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Deciphering Potential Roles of Earthworms in Mitigation of Antibiotic Resistance in the Soils from Diverse Ecosystems.

Environ Sci Technol 2021 May 12. Epub 2021 May 12.

State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.

Earthworms are capable of redistributing bacteria and antibiotic resistance genes (ARGs) through soil profiles. However, our understanding of the earthworm gut microbiome and its interaction with the antibiotic resistome is still lacking. Here, we characterized the earthworm gut and soil microbiome and antibiotic resistome in natural and agricultural ecosystems at a national scale, and microcosm studies and field experiments were also employed to test the potential role of earthworms in dynamics of soil ARGs. Read More

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Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil.

mBio 2021 May 11;12(3). Epub 2021 May 11.

Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA

In agricultural settings, microbes and antimicrobial resistance genes (ARGs) have the potential to be transferred across diverse environments and ecosystems. The consequences of these microbial transfers are unclear and understudied. On dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. Read More

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Soil type shapes the antibiotic resistome profiles of long-term manured soil.

Sci Total Environ 2021 Apr 27;786:147361. Epub 2021 Apr 27.

College of Resources and Environment, Southwest University, Chongqing 400716, China. Electronic address:

Animal manure fertilization facilitates the proliferation and dissemination of antibiotic resistance genes (ARGs) in soil, posing high risks to humans and ecosystem health. Although studies suggest that soil types could shape the ARG profiles in greenhouse soil, there is still a lack of comparative studies on the fate of ARGs in different types of manured soils under field trials. Thus, a metagenomic approach was used to decipher the fate of ARGs in 12-year long-term fertilized (inorganic fertilizer, compost manure and a mix of them) acidic, near-neutral and alkaline soils. Read More

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Ecological insights into the elevational biogeography of antibiotic resistance genes in a pristine river: Metagenomic analysis along the Yarlung Tsangpo River on the Tibetan Plateau.

Environ Pollut 2021 Apr 10;286:117101. Epub 2021 Apr 10.

Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China.

Presently, the prevalence of antibiotic resistance genes (ARGs) is regarded as an emerging environmental issue, and many studies have illuminated biogeographical patterns of the antibiotic resistome. However, few studies have investigated elevational biogeography and associated assembly mechanisms of ARGs in natural river systems. Accordingly, in the present study, we used metagenomics approaches to analyze the biogeographical pattern of ARGs along the pristine Yarlung Tsangpo River on the Tibetan Plateau. Read More

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Toxicity Assessment of Nano-ZnO Exposure on the Human Intestinal Microbiome, Metabolic Functions, and Resistome Using an In Vitro Colon Simulator.

Environ Sci Technol 2021 May 9. Epub 2021 May 9.

Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), IRDR ICoE on Risk Interconnectivity and Governance on Weather/Climate Extremes Impact and Public Health, Fudan Tyndall Centre, Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China.

Nano-ZnO, as a commonly used nanomaterial, has been found in drinking water, food, and medicine; therefore, it poses potential health risks via the digestion system. However, little is known about the toxicity of nano-ZnO on the human intestinal microbiome, which plays critical roles in human health. This study comprehensively investigated the impact of nano-ZnO on the human gut microbiome, metabolic functions, and resistome using an in vitro colon simulator. Read More

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Performance of full scale constructed wetlands in removing antibiotics and antibiotic resistance genes.

Sci Total Environ 2021 Apr 28;786:147368. Epub 2021 Apr 28.

Department of Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, the Netherlands. Electronic address:

Additional treatment of wastewater, such as constructed wetlands (CWs), is a possible solution to reduce the discharge of antibiotics and antibiotic resistance genes (ARGs) from households and industry to the environment. This study aims to investigate the occurrence and removal of antibiotics and ARGs by two full scale CWs operated at different hydraulic retention times (HRT), namely 1 day and 3 days. Both CWs were receiving the same wastewater treatment plant (WWTP) effluent. Read More

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Functional Metagenomics for Identification of Antibiotic Resistance Genes (ARGs).

Methods Mol Biol 2021 ;2242:173-183

Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.

