
Affiliation(s)
- Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ming Sun
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Tao Lin
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Youxiong Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xianhu Wei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shuhong Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhenjie Liu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ling Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Wei Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiuhua Lin
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| |
Collapse
|
24
|
Chen J, Yang Y, Jiang X, Ke Y, He T, Xie S. Metagenomic insights into the profile of antibiotic resistomes in sediments of aquaculture wastewater treatment system. J Environ Sci (China) 2022; 113:345-355. [PMID: 34963542 DOI: 10.1016/j.jes.2021.06.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 06/14/2023]
Abstract
To meet the rapidly growing global demand for aquaculture products, large amounts of antibiotics were used in aquaculture, which might accelerate the evolution of antibiotic-resistant bacteria (ARB) and the propagation of antibiotic genes (ARGs). In our research, we revealed the ARGs profiles, their co-occurrence with mobile genetic elements (MGEs), and potential hosts in sediments of a crab pond wastewater purification system based on metagenomic analysis. The residual antibiotic seems to increase the propagation of ARGs in the crab pond, but there was no clear relationship between a given antibiotic type and the corresponding resistance genes. The effect of aquaculture on sediment was not as profound as that of other anthropogentic activities, but increased the relative abundance of sulfonamide resistance gene. A higher abundance of MGEs, especially plasmid, increased the potential ARGs dissemination risk in crab and purification ponds. Multidrug and sulfonamide resistance genes had greater potential to transfer because they were more frequently carried by MGEs. The horizontal gene transfer was likely to occur among a variety of microorganisms, and various ARGs hosts including Pseudomonas, Acinetobacter, Escherichia, and Klebsiella were identified. Bacterial community influenced the composition of ARG hosts, and Proteobacteria was the predominant hosts. Overall, our study provides novel insights into the environmental risk of ARGs in sediments of aquaculture wastewater treatment system.
Collapse
Affiliation(s)
- Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xinshu Jiang
- State Key Joint Laboratory of Environment Simulation and Pollution Control (SKJLESPC), Beijing Key Laboratory for Emerging Organic Contaminants Control (BKLEOC), School of Environment, POPs Research Center, Tsinghua University, Beijing 100084, China
| | - Yanchu Ke
- State Key Joint Laboratory of Environment Simulation and Pollution Control (SKJLESPC), Beijing Key Laboratory for Emerging Organic Contaminants Control (BKLEOC), School of Environment, POPs Research Center, Tsinghua University, Beijing 100084, China
| | - Tao He
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China.
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| |
Collapse
|
25
|
Hu Y, Jiang L, Sun X, Wu J, Ma L, Zhou Y, Lin K, Luo Y, Cui C. Risk assessment of antibiotic resistance genes in the drinking water system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149650. [PMID: 34426368 DOI: 10.1016/j.scitotenv.2021.149650] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 05/17/2023]
Abstract
Antibiotic resistance genes (ARGs) are extensively detected in various environmental media, whose risk assessment in the drinking water systems has not been comprehensive. This study established a new risk assessment of ARGs in the drinking water systems, considering the chlorine-resistance ability, transferability, and ARGs harboring potential of pathogens. The risk of ARGs in a typical drinking water reservoir was also evaluated based on the detection of ARGs and antibiotic-resistant bacteria (ARB). Fourteen ARGs were detected with a relative concentration range of 10-4-10-3 (ARGs/16S rRNA gene). Five isolated ARB were identified as human opportunistic pathogens, one of which (Pseudomonas aeruginosa HLS-6, CCTCC AB 2017269) is resistant to hundreds of milligrams per liter levels of antibiotics and low-level chlorine. This result indicated that ARB tolerant to high-levels of antibiotics could be isolated from environments containing trace levels of antibiotics. Moreover, complete genome sequencing confirmed the inclusion of ARGs (sul1, aadA2) on the class I integron in HLS-6, indicating that the risk of ARGs in this drinking water reservoir could be classified as resistance risk ranking in drinking water system 1 (R3DW 1). The risk assessment of ARGs in this study provides a clear understanding of ARG risk in drinking water systems. The results reveal that the ARGs and ARB contamination of drinking water reservoirs pose significant challenges for drinking water treatment efficiency and affect drinking water safety.
