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Robins K, O'Donnell G, Neumann A, Schmidt W, Hart A, Graham DW. Antimicrobial resistance in rural rivers: Comparative study of the Coquet (Northumberland) and Eden (Cumbria) River catchments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172348. [PMID: 38614353 DOI: 10.1016/j.scitotenv.2024.172348] [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: 12/20/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Many studies have characterised resistomes in river microbial communities. However, few have compared resistomes in parallel rural catchments that have few point-source inputs of antimicrobial genes (ARGs) and organisms (i.e., AMR) - catchments where one can contrast more nebulous drivers of AMR in rural rivers. Here, we used quantitative microbial profiling (QMP) to compare resistomes and microbiomes in two rural river catchments in Northern England, the Coquet and Eden in Northumberland and Cumbria, respectively, with different hydrological and geographical conditions. The Eden has higher flow rates, higher annual surface runoff, and longer periods of soil saturation, whereas the Coquet is drier and has lower flowrates. QMP analysis showed the Eden contained significantly more abundant microbes associated with soil sources, animal faeces, and wastewater than the Coquet, which had microbiomes like less polluted rivers (Wilcoxon test, p < 0.01). The Eden also had greater ARG abundances and resistome diversity (Kruskal Wallis, p < 0.05), and higher levels of potentially clinically relevant ARGs. The Eden catchment had greater and flashier runoff and more extensive agricultural land use in its middle reach, which explains higher levels of AMR in the river. Hydrological and geographic factors drive AMR in rural rivers, which must be considered in environmental monitoring programmes.
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Affiliation(s)
- Katie Robins
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Greg O'Donnell
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Anke Neumann
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Wiebke Schmidt
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Alwyn Hart
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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Wen X, Xu J, Worrich A, Li X, Yuan X, Ma B, Zou Y, Wang Y, Liao X, Wu Y. Priority establishment of soil bacteria in rhizosphere limited the spread of tetracycline resistance genes from pig manure to soil-plant systems based on synthetic communities approach. ENVIRONMENT INTERNATIONAL 2024; 187:108732. [PMID: 38728817 DOI: 10.1016/j.envint.2024.108732] [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: 02/16/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
The spread of antibiotic resistance genes (ARGs) in agroecosystems through the application of animal manure is a global threat to human and environmental health. However, the adaptability and colonization ability of animal manure-derived bacteria determine the spread pathways of ARG in agroecosystems, which have rarely been studied. Here, we performed an invasion experiment by creating a synthetic communities (SynCom) with ten isolates from pig manure and followed its assembly during gnotobiotic cultivation of a soil-Arabidopsis thaliana (A. thaliana) system. We found that Firmicutes in the SynCom were efficiently filtered out in the rhizosphere, thereby limiting the entry of tetracycline resistance genes (TRGs) into the plant. However, Proteobacteria and Actinobacteria in the SynCom were able to establish in all compartments of the soil-plant system thereby spreading TRGs from manure to soil and plant. The presence of native soil bacteria prevented the establishment of manure-borne bacteria and effectively reduced the spread of TRGs. Achromobacter mucicolens and Pantoea septica were the main vectors for the entry of tetA into plants. Furthermore, doxycycline stress promoted the horizontal gene transfer (HGT) of the conjugative resistance plasmid RP4 within the SynCom in A. thaliana by upregulating the expression of HGT-related mRNAs. Therefore, this study provides evidence for the dissemination pathways of ARGs in agricultural systems through the invasion of manure-derived bacteria and HGT by conjugative resistance plasmids and demonstrates that the priority establishment of soil bacteria in the rhizosphere limited the spread of TRGs from pig manure to soil-plant systems.
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Affiliation(s)
- Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan 512005, China; Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany
| | - Jiaojiao Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany.
| | - Xianghui Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xingyun Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Resources and Environment, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 525000, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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Yang L, Zhao F, Feng Q, Li M, Wang X, Tang J, Bu Q, Chen L. A landscape source-sink model to understanding the seasonal dynamics of antibiotics in soils at watershed scale. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133224. [PMID: 38101022 DOI: 10.1016/j.jhazmat.2023.133224] [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: 09/18/2023] [Revised: 11/23/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Human and veterinary antibiotics occur widely in soil ecosystems and pose a serious threat to soil health. Landscape structure can be linked to Earth surface processes and anthropogenic footprints and may influence the variability of antibiotics in soil. In this study, an improved landscape source-sink model was used to characterize source-sink structures using the location-weighted landscape index (LWLI), which can be linked to antibiotic seasonality. The topographic wetness index was employed to identify source and sink landscapes, which represent antibiotic transport pathways via topography-driven hydrological processes. The results indicate that LWLI values and antibiotic seasonality are typically higher in farmland soils than in forest and orchard soils. LWLI values exhibit significant positive correlations with antibiotic seasonality in soils (R2: 0.33-0.58). Furthermore, landscape source-sink structures have a significant influence on antibiotic seasonality between winter and other seasons in farmland soils; however, these structures affect antibiotic seasonality between summer and other seasons in forest and orchard soils. The results of this study indicate that water movement regulated by landscape structure may play a crucial role in influencing antibiotic seasonality in soils at the watershed scale, and the landscape source-sink model can be used to quantitatively evaluate antibiotic seasonality in soil environment.
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Affiliation(s)
- Lei Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangkai Zhao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China
| | - Qingyu Feng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinmiao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianfeng Tang
- Key laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qingwei Bu
- School of Chemical& Environmental Engineering, China University of Mining & Technology-Beijing, Beijing 100083, China
| | - Liding Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Zhao C, Liu X, Tan H, Bian Y, Khalid M, Sinkkonen A, Jumpponen A, Rahman SU, Du B, Hui N. Urbanization influences the indoor transfer of airborne antibiotic resistance genes, which has a seasonally dependent pattern. ENVIRONMENT INTERNATIONAL 2024; 185:108545. [PMID: 38447454 DOI: 10.1016/j.envint.2024.108545] [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: 01/19/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
Over the last few years, the cumulative use of antibiotics in healthcare institutions, as well as the rearing of livestock and poultry, has resulted in the accumulation of antibiotic resistance genes (ARGs). This presents a substantial danger to human health worldwide. The characteristics of airborne ARGs, especially those transferred from outdoors to indoors, remains largely unexplored in neighborhoods, even though a majority of human population spends most of their time there. We investigated airborne ARGs and mobile genetic element (MGE, IntI1), plant communities, and airborne microbiota transferred indoors, as well as respiratory disease (RD) prevalence using a combination of metabarcode sequencing, real-time quantitative PCR and questionnaires in 72 neighborhoods in Shanghai. We hypothesized that (i) urbanization regulates ARGs abundance, (ii) the urbanization effect on ARGs varies seasonally, and (iii) land use types are associated with ARGs abundance. Supporting these hypotheses, during the warm season, the abundance of ARGs in peri-urban areas was higher than in urban areas. The abundance of ARGs was also affected by the surrounding land use and plant communities: an increase in the proportion of gray infrastructure (e.g., residential area) around neighborhoods can lead to an increase in some ARGs (mecA, qnrA, ermB and mexD). Additionally, there were variations observed in the relationship between ARGs and bacterial genera in different seasons. Specifically, Stenotrophomonas and Campylobacter were positively correlated with vanA during warm seasons, whereas Pseudomonas, Bacteroides, Treponema and Stenotrophomonas positively correlated with tetX in the cold season. Interstingly, a noteworthy positive correlation was observed between the abundance of vanA and the occurrence of both rhinitis and rhinoconjunctivitis. Taken together, our study underlines the importance of urbanization and season in controlling the indoor transfer of airborne ARGs. Furthermore, we also highlight the augmentation of green-blue infrastructure in urban environments has the potential to mitigate an excess of ARGs.
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Affiliation(s)
- Chang Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, 200240, Shanghai, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd., 200240, Shanghai, China.
| | - Xinxin Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China; Faculty of Biological and Environmental Sciences, University of Helsinki, Niemenkatu 73, Lahti 15140 Finland.
| | - Haoxin Tan
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China.
| | - Yucheng Bian
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China.
| | - Muhammad Khalid
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China.
| | - Aki Sinkkonen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Niemenkatu 73, Lahti 15140 Finland; Horticulture Technologies, Unit of Production Systems, Natural Resources Institute Finland, Turku, Finland.
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, KS, USA.
| | - Saeed Ur Rahman
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China.
| | - Baoming Du
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China.
| | - Nan Hui
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China; Faculty of Biological and Environmental Sciences, University of Helsinki, Niemenkatu 73, Lahti 15140 Finland.
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5
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Seyoum MM, Ashworth AJ, Feye KM, Ricke SC, Owens PR, Moore PA, Savin M. Long-term impacts of conservation pasture management in manuresheds on system-level microbiome and antibiotic resistance genes. Front Microbiol 2023; 14:1227006. [PMID: 37886073 PMCID: PMC10598662 DOI: 10.3389/fmicb.2023.1227006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/13/2023] [Indexed: 10/28/2023] Open
Abstract
Animal manure improves soil fertility and organic carbon, but long-term deposition may contribute to antibiotic resistance genes (ARGs) entering the soil-water environment. Additionally, long-term impacts of applying animal manure to soil on the soil-water microbiome, a crucial factor in soil health and fertility, are not well understood. The aim of this study is to assess: (1) impacts of long-term conservation practices on the distribution of ARGs and microbial dynamics in soil, and runoff; and (2) associations between bacterial taxa, heavy metals, soil health indicators, and ARGs in manures, soils, and surface runoff in a study following 15 years of continuous management. This management strategy consists of two conventional and three conservation systems, all receiving annual poultry litter. High throughput sequencing of the 16S ribosomal RNA was carried out on samples of cattle manure, poultry litter, soil, and runoff collected from each manureshed. In addition, four representative ARGs (intl1, sul1, ermB, and blactx-m-32) were quantified from manures, soil, and runoff using quantitative PCR. Results revealed that conventional practice increased soil ARGs, and microbial diversity compared to conservation systems. Further, ARGs were strongly correlated with each other in cattle manure and soil, but not in runoff. After 15-years of conservation practices, relationships existed between heavy metals and ARGs. In the soil, Cu, Fe and Mn were positively linked to intl1, sul1, and ermB, but trends varied in runoff. These findings were further supported by network analyses that indicated complex co-occurrence patterns between bacteria taxa, ARGs, and physicochemical parameters. Overall, this study provides system-level linkages of microbial communities, ARGs, and physicochemical conditions based on long-term conservation practices at the soil-water-animal nexus.
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Affiliation(s)
- Mitiku Mihiret Seyoum
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Amanda J. Ashworth
- USDA-ARS, Poultry Production and Product Safety Research Unit, Fayetteville, AR, United States
| | - Kristina M. Feye
- Cellular and Molecular Biology, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science & Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Phillip R. Owens
- USDA-ARS, Dale Bumpers Small Farms Research Center, Booneville, AR, United States
| | - Philip A. Moore
- USDA-ARS, Poultry Production and Product Safety Research Unit, Fayetteville, AR, United States
| | - Mary Savin
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
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Fry KL, McPherson VJ, Gillings MR, Taylor MP. Tracing the Sources and Prevalence of Class 1 Integrons, Antimicrobial Resistance, and Trace Elements Using European Honey Bees. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:10582-10590. [PMID: 37417314 DOI: 10.1021/acs.est.3c03775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Surveillance of antimicrobial resistance is essential for an effective One Health response. This study explores the efficacy of European honey bees (Apis mellifera) for biomonitoring antimicrobial resistance (AMR) in urban areas. Class 1 integrons (intI1) are investigated as a universal AMR indicator, as well as associated cassette arrays and trace element contaminants at a city-wide scale. Class 1 integrons were found to be pervasive across the urban environment, occurring in 52% (75/144) of the honey bees assessed. The area of waterbodies within the honey bee's foraging radius was associated with intI1 prevalence, indicating an exposure pathway for future investigation to address. Trace element concentrations in honey bees reflected urban sources, supporting the application of this biomonitoring approach. As the first study of intI1 in honey bees, we provide insights into the environmental transfer of bacterial DNA to a keystone species and demonstrate how intI1 biomonitoring can support the surveillance of AMR.