The identification of antibiotic resistance genes (ARGs) in microbial communities is one of the most challenging tasks in biology. The evolution and improvement of genome sequencing techniques, combined with the improvement of computational analysis techniques, have allowed us to acquire increasingly detailed information on the complex and varied microbial community that coexists and coevolves in the most heterogeneous environment. This chapter describes how to identify and quantify ARGs, using specific tools (Bowtie2, Bedtools for coverage, G/C content, and the estimated number of reads mapping each open reading frame; RGI tool, with the support of CARD database, to inspect the distribution of antibiotic resistance genes). Read More

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January 2021

Microbial and chemical pollutants on the manure-crops pathway in the perspective of "One Health" holistic approach.

Sci Total Environ 2021 Apr 29;785:147411. Epub 2021 Apr 29.

The Biotechnology Centre, Silesian University of Technology, Krzywoustego 8 Str., 44-100 Gliwice, Poland; Department of Inorganic, Analytical Chemistry and Electrochemistry, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 6 Str., 44-100 Gliwice, Poland.

This study determined the impact of poultry and bovine manure fertilization on the content of antibiotics, heavy metals (HMs), and the quantitative and qualitative composition of integrase and antibiotic resistance genes in soil, groundwater, and crops cultivated on manure-amended plots. Antibiotic concentration levels were analyzed using the HPLC-MS/MS, heavy metal concentration level were measured by HGAAS and ICP-OES, while the integrase genes and ARGs were quantified using Real-Time PCR (qPCR) method. Manure, soil, and crops samples contained the highest concentration of Zn (10-10 ng g) and Cu (10-10 ng g) of all HMs tested. Read More

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Assessing visitor use impact on antibiotic resistant bacteria and antibiotic resistance genes in soil and water environments of Rocky Mountain National Park.

Sci Total Environ 2021 Apr 21;785:147122. Epub 2021 Apr 21.

Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA. Electronic address:

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. Read More

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The fate of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) from livestock wastewater (dominated by quinolone antibiotics) treated by microbial fuel cell (MFC).

Ecotoxicol Environ Saf 2021 Apr 28;218:112267. Epub 2021 Apr 28.

College of Civil Engineering, Sichuan Agricultural University, Dujiangyan 611830, PR China.

The removal characteristics of antibiotic resistance genes and mobile genetic elements from livestock wastewater (dominated by quinolone antibiotics) treated with MFC were evaluated by High-throughput quantitative (HT-qPCR). The results showed that 144 ARGs and 8 MEGs were detected in the livestock wastewater. After MFC treatment, the number of AGRs decreased as a whole, and the relative abundance of macrolide-lincosamide-streptogramin group B (MLSB) and aminoglycosider decreased by 62. Read More

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Metagenomics analysis reveals the distribution and communication of antibiotic resistance genes within two different red swamp crayfish Procambarus clarkii cultivation ecosystems.

Environ Pollut 2021 Apr 16;285:117144. Epub 2021 Apr 16.

Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China. Electronic address:

Antibiotic resistance genes (ARGs) are emerging contaminants that pose a potential risk to human health worldwide. In this study, a metagenomic analysis was performed to investigate the distribution of ARGs in paddy field ecosystems, crayfish monoculture pond ecosystems, and rice-crayfish cultivation field ecosystems. The results showed that MacB and BcrA are two dominant ARGs, and macrolide is the dominant antibiotic not only in the water, but also in the sediment and gut of crayfish, in both the crayfish monoculture and the rice-crayfish cultivation ecosystems. Read More

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Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts.

Microorganisms 2021 Apr 27;9(5). Epub 2021 Apr 27.

Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 16628 Prague 6, Czech Republic.

The aspiration these days is to apply rapid methods for parallel analysis of bacteriome and resistome of food samples to increase food safety and prevent antibiotic resistance genes (ARGs) spreading. In this work, we used nanopore sequencing (NS) to determine the diversity and dynamics of the microbiome and resistome in two types of bean sprouts. We proved that NS provided an easy, quick, and reliable way to identify the microbiome and resistome of a food sample also. Read More

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Combining Functional Genomics and Whole-Genome Sequencing to Detect Antibiotic Resistance Genes in Bacterial Strains Co-Occurring Simultaneously in a Brazilian Hospital.