Collapse
Affiliation(s)
- Yaru Hu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Lei Jiang
- National Engineering Research Center of Urban Water Resources, Shanghai 200082, China
| | - Xiaoyan Sun
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jianqiang Wu
- Shanghai Academy of Environmental Sciences, Shanghai 200233, China
| | - Lei Ma
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yanbo Zhou
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Kuangfei Lin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, Tianjin 300071, China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| |
Collapse
|
26
|
Niegowska M, Sanseverino I, Navarro A, Lettieri T. Knowledge gaps in the assessment of antimicrobial resistance in surface waters. FEMS Microbiol Ecol 2021; 97:fiab140. [PMID: 34625810 PMCID: PMC8528692 DOI: 10.1093/femsec/fiab140] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/06/2021] [Indexed: 11/26/2022] Open
Abstract
The spread of antibiotic resistance in the water environment has been widely described. However, still many knowledge gaps exist regarding the selection pressure from antibiotics, heavy metals and other substances present in surface waters as a result of anthropogenic activities, as well as the extent and impact of this phenomenon on aquatic organisms and humans. In particular, the relationship between environmental concentrations of antibiotics and the acquisition of ARGs by antibiotic-sensitive bacteria as well as the impact of heavy metals and other selective agents on antimicrobial resistance (AMR) need to be defined. Currently, established safety values are based on the effects of antibiotic toxicity neglecting the question of AMR spread. In turn, risk assessment of antibiotics in waterbodies remains a complex question implicating multiple variables and unknowns reinforced by the lack of harmonized protocols and official guidelines. In the present review, we discussed current state-of-the-art and the knowledge gaps related to pressure exerted by antibiotics and heavy metals on aquatic environments and their relationship to the spread of AMR. Along with this latter, we reflected on (i) the risk assessment in surface waters, (ii) selective pressures contributing to its transfer and propagation and (iii) the advantages of metagenomics in investigating AMR. Furthermore, the role of microplastics in co-selection for metal and antibiotic resistance, together with the need for more studies in freshwater are highlighted.
Collapse
Affiliation(s)
- Magdalena Niegowska
- European Commission, Joint Research Centre (JRC), Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Isabella Sanseverino
- European Commission, Joint Research Centre (JRC), Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Anna Navarro
- European Commission, Joint Research Centre (JRC), Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Teresa Lettieri
- European Commission, Joint Research Centre (JRC), Via Enrico Fermi 2749, 21027 Ispra, Italy
| |
Collapse
|
27
|
Bueno I, Beaudoin A, Arnold WA, Kim T, Frankson LE, LaPara TM, Kanankege K, Wammer KH, Singer RS. Quantifying and predicting antimicrobials and antimicrobial resistance genes in waterbodies through a holistic approach: a study in Minnesota, United States. Sci Rep 2021; 11:18747. [PMID: 34548591 PMCID: PMC8455696 DOI: 10.1038/s41598-021-98300-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/03/2021] [Indexed: 11/25/2022] Open
Abstract
The environment plays a key role in the spread and persistence of antimicrobial resistance (AMR). Antimicrobials and antimicrobial resistance genes (ARG) are released into the environment from sources such as wastewater treatment plants, and animal farms. This study describes an approach guided by spatial mapping to quantify and predict antimicrobials and ARG in Minnesota’s waterbodies in water and sediment at two spatial scales: macro, throughout the state, and micro, in specific waterbodies. At the macroscale, the highest concentrations across all antimicrobial classes were found near populated areas. Kernel interpolation provided an approximation of antimicrobial concentrations and ARG abundance at unsampled locations. However, there was high uncertainty in these predictions, due in part to low study power and large distances between sites. At the microscale, wastewater treatment plants had an effect on ARG abundance (sul1 and sul2 in water; blaSHV, intl1, mexB, and sul2 in sediment), but not on antimicrobial concentrations. Results from sediment reflected a long-term history, while water reflected a more transient record of antimicrobials and ARG. This study highlights the value of using spatial analyses, different spatial scales, and sampling matrices, to design an environmental monitoring approach to advance our understanding of AMR persistence and dissemination.
Collapse
Affiliation(s)
- Irene Bueno
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, USA.