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Affiliation(s)
- Kara L Fry
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
- EPA Science, Centre for Applied Sciences, Environment Protection Authority Victoria, Ernest Jones Drive, Macleod, Victoria 3085, Australia
| | - Vanessa J McPherson
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Michael R Gillings
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Mark Patrick Taylor
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
- EPA Science, Centre for Applied Sciences, Environment Protection Authority Victoria, Ernest Jones Drive, Macleod, Victoria 3085, Australia
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7
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Wang W, Shen P, Lu Z, Mo F, Liao Y, Wen X. Metagenomics reveals the abundance and accumulation trend of antibiotic resistance gene profile under long-term no tillage in a rainfed agroecosystem. Front Microbiol 2023; 14:1238708. [PMID: 37547681 PMCID: PMC10397733 DOI: 10.3389/fmicb.2023.1238708] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023] Open
Abstract
Widespread soil resistance can seriously endanger sustainable food production and soil health. Conservation tillage is a promising practice for improving soil structure and health. However, the impact of long-term no-tillage on the presence of antibiotic resistance genes in agricultural soils remains unexplored. Based on the long-term (>11 yr) tillage experimental fields that include both conservation tillage practices [no tillage (ZT)] and conventional tillage practices [plough tillage (PT)], we investigated the accumulation trend of antibiotic resistance genes (ARGs) in farmland soils under long-term no-tillage conditions. We aimed to provide a scientific basis for formulating agricultural production strategies to promote ecological environment safety and human health. In comparison to PT, ZT led to a considerable reduction in the relative abundance of both antibiotic resistance genes and antibiotic target gene families in the soil. Furthermore, the abundance of all ARGs were considerably lower in the ZT soil. The classification of drug resistance showed that ZT substantially decreased the relative abundance of Ethambutol (59.97%), β-lactams (44.87%), Fosfomycin (35.82%), Sulfonamides (34.64%), Polymyxins (33.67%), MLSB (32.78%), Chloramphenicol (28.57%), Multi-drug resistance (26.22%), Efflux pump (23.46%), Aminoglycosides (16.79%), Trimethoprim (13.21%), Isoniazid (11.34%), Fluoroquinolone (6.21%) resistance genes, compared to PT soil. In addition, the abundance of the bacterial phyla Proteobacteria, Actinobacteria, Acidobacteria, and Gemmatimonadetes decreased considerably. The Mantel test indicated that long-term ZT practices substantially increased the abundance of beneficial microbial flora and inhibited the enrichment of ARGs in soil by improving soil microbial diversity, metabolic activity, increasing SOC, TN, and available Zn, and decreasing pH. Overall, long-term no-tillage practices inhibit the accumulation of antibiotic resistance genes in farmland soil, which is a promising agricultural management measure to reduce the accumulation risk of soil ARGs.
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Affiliation(s)
- Weiyan Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Low-carbon Green Agriculture in Northwestern China, Ministry of Agriculture and Rural Affairs, Yangling, Shaanxi, China
- Key Laboratory of Crop Physi-ecology and Tillage Science in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Pengfei Shen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhiqiang Lu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Fei Mo
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuncheng Liao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoxia Wen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Low-carbon Green Agriculture in Northwestern China, Ministry of Agriculture and Rural Affairs, Yangling, Shaanxi, China
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Fu C, Qin Y, Xiang Q, Qiao M, Zhu Y. pH drives the spatial variation of antibiotic resistance gene profiles in riparian soils at a watershed scale. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 326:121486. [PMID: 36963452 DOI: 10.1016/j.envpol.2023.121486] [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: 02/05/2023] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
Owing to convenient water access, riparian areas are often sites for intensive livestock breeding industries and agriculture, which can increase the spread of antibiotic resistance genes (ARGs). However, studies on ARG profiles in riparian soils are limited and there is little information regarding the factors influencing ARGs at a watershed scale. Here, we analyzed ARG profiles, bacterial communities, and soil properties in riparian soils under different land-use types. A total of 124 ARGs and 25 mobile genetic elements (MGEs) were detected in the riparian soils, which covered almost all major classes of antibiotics. Non-metric multidimensional scaling analysis showed that both the distance to the water reservoir and land-use types played important roles in shaping ARG profiles in riparian soils at a watershed scale. Downstream soils harbored three times the abundance of ARGs compared with upstream and midstream soils. Distance-decay analysis indicated that the similarity of ARG profiles and bacterial community composition decreased significantly with the increase of geographical distance (p < 0.001). When taking the land-use type into consideration, the relative abundance and diversity of ARGs and MGEs in orchard and farmland soils were significantly higher than those in wasteland soils. This indicated that anthropogenic activities can also affect ARG patterns in riparian soils. MGE abundance was identified as major driving factors of ARG profiles. In addition, among all the examined soil properties, soil pH was found to be more important than nutrients and organic carbon in shaping ARG profiles. Our findings provide valuable data on ARG distribution in riparian soils in a reservoir catchment and highlight downstream soils is crucial for ensuring water source security.
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Affiliation(s)
- Chenxi Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Yuan Qin
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Qian Xiang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, China
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China.
| | - Yongguan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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9
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Spets P, Ebert K, Dinnétz P. Spatial analysis of antimicrobial resistance in the environment. A systematic review. GEOSPATIAL HEALTH 2023; 18. [PMID: 37246541 DOI: 10.4081/gh.2023.1168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/20/2023] [Indexed: 05/30/2023]
Abstract
Antimicrobial resistance (AMR) is a global major health concern. Spatial analysis is considered an invaluable method in health studies. Therefore, we explored the usage of spatial analysis in Geographic Information Systems (GIS) in studies on AMR in the environment. This systematic review is based on database searches, a content analysis, ranking of the included studies according to the preference ranking organization method for enrichment evaluations (PROMETHEE) and estimation of data points per km2. Initial database searches resulted in 524 records after removal of duplicates. After the last stage of full text screening, 13 greatly heterogeneous articles with diverse study origins, methods and design remained. In the majority of studies, the data density was considerably less than one sampling site per km2 but exceeded 1,000 sites per km2 in one study. The results of the content analysis and ranking showed a variation between studies that primarily used spatial analysis and those that used spatial analysis as a sec ondary method. We identified two distinct groups of GIS methods. The first was focused on sample collection and laboratory testing, with GIS as supporting method. The second group used overlay analysis as the primary method to combine datasets in a map. In one case, both methods were combined. The low number of articles that met our inclusion criteria highlights a research gap. Based on the findings of this study we encourage application of GIS to its full potential in studies of AMR in the environment.
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Affiliation(s)
- Patrick Spets
- Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge.
| | - Karin Ebert
- Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge.
| | - Patrik Dinnétz
- Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge.
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Hu NW, Yu HW, Deng BL, Hu B, Zhu GP, Yang XT, Wang TY, Zeng Y, Wang QY. Levels of heavy metal in soil and vegetable and associated health risk in peri-urban areas across China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 259:115037. [PMID: 37210996 DOI: 10.1016/j.ecoenv.2023.115037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/28/2023] [Accepted: 05/17/2023] [Indexed: 05/23/2023]
Abstract
Peri-urban vegetable field plays an essential role in providing vegetables for local residents. Because of its particularity, it is affected by both industrial and agricultural activities which have led to the accumulations of heavy metal in soil. So far, information on heavy metal pollution status, spatial features, and human health risks in peri-urban vegetable areas across China is still scarce. To fill this gap, we systematically compiled soil and vegetable data collected from 123 articles published between 2010 and 2022 at a national level. The pollution status of heavy metals (i.e., cadmium (Cd), mercury (Hg), arsenic (As), lead (Pb), chromium (Cr), copper (Cu), nickel (Ni), and zinc (Zn)) in peri-urban vegetable soils and vegetables were investigated. To evaluate the levels of heavy metal pollution in soil and human health risks, the geoaccumulation index (Igeo) and target hazard quotient (HQ) were calculated. The results showed that mean concentrations of Cd, Hg, As, Pb, Cr, Cu, Ni, and Zn in peri-urban vegetable soils were 0.50, 0.53, 12.03, 41.97, 55.56, 37.69, 28.55, and 75.38 mg kg-1, respectively. The main pollutants in peri-urban vegetable soil were Cd and Hg, and 85.25% and 92.86% of the soil samples had Igeo > 1, respectively. The mean Igeo values of this regions followed the order of northwest > central > south > north > east > southwest > northeast for Cd and northeast > northwest > north > southwest > east > central > south for Hg. The mean Cd, Hg, As, Pb, Cr, Cu, Ni, and Zn concentrations in vegetables were 0.30, 0.26, 0.37, 0.54, 1.17, 6.17, 1.96, and 18.56 mg kg-1, respectively. Approximately 87.01% (Cd), 71.43% (Hg), 20% (As), 65.15% (Pb), 27.08% (Cr) of the vegetable samples exceeded the safety requirement values. The vegetables grown in central, northwest, and northern China accumulated much more heavy metals than those grown in other regions. As the HQ values for adults, 53.25% (Cd), 71.43% (Hg), 84.00% (As), and 58.33% (Cr) of the sampled vegetables were higher than 1. For children, the HQ values were higher than 1 for 66.23% (Cd), 73.81% (Hg), 86.00% (As), and 87.50% (Cr) of the sampled vegetables. The findings of this study demonstrate that the situation of heavy metal pollution in peri-urban vegetable areas across China are not optimistic and residents who consume the vegetables are at high risk of health issues. To ensure soil quality and human health, strategies should be taken to guide vegetable production and remedy soil pollution in peri-urban areas with the rapidly urbanizing China.
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Affiliation(s)
- Nai-Wen Hu
- Key Laboratory of Wet Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Wen Yu
- Key Laboratory of Wet Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Bo-Ling Deng
- Key Laboratory of Wet Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Hu
- Agricultural Technology and Extension Center of Jilin Province, Changchun 130033, China
| | - Guo-Peng Zhu
- Key Laboratory of Wet Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiu-Tao Yang
- Key Laboratory of Wet Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Tian-Ye Wang
- Key Laboratory of Wet Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Ying Zeng
- Key Laboratory of Wet Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Quan-Ying Wang
- Key Laboratory of Wet Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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11
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Marutescu LG. Current and Future Flow Cytometry Applications Contributing to Antimicrobial Resistance Control. Microorganisms 2023; 11:1300. [PMID: 37317273 DOI: 10.3390/microorganisms11051300] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
Antimicrobial resistance is a global threat to human health and welfare, food safety, and environmental health. The rapid detection and quantification of antimicrobial resistance are important for both infectious disease control and public health threat assessment. Technologies such as flow cytometry can provide clinicians with the early information, they need for appropriate antibiotic treatment. At the same time, cytometry platforms facilitate the measurement of antibiotic-resistant bacteria in environments impacted by human activities, enabling assessment of their impact on watersheds and soils. This review focuses on the latest applications of flow cytometry for the detection of pathogens and antibiotic-resistant bacteria in both clinical and environmental samples. Novel antimicrobial susceptibility testing frameworks embedding flow cytometry assays can contribute to the implementation of global antimicrobial resistance surveillance systems that are needed for science-based decisions and actions.