Antibiotics (Basel) 2021 Apr 11;10(4). Epub 2021 Apr 11.

Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-901, Brazil.

(1) Background: The rise of multi-antibiotic resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. (2) Methods: We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 34 strains of Gram-negative and Gram-positive bacteria, providing the first genomic description of and clinical isolates from South America. Read More

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Potential Environmental and Human Health Risks Caused by Antibiotic-Resistant Bacteria (ARB), Antibiotic Resistance Genes (ARGs) and Emerging Contaminants (ECs) from Municipal Solid Waste (MSW) Landfill.

Antibiotics (Basel) 2021 Apr 1;10(4). Epub 2021 Apr 1.

Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, Ourense Campus, University of Vigo, E-32004 Ourense, Spain.

The disposal of municipal solid waste (MSW) directly at landfills or open dump areas, without segregation and treatment, is a significant concern due to its hazardous contents of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and metal resistance genes (MGEs). The released leachate from landfills greatly effects the soil physicochemical, biological, and groundwater properties associated with agricultural activity and human health. The abundance of ARB, ARGs, and MGEs have been reported worldwide, including MSW landfill sites, animal husbandry, wastewater, groundwater, soil, and aerosol. Read More

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Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach.

Microb Drug Resist 2021 Apr 28. Epub 2021 Apr 28.

Virology Unit and Bioinformatics Centre, and Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India.

In this study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community, and antibiotic resistance genes (ARGs). Utilizing data from Illumina platform, 4,174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, ∼86. Read More

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Proliferation of antibiotic-resistant microorganisms and associated genes during composting: An overview of the potential impacts on public health, management and future.

Sci Total Environ 2021 Apr 19;784:147191. Epub 2021 Apr 19.

Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State, Nigeria; Bioconversion and Renewable Energy Research Unit, University of Nigeria, Nsukka, Enugu State, Nigeria. Electronic address:

Antibiotic residues together with non-antibiotic drugs and heavy metals act as a selective pressure for the spread of antibiotic-resistant microorganisms (ARMs), antibiotic-resistant genes (ARGs), and mobile genetic elements (MGEs) during composting of livestock manure. ARMs, ARGs and MGEs have become emerging contaminants since they are regularly implicated in the majority of compost produced from livestock manure. The prevalence of these contaminants in agricultural soil receiving compost has drawn huge attention globally due to the risks they pose to the total environment. Read More

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Comparison of bacterial communities and antibiotic resistance genes in oxidation ditches and membrane bioreactors.

Sci Rep 2021 Apr 26;11(1):8955. Epub 2021 Apr 26.

College of Resource and Environmental Science, Xinjiang University, No. 666 Shengli Road, Tianshan District, Urumqi, China.

Oxidation ditches (ODs) and membrane bioreactors (MBRs) are widely used in wastewater treatment plants (WWTPs) with bacteria and antibiotic resistance genes (ARGs) running through the whole system. In this study, metagenomic sequencing was used to compare the bacterial communities and ARGs in the OD and MBR systems, which received the same influent in a WWTP located in Xinjiang, China. The results showed that the removal efficiency of pollutants by the MBR process was better than that by the OD process. Read More

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Ryegrass (Lolium multiflorum L.) and Indian mustard (Brassica juncea L.) intercropping can improve the phytoremediation of antibiotics and antibiotic resistance genes but not heavy metals.

Sci Total Environ 2021 Apr 16;784:147093. Epub 2021 Apr 16.

Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China. Electronic address:

Lolium multiflorum and Brassica juncea display phytoremediation potential for heavy metals and antibiotics pollution. However, there is limited understanding of their function in removing combined pollutants (heavy metals, antibiotics and antibiotic resistance genes (ARGs)) under different cropping patterns. Sole cropping had little effect on heavy metals, but reduced antibiotics by 2. Read More

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The association between antimicrobials and the antimicrobial-resistant phenotypes and resistance genes of Escherichia coli isolated from hospital wastewaters and adjacent surface waters in Sri Lanka.