| | - Amanda Beaudoin
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, USA.,Minnesota Department of Health, P.O. Box 64975, St. Paul, MN, 55164-0975, USA
| | - William A Arnold
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, MN, 55455, USA.,Water Resources Science Program, University of Minnesota, 1985 Buford Ave., St. Paul, MN, 55108, USA
| | - Taegyu Kim
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, MN, 55455, USA
| | - Lara E Frankson
- Water Resources Science Program, University of Minnesota, 1985 Buford Ave., St. Paul, MN, 55108, USA
| | - Timothy M LaPara
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Dr. SE, Minneapolis, MN, 55455, USA
| | - Kaushi Kanankege
- Center for Animal Health and Food Safety, College of Veterinary Medicine, University of Minnesota, 1354 Eckles Ave., St. Paul, MN, 55108, USA
| | - Kristine H Wammer
- College of Arts & Sciences, University of St. Thomas, 2115 Summit Ave., St. Paul, MN, 55105, USA
| | - Randall S Singer
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Ave., St. Paul, MN, 55108, USA
| |
Collapse
|
28
|
Zhang B, Qin S, Guan X, Jiang K, Jiang M, Liu F. Distribution of Antibiotic Resistance Genes in Karst River and Its Ecological Risk. WATER RESEARCH 2021; 203:117507. [PMID: 34392041 DOI: 10.1016/j.watres.2021.117507] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
In recent years, karst water has been polluted by emerging pollutants such as antibiotics. In this study, the bacterial communities and antibiotic resistance genes (ARGs) in antibiotics contaminated karst river was studied in summer and winter. The concentration of antibiotics in winter karst river is higher than that in summer, and there are significant differences in structure of bacterial community and ARGs between karst river water samples. Aminoglycoside, beta-lactamase and multidrug are the main types of ARGs, and transposons play an important role in the spread of ARGs. The horizontal gene transfer (HGT) of ARGs between bacteria mediated by mobile genetic elements (MGEs) would cause the spread of ARGs and bring potential ecological risks. In addition, we found that the risk of antibiotic resistant pathogenic bacteria (ARPB) in winter was possibly higher than that in summer. It was suggested that the discharge of antibiotics, water amount and seasonal occurrence time of human intestinal diseases affect the risks caused by antibiotics contaminants. This study helps us to understand the transmission mechanism of ARGs and their potential seasonal ecological risks in complex karst water systems.
Collapse
Affiliation(s)
- Biao Zhang
- School of Ocean Sciences, China University of Geosciences, Beijing, China; The Fifth Geology Company of Hebei Geology and Minerals Bureau, Tangshan, Hebei, China
| | - Shang Qin
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Xiangyu Guan
- School of Ocean Sciences, China University of Geosciences, Beijing, China; Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences, Beijing 100083, China.
| | - Kaidi Jiang
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences, Beijing 100083, China
| | - Minhui Jiang
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Fei Liu
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences, Beijing 100083, China
| |
Collapse
|
29
|
Antibiotic Resistance in Wastewater and Its Impact on a Receiving River: A Case Study of WWTP Brno-Modřice, Czech Republic. WATER 2021. [DOI: 10.3390/w13162309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Antibiotic resistance has become a global threat in which the anthropogenically influenced aquatic environment represents not only a reservoir for the spread of antibiotic resistant bacteria (ARB) among humans and animals but also an environment where resistance genes are introduced into natural microbial ecosystems. Wastewater is one of the sources of antibiotic resistance. The aim of this research was the evaluation of wastewater impact on the spread of antibiotic resistance in the water environment. In this study, qPCR was used to detect antibiotic resistance genes (ARGs)—blaCTX-M-15, blaCTX-M-32, ampC, blaTEM, sul1, tetM and mcr-1 and an integron detection primer (intl1). Detection of antibiotic resistant Escherichia coli was used as a complement to the observed qPCR results. Our results show that the process of wastewater treatment significantly reduces the abundances of ARGs and ARB. Nevertheless, treated wastewater affects the ARGs and ARB number in the receiving river.
Collapse
|
30
|
Nogueira T, Botelho A. Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures. Antibiotics (Basel) 2021; 10:787. [PMID: 34203511 PMCID: PMC8300701 DOI: 10.3390/antibiotics10070787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/20/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022] Open
Abstract
The shortage of wild fishery resources and the rising demand for human nutrition has driven a great expansion in aquaculture during the last decades in terms of production and economic value. As such, sustainable aquaculture production is one of the main priorities of the European Union's 2030 agenda. However, the intensification of seafood farming has resulted in higher risks of disease outbreaks and in the increased use of antimicrobials to control them. The selective pressure exerted by these drugs provides the ideal conditions for the emergence of antimicrobial resistance hotspots in aquaculture facilities. Omics technology is an umbrella term for modern technologies such as genomics, metagenomics, transcriptomics, proteomics, culturomics, and metabolomics. These techniques have received increasing recognition because of their potential to unravel novel mechanisms in biological science. Metagenomics allows the study of genomes in microbial communities contained within a certain environment. The potential uses of metagenomics in aquaculture environments include the study of microbial diversity, microbial functions, and antibiotic resistance genes. A snapshot of these high throughput technologies applied to microbial diversity and antimicrobial resistance studies in aquacultures will be presented in this review.
Collapse
Affiliation(s)
- Teresa Nogueira
- Laboratory of Bacteriology and Mycology, INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal;
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Evolutionary Ecology of Microorganisms Group, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Ana Botelho
- Laboratory of Bacteriology and Mycology, INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal;
| |
Collapse
|
31
|
The Effect of the Effluent from a Small-Scale Conventional Wastewater Treatment Plant Treating Municipal Wastewater on the Composition and Abundance of the Microbial Community, Antibiotic Resistome, and Pathogens in the Sediment and Water of a Receiving Stream. WATER 2021. [DOI: 10.3390/w13060865] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The effluents of wastewater treatment plants (WWTPs) are major contributors of nutrients, microbes—including those carrying antibiotic resistance genes (ARGs)—and pathogens to receiving waterbodies. The effect of the effluent of a small-scale activated sludge WWTP treating municipal wastewater on the composition and abundance of the microbial community as well as the antibiotic resistome and pathogens in the sediment and water of the receiving stream and river was studied using metagenome sequencing and a quantitative approach. Elevated Bacteroidetes proportions in the prokaryotic community, heightened sulfonamide and aminoglycoside resistance determinants proportions, and an increase of up to three orders of magnitude of sul1–sul2–aadA–blaOXA2 gene cluster abundances were recorded in stream water and sediments 0.3 km downstream of a WWTP discharge point. Further downstream, a gradual recovery of affected microbial communities along a distance gradient from WWTP was recorded, culminating in the mostly comparable state of river water and sediment parameters 3.7 km downstream of WWTP and stream water and sediments upstream of the WWTP discharge point. Archaea, especially Methanosarcina, Methanothrix, and Methanoregula, formed a substantial proportion of the microbial community of WWTP effluent as well as receiving stream water and sediment, and were linked to the spread of ARGs. Opportunistic environmental-origin pathogens were predominant in WWTP effluent and receiving stream bacterial communities, with Citrobacter freundii proportion being especially elevated in the close vicinity downstream of the WWTP discharge point.
Collapse
|
32
|
Sánchez-Baena AM, Caicedo-Bejarano LD, Chávez-Vivas M. Structure of Bacterial Community with Resistance to Antibiotics in Aquatic Environments. A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:2348. [PMID: 33673692 PMCID: PMC7957730 DOI: 10.3390/ijerph18052348] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/11/2022]
Abstract
Aquatic environments have been affected by the increase in bacterial resistant to antibiotics. The aim of this review is to describe the studies carried out in relation to the bacterial population structure and antibiotic resistance genes in natural and artificial water systems. We performed a systematic review based on the PRISMA guideline (preferred reporting items for systematic reviews and meta-analyzes). Articles were collected from scientific databases between January 2010 and December 2020. Sixty-eight papers meeting the inclusion criteria, i.e., "reporting the water bacterial community composition", "resistance to antibiotics", and "antibiotic resistance genes (ARG)", were evaluated according to pre-defined validity criteria. The results indicate that the predominant phyla were Firmicutes and Bacteroidetes in natural and artificial water systems. Gram-negative bacteria of the family Enterobacteraceae with resistance to antibiotics are commonly reported in drinking water and in natural water systems. The ARGs mainly reported were those that confer resistance to β-lactam antibiotics, aminoglycosides, fluoroquinolones, macrolides and tetracycline. The high influence of anthropogenic activity in the environment is evidenced. The antibiotic resistance genes that are mainly reported in the urban areas of the world are those that confer resistance to the antibiotics that are most used in clinical practice, which constitutes a problem for human and animal health.