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Affiliation(s)
- Luminita Gabriela Marutescu
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 91-95 Spl. Independentei, 050095 Bucharest, Romania
- Research Institute of the University of Bucharest, 050095 Bucharest, Romania
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12
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Zhang S, Li T, Hu J, Li K, Liu D, Li H, Wang F, Chen D, Zhang Z, Fan Q, Cui X, Che R. Reforestation substantially changed the soil antibiotic resistome and its relationships with metal resistance genes, mobile genetic elements, and pathogens. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 342:118037. [PMID: 37178462 DOI: 10.1016/j.jenvman.2023.118037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Revealing the effects of reforestation on soil antibiotic resistome is essential for assessing ecosystem health, yet related studies remain scarce. Here, to determine the responses of the soil antibiotic resistome to reforestation, 30 pairs of cropland and forest soil samples were collected from southwestern China, a region with high environmental heterogeneity. All the forests had been derived from croplands more than one decade ago. The diversity and abundance of soil antibiotic resistance genes (ARGs), metal resistance genes (MRGs), mobile genetic elements (MGEs), and pathogens were determined by metagenomic sequencing and real-time PCR. The results showed that reforestation significantly increased soil microbial abundance and the contents of Cu, total carbon, total nitrogen, total organic carbon, and ammonium nitrogen. Nevertheless, it decreased the contents of soil Zn, Ba, nitrate nitrogen, and available phosphorus. The main soil ARGs identified in this region were vancomycin, multidrug, and bacitracin resistance genes. Reforestation significantly increased the soil ARG abundance by 62.58%, while it decreased the ARG richness by 16.50%. Reforestation exerted no significant effects on the abundance of heavy metal resistance genes and pathogens, but it doubled the abundance of MGEs. Additionally, reforestation substantially decreased the co-occurrence frequencies of ARGs with MRGs and pathogens. In contrast, the correlation between ARGs and MGEs was greatly enhanced by reforestation. Similarly, the correlations between soil ARG abundance and environmental factors were also strengthened by reforestation. These findings suggest that reforestation can substantially affect the soil antibiotic resistome and exerts overall positive effects on soil health by decreasing ARG richness, providing critical information for assessing the effects of "grain for green" project on soil health.
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Affiliation(s)
- Song Zhang
- Institute of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University, Kunming, 650500, China; State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Ting Li
- Institute of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University, Kunming, 650500, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinming Hu
- Institute of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University, Kunming, 650500, China
| | - Kexin Li
- Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Dong Liu
- School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Haixia Li
- Faculty of Land Resource Engineering, Kunming University of Science and Technology, Kunming, 650093, China
| | - Fang Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danhong Chen
- Institute of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University, Kunming, 650500, China
| | - Zejin Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiuping Fan
- Institute of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University, Kunming, 650500, China
| | - Xiaoyong Cui
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rongxiao Che
- Institute of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Yunnan University, Kunming, 650500, China.
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13
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Ke Z, Tang J, Yang L, Sun J, Xu Y. Linking pharmaceutical residues to dissolved organic matter and aquatic bacterial communities in a highly urbanized bay. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162027. [PMID: 36740058 DOI: 10.1016/j.scitotenv.2023.162027] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Pharmaceuticals are causing environmental concerns associated with their widespread distribution in aquatic ecosystems. The environmental fate and behavior of pharmaceutical residues are related to dissolved organic matter and bacterial communities, both of which are strongly influenced by human activities. However, the relationships among pharmaceutical pollution, dissolved organic matter pool, and bacterial community structure under the pressure of human activities are still unclear, especially in highly urbanized bay areas. In this study, we investigated the occurrence and distribution of 35 pharmaceuticals in a typical urbanized bay (Hangzhou Bay) in Eastern China, and analyzed their relationships with dissolved organic matter and aquatic bacterial community structure. The target pharmaceuticals were ubiquitously detected in surface water samples, with their concentrations ranging from undetectable to 263 ng/L. The detected pharmaceuticals were mostly sulfonamides, macrolides, antidepressants, and metabolites of stimulants. Significant positive correlations were observed between the concentrations of pharmaceuticals and the intensity of human activities. Strong correlations also emerged between the concentration of antidepressants and the speed of urban expansion, as well as between the concentration of cardiovascular drugs and the population density or nightlight index. Three fluorescent components (protein-like C1, terrestrial humic-like C2, protein tryptophan-like C3) were significantly positively correlated with the total concentration of pharmaceuticals. Pharmaceutical pollution reshaped aquatic bacterial communities, based on the close correlation observed between pharmaceutical concentration and bacterial community structure. The results elucidate the potential dynamics of dissolved organic matter pool and aquatic bacterial communities in response to pharmaceutical pollution in urbanized bay ecosystems.
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Affiliation(s)
- Ziyan Ke
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315800, China
| | - Jianfeng Tang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315800, China.
| | - Lei Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jing Sun
- College of Resources and Environment, Chengdu University of Information Technology, Chengdu 610225, China
| | - Yaoyang Xu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315800, China
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14
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Zhao F, Yang L, Tang J, Fang L, Yu X, Li M, Chen L. Urbanization-land-use interactions predict antibiotic contamination in soil across urban-rural gradients. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161493. [PMID: 36634779 DOI: 10.1016/j.scitotenv.2023.161493] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Antibiotics ubiquitously occur in soils and pose a potential threat to ecosystem health. Concurrently, urbanization and land-use intensification have transformed soil ecosystems, but how they affect antibiotic contamination remain largely unknown. Therefore, we profiled a broad-scale pattern of antibiotics in soil from agricultural lands and green spaces across urbanization gradients, and explored the hypothetical models to verify the effects of urbanization and land-use intensity on antibiotic contamination. The results showed that antibiotic concentrations and seasonality were higher in agricultural soil than in green spaces, which respectively showed linear or hump-shaped declines along with the increasing distance to urban centers. However, the response of antibiotic pollution to land-use intensity depended strongly on the urbanization level. More importantly, interactions between urbanization and land-use explained, on average, 59.6 % of the variation in antibiotic concentrations in soil across urbanization gradients. The proposed interactions can predict the non-linear changes in soil vulnerability to antibiotic contamination. Our study revealed that the urbanization can modulate the effects of land-use intensity on antibiotic concentration and seasonality in the soil environment, and that there is high stress on peri-urban soil ecosystems due to ongoing land-use changes arising from rapid urbanization processes.
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Affiliation(s)
- Fangkai Zhao
- School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lei Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianfeng Tang
- CAS Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Li Fang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan 316021, China
| | - Xinwei Yu
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan 316021, China
| | - Min Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liding Chen
- School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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15
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Hilal MG, Han B, Yu Q, Feng T, Su W, Li X, Li H. Insight into the dynamics of drinking water resistome in China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 322:121185. [PMID: 36736566 DOI: 10.1016/j.envpol.2023.121185] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/12/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Antibiotic resistance (AR) is a serious environmental hazard of the current age. Antibiotic resistance genes (ARGs) are the fundamental entities that spread AR in the environment. ARGs are likely to be transferred from the non-pathogenic to pathogenic microbes that might ultimately be responsible for the AR in humans and other organisms. Drinking water (DW) is the primary interaction route between ARGs and humans. Being the highest producer and consumer of antibiotics China poses a potential threat to developing superbugs and ARGs dissemination. Herein, we comprehensively seek to review the ARGs from dominant DW sources in China. Furthermore, the origin and influencing factors of the ARGs to the DW in China have been evaluated. Commonly used methods, both classical and modern, are being compiled. In addition, the risk posed and mitigation strategies of DW ARGs in China have been outlined. Overall, we believe this review would contribute to the assessment of ARGs in DW of China and their dissemination to humans and other animals and ultimately help the policymakers and scientists in the field to counteract this problem on an emergency basis.
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Affiliation(s)
- Mian Gul Hilal
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China; MOE, Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China
| | - Binghua Han
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qiaoling Yu
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Tianshu Feng
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Wanghong Su
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Xiangkai Li
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, 730000, Gansu, PR China
| | - Huan Li
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, 730000, China.
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16
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Xiang Q, Zhu D, Qiao M, Yang XR, Li G, Chen QL, Zhu YG. Temporal dynamics of soil bacterial network regulate soil resistomes. Environ Microbiol 2023; 25:505-514. [PMID: 36478095 DOI: 10.1111/1462-2920.16298] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
Soil bacteria are diverse and form complicated ecological networks through various microbial interactions, which play important roles in soil multi-functionality. However, the seasonal effects on the bacterial network, especially the relationship between bacterial network topological features and soil resistomes remains underexplored, which impedes our ability to unveil the mechanisms of the temporal-dynamics of antibiotic resistance genes (ARGs). Here, a field investigation was conducted across four seasons at the watershed scale. We observed significant seasonal variation in bacterial networks, with lower complexity and stability in autumn, and a wider bacterial community niche in summer. Similar to bacterial communities, the co-occurrence networks among ARGs also shift with seasonal change, particularly with respect to the topological features of the node degree, which on average was higher in summer than in the other seasons. Furthermore, the nodes with higher betweenness, stress, degree, and closeness centrality in the bacterial network showed strong relationships with the 10 major classes of ARGs. These findings highlighted the changes in the topological properties of bacterial networks that could further alter antibiotic resistance in soil. Together, our results reveal the temporal dynamics of bacterial ecological networks at the watershed scale, and provide new insights into antibiotic resistance management under environmental changes.
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Affiliation(s)
- Qian Xiang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
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17
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Scott LC, Aubee A, Wilson MJ, Esser S, Descamps D, Lee N, Distler E, Aw TG. Leave No Trace? Ecological and anthropogenic determinants of antibiotic resistant bacteria in a recreational alpine environment. ENVIRONMENTAL RESEARCH 2023; 216:114617. [PMID: 36273598 DOI: 10.1016/j.envres.2022.114617] [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: 06/18/2022] [Revised: 10/05/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic resistant bacteria (ARB) have been detected in remote environments, but the degree to which their presence is due to anthropogenic contamination remains unclear. Here, anthropogenic and ecological determinants of ARB were characterized in remote and highly visited areas of Rocky Mountain National Park in the United States. Soil and water samples were collected from 29 sites once a month for three months and measured for bacteria resistant to seven antibiotics with flow cytometry. A novel index of the likelihood of human presence (HPI) was generated for estimating human impact on ARB abundance. The HPI accounted for 44% of variation in ARB abundance in water samples (p < 0.0001) and 51% of variation in soil samples (p < 0.00001). Human presence index was illustrated as a reliable predictor of ARB abundance despite a tendency to underpredict at higher levels of human impact. Ecological determinants such as temperature, elevation, slope, and aspect were also found to be significantly associated with ARB abundance. These findings suggest that human presence drives the abundance of ARB in Rocky Mountain National Park, but ecological variables play a significant role in their presence and dispersal.
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Affiliation(s)
- Laura C Scott
- Tulane University School of Public Health and Tropical Medicine, Department of Environmental Health Sciences, New Orleans, LA, 70112, USA.
| | - Alexandra Aubee
- Tulane University School of Public Health and Tropical Medicine, Department of Environmental Health Sciences, New Orleans, LA, 70112, USA
| | - Mark J Wilson
- Tulane University School of Public Health and Tropical Medicine, Department of Environmental Health Sciences, New Orleans, LA, 70112, USA
| | - Scott Esser
- Continental Divide Research Learning Center, Rocky Mountain National Park, National Park Service, Estes Park, CO, 80517, USA
| | - Denisse Descamps
- Tulane University School of Public Health and Tropical Medicine, Department of Epidemiology, New Orleans, LA, 70112, USA
| | - Nicholas Lee
- Tulane University School of Public Health and Tropical Medicine, Department of Environmental Health Sciences, New Orleans, LA, 70112, USA
| | - Emiko Distler
- Tulane University School of Public Health and Tropical Medicine, Department of Environmental Health Sciences, New Orleans, LA, 70112, USA
| | - Tiong Gim Aw
- Tulane University School of Public Health and Tropical Medicine, Department of Environmental Health Sciences, New Orleans, LA, 70112, USA.
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18
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Zhang L, Ju Z, Su Z, Fu Y, Zhao B, Song Y, Wen D, Zhao Y, Cui J. The antibiotic resistance and risk heterogeneity between urban and rural rivers in a pharmaceutical industry dominated city in China: The importance of social-economic factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158530. [PMID: 36063953 DOI: 10.1016/j.scitotenv.2022.158530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Rivers are important environmental sources of human exposure to antibiotic resistance. Many factors can change antibiotic resistance in rivers, including bacterial communities, human activities, and environmental factors. However, the systematic comparison of the differences in antibiotics resistance and risks between urban rivers (URs) and rural rivers (RRs) in a pharmaceutical industry dominated city is still rare. In this study, Shijiazhuang City (China) was selected as an example to compare the differences in antibiotics resistance and risks between URs and RRs. The results showed higher concentrations of total quinolones (QNs) antibiotics in both water and sediment samples collected from URs than those from RRs. The subtypes and abundances of antibiotic resistance genes (ARGs) in URs were significantly higher than those in RRs, and most emerging ARGs (including OXA-type, GES-type, MCR-type, and tet(X)) were only detected in URs. The ARGs were mainly influenced by QNs in URs and social-economic factors (SEs) in RRs. The composition of the bacterial community was significantly different between URs and RRs. The abundance of antibiotic-resistant pathogenic bacteria (ARPBs) and virulence factors (VFs) were higher in URs than those in RRs. Therein, 371 and 326 pathogen types were detected in URs and RRs, respectively. Most emerging ARGs showed a significantly positive correlation with priority ARPBs. Variance partitioning analysis revealed that SEs were the main driving factors of ARGs (80 %) and microbial communities (92 %) both in URs and RRs. Structural equation models indicated that antibiotics (QNs) and microbial communities were the most direct influence of ARGs in URs and RRs, respectively. The cumulative resistance risk of QNs was high in URs, but relatively low in RRs. Enrofloxacin and flumequine posed the highest risk in water and sediment, respectively. This study could help us to better manage and control the risk of antibiotic resistance in different rivers.
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Affiliation(s)
- Lulu Zhang
- College of Environment Science and Engineering, Hebei University of Science and Technology, 050000 Shijiazhuang, Hebei Province, China; College of Environmental Science and Engineering, Peking University, 100871 Beijing, China.
| | - Zejia Ju
- College of Environment Science and Engineering, Hebei University of Science and Technology, 050000 Shijiazhuang, Hebei Province, China
| | - Zhiguo Su
- College of Environmental Science and Engineering, Peking University, 100871 Beijing, China
| | - Yu Fu
- College of Environment Science and Engineering, Hebei University of Science and Technology, 050000 Shijiazhuang, Hebei Province, China
| | - Bo Zhao
- College of Environment Science and Engineering, Hebei University of Science and Technology, 050000 Shijiazhuang, Hebei Province, China
| | - Yuanmeng Song
- College of Environment Science and Engineering, Hebei University of Science and Technology, 050000 Shijiazhuang, Hebei Province, China
| | - Donghui Wen
- College of Environmental Science and Engineering, Peking University, 100871 Beijing, China
| | - Yu Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China
| | - Jiansheng Cui
- College of Environment Science and Engineering, Hebei University of Science and Technology, 050000 Shijiazhuang, Hebei Province, China
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19
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Feng T, Han Q, Su W, Yu Q, Yang J, Li H. Microbiota and mobile genetic elements influence antibiotic resistance genes in dust from dense urban public places. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 311:119991. [PMID: 35987288 DOI: 10.1016/j.envpol.2022.119991] [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: 05/04/2022] [Revised: 08/01/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Many contaminants were carried by dust, a common environment media that is easy to contact with human beings, and antibiotic resistance genes (ARGs) as an emergency pollutant also harbor in dust and pose serious threats to human health especially those carried by opportunistic pathogens because inactivation of antibiotics caused by ARGs may enhance pathogenicity. Considering there is a gap of investigation of dust ARGs, 16 S rRNA gene sequences and high-throughput quantitative PCR were employed to obtain information of microbial communities and accumulated ARGs in dust from different urban places, including the malls, hospitals, schools and parks, to investigate the distribution and influencing factors of ARGs and discover the potential hosts of ARGs in dust. Here, 9 types of ARGs such as sulfonamide, tetracycline, and beta-lactamase and 71 subtypes of ARGs like sul1, tetM-01, and drfA1 were detected in dust. ARGs had varying distribution in different public places and seasons in dust. The abundances of total ARGs, MLSB and tetracycline genes were higher in spring than summer. The diversity of ARGs was highest in malls, follow by hospitals, schools, and parks. Additionally, multi-drug resistance genes in dust were more abundant in hospitals than in schools and parks. The microbes were distinguished as the most important driving factors for ARGs in dust, followed by the mobile genetic elements (MGEs) and different places, while dust physicochemical parameters only exert a negligible impact. Notably, several opportunistic pathogens like the Streptococcus, Vibrio, and Pseudomonas were inferred as potential hosts of high-risk ARGs such as mecA, tetM-02, and tetO-01 in dust because of strongly positive co-occurrence. These results imply that dust is likely an important reservoir of ARGs. We should realize that ARGs may be harbored in some opportunistic pathogens occur in dust and endanger human health because of dust contacting to human easily.
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Affiliation(s)
- Tianshu Feng
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou, 730000, China; State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.
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Wang J, Zhang Q, Chu H, Shi Y, Wang Q. Distribution and co-occurrence patterns of antibiotic resistance genes in black soils in Northeast China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 319:115640. [PMID: 35809539 DOI: 10.1016/j.jenvman.2022.115640] [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: 12/30/2021] [Revised: 06/22/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Black soils (Mollisols) are among the most important soil resources for crop production and food security. In China, they are mainly distributed in the northeastern region. To investigate soil antibiotic resistance distribution patterns and monitor soil quality, we randomly chose nine corn fields in Northeast China and analyzed the antibiotic resistance gene (ARG) distribution and co-occurrence patterns on the basis of high-throughput approaches and network analyses. High genetic diversity (136 unique genes) and low ARG abundances (10-5-10-2 copies/16S rRNA gene copy) were detected, with relatively few interactions among ARGs. Type I integron genes were prevalent in the soil and were positively correlated with ARGs, which may increase the risk of ARG transmission. Most ARGs were strongly associated with microorganisms. Moreover, several ARGs were significantly correlated with antibiotics, nutrients, and metal elements. The generation and dissemination of ARGs, which were most likely mediated by mobile genetic elements (MGEs) and bacteria, were affected by environmental conditions. These results provide insights into the widespread co-occurrence patterns in soil resistomes.
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Affiliation(s)
- Jianmei Wang
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 100081, PR China; Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Qianru Zhang
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 100081, PR China.
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, PR China
| | - Qing Wang
- Hebei Key Laboratory of Air Pollution Cause and Impact (Preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, PR China
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Zhao F, Yang L, Yen H, Yu X, Fang L, Li M, Chen L. Can agricultural land use alter the responses of soil biota to antibiotic contamination? JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129350. [PMID: 35749896 DOI: 10.1016/j.jhazmat.2022.129350] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/27/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Antibiotics accumulate in soils via various agricultural activities, endangering soil biota that play fundamental roles in maintaining agroecosystem function. However, the effects of land-use heterogeneity on soil biota tolerance to antibiotic stresses are not well understood. In this study, we explored the relationships between antibiotic residues, bacterial communities, and earthworm populations in areas with different land-use types (forest, maize, and peanut fields). The results showed that antibiotic levels were generally higher in maize and peanut fields than in forests. Furthermore, land use modulated the effects of antibiotics on soil bacterial communities and earthworm populations. Cumulative antibiotic concentrations in peanut fields were negatively correlated with bacterial diversity and earthworm abundance, whereas no significant correlations were detected in maize fields. In contrast, antibiotics improved bacterial diversity and richness in forest soils. Generally, earthworm populations showed stronger tolerance to antibiotics than did soil bacterial communities. Agricultural land use differentially modified the responses of the soil bacterial community and earthworm population to antibiotic contamination, and earthworms might provide an alternative for controlling antibiotic contamination.
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Affiliation(s)
- Fangkai Zhao
- School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lei Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haw Yen
- School of Forestry and Wildlife Sciences, Auburn University, Auburn 36849, USA; Environmental Exposure Modeling, Bayer US Crop Science Division, Chesterfield 63017, USA
| | - Xinwei Yu
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, 316021, China
| | - Li Fang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, 316021, China
| | - Min Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liding Chen
- School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Yan M, Zhu C, Song T, Li B, Su S, Li H. Impact of different manure-derived dissolved organic matters on the fate of arsenic-antibiotic in co-contaminated paddy soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119376. [PMID: 35491001 DOI: 10.1016/j.envpol.2022.119376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/12/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
Manure application increases the transfer risk of antibiotic resistance to farmland. Especially, its impact remains unclear when it occurs in arsenic (As)-contaminated paddy soils, which is considered as a global environmental problem. In this work, we investigated the fate of antibiotic resistance genes (ARGs) in As-antibiotic co-contaminated paddy soils under the application of manure from different sources (pig manure, cow dung, and chicken manure). Differences in the aliphatic carbon and electron-donating capacities of these dissolved organic matters (DOM) regulated the transformation of iron and As by both biotic and abiotic processes. The regulation by pig manure was stronger than that by cow dung and chicken manure. DOM regulation increased the abundance of As-related functional genes (arsC, arrA, aioA, and arsM) in the soil and accelerated the transformation of As speciation, the highest proportion of As(III) being 45%-61%. Meanwhile, the continuous selection pressure provided by the highly toxic As(III) increased the risk of ARGs and mobile genetic elements (MGEs) via horizontal gene transfer. As-resistant bacteria, including Bacillus, Geobacter, and Desulfitobacterium, were finally considered as potential host bacteria for ARGs and MGEs. In summary, this study clarified the synergistic mechanism of As-antibiotic on the fate of ARGs in co-contaminated paddy soils, and provided practical guidance for the proper application of organic fertilizers.
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Affiliation(s)
- Mengmeng Yan
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Changxiong Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Tingting Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Binxu Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Shiming Su
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Hongna Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
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Wang Z, Han R, Muhammad A, Guan DX, Zama E, Li G. Correlative distribution of DOM and heavy metals in the soils of the Zhangxi watershed in Ningbo city, East of China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 299:118811. [PMID: 35007678 DOI: 10.1016/j.envpol.2022.118811] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/02/2021] [Accepted: 01/06/2022] [Indexed: 05/27/2023]
Abstract
In peri-urban critical zones, soil ecosystems are highly affected by increasing urbanization, causing probably an intense interaction between dissolved organic matter (DOM) and heavy metals in soil. Such interaction is critical for understanding the biogeochemical cycles of both organic matter and heavy metals in these zones. However, limited research has reported the correlative distribution of DOM and heavy metals at high seasonal and spatial resolutions in peri-urban critical zones. In this study, 160 soil samples were collected from the farmland and forestland of Zhangxi watershed, in Ningbo, eastern China during spring, summer, fall and winter four seasons. UV-visible absorption and fluorescent spectroscopy were used to explore the optical characteristics of DOM. The results indicated a mixture of exogenous and autogenous sources of DOM in the Zhangxi watershed, while DOM in farmland exhibited a higher degree of aromaticity and humification than that in forestland. Fluorescent results showed that humic acid-like, fulvic acid-like and microbial-derived humic-like fractions were mostly affected by seasons. The distribution of heavy metals was affected mainly by land-use changes and seasons. Correlation analysis between heavy metals and DOM characteristics and components suggested that aromatic and humic substances were more favorable in binding with EDTA extractable Ni, Cu, Zn and Cd. The bioavailable Cd and Pb decreased due to binding with humic fractions, indicating its great effects on the bioavailability of Cd and Pb. Overall, these findings provide an insight into the correlative distributions of DOM and heavy metals in peri-urban areas, thereby highlighting their biogeochemical cycling in the soil environment.
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Affiliation(s)
- Zhe Wang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, PR China
| | - Ruixia Han
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, PR China
| | - Azeem Muhammad
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, PR China
| | - Dong-Xing Guan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Eric Zama
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, PR China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, PR China.
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Nugent A, Allison SD. A framework for soil microbial ecology in urban ecosystems. Ecosphere 2022. [DOI: 10.1002/ecs2.3968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Andie Nugent
- Department of Ecology and Evolutionary Biology University of California–Irvine Irvine California USA
| | - Steven D. Allison
- Department of Ecology and Evolutionary Biology University of California–Irvine Irvine California USA
- Department of Earth System Science University of California–Irvine Irvine California USA
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25
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Distribution and Transfer of Antibiotic Resistance Genes in Coastal Aquatic Ecosystems of Bohai Bay. WATER 2022. [DOI: 10.3390/w14060938] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Antibiotic resistance genes (ARGs) are abundant in diverse ecosystems and the resistome may constitute a health threat for humans and animals. It is necessary to uncover ARGs and the accumulation mechanisms from different environmental sources. Various habitats, such as soil, seawater and fish intestines, could overflow a considerable amount of ARGs and the horizontal transfer of ARGs may occur in these environments. Thus, we assessed the composition and abundance of ARGs in seawater, soil and intestinal tracts of Cynoglossus semilaevis collected from different sites in Bohai Bay (China), including a natural area and three fish farms, through a high-throughput qPCR array. In total, 243 ARGs were uncovered, governing the resistance to aminoglycoside, multidrug, beta-lactamase, macrolide lincosamide streptomycin B (MLSB), chloramphenicol, sulfonamide, tetracycline, vancomycin and other antibiotics. The action mechanisms of these ARGs were mainly antibiotic deactivation, efflux pump and cellular protection. Importantly, similar ARGs were detected in different samples but show dissimilar enrichment levels. ARGs were highly enriched in the fish farms compared to the natural sea area, with more genes detected, while some ARGs were detected only in the natural sea area samples, such as bacA-02, tetL-01 and ampC-06. Regarding sample types, water samples from all locations shared more ARGs in common and held the highest average level of ARGs detected than in the soil and fish samples. Mobile genetic elements (MGEs) were also detected in three sample types, in the same trend as ARGs. This is the first study comparing the resistome of different samples of seawater, soil and intestines of C. semilaevis. This study contributes to a better understanding of ARG dissemination in water sources and could facilitate the effective control of ARG contamination in the aquatic environment.
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Wang L, Chai B. Fate of Antibiotic Resistance Genes and Changes in Bacterial Community With Increasing Breeding Scale of Layer Manure. Front Microbiol 2022; 13:857046. [PMID: 35356511 PMCID: PMC8959713 DOI: 10.3389/fmicb.2022.857046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/22/2022] [Indexed: 11/24/2022] Open
Abstract
The use of antimicrobials in intensive poultry production is becoming increasingly common because of its high throughput of meat and egg products. However, the profile of antibiotic resistance genes (ARGs) and the underlying mechanisms in different breeding scale farms were not fully explored. The study examined the profiles of ARGs in layer manure from three free-range and 12 intensive layer farms with different scales (N500, N5000, N10000, and N20000). A quantitative PCR (qPCR) array was used to quantify ARGs, and microbial community structure was analyzed by 16S rRNA gene sequencing. A total of 48 ARGs, belonging to seven major types, were identified in the layer manure samples, with sul2, tetM-01, and ermB being the predominant ones. The abundance, diversity, and mobility potential of ARGs in layer manure changed significantly with the increasing of the breeding scale. The abundances of total ARGs had significantly positive correlations with mobile genetic elements (MGEs), suggesting the mobility potential of ARGs in layer manure samples. Bacterial abundance did not show significant differences among the five group manure samples. However, bacterial diversity showed an increasing trend along the breeding scale. Pathogenic Bacteroidetes increased in the largest-scale layer manure samples and showed significant positive correlations with most ARGs. Network analysis revealed significant co-occurrence patterns between ARGs and microbial taxa, indicating ARGs had a wide range of bacterial hosts. Proteobacteria and Firmicutes were potential hosts for tetracycline and macrolide-lincosamide-streptogramin B (MLSB) resistant genes. Our results indicated that the expansion of the breeding scale of a farm promotes the abundance, diversity, and mobility potential of ARGs in layer manure.
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Hobeika W, Gaschet M, Ploy MC, Buelow E, Sarkis DK, Dagot C. Resistome Diversity and Dissemination of WHO Priority Antibiotic Resistant Pathogens in Lebanese Estuaries. Antibiotics (Basel) 2022; 11:antibiotics11030306. [PMID: 35326767 PMCID: PMC8944630 DOI: 10.3390/antibiotics11030306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 11/23/2022] Open
Abstract
Anthropogenic pressure is known to be a key driver of antimicrobial resistance (AMR) dissemination in the environment. Especially in lower income countries, with poor infrastructure, the level of AMR dissemination is high. Therefore, we assessed the levels and diversity of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in Lebanese rivers at estuaries’ sites (n = 72) of the Mediterranean Sea in spring 2017 and winter 2018. Methods: A combined approach using culture techniques and high throughput qPCR were applied to identify ARB and ARGs in rivers along the Lebanese coast. Results: Multidrug-resistant Gram-negative (Enterobacterales and Pseudomonas spp.) and Gram-positive bacterial pathogens were isolated. Levels of ARGs were highest in the winter campaign and areas with high anthropogenic activities and population growth with an influx of refugees. Conclusion: Qualitative analysis of ARB and the analysis of the Lebanese estuaries’ resistome revealed critical levels of contamination with pathogenic bacteria and provided significant information about the spread of ARGs in anthropogenically impacted estuaries.
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Affiliation(s)
- Wadad Hobeika
- Université de Limoges, INSERM, CHU Limoges, 87085 Limoges, France; (W.H.); (M.G.); (M.-C.P.)
- Microbiology Laboratory, School of Pharmacy, Saint-Joseph University, Beirut 17-5208, Lebanon;
| | - Margaux Gaschet
- Université de Limoges, INSERM, CHU Limoges, 87085 Limoges, France; (W.H.); (M.G.); (M.-C.P.)
| | - Marie-Cécile Ploy
- Université de Limoges, INSERM, CHU Limoges, 87085 Limoges, France; (W.H.); (M.G.); (M.-C.P.)
| | - Elena Buelow
- Université Grenoble Alpes, CNRS, TIMC, 38000 Grenoble, France
- Correspondence: (E.B.); (C.D.)
| | - Dolla Karam Sarkis
- Microbiology Laboratory, School of Pharmacy, Saint-Joseph University, Beirut 17-5208, Lebanon;
| | - Christophe Dagot
- Université de Limoges, INSERM, CHU Limoges, 87085 Limoges, France; (W.H.); (M.G.); (M.-C.P.)
- Correspondence: (E.B.); (C.D.)
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28
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Wang H, Su X, Su J, Zhu Y, Ding K. Profiling the antibiotic resistome in soils between pristine and human-affected sites on the Tibetan Plateau. J Environ Sci (China) 2022; 111:442-451. [PMID: 34949372 DOI: 10.1016/j.jes.2021.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 06/14/2023]
Abstract
With increasing pressure from anthropogenic activity in pristine environments, the comprehensive profiling of antibiotic resistance genes (ARGs) is essential to evaluate the potential risks from human-induced antibiotic resistance in these under-studied places. Here, we characterized the microbial resistome in relatively pristine soil samples collected from four distinct habitats on the Tibetan Plateau, using a Smart chip based high-throughput qPCR approach. We compared these to soils from the same habitats that had been subjected to various anthropogenic activities, including residential sewage discharge, animal farming, atmospheric deposition, and tourism activity. Compared to pristine samples, an average of 23.7% more ARGs were detected in the human-affected soils, and the ARGs enriched in these soils mainly encoded resistances to aminoglycoside and beta-lactam. Of the four habitats studied, soils subjected to animal farming showed the highest risks of ARG enrichment and dissemination. As shown, the number of ARGs enriched (a total of 42), their fold changes (17.6 fold on average), and the co-occurrence complexity between ARGs and mobile genetic elements were all the highest in fecal-polluted soils. As well as antibiotics themselves, heavy metals also influenced ARG distributional patterns in Tibetan environments. However, compared to urban areas, the Tibetan Plateau had a low potential for ARG selection and exhibited low carriage of ARGs by mobile genetic elements, even in environments impacted by humans, suggesting that these ARGs have a limited capacity to disseminate. The present study examined the effects of multiple anthropogenic activities on the soil resistomes in relatively pristine environments.
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Affiliation(s)
- Hang Wang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming 650224, China; National Plateau Wetlands Research Center, Southwest Forestry University, Kunming 650224, China
| | - Xiaoxuan Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jianqiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yongguan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Kai Ding
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021; 34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.
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Affiliation(s)
- F. Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. L. Martínez
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - V. F. Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Central Bioinformatics Unit, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - J. Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. C. Galán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A. San Millán
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - R. Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - T. M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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Mafiz AI, He Y, Zhang W, Zhang Y. Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer. Front Microbiol 2021; 12:771707. [PMID: 34887843 PMCID: PMC8650581 DOI: 10.3389/fmicb.2021.771707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022] Open
Abstract
Fifteen soil and 45 vegetable samples from Detroit community gardens were analyzed for potential antimicrobial resistance contamination. Soil bacteria were isolated and tested by antimicrobial susceptibility profiling, horizontal gene transfer, and whole-genome sequencing. High-throughput 16S rRNA sequencing analysis was conducted on collected soil samples to determine the total bacterial composition. Of 226 bacterial isolates recovered, 54 were from soil and 172 from vegetables. A high minimal inhibitory concentration (MIC) was defined as the MIC greater than or equal to the resistance breakpoint of Escherichia coli for Gram-negative bacteria or Staphylococcus aureus for Gram-positive bacteria. The high MIC was observed in 63.4 and 69.8% of Gram-negative isolates from soil and vegetables, respectively, against amoxicillin/clavulanic acid, as well as 97.5 and 82.7% against ampicillin, 97.6 and 90.7% against ceftriaxone, 85.4 and 81.3% against cefoxitin, 65.8 and 70.5% against chloramphenicol, and 80.5 and 59.7% against ciprofloxacin. All Gram-positive bacteria showed a high MIC to gentamicin, kanamycin, and penicillin. Forty of 57 isolates carrying tetM (70.2%) successfully transferred tetracycline resistance to a susceptible recipient via conjugation. Whole-genome sequencing analysis identified a wide array of antimicrobial resistance genes (ARGs), including those encoding AdeIJK, Mex, and SmeDEF efflux pumps, suggesting a high potential of the isolates to become antimicrobial resistant, despite some inconsistency between the gene profile and the resistance phenotype. In conclusion, soil bacteria in urban community gardens can serve as a reservoir of antimicrobial resistance with the potential to transfer to clinically important pathogens, resulting in food safety and public health concerns.
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Affiliation(s)
- Abdullah Ibn Mafiz
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States.,Department of Human Sciences, Tennessee State University, Nashville, TN, United States
| | - Yingshu He
- Department of Food Science and Nutrition, Illinois Institute of Technology, Chicago, IL, United States.,Center for Food Safety, University of Georgia, Griffin, GA, United States
| | - Wei Zhang
- Department of Food Science and Nutrition, Illinois Institute of Technology, Chicago, IL, United States
| | - Yifan Zhang
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, United States
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Ma X, Yang Z, Xu T, Qian M, Jiang X, Zhan X, Han X. Chlortetracycline alters microbiota of gut or faeces in pigs and leads to accumulation and migration of antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:148976. [PMID: 34273831 DOI: 10.1016/j.scitotenv.2021.148976] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/11/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
In this study, we investigated the effect of long-term use of chlortetracycline (CTC) on the gut microbiota composition and metabolism profiles in pigs, and the variation of antibiotic resistance genes (ARGs) and microbial communities in faeces and manure during aerobic composting (AC) and anaerobic digestion (AD). The pigs were fed the same basal diet supplemented with or without 75 mg/kg CTC, and fresh faeces of 30-, 60-, 90-, and 120-day-old pigs were collected from the CTC group. The results showed that CTC reduced the diversity of the gut microbiota significantly and changed its structure. Metabolomics analysis of intestinal contents revealed 23 differentially abundant metabolites, mainly organic acids, carbohydrates, and amino acids. Metabolic pathways, such as the TCA cycle, propionate metabolism, and pyruvate metabolism, were changed. From 30 to 120 days of age, the amount of CTC residues in faeces and the abundance of 3 tetracycline resistance genes increased significantly, and it was positively correlated with tetC, tetG, tetW, sul1 and intI2. CTC residue levels and ARGs abundance gradually decreased with fermentation time, and AC was better than AD at reducing ARGs abundance. The results suggest that in-feed CTC can reduce the diversity of the gut microbiota, change the structure, function and metabolism of the bacterial community, and increase the abundance of ARGs in faeces.
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Affiliation(s)
- Xin Ma
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Zhiren Yang
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Science, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Hainan, China
| | - Tingting Xu
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Mengqi Qian
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Xuemei Jiang
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Xiuan Zhan
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Science, Zhejiang University, Hangzhou 310058, China.
| | - Xinyan Han
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Science, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Hainan, China.
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32
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Na G, Zhang K, Gao H, Li R, Jin S, Zhao F, Zhang H, Li S. Occurrence and distribution characteristics of antibiotic resistance genes in sediments between urban and rural of the Liaohe River Basin, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:54002-54014. [PMID: 34043168 DOI: 10.1007/s11356-021-13560-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Antibiotic resistance genes (ARGs) are considered to be emerging pollutants related to human activities. The rapid development of global urbanization has expanded human activities, thereby exacerbating the global human health risks caused by antibiotic resistance genes. The effects of urban and rural environments are multifarious, which makes the source and distribution of ARGs in the environment diversification. Understanding the distribution and spread of ARGs is essential for studying the environmental behavior of ARGs. In this study, the occurrence 296 genes were detected by the high-throughput qPCR technology, and FC value was used to analyze the diversity of ARGs and mobile genetic elements (MGEs) in sediments between urban and rural areas of the Liaohe River Basin, China. The co-occurrence of MGEs and ARGs was analyzed using network to decipher core genes. A total of 187 ARGs and 10 MGEs were detected in all sediment samples. The average number of genes detected in urban sites is 89 higher than that in rural sites. The high abundance and various types of ARGs and MGEs detected in urban river sediments indicate that the occurrence of urban ARGs is more complex. MGEs were detected high levels and were significantly correlated with the abundance and diversity of ARGs in river sediments providing evidence that MGEs were related to the occurrence and distribution of ARGs and tnpA (tnpA-07, tnpA-01, and tnpA-03) gene were at the key position of co-occurrence of various types of ARGs.
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Affiliation(s)
- Guangshui Na
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China.
- National Marine Environmental Monitoring Center, Dalian, 116023, China.
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya, 572022, China.
| | - Keyu Zhang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China
- National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Hui Gao
- National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Ruijing Li
- National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Shuaichen Jin
- National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Fuqiang Zhao
- National Marine Environmental Monitoring Center, Dalian, 116023, China
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, 116023, China
| | - Haibo Zhang
- National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Shisheng Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China
- National Marine Environmental Monitoring Center, Dalian, 116023, China
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33
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Hou L, Wang H, Chen Q, Su JQ, Gad M, Li J, Mulla SI, Yu CP, Hu A. Fecal pollution mediates the dominance of stochastic assembly of antibiotic resistome in an urban lagoon (Yundang lagoon), China. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126083. [PMID: 34000699 DOI: 10.1016/j.jhazmat.2021.126083] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/19/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Sewage and fecal pollution cause antibiotic resistance genes (ARGs) pollution in urban lagoons. Seasonality also affects ARG dynamics. However, knowledge of factors controlling ARG community assembly across seasons is still limited. Here, we revealed the seasonal variation of ARGs and depict the underlying assembly processes and drivers via high-throughput quantitative PCR in an urban lagoon, China. A higher richness and abundance of ARGs were observed in summer and winter compared to spring and fall (Kruskal-Wallis test, P < 0.05). Both ARG and prokaryotic communities were mainly governed by stochastic processes, however, these processes drove ARGs and prokaryotes differently across seasons. Stochastic processes played a more dominant role in shaping ARG communities in summer (average stochasticity: 83%) and winter (75%), resulting in a stable antibiotic resistome. However, no such seasonal pattern of stochastic processes was determined for prokaryotes, indicating a decoupling of the assembly process of ARGs and prokaryotes. Moreover, fecal microorganisms (e.g., Bacteroidetes and Faecalibacterium) mediated the stochastic processes of ARG profiles, via enhancement of prokaryotic biomass and mobile genetic element abundances. The tnpA-07 transposase was the key for the horizontal gene transfer. These findings will enhance our understanding of how fecal pollution shapes ARG community assembly in urban lagoons.
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Affiliation(s)
- Liyuan Hou
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hongjie Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qingfu Chen
- Yundang Lake Management Center, Xiamen, Fujian 361004, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China
| | - Mahmoud Gad
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Water Pollution Research Department, National Research Centre, Giza 12622, Egypt
| | - Jiangwei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Sikandar I Mulla
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Department of Biochemistry, School of Applied Sciences, Reva University, Bangalore 560064, India
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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34
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Scott LC, Wilson MJ, Esser SM, Lee NL, Wheeler ME, Aubee A, Aw TG. Assessing visitor use impact on antibiotic resistant bacteria and antibiotic resistance genes in soil and water environments of Rocky Mountain National Park. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 785:147122. [PMID: 33932658 DOI: 10.1016/j.scitotenv.2021.147122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have been detected in soil and water in close proximity to anthropogenic sources, but the extent to which human impact plays into ARB and ARGs entering the environment is not well described. This study aimed to determine the impact of visitor use on ARB and ARGs in a national park environment. Soil (n = 240) and water (n = 210) samples were collected across a gradient of human activity in Rocky Mountain National Park and analyzed for bacteria resistant to doxycycline, levofloxacin, and vancomycin. Amount of physical effort required to access a sampling site was used as a metric for the likelihood of human presence. A subset of samples was analyzed for the presence and abundance of six ARGs using quantitative polymerase chain reaction. Linear regression analysis demonstrated that anthropogenic factors including hiking effort and proximity to a toilet significantly contributed to the variance of the abundance of ARB for multiple antibiotics in soil and water. Additionally, ecological factors such as water movement, soil texture, and season may play a role in the detection of ARB and ARGs. Predictive analysis suggests that both human presence and human activities, such as waste elimination, significantly contributed to the abundance of ARB in soil and water. The results of this work evidence that the ecology of antibiotic resistance in remote environments is more complex than anthropogenic impact alone, necessitating further environmental characterization of ARB and ARGs.
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Affiliation(s)
- Laura C Scott
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Mark J Wilson
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Scott M Esser
- Continental Divide Research Learning Center, Rocky Mountain National Park. Estes Park, CO, USA
| | - Nicholas L Lee
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Michael E Wheeler
- School of Renewable Natural Resources, Louisiana State University, Baton Rouge, LA, USA
| | - Alexandra Aubee
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA.
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35
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Liu S, Wang P, Wang C, Wang X, Chen J. Anthropogenic disturbances on antibiotic resistome along the Yarlung Tsangpo River on the Tibetan Plateau: Ecological dissemination mechanisms of antibiotic resistance genes to bacterial pathogens. WATER RESEARCH 2021; 202:117447. [PMID: 34325101 DOI: 10.1016/j.watres.2021.117447] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/05/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Human activities can accelerate the antibiotic resistome prevalence and pose threats to ecological safety and public health globally. However, antibiotic resistance gene (ARG) mobility and dissemination into bacterial pathogens under anthropogenic disturbances are still poorly understood. Here, we used a metagenomic approach to profile the biogeography of ARGs and pathogenic antibiotic resistant bacteria (PARB) under anthropogenic disturbances along the Yarlung Tsangpo River. Results showed the ARGs was dominated by bacA gene along the Yarlung Tsangpo River on the Tibetan Plateau. The ARG composition was differently impacted by rapid urbanization and dam construction, which urbanization could promote ARGs resistant to sulfonamide and tetracycline, whereas dam construction could elevate the resistance to chloramphenicol and aminoglycoside. Land use pattern was identified as a critical factor influencing ARG composition under anthropogenic disturbances, as it could directly reflect the land degradation level and indicate the inputs of ARG-selective chemicals of different human activities. Moreover, despite of the lack of variation in ARG relative abundance, PARB were highly promoted by anthropogenic activities, indicating increasing ARG dissemination to pathogen. We found that human-impacted environments harbored high proportion of mobile genetic elements (MGEs), and the MGE carrying ARGs also increased under anthropogenic disturbances in the pathogenic hosts, which confirmed that anthropogenic activities could promote ARG horizontal gene transfer. Furthermore, anthropogenic activities could influence PARB assembly processes. Basically, stochastic processes dominated PARB assembly along the river, and with increasing level of anthropogenic activities, these processes shifted from undominated stochastic processes to dispersal limitation. In summary, this study provides useful strategies in watershed resistome management and reduction of ARG dissemination to pathogens, which should consider the mode and intensity of human activity and its potential influence on horizontal gene transfer and assembly processes.
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Affiliation(s)
- Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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36
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Guo Y, Qiu T, Gao M, Sun Y, Cheng S, Gao H, Wang X. Diversity and abundance of antibiotic resistance genes in rhizosphere soil and endophytes of leafy vegetables: Focusing on the effect of the vegetable species. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125595. [PMID: 34088171 DOI: 10.1016/j.jhazmat.2021.125595] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/04/2021] [Accepted: 03/03/2021] [Indexed: 05/27/2023]
Abstract
Antibiotic resistance genes (ARGs) in the endophytes of vegetables represent a potential route of human exposure to the soil resistome. However, the effect of vegetable species on the endophytic ARG profiles is unclear, hampering our understanding of how ARGs migrate into the soil-vegetable system and their potential health risks. Here, we planted four leafy vegetables (cilantro, endive, lettuce, and pak choi), which are commonly eaten raw, and analyzed the resistomes and microbiomes in three sample types (rhizosphere soil, root, and leaf endophytes). A total of 150 ARG subtypes were detected using high-throughput quantitative PCR. Vegetable species had a significant effect on ARG diversity and abundance, and pak choi accumulated more ARGs in its associated microbiome than the other three vegetables. The bacterial community was the primary factor shaping ARG profiles and was significantly correlated with ARG subtypes. We identified aadE, tet(34), and vanSB as shared ARGs among leaves of the four vegetables; the bacterial families correlated with tet(34) and vanSB were also shared across the vegetables and belonged to Proteobacteria. This study deepens our understanding of how endophytic ARG profiles vary among different vegetables and highlights the potential health risk associated with consuming these vegetables raw.
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Affiliation(s)
- Yajie Guo
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Tianlei Qiu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Min Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanmei Sun
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, Shaanxi 710069, China
| | - Shoutao Cheng
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Haoze Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xuming Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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37
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Xiang Q, Qiao M, Zhu D, Giles M, Neilson R, Yang XR, Zhu YG, Chen QL. Seasonal change is a major driver of soil resistomes at a watershed scale. ISME COMMUNICATIONS 2021; 1:17. [PMID: 36732354 PMCID: PMC9723683 DOI: 10.1038/s43705-021-00018-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 04/27/2023]
Abstract
Soils harbor the most diverse naturally evolved antibiotic resistomes on Earth that threaten human health, ecosystem processes, and food security. Yet the importance of spatial and temporal variability in shaping the distribution of soil resistomes is not well explored. Here, a total of 319 topsoil samples were collected at a watershed scale during four seasons (spring to winter) and high-throughput quantitative PCR (HT-qPCR) was used to characterize the profiles of soil antibiotic resistance genes (ARGs). A significant and negative correlation was observed between soil ARG profiles and seasonal dissimilarity, which along with seasonally dependent distance-decay relationships highlight the importance of seasonal variability in shaping soil antibiotic resistomes. Significant, though weak, distance-decay relationships were identified in spring, summer and winter, for ARG similarities with geographic distances. There were also strong interactions between specific soil ARGs and Actinobacteria, Firmicutes and Proteobacteria. Moreover, we found that the relative abundance of soil Actinobacteria, Firmicutes and Proteobacteria correlated significantly with annual mean temperature and annual mean precipitation at a watershed scale. A random forest model showed that seasonal change rather than spatial variation was the most important predictor of the composition of soil ARGs. Together, these results constitute an advance in our understanding of the relative importance of spatial and temporal variability in shaping soil ARG profiles, which will provide novel insights allowing us to forecast their distribution under a changing environment.
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Affiliation(s)
- Qian Xiang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Madeline Giles
- Ecological Sciences, The James Hutton Institute, Dundee, Scotland, UK
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, Scotland, UK
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Qing-Lin Chen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.
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38
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Jiang C, Diao X, Wang H, Ma S. Diverse and abundant antibiotic resistance genes in mangrove area and their relationship with bacterial communities - A study in Hainan Island, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 276:116704. [PMID: 33652188 DOI: 10.1016/j.envpol.2021.116704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Antibiotic resistance genes (ARGs) are emerging contaminants in the environment and have been highlighted as a worldwide environmental and health concern. As important participants in the biogeochemical cycles, mangrove ecosystems are subject to various anthropogenic disturbances, and its microbiota may be affected by various contaminants such as ARGs. This study selected 13 transects of mangrove-covered areas in Hainan, China for sediment sample collection. The abundance and diversity of ARGs and mobile genetic elements (MGEs) were investigated using high-throughput quantitative polymerase chain reaction (HT-qPCR), and high-throughput sequencing was used to study microbial structure and diversity. A total of 179 ARGs belonging to 9 ARG types were detected in the study area, and the detection rates of vanXD and vatE-01 were 100%. The abundance of ARGs was 8.30 × 107-6.88 × 108 copies per g sediment (1.27 × 10-2-3.39 × 10-2 copies per 16S rRNA gene), which was higher than similar studies, and there were differences in the abundance of ARGs in these sampling transects. The multidrug resistance genes (MRGs) accounted for the highest proportion (69.0%), which indicates that the contamination of ARGs in the study area was very complicated. The ARGs significantly positively correlated with MGEs, which showed that the high level of ARGs was related to its self-enhancement. The dominant bacteria at the genus level were Desulfococcus, Clostridium, Rhodoplanes, Bacillus, Vibrio, Enterococcus, Sedimentibacter, Pseudoalteromonas, Paracoccus, Oscillospira, Mariprofundus, Sulfurimonas, Aminobacterium, and Novosphingobium. There was a significant positive correlation between 133 bacterial genera and some ARGs. Chthoniobacter, Flavisolibacter, Formivibrio, Kaistia, Moryella, MSBL3, Perlucidibaca, and Zhouia were the main potential hosts of ARGs in the sediments of Hainan mangrove area, and many of these bacteria are important participants in biogeochemical cycles. The results contribute to our understanding of the distribution and potential hosts of ARGs and provide a scientific basis for the protection and management of Hainan mangrove ecosystem.
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Affiliation(s)
- Chunxia Jiang
- College of Ecology and Environment, Hainan University, Haikou, 570228, China; State Key Laboratory of Marine Resources Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Xiaoping Diao
- State Key Laboratory of Marine Resources Utilization in South China Sea, Hainan University, Haikou, 570228, China; College of Life Science, Hainan Normal University, Haikou, 571158, China.
| | - Haihua Wang
- College of Ecology and Environment, Hainan University, Haikou, 570228, China; State Key Laboratory of Marine Resources Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Siyuan Ma
- College of Life Science, Hainan Normal University, Haikou, 571158, China
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39
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Zhang Y, Xu R, Xiang Y, Lu Y, Jia M, Huang J, Xu Z, Cao J, Xiong W, Yang Z. Addition of nanoparticles increases the abundance of mobile genetic elements and changes microbial community in the sludge anaerobic digestion system. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:124206. [PMID: 33535360 DOI: 10.1016/j.jhazmat.2020.124206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 06/12/2023]
Abstract
This study explored the fate of mobile genetic elements (MGEs) in anaerobic digestion (AD) system with four nanoparticles (NPs) added, including carbon NPs, Al2O3 NPs, ZnO NPs, and CuO NPs. 16S rRNA amplicon sequencing and quantitative PCR to investigate the microbial community, MGEs abundance and the potential host in the AD process. The results of high-throughput sequencing showed that ZnO NPs and CuO NPs significantly reduced the microbial diversity and significantly changed the microbial community structure. Simultaneously, the absolute abundance of MGEs increased by 145.01%, 159.67%, 354.70%, and 132.80% on the carbon NPs, Al2O3 NPs, ZnO NPs, and CuO NPs. The enrichment rate of tnpA-03 in ZnO NPs group was the highest, which could reach up to 2854.80%. Co-occurrence analysis revealed that Proteobacteria harbored the vast majority of MGEs followed by Firmicutes. Redundancy analysis and variation partitioning analysis showed that metabolites were the main factors that shifted the succession of bacterial communities. Moreover, there were significant positive correlations between metabolites and part MGEs (such as tnpA-01, tnpA-02, tnpA-03, tnpA-04, tnpA-05, tnpA-07 and ISCR1). This study provides a new perspective that NPs increase the risk of antibiotic resistance through MGEs during AD process.
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Affiliation(s)
- Yanru Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Rui Xu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science Technology, Guangzhou 510650, PR China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, PR China
| | - Yinping Xiang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yue Lu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Meiying Jia
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Jing Huang
- Hunan Academy of Forestry and State Key Laboratory of Utilization of Woody Oil Resource, Changsha 410004, PR China
| | - Zhengyong Xu
- Hunan Provincial Science and Technology Affairs Center, Changsha 410013, PR China
| | - Jiao Cao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Weiping Xiong
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
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Jauregi L, Epelde L, Alkorta I, Garbisu C. Antibiotic Resistance in Agricultural Soil and Crops Associated to the Application of Cow Manure-Derived Amendments From Conventional and Organic Livestock Farms. Front Vet Sci 2021; 8:633858. [PMID: 33708812 PMCID: PMC7940349 DOI: 10.3389/fvets.2021.633858] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/03/2021] [Indexed: 11/28/2022] Open
Abstract
The application of organic amendments to agricultural soil can enhance crop yield, while improving the physicochemical and biological properties of the recipient soils. However, the use of manure-derived amendments as fertilizers entails environmental risks, such as the contamination of soil and crops with antibiotic residues, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). In order to delve into these risks, we applied dairy cow manure-derived amendments (slurry, fresh manure, aged manure), obtained from a conventional and an organic farm, to soil. Subsequently, lettuce and wheat plants were grown in the amended soils. After harvest, the abundance of 95 ARGs and MGE-genes from the amended soils and plants were determined by high-throughput qPCR. The structure of soil prokaryotic communities was determined by 16S rRNA amplicon sequencing and qPCR. The absolute abundance of ARGs and MGE-genes differed between treatments (amended vs. unamended), origins of amendment (conventional vs. organic), and types of amendment (slurry vs. fresh manure vs. aged manure). Regarding ARG-absolute abundances in the amendments themselves, higher values were usually found in slurry vs. fresh or aged manure. These abundances were generally higher in soil than in plant samples, and higher in wheat grain than in lettuce plants. Lettuce plants fertilized with conventional amendments showed higher absolute abundances of tetracycline resistance genes, compared to those amended with organic amendments. No single treatment could be identified as the best or worst treatment regarding the risk of antibiotic resistance in soil and plant samples. Within the same treatment, the resistome risk differed between the amendment, the amended soil and, finally, the crop. In other words, according to our data, the resistome risk in manure-amended crops cannot be directly inferred from the analysis of the amendments themselves. We concluded that, depending on the specific question under study, the analysis of the resistome risk should specifically focus on the amendment, the amended soil or the crop.
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Affiliation(s)
- Leire Jauregi
- Department of Conservation of Natural Resources, NEIKER – Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Lur Epelde
- Department of Conservation of Natural Resources, NEIKER – Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Carlos Garbisu
- Department of Conservation of Natural Resources, NEIKER – Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Spain
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Song M, Song D, Jiang L, Zhang D, Sun Y, Chen G, Xu H, Mei W, Li Y, Luo C, Zhang G. Large-scale biogeographical patterns of antibiotic resistome in the forest soils across China. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123990. [PMID: 33265028 DOI: 10.1016/j.jhazmat.2020.123990] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 08/14/2020] [Accepted: 09/12/2020] [Indexed: 05/26/2023]
Abstract
Soil is a reservoir of environmental resistomes. Information about their distribution, profiles, and driving forces in undisturbed environments is essential for understanding and managing modern antibiotic resistance genes (ARGs) in human disturbed environments. However, knowledge about the resistomes in pristine soils is limited, particularly at national scale. Here, we conducted a national-scale investigation of soil resistomes in pristine forests across China. Although the antibiotics content was low and ranged from below limit of detection (LOD) to 0.290 μg/kg, numerous detected ARGs conferring resistance to major classes of modern antibiotics were identified and indicated forest soils as a potential source of resistance traits. ARGs ranged from 6.20 × 10-7 to 2.52 × 10-3 copies/16S-rRNA and were predominated by those resisting aminoglycoside and encoding deactivation mechanisms. Low abundance of mobile genetic elements (MGEs) and its scarcely positive connections with ARGs suggest the low potential of horizontal gene transfer. The geographic patterns of ARGs and ARG-hosts in pristine forest soils were mainly driven by soil physiochemical variables and followed a distance-decay relationship. This work focusing on pristine soils can provide valuably new information for our understanding of the ARGs in human disturbed environments.
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Affiliation(s)
- Mengke Song
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China
| | - Dandan Song
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Longfei Jiang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yingtao Sun
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guoen Chen
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Huijuan Xu
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China
| | - Weiping Mei
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yongtao Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China.
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Davis BC, Riquelme MV, Ramirez-Toro G, Bandaragoda C, Garner E, Rhoads WJ, Vikesland P, Pruden A. Demonstrating an Integrated Antibiotic Resistance Gene Surveillance Approach in Puerto Rican Watersheds Post-Hurricane Maria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15108-15119. [PMID: 33205660 DOI: 10.1021/acs.est.0c05567] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Comprehensive surveillance approaches are needed to assess sources, clinical relevance, and mobility of antibiotic resistance genes (ARGs) in watersheds. Here, we examined metrics derived from shotgun metagenomic sequencing and relationship to human fecal markers (HFMs; crAssphage, enterococci) and anthropogenic antibiotic resistance markers (AARMs; intI1, sul1) in three distinct Puerto Rican watersheds as a function of adjacent land use and wastewater treatment plant (WWTP) input 6 months after Hurricane Maria, a category V storm. Relative abundance and diversity of total ARGs increased markedly downstream of WWTP inputs, with ARGs unique to WWTP and WWTP-impacted river samples predominantly belonging to the aminoglycoside and β-lactam resistance classes. WWTP and other anthropogenic inputs were similarly associated with elevated resistome risk scores and mobility incidence (M%). Contig analysis indicated a wide variety of mobile β-lactam ARGs associated with pathogens downstream of WWTP discharge that were consistent with regional clinical concern, e.g., Klebsiella pneumoniae contigs containing KPC-2 within an ISKpn6-like transposase. HFMs and AARMs correlated strongly with the absolute abundance of total ARGs, but AARMs better predicted the majority of ARGs in general (85.4 versus <2%) and β-lactam ARGs in particular. This study reveals sensitive, quantitative, mobile, clinically relevant, and comprehensive targets for antibiotic resistance surveillance in watersheds.
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Affiliation(s)
- Benjamin C Davis
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Maria Virginia Riquelme
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Graciela Ramirez-Toro
- Center for Environmental Education, Conservation and Research, Inter American University, San Germán, Puerto Rico 00683, United States
| | - Christina Bandaragoda
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Emily Garner
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - William J Rhoads
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Peter Vikesland
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
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43
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Li LG, Huang Q, Yin X, Zhang T. Source tracking of antibiotic resistance genes in the environment - Challenges, progress, and prospects. WATER RESEARCH 2020; 185:116127. [PMID: 33086465 DOI: 10.1016/j.watres.2020.116127] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance has become a global public health concern, rendering common infections untreatable. Given the widespread occurrence, increasing attention is being turned toward environmental pathways that potentially contribute to antibiotic resistance gene (ARG) dissemination outside the clinical realm. Studies during the past decade have clearly proved the increased ARG pollution trend along with gradient of anthropogenic interference, mainly through marker-ARG detection by PCR-based approaches. However, accurate source-tracking has been always confounded by various factors in previous studies, such as autochthonous ARG level, spatiotemporal variability and environmental resistome complexity, as well as inherent method limitation. The rapidly developed metagenomics profiles ARG occurrence within the sample-wide genomic context, opening a new avenue for source tracking of environmental ARG pollution. Coupling with machine-learning classification, it has been demonstrated the potential of metagenomic ARG profiles in unambiguously assigning source contribution. Through identifying indicator ARG and recovering ARG-host genomes, metagenomics-based analysis will further increase the resolution and accuracy of source tracking. In this review, challenges and progresses in source-tracking studies on environmental ARG pollution will be discussed, with specific focus on recent metagenomics-guide approaches. We propose an integrative metagenomics-based framework, in which coordinated efforts on experimental design and metagenomic analysis will assist in realizing the ultimate goal of robust source-tracking in environmental ARG pollution.
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Affiliation(s)
- Li-Guan Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong
| | - Qi Huang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong
| | - Xiaole Yin
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, 999077, Hong Kong.
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44
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Neher TP, Ma L, Moorman TB, Howe A, Soupir ML. Seasonal variations in export of antibiotic resistance genes and bacteria in runoff from an agricultural watershed in Iowa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:140224. [PMID: 32806354 DOI: 10.1016/j.scitotenv.2020.140224] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Seasonal variations of antimicrobial resistance (AMR) indicators in runoff water can help improve our understanding of AMR sources and transport within an agricultural watershed. This study aimed to monitor multiple areas throughout the Black Hawk Lake (BHL) watershed (5324 ha) in central Iowa during 2017 and 2018 that consists of both swine and cattle feeding operations as well as known areas with manure application. The measured indicators included plate counts for fecal indicator bacteria (FIB) E. coli, Enterococcus, antibiotic resistant fecal indicator bacteria (ARBs) tylosin resistant Enterococcus, tetracycline resistant Enterococcus, and antibiotic resistance genes (ARGs): ermB, ermF (macrolide), tetA, tetM, tetO, tetW (tetracycline), sul1, sul2 (sulfonamide), aadA2 (aminoglycoside), vgaA, and vgaB (pleuromutilin). Both the plate count and the ARG analyses showed seasonal trends. Plate counts were significantly greater during the growing season, while the ARGs were greater in the pre-planting and post-harvest seasons (Wilcoxon Rank-Sum Test p < 0.05). The ermB gene concentration was significantly correlated (p < 0.05) with E. coli and Enterococcus concentrations in 2017, suggesting a potential use of this ARG as an indicator of environmental AMR and human health risk. Flow rate was not a significant contributor to annual variations in bacteria and AMR indicators. Based on observed seasonal patterns, we concluded that manure application was the likely contributor to elevated ARG indicators observed in the BHL watershed, while the driver of elevated ARB indictors in the growing season can only be speculated. Understanding AMR export patterns in agricultural watersheds provides public health officials knowledge of seasonal periods of higher AMR load to recreational waters.
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Affiliation(s)
- Timothy P Neher
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States.
| | - Lanying Ma
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Thomas B Moorman
- National Laboratory for Agriculture and the Environment, USDA-ARS, IA, United States
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Michelle L Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
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Xiang Q, Chen QL, Zhu D, Yang XR, Qiao M, Hu HW, Zhu YG. Microbial functional traits in phyllosphere are more sensitive to anthropogenic disturbance than in soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114954. [PMID: 32544665 DOI: 10.1016/j.envpol.2020.114954] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Soil-plant microbiome plays a critical role in the regulation of terrestrial ecosystem function and service, including biogeochemical cycling and primary production. The lack of knowledge regarding the differences in microbial functional traits, i.e. the functional genes related to carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles, between soil and plant microbiomes hampers our prediction of the terrestrial nutrient cycling processes under the pressure of anthropogenic disturbance. Herein, a quantitative microbial element cycling (QMEC) method and amplicon sequencing was employed to characterize CNPS cycling genes and microbial communities in soil and plant samples collected from peri-urban farmland with high anthropogenic disturbance and forest ecosystem with minimal disturbance. The soil-plant system harbored a diverse array of CNPS cycling genes, which were significantly more abundant in soil than in phyllosphere. The overall CNPS gene profiles in farmland samples was distinct from that of forest samples in both soil and plant phyllosphere. Farmland samples had a lower abundance of CNPS cycling genes than forest samples, indicating that intensive agricultural management practices may consequently compromise the biogeochemical cycling potential of nutrients. Significant positive correlations between the abundance of CNPS cycling genes and microbial diversity were observed in phyllosphere microbiome but not in soil, suggesting that the functional redundancy in soil microbiome may be higher than that of phyllosphere microbiome. Taken together, we provide experimental evidence for the substantial impacts of anthropogenic disturbance on CNPS cycling genes in the soil-plant system and necessitate future efforts to unravel the plant microbiome diversity and functionality under the pressure of global changes.
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Affiliation(s)
- Qian Xiang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
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46
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Chen QL, Ding J, Li CY, Yan ZZ, He JZ, Hu HW. Microbial functional attributes, rather than taxonomic attributes, drive top soil respiration, nitrification and denitrification processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 734:139479. [PMID: 32464393 DOI: 10.1016/j.scitotenv.2020.139479] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/13/2020] [Accepted: 05/14/2020] [Indexed: 06/11/2023]
Abstract
We lack empirical evidence for the relative importance of microbial functional attributes vs taxonomic attributes in regulating specified soil processes related to carbon (C) and nitrogen (N) cycling, which has hindered our ability to predict the responses of ecosystem multifunctionality to environmental changes. Here, we collected soil samples from a long-term experimental field with eight inorganic and organic fertilization treatments and evaluated the linkage between microbial functional attributes (abundance of functional genes), taxonomic attributes (microbial taxonomic composition), and soil processes including soil respiration, denitrification and nitrification. Long-term fertilization had no significant effect on the bacterial or fungal alpha-diversity. The treatments of chicken manure and sewage sludge addition significantly altered the rates of soil respiration, denitrification and nitrification, which were significantly correlated with the abundances of relevant functional genes. Random forest model indicated that the abundance of functional genes was the main diver for the rate of soil processes. The predominant effect of microbial functional attributes in driving soil processes was maintained when simultaneously accounting for multiple abiotic (total C, total N and soil pH) and biotic drivers (bacterial and fungal community structure), indicating that microbial functional attributes were the predominant driver predicting the rate of soil respiration, denitrification and nitrification. Our results suggested the importance of developing a functional gene-centric framework to incorporate microbial communities into biogeochemical models, which may provide new insights into the biodiversity-functions relationship and have implications for future management of the consequences of biodiversity loss for ecosystem multifunctionality.
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Affiliation(s)
- Qing-Lin Chen
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Jing Ding
- School of Environmental and Material Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Chao-Yu Li
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Zhen-Zhen Yan
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ji-Zheng He
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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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.
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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
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Scott LC, Lee N, Aw TG. Antibiotic Resistance in Minimally Human-Impacted Environments. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17113939. [PMID: 32498349 PMCID: PMC7313453 DOI: 10.3390/ijerph17113939] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/28/2022]
Abstract
Antibiotic resistant bacteria (ARB) have become contaminants of concern in environmental systems. Studies investigating environmental ARB have primarily focused on environments that are greatly impacted by anthropogenic activity. Background concentrations of ARB in natural environments is not well understood. This review summarizes the current literature on the monitoring of ARB and antibiotic resistance genes (ARGs) in environments less impacted by human activity. Both ARB and ARGs have been detected on the Antarctic continent, on isolated glaciers, and in remote alpine environments. The methods for detecting and quantifying ARB and ARGs from the environment are not standardized and warrant optimization. Further research should be focused on the detection and quantification of ARB and ARGs along human gradients to better characterize the factors leading to their dissemination in remote environments.
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49
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Zhao X, Shen JP, Zhang LM, Du S, Hu HW, He JZ. Arsenic and cadmium as predominant factors shaping the distribution patterns of antibiotic resistance genes in polluted paddy soils. JOURNAL OF HAZARDOUS MATERIALS 2020; 389:121838. [PMID: 31848095 DOI: 10.1016/j.jhazmat.2019.121838] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 11/29/2019] [Accepted: 12/05/2019] [Indexed: 05/28/2023]
Abstract
Heavy metals have been recognized as potential factors driving the evolution and development of antibiotic resistance. However, the relative effects of cadmium (Cd) and arsenic (As) on the prevalence and distribution of antibiotic resistance genes (ARGs) remain unclear. We investigated the co-selection effects of Cd and As on ARGs in 45 paddy soils polluted by heavy metals, using high-throughput quantitative PCR. A total of 119 ARGs and 9 mobile genetic elements (MGEs) were detected in all samples. Regression analysis showed that the single pollution index (PIAs and PICd) and Nemerow integrated pollution index (NIPI) both had significant and positive correlations with ARGs (P < 0.05), indicating the co-selective effects of Cd and As on ARGs distribution. The significant correlations between bacterial taxa and different ARGs in network analysis revealed potential hosts of ARGs. Structural equation models indicated that the effects of As on ARGs were stronger than that of Cd. The profile of ARGs could be impacted by Cd and As indirectly by strongly affecting the bacterial abundance. Overall, this study extended our knowledge about the co-selection of Cd and As on ARGs in paddy soil, and had important implications for assessing the potential risks of ARGs in paddy soils.
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Affiliation(s)
- Xiang Zhao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100085, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100085, China.
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100085, China
| | - Shuai Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100085, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville Victoria 3010, Australia
| | - Ji-Zheng He
- University of Chinese Academy of Sciences, Beijing, 100085, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville Victoria 3010, Australia
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Guo HG, Chen QL, Hu HW, He JZ. Fate of antibiotic resistance genes during high-solid anaerobic co-digestion of pig manure with lignite. BIORESOURCE TECHNOLOGY 2020; 303:122906. [PMID: 32028218 DOI: 10.1016/j.biortech.2020.122906] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/24/2020] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
Lignite could be used to promote methane production during high-solid anaerobic co-digestion (HS-AcoD) of pig manure, however, the effects of lignite amendment on the fate of ARGs during HS-AcoD are unknown. Here, we explored the influence of lignite (0%, 8%, 16%, 32%, and 64%) on the fate of ARGs during HS-AcoD of pig manure. The results showed that 16% lignite reduced the absolute abundance of ARGs by 28.71% compared with the 0% lignite treatment. Variation partitioning analysis suggested the combined effect of microbial community, mobile genetic elements (MGEs) and environmental factors was the major driver shaping the pattern of ARGs. The potential hosts of ARGs were Bifidobacterium, Lactobacillus, Tissierella and Streptococcus. Structural equation models analysis suggested lignite indirectly impacted the pattern of ARGs by significantly reducing the abundance of microbial community and MGEs. These findings give an insight into the mechanistic understanding of the lignite influence on the reduction of ARGs during HS-AcoD.
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Affiliation(s)
- Hai-Gang Guo
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056038, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia; Huayu Agricultural Science and Technology Co., LTD, Handan 057153, China
| | - Qing-Lin Chen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia.
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