Chemosphere 2021 Apr 17;279:130591. Epub 2021 Apr 17.

National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, 305-0856, Ibaraki, Japan.

The presence of antimicrobials, antimicrobial-resistant bacteria (ARB), and the associated antimicrobial resistance genes (ARGs) in the environment is a global health concern. In this study, the concentrations of 25 antimicrobials, the resistance of Escherichia coli (E. coli) strains in response to the selection pressure imposed by 15 antimicrobials, and enrichment of 20 ARGs in E. Read More

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[Distribution of Antibiotic Resistance Genes and Microbial Communities in a Fishery Reclamation Mining Subsidence Area].

Huan Jing Ke Xue 2021 May;42(5):2541-2549

Low Carbon Energy Institute, China University of Ming and Technology, Xuzhou 221000, China.

The widespread use of antibiotics in the aquaculture industry has caused antibiotic resistance genes (ARGs) pollution. Metagenomics technology was used to detect and analyze the relative abundance of ARGs and microbial community structure in a fishery reclamation mining subsidence area. A total of 29 ARGs were detected, and had the highest relative abundance in all the samples, reaching 1. Read More

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[Effects of Activated Carbon on the Fate of Antibiotic Resistance Genes During Anaerobic Digestion of the Organic Fraction of Municipal Solid Waste].

Huan Jing Ke Xue 2021 May;42(5):2413-2421

Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China.

The organic fraction of municipal solid waste (OFMSW) has become one of the sources and reservoirs of antibiotic resistance genes (ARGs). It is essential to explore the fate of ARGs during biological treatment of OFMSW. Therefore, the changes in several types of ARGs and integron genes during anaerobic digestion of the OFMSW were analyzed by quantitative PCR. Read More

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Identification and validation of autophagy-related prognostic signature for head and neck squamous cell carcinoma.

Transl Oncol 2021 Apr 17;14(7):101094. Epub 2021 Apr 17.

Department of Otorhinolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430000, China. Electronic address:

Background: Many studies have demonstrated that autophagy plays a significant role in regulating tumor growth and progression. However, the effect of autophagy-related genes (ARGs) on the prognosis have rarely been analyzed in head and neck squamous cell carcinoma (HNSCC).

Methods: We obtained differentially expressed ARGs from HNSCC mRNA data in The Cancer Genome Atlas (TCGA) database. Read More

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Antibiotic resistance genes are enriched with prolonged age of refuse in small and medium-sized landfill systems.

Environ Res 2021 Apr 18;197:111194. Epub 2021 Apr 18.

School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China. Electronic address:

Landfills are sites for the disposal of waste over decades. The dynamics of contaminants during landfill treatment influence the functions and environmental risks of the landfill systems, but the patterns of these dynamics are not fully characterized, especially for antibiotic resistant genes (ARGs), an emerging contaminant of global concern. Here, seventeen typical ARG subtypes were quantitatively investigated in refuse samples from small and medium-sized landfills with ages of <3 years, ~5 years, and 8-10 years. Read More

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Resistome and microbial profiling of pediatric patient's gut infected with multidrug-resistant diarrhoeagenic using next-generation sequencing; the first study from Pakistan.

Libyan J Med 2021 Dec;16(1):1915615

Department of Biology Education, Kyungpook National University, Daegu, Republic of Korea.

A high prevalence of multidrug-resistant (MDR) pathogens has been reported in adult and pediatric populations of Pakistan. However, data describing the effect of MDR microbes on the gut microbiota is scarce. We designed a cross-sectional pediatric study to investigate the effect of MDR microbes' infection on the gut microbiome and its resistome of children using high-throughput next-generation sequencing (NGS). Read More

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December 2021

Faecal microbiota and antibiotic resistance genes in migratory waterbirds with contrasting habitat use.

Sci Total Environ 2021 Apr 1;783:146872. Epub 2021 Apr 1.

Water Quality, Institut Català de Recerca de l'Aigua (ICRA), Carrer Emili Grahit 101, E-17003 Girona, Spain; Grup d'Ecologia Microbiana Molecular, Institut d'Ecologia Aquàtica, Universitat de Girona, Campus de Montilivi, E-17003 Girona, Spain.

Migratory birds may have a vital role in the spread of antimicrobial resistance across habitats and regions, but empirical data remain scarce. We investigated differences in the gut microbiome composition and the abundance of antibiotic resistance genes (ARGs) in faeces from four migratory waterbirds wintering in South-West Spain that differ in their habitat use. The white stork Ciconia ciconia and lesser black-backed gull Larus fuscus are omnivorous and opportunistic birds that use highly anthropogenic habitats such as landfills and urban areas. Read More

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Fate of antibiotic resistance genes in farmland soil applied with three different fertilizers during the growth cycle of pakchoi and after harvesting.

J Environ Manage 2021 Jul 14;289:112576. Epub 2021 Apr 14.

State Key Laboratory of Environmental Criteria and Risk Assessment, State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China. Electronic address:

The increasing prevalence of antibiotic resistance genes (ARGs) in the soil environment poses a serious threat to crop safety and even public health. In this study, the fate of ARGs in the soil was investigated during the growth period of pakchoi and after harvesting with the application of different kinds of fertilizers. The result showed that increasing rate of soil ARGs during the growth period of pakchoi followed the order of composted manure > commercial fertilizer > mineral fertilizer. Read More

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Bioaerosol is an important transmission route of antibiotic resistance genes in pig farms.

Environ Int 2021 Apr 14;154:106559. Epub 2021 Apr 14.

Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia. Electronic address:

Although pig farms are hotspots of antibiotic resistance due to intensive use of antibiotics, little is known about the abundance, diversity and transmission of airborne antibiotic resistance genes (ARGs). This study reports that bioaerosol is an important spread route of ARGs in pig farms. ARGs, mobile genetic elements (MGEs), and bacterial communities were investigated in both air and feces samples during winter and summer. Read More

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The variation of antibiotic resistance genes and their links with microbial communities during full-scale food waste leachate biotreatment processes.

J Hazard Mater 2021 Apr 1;416:125744. Epub 2021 Apr 1.

Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Engineering Research Center for Nanophotonics and Advanced Instrument, Ministry of Education, East China Normal University, Shanghai 200062, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China. Electronic address:

The prevalence of antibiotic resistance genes (ARGs) has been widely reported in various environments. However, little is known of them in food waste (FW) leachate with high organic content and how their distribution is influenced by biotreatment processes. Here, twelve ARGs, two integrase genes and bacterial communities were investigated during two full-scale FW biotreatment processes. Read More

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Heavy metal could drive co-selection of antibiotic resistance in terrestrial subsurface soils.

J Hazard Mater 2021 Jun 14;411:124848. Epub 2020 Dec 14.

Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

Terrestrial surface ecosystems are important sinks for antibiotic resistance genes (ARGs) due to the continuous discharge of contaminants from human-impacted ecosystems. However, the abundance and resistance types of ARGs and their influencing factors in terrestrial subsurface soils are not well known. In this study, we investigated the abundance and diversity of ARGs, and their correlations with metal resistance genes (MRGs), mobile genetic elements (MGEs), bacteria, and heavy metals in subsurface soils using high throughput quantitative PCR and metagenomic sequencing approaches. Read More

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Environmental antimicrobial resistance is associated with faecal pollution in Central Thailand's coastal aquaculture region.

J Hazard Mater 2021 Mar 23;416:125718. Epub 2021 Mar 23.

School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom. Electronic address:

We assessed antimicrobial resistance (AMR) potential to seven major classes of antibiotics in Central Thailand's coastal aquaculture region using high-throughput qPCR targeting 295 antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). In parallel, we used MinION next generation sequencing (NGS) of 16S rRNA gene amplicons, qPCR of faecal pollution makers, and conventional plate count methods for the comprehensive characterization of environmental microbiomes. We tested the hypothesis that aquaculture increases environmental AMR by comparing ARGs and MGEs in water and sediment samples from five aquaculture sites and their associated canals. Read More

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