Collapse
Affiliation(s)
- Ana María Sánchez-Baena
- Department of Natural Sciences, Exact and Statistics, Faculty of Basic Sciences, Campus Pampalinda, Universidad Santiago de Cali, Cali Calle 5 # 62-00, Colombia;
| | - Luz Dary Caicedo-Bejarano
- Department of Natural Sciences, Exact and Statistics, Faculty of Basic Sciences, Campus Pampalinda, Universidad Santiago de Cali, Cali Calle 5 # 62-00, Colombia;
| | - Mónica Chávez-Vivas
- Department of Biomedical Sciences, Faculty of Health, Campus Pampalinda, Universidad Santiago de Cali, Cali Calle 5 # 62-00, Colombia;
| |
Collapse
|
33
|
Zhang W, Zhang Q, Li M, Wang H, Li Y, Peng H, Feng J. Microbial community and function evaluation in the start-up period of bioaugmented SBR fed with aniline wastewater. BIORESOURCE TECHNOLOGY 2021; 319:124148. [PMID: 32987279 DOI: 10.1016/j.biortech.2020.124148] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/13/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
An enhanced sequencing batch reactor (SBR) system was developed to treat synthetic wastewater rich in 600 mg/L aniline. The aniline degradation efficiency was almost 100%, and the total nitrogen (TN) removal rate was more than 50%. Metagenomics technology revealed the community structure, functional genes and metabolic mechanism during the start-up of the enhanced reactor. Sequencing results showed that Proteobacteria, Bacteroidetes, Chloroflexi and Actinobacteria were dominant phylum. The proportion of degradation of aromatic compounds function increased gradually, but the proportion of nitrogen metabolism function changed little. Functional genes involved in aniline degradation including benA-xylX and dmpB/xylE were detected. The functional genes of nitrogen metabolism were involved in complete nitrification, traditional denitrification, assimilation nitrate reduction and dissimilation nitrate reduction. The functional contribution analysis and network analysis showed that the cooperation and competition of Thauera, Delftia, Diaphorobacter, Micavibrio and Azoarcus ensured the effective removal of aniline and nitrogen.
Collapse
Affiliation(s)
- Wenli Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan 430070, PR China
| | - Qian Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan 430070, PR China.
| | - Meng Li
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan 430070, PR China
| | - Hongyu Wang
- School of Civil Engineering, Wuhan University, Wuhan 430072, PR China
| | - Yao Li
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan 430070, PR China
| | - Haojin Peng
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan 430070, PR China
| | - Jiapeng Feng
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan 430070, PR China
| |
Collapse
|
34
|
Zhou R, Zeng S, Hou D, Liu J, Weng S, He J, Huang Z. Temporal variation of antibiotic resistance genes carried by culturable bacteria in the shrimp hepatopancreas and shrimp culture pond water. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 199:110738. [PMID: 32447139 DOI: 10.1016/j.ecoenv.2020.110738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
The increasing prevalence of antibiotic resistance genes (ARGs) is a challenge to the health of humans, animals and the environments. Human activities and aquatic environments can increase ARGs. Few studies have focused on the temporal variation of aquatic bacteria with multiple ARGs in aquatic environments affected by human production activity. We studied culturable bacteria (CB) carrying ARGs, including sul1, sul2, floR, strA and gyrA in the shrimp hepatopancreas (HP) and in pond water during shrimp culture. The relative abundance of ARGs carried by CB in HP was higher than that in water (P < 0.05). However, CB carrying ARGs generally varied in random pattern. The correlation of sul2 abundance was significantly positive in HP, while that of strA abundance was significantly negative in water (P < 0.05) during shrimp culture. Among all of the CB, 33.59% carried multiple ARGs. Temporal distance-decay analysis indicated that CB carrying ARGs in water were more resistant to the effects of human activity. CB carrying ARGs varied temporally in HP and pond water during shrimp culture. These results demonstrate that multiple ARGs are carried by CB, and these varied with the phase of aquatic culture.
Collapse
Affiliation(s)
- Renjun Zhou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Shenzheng Zeng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Dongwei Hou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Jian Liu
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China.
| | - Zhijian Huang
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China.
| |
Collapse
|
35
|
Anthony ET, Ojemaye MO, Okoh OO, Okoh AI. A critical review on the occurrence of resistomes in the environment and their removal from wastewater using apposite treatment technologies: Limitations, successes and future improvement. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:113791. [PMID: 32224385 DOI: 10.1016/j.envpol.2019.113791] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/08/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Recent reports are pointing towards the potential increasing risks of resistomes in human host. With no permissible limit in sight, resistomes are continually multiplying at an alarming rate in the ecosystem, with a disturbing level in drinking water source. The morphology and chemical constituent of resistomes afford them to resist degradation, elude membrane and counter ionic charge, thereby, rendering both conventional and advanced water and wastewater treatment inefficient. Water and wastewater matrix may govern the propagation of individual resistomes sub-type, co-selection and specific interaction towards precise condition may have enhanced the current challenge. This review covers recent reports (2011-2019) on the occurrence of ARB/ARGs and ease of spread of resistance genes in the aquatic ecosystem. The contributions of water matrix to the spread and mitigation, treatment options, via bulk removal or capture, and intracellular and extracellular DNA lysis were discussed. A complete summary of recent occurrences of ARB/ARGs, fate after disinfection and optimum conditions of individual treatment technology or in tandem, including process limitations, with a brief assessment of removal or degradation mechanism were highlighted.
Collapse
Affiliation(s)
- Eric Tobechukwu Anthony
- Department of Pure and Applied Chemistry, University of Fort Hare, Alice, 5700, South Africa; SAMRC, Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa; AEMREG, Applied and Environmental Microbiology Research Group, University of Fort Hare, Alice, South Africa.
| | - Mike O Ojemaye
- Department of Pure and Applied Chemistry, University of Fort Hare, Alice, 5700, South Africa; SAMRC, Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa; AEMREG, Applied and Environmental Microbiology Research Group, University of Fort Hare, Alice, South Africa
| | - Omobola O Okoh
- Department of Pure and Applied Chemistry, University of Fort Hare, Alice, 5700, South Africa; SAMRC, Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa; AEMREG, Applied and Environmental Microbiology Research Group, University of Fort Hare, Alice, South Africa
| | - Anthony I Okoh
- SAMRC, Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa; AEMREG, Applied and Environmental Microbiology Research Group, University of Fort Hare, Alice, South Africa
| |
Collapse
|
36
|
Cheng J, Tang X, Liu C. Occurrence and distribution of antibiotic resistance genes in various rural environmental media. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:29191-29203. [PMID: 32436087 DOI: 10.1007/s11356-020-09287-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance genes (ARGs) in rural environments have been poorly characterized in the literature. In this study, the diversity, abundance, and distribution of ARGs in surface waters, soils, and sediments of a typical hilly rural area in the Upper Yangtze River watershed were investigated using the high-throughput quantitative polymerase chain reaction, and their relationships with chemical properties of the samples were analyzed. No significant differences in the diversity and abundance of ARGs were observed among the three medium types while the ARG distribution pattern in the sediments was obviously different from that of the surface waters. According to the co-occurrence pattern of ARGs subtypes obtained by network analysis, blaOXA10-02, blaPSE, lnuB-02, and qacEΔ1-01 can be used to estimate the relative abundance of total ARGs for the study area. It appeared that the prevalence of ARGs in the sediments was promoted by the horizontal gene transfer (HGT) and vertical gene transfer together, while their spread in the surface waters and soils were facilitated by the supply of biogenic elements and HGT, respectively. Mobile genetic elements (MGEs) were abundant and detected in all samples, and their abundance was significantly and positively correlated with that of ARGs, implying that the potential horizontal transfer of ARGs to other bacteria and pathogens in rural environments should not be overlooked.
Collapse
Affiliation(s)
- Jianhua Cheng
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiangyu Tang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Chen Liu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| |
Collapse
|
37
|
Ekwanzala MD, Dewar JB, Momba MNB. Environmental resistome risks of wastewaters and aquatic environments deciphered by shotgun metagenomic assembly. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 197:110612. [PMID: 32302860 DOI: 10.1016/j.ecoenv.2020.110612] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
In this paper, we deciphered the core resistome disseminating from hospital wastewater to the aquatic environment by characterising the resistome, plasmidome, mobilome and virulome using metagenomic analysis. This study also elucidated different environmental resistome risks using shotgun-metagenomic assembly. The results showed that clinically relevant taxa were found in assessed matrices (Salmonella spp., Acinetobacter spp, Escherichia-Shigella spp., Pseudomonas spp., Staphylococcus spp. and Vibrio spp.). For the plasmidome, we found 249 core plasmidome sequences that were shared among all assessed matrices. The core mobilome of 2424 mobile genetic elements shared among all assessed matrices was found. Regarding the virulome, we found 148 core virulence factors shared among all assessed samples, and the core virulome content was consistently shared across the most abundant bacterial genera. Although influent of wastewater showed considerable higher relative bacterial abundance (P = 0.008), hospital wastewater showed significant higher environmental resistome risk scores against all other assessed matrices, with an average of 46.34% (P = 0.001). These results suggest hospital wastewater, effluent and sewage sludge should be subjected to stringent mitigating measures to minimise such dissemination.
Collapse
Affiliation(s)
- Mutshiene Deogratias Ekwanzala
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Private BagX680, Pretoria, 0001, South Africa.
| | - John Barr Dewar
- Department of Life and Consumer Sciences, University of South Africa, Florida Campus, Johannesburg, South Africa
| | - Maggy Ndombo Benteke Momba
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Private BagX680, Pretoria, 0001, South Africa.
| |
Collapse
|
38
|
Ohore OE, Addo FG, Han N, Li X, Zhang S. Profiles of ARGs and their relationships with antibiotics, metals and environmental parameters in vertical sediment layers of three lakes in China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 255:109583. [PMID: 31739203 DOI: 10.1016/j.jenvman.2019.109583] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/22/2019] [Accepted: 09/15/2019] [Indexed: 06/10/2023]
Abstract
Antibiotic resistance is a global health problem, and the role of antibiotics and metal pollution in antibiotic resistance in sediment biocenosis is limited. The occurrence and relationship between antibiotic resistance genes (ARGs), antibiotics, metals and environmental parameters were investigated in vertical layers of sediments in rural and urban lakes. Generally, the total concentrations of seven antibiotics were significantly higher in the rural lake (Lake Taihu = 96%) than in the urban lakes (Xuanwu = 0.3%, Wulongtan = 3%), while similar concentrations were observed for metals (Taihu (34%), Xuanwu (33%) and Wulongtan (33%)). The concentration of metals and antibiotics were mostly higher in the surface sediment layers than the deeper ones (for antibiotics; surface layers = 89%, deeper layer = 11%, for metals; surface = 65%, deep = 35%). The ARGs showed no significant difference between surface and deeper sediments (surface = 48%, deep = 52%, p < 0.05). The potential ecological risk index of Ni, Cu, Zn, Cr, Mn, As, Cd, and Pb contamination showed that Lake Taihu and Wulongtan had moderate ecological risks while Lake Xuanwu had a low ecological risk. Pearson coefficient and network analysis showed that direct and indirect relationship existed among antibiotics, metals, environmental parameters, and ARGs, and the relationship was linked by key environmental components. tetA, blaTEM, SDZ, TOC, OFL, Cd, OTC, NOR, Ni, sulA, AUR, TC, DOX and TN were the major factors that influence the distribution of resistance genes, forming a complex network mechanism of antibiotic resistance. Our study revealed that antibiotics and heavy metals are widely distributed in the surficial sediments and the proliferation of ARGs are influenced by some key environmental components.
Collapse
Affiliation(s)
- Okugbe Ebiotubo Ohore
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, China
| | - Felix Gyawu Addo
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, China
| | - Nini Han
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, China
| | - Xin Li
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, China
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing, 210098, China.
| |
Collapse
|
39
|
Pu C, Yu Y, Diao J, Gong X, Li J, Sun Y. Exploring the persistence and spreading of antibiotic resistance from manure to biocompost, soils and vegetables. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 688:262-269. [PMID: 31229823 DOI: 10.1016/j.scitotenv.2019.06.081] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
The main avenue in which antibiotic resistance enters soils is through the application of livestock manure. However, whether antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) persist and spread to vegetables with the application of manure and manure products is still unclear. This study assessed seven kinds of cultured ARB, 221 ARGs subtypes and three transposon genes in the vegetable production chain (from manure to biocompost, soils and vegetables). Results showed that at least 80% of ARB, ARGs and transposon genes were removed after aerobic composting. However, aerobic composting did not reduce the diversity of ARGs in pig and chicken manure. A total of 19 ARGs subtypes still persisted during aerobic composting. Compared to the temperature-thermophilic stage, the number of bacteria resistant to erythromycin, the relative abundance of ARGs and IS613 increased 1.7-4.9 times at the temperature-decreasing stage. Direct application of biocompost introduced 11 ARGs subtypes to pakchoi, but these ARGs did not present in biocompost-amended soil. A transposon gene tnpA was also detected in the biocompost-amended soil, but surprisingly was found in the control vegetable. This demonstrated that the transposon gene is intrinsic in pakchoi. Bacterial community analysis and network analysis revealed that a specific genus Terrisporobacter carrying tetO, tetW ermB and tnpA persisted in the vegetable production chain, which may generate a potential risk in the following production. Our study illuminates the persistence and spreading of antibiotic resistance in the vegetable production chain which could help manage the ecological risks arising from antibiotic resistance in manure sources.
Collapse
Affiliation(s)
- Chengjun Pu
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Yao Yu
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Jianxiong Diao
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Xiaoyan Gong
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Ji Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Ying Sun
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
40
|
Chen Y, Li P, Huang Y, Yu K, Chen H, Cui K, Huang Q, Zhang J, Yew-Hoong Gin K, He Y. Environmental media exert a bottleneck in driving the dynamics of antibiotic resistance genes in modern aquatic environment. WATER RESEARCH 2019; 162:127-138. [PMID: 31260828 DOI: 10.1016/j.watres.2019.06.047] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 05/26/2023]
Abstract
With the rapid construction of dams worldwide, reservoir system has become a representation of modern aquatic environment. However, the profiles of antibiotic resistance genes (ARGs) and associated factor influencing their dynamics in modern aquatic environment (e.g., water phase, sediment phase, and soil phase) are largely unknown. Here, we comprehensively characterized the diversity, abundance, distribution of ARGs in a large drinking water reservoir using high-throughput quantitative PCR, as well as ranked the factors (e.g., mobile genetic elements (MGEs), bacteria community, bacterial biomass, antibiotics, and basic properties) influencing the profiles of ARGs on the basis of structural equation models (SEMs). Water phase was prone to harbor more diverse ARGs as compared to sediment phase and soil phase, and soil phase in drawdown area was a potential reservoir and hotspot for ARGs. Environmental media partially affected the ARG diversity in modern aquatic environment, while it observably influenced the distributions of ARGs and MGEs and their co-occurrence patterns. The pathways for the proliferation and spread of ARGs in water phase were both the horizontal gene transfer (HGT) and vertical gene transfer (VGT), while the dominant pathways in sediment phase and soil phase were the HGT and VGT, respectively. The SEMs demonstrated that MGEs contributed the most to drive the ARG dynamics in both water phase and sediment phase, while the most dominant factor for this in soil phase was bacterial community. Overall, environmental media exerted a bottleneck in driving the dynamics of ARGs in modern aquatic environment probably via diversifying the MGEs, bacterial community, bacterial biomass, antibiotics and basic properties.
Collapse
Affiliation(s)
- Yihan Chen
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China.
| | - Peng Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuansheng Huang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kaifeng Yu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongjie Chen
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, #02-01, Singapore, 117411, Singapore; Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, E1A 07-03, Singapore, 117576, Singapore
| | - Kangping Cui
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Qianli Huang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, #02-01, Singapore, 117411, Singapore; Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, E1A 07-03, Singapore, 117576, Singapore
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; Shanghai Institute of Pollution Control and Ecological Security, 800 Dongchuan Road, Shanghai, 200240, China.
| |
Collapse
|
41
|
Zhang Y, Zhang Y, Kuang Z, Xu J, Li C, Li Y, Jiang Y, Xie J. Comparison of Microbiomes and Resistomes in Two Karst Groundwater Sites in Chongqing, China. GROUND WATER 2019; 57:807-818. [PMID: 31297792 DOI: 10.1111/gwat.12924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
Karst groundwater is an important water resource, as it accounts for about 15% of the total landscape of the earth and supplies 20% of potable water worldwide. The antibiotics resistance is an emerging global concern, and antibiotics residual and increase of antibiotic resistance genes represent serious global concerns and emerging pollutants. There is no report on the antibiotic resistance genes in groundwater. To survey resistome and microbiome in karst groundwater, two karst water samples were chosen for metagenome and metatranscriptome study, namely the 37th spring (C) and Dongcao spring (R) in Beibei, Chongqing, China. The two sites differ significantly in sulfur content, geochemical parameters, community structure, antibiotic resistance genes, and mechanisms, and these results may be influenced by anthropogenic activities. Combining with the Antibiotic Resistance Genes Database, three types of resistance genes baca, sul2, sul1 are present in R and C, and ant3ia, ermc, tetpa are also present in R. The number of all resistance genes in R was more than C, and Proteobacteria, Bacteroidetes, Nitrospirae are the main sources of antibiotic resistance genes. In addition, a large number of genes related to antibiotic gene transmission and drug resistance were found in both samples. Karst groundwater is an important source of drinking water and a possible venue for the transmission of microbial antibiotic resistance genes. However, few studies addressed this issue in karst groundwater, despite its widespread and great importance to global ecosystem. Karst groundwater is a reservoir for antibiotic resistant genes, and measures to control these resistant genes are urgently needed.
Collapse
Affiliation(s)
- Yuan Zhang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, 2 Tiansheng, Chongqing, China
| | - Yuanzhu Zhang
- Chongqing Key Laboratory of Karst Environment, School of Geographical Sciences, Southwest University, 2 Tiansheng, Chongqing, 400715, China
| | - Zhongmei Kuang
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, 2 Tiansheng, Chongqing, China
| | - Junqi Xu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, 2 Tiansheng, Chongqing, China
| | - Chunyan Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environment of Three Gorges Reservoir, Ministry of Education, School of Life Sciences, Southwest University, 2 Tiansheng, Chongqing, China
| | - Yong Li
- Chongqing Key Laboratory of Karst Environment, School of Geographical Sciences, Southwest University, 2 Tiansheng, Chongqing, 400715, China
| | - Yongjun Jiang
- Chongqing Key Laboratory of Karst Environment, School of Geographical Sciences, Southwest University, 2 Tiansheng, Chongqing, 400715, China
| | | |
Collapse
|