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Durán-Viseras A, Lindner BG, Hatt JK, Lai A, Wallace R, Ginn O, Brown J, Konstantinidis KT. Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170772. [PMID: 38346660 DOI: 10.1016/j.scitotenv.2024.170772] [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: 12/19/2023] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 02/20/2024]
Abstract
In recent decades, human food consumption has led to an increased demand for animal-based foods, particularly chicken meat production. The state of Georgia, USA is one of the top broiler chicken producers in the United States, where animals are raised in Concentrated Animal Feeding Operations (CAFOs). Without proper management, CAFOs could negatively impact the environment and become a public health risk as a source of water and air pollution and/or by spreading antimicrobial resistance genes. In this study, we used metagenome sequencing to investigate the impact of the application of the CAFO's litter on adjacent soils and downstream creek waters in terms of microbial diversity and antimicrobial resistance profile changes. Our data indicate that while a few microbial groups increased in abundance within a short period of time after litter application, these populations subsequently decreased to levels similar to those found prior to the litter application or to below the detection limit of our metagenome sequencing effort. Microbial taxonomic composition analyses, relative abundance of Metagenome-Assembled Genomes (MAGs) and detection of Antimicrobial Resistance Genes (ARGs) allow us to conclude that this practice of litter application had a negligible effect on the microbiome or resistome profile of these soils and nearby waterways, likely due to its dilution in the field and/or outcompetition by indigenous microbes, revealing a minimal impact of these poultry facilities on the natural microbial communities.
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Affiliation(s)
- Ana Durán-Viseras
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla 41012, Spain; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Amanda Lai
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Robert Wallace
- Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Olivia Ginn
- Chemical, Materials and Biomedical Engineering Department and Institute for Bioinformatics, University of Georgia, Athens, GA 30601, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Męcik M, Buta-Hubeny M, Paukszto Ł, Maździarz M, Wolak I, Harnisz M, Korzeniewska E. Poultry manure-derived microorganisms as a reservoir and source of antibiotic resistance genes transferred to soil autochthonous microorganisms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 348:119303. [PMID: 37832303 DOI: 10.1016/j.jenvman.2023.119303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023]
Abstract
Animal husbandry is increasing yearly due to the growing demand for meat and livestock products, among other reasons. To meet these demands, prophylactic antibiotics are used in the livestock industry (i.e., poultry farming) to promote health and stimulate animal growth. However, antibiotics are not fully metabolized by animals, and they are evacuated to the environment with excreta. Animal manure is used as fertilizer to reduce the volume of waste generated in the livestock sector. However, manure often contains microorganisms harboring antibiotic resistance genes (ARGs). Then, the microbiome of manure applicate to the soil may contribute to the spread of antibiotic resistance in the environment, including autochthonous soil-dwelling microorganisms. The present study was conducted during the crops growing season in Poland (May to September 2019) to determine the influence of poultry manure as well as poultry manure supplemented with selected antibiotics on the diversity of the soil microbiome in treatments that had not been previously fertilized with manure and the ability of antibiotic-resistant bacteria to transfer ARGs to other soil bacteria. Antibiotic concentrations were elevated at the beginning of the study and decreased over time. Poultry manure induced significant changes in the structure of microbial communities in soil; the diversity of the soil microbiome decreased, and the abundance of bacterial genera Bradyrhizobium, Streptomyces, and Pseudomonas, which are characteristic of the analyzed manure, increased. Over time, soil microbial diversity was restored to the state observed before the application of manure. Genes conferring resistance to multiple drugs as well as genes encoding resistance to bacitracin and aminoglycosides were the most frequently identified ARGs in the analyzed bacteria, including on mobile genetic elements. Multidrug resistance was observed in 17 bacterial taxa, whereas ARGs were identified in 32 bacterial taxa identified in the soil microbiome. The results of the study conclude that the application of poultry manure supplemented with antibiotics initially affects soil microbiome and resistome diversity but finally, the soil shows resilience and returns to its original state after time, with most antibiotic resistance genes disappearing. This phenomenon is of great importance in sustainable soil health after manure application.
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Affiliation(s)
- Magdalena Męcik
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Martyna Buta-Hubeny
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-721, Olsztyn, Poland
| | - Mateusz Maździarz
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-721, Olsztyn, Poland
| | - Izabela Wolak
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Monika Harnisz
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland.
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Guo R, Zhu D, He J, Ma W, Li L, Li X, Wang Y. Influence of copper and aging on freely dissolved tetracycline concentration in soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:115994-116003. [PMID: 37897579 DOI: 10.1007/s11356-023-30640-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
Copper (Cu) and tetracyclines (TCs) often coexist in agricultural soils because of the use of manures on farmland; however, the influence of Cu on the bioavailability of TCs is still unclear, especially for cases with aging Cu. The freely dissolved concentrations (FDCs) of TCs are believed to be directly related to their bioavailability. In the present study, the FDCs of TCs were determined using organic-diffusive gradients in thin films (o-DGT), and the influence of Cu on the FDCs of TCs in soils was evaluated. The results showed that the FDCs of tetracycline (TC), oxytetracycline (OTC), and chlortetracycline (CTC) were 0.11-0.93, 0.28-1.02, and 0.24-0.53 μg/kg in the CK groups (no Cu added) and accounted for 0.09-0.58, 0.10-1.40, and 0.05-1.19‰ of their total concentrations which ranged from 0.2 to 10.0 mg/kg for TC, OTC, and CTC, respectively. The co-contamination of Cu reduced the FDCs of TCs in most cases, and aging increased the influence of Cu. The presence of Cu resulted in a decrease in the TC FDC by 35.48-95.04% in aged soils and 3.42-87.19% in newly prepared soils. FTIR analysis revealed that aging facilitated the bonding of Cu to soil particles via Cu-O, and Cu bonded to groups such as hydroxyl groups (-OH) in TCs. Our results suggested that the presence of Cu might reduce the bioavailability of TCs, and aging would enhance these effects. This is helpful for the bioavailability analysis of TCs under co-contamination of heavy metals.
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Affiliation(s)
- Ruichao Guo
- National Demonstration Center for Environmental and Planning, College of Environment and Planning, Henan University, Kaifeng, 475004, China
- Henan Engineering Research Centre for Control & Remediation of Soil Heavy Metal Pollution, Henan University, Kaifeng, 475004, China
| | - Deyuan Zhu
- National Demonstration Center for Environmental and Planning, College of Environment and Planning, Henan University, Kaifeng, 475004, China
- Henan Engineering Research Centre for Control & Remediation of Soil Heavy Metal Pollution, Henan University, Kaifeng, 475004, China
| | - Jimei He
- National Demonstration Center for Environmental and Planning, College of Environment and Planning, Henan University, Kaifeng, 475004, China
- Henan Engineering Research Centre for Control & Remediation of Soil Heavy Metal Pollution, Henan University, Kaifeng, 475004, China
| | - Wencong Ma
- National Demonstration Center for Environmental and Planning, College of Environment and Planning, Henan University, Kaifeng, 475004, China
- Henan Engineering Research Centre for Control & Remediation of Soil Heavy Metal Pollution, Henan University, Kaifeng, 475004, China
| | - Lin Li
- National Demonstration Center for Environmental and Planning, College of Environment and Planning, Henan University, Kaifeng, 475004, China
- Henan Engineering Research Centre for Control & Remediation of Soil Heavy Metal Pollution, Henan University, Kaifeng, 475004, China
| | - Xuhui Li
- National Demonstration Center for Environmental and Planning, College of Environment and Planning, Henan University, Kaifeng, 475004, China.
- Henan Engineering Research Centre for Control & Remediation of Soil Heavy Metal Pollution, Henan University, Kaifeng, 475004, China.
| | - Yulong Wang
- National Demonstration Center for Environmental and Planning, College of Environment and Planning, Henan University, Kaifeng, 475004, China
- Henan Engineering Research Centre for Control & Remediation of Soil Heavy Metal Pollution, Henan University, Kaifeng, 475004, China
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Mu M, Yang F, Han B, Ding Y, Zhang K. Insights into the panorama of antibiotic resistome in cropland soils amended with vermicompost in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161658. [PMID: 36649763 DOI: 10.1016/j.scitotenv.2023.161658] [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: 11/21/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
The accumulation and propagation of animal-derived antibiotic resistance genes (ARGs) pose great challenges to agricultural ecosystems. Vermicompost has drawn global attention as a new type of eco-friendly organic fertilizer. However, the effects of vermicompost application on ARGs in soil are still unclear. Here, we conducted a nationwide large-scale survey to explore the impact of vermicompost application on ARGs and the host in cropland fields as well as their regional differences. Vermicompost application was found to alter the pattern of ARGs, reduce the transfer of mobile genetic elements (MGEs), and mitigate the proliferation of high-risk bla-ARGs in soil. Regional differences in vermicompost-derived ARGs were observed in croplands, with less ARG-spreading risk in brown and yellow-brown soils. Total ARG abundance was present at the lowest level (1.24 × 105-3.57 × 107 copies/g) in vermicomposted soil compared with the croplands using animal manure (e.g., swine, chicken, and cow manure). Furthermore, vermicompost application increased the abundance of beneficial bacteria like Ilumatobacter and Gaiella, while reducing the abundance of Acidobacteria and Pseudarthrobacter. Network analysis showed that vermicompost altered ARG host bacteria and reduced the numbers of potential ARG hosts in soil. Microbes played a key role in ARG changes in vermicompost-treated soil. Our study provides valuable insight into the response of soil ARGs and the host to vermicompost in cropland ecosystem, and also provides a novel pathway for controlling the propagation of animal-derived ARGs.
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Affiliation(s)
- Meirui Mu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China.
| | - Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China
| | - Yongzhen Ding
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China; Key Laboratory of Low-carbon Green Agriculture in North China, Ministry of Agriculture and Rural Affairs, PR China.
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Tack B, Phoba MF, Thong P, Lompo P, Hupko C, Desmet S, Martiny D, Mattheus W, De La Gandara MP, Mbuyi-Kalonji L, Kuijpers L, Prevost B, Barbé B, Vandenberg O, Lunguya O, Ruiz J, Jacobs J, Hardy L. Epidemiological cut-off value and antibiotic susceptibility test methods for azithromycin in a collection of multi-country invasive non-typhoidal Salmonella. Clin Microbiol Infect 2022; 28:1615-1623. [PMID: 35738320 DOI: 10.1016/j.cmi.2022.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Azithromycin is an alternative to treat invasive non-typhoidal Salmonella (iNTS) infections. We determined its epidemiological cut-off (ECOFF) and compared azithromycin susceptibility testing methods for iNTS. METHODS We used EUCAST ECOFFinder to determine the minimum inhibitory concentrations (MIC; obtained by broth microdilution) ECOFF and corresponding disk zone diameters of 515 iNTS from blood cultures in DR Congo, Burkina Faso, Rwanda, and Cambodia. Transferable resistance mechanisms were determined by polymerase chain reaction. We compared azithromycin susceptibility testing by semi-automated broth microdilution (customized Sensititre panel; reference), agar dilution, gradient tests (bioMérieux, Liofilchem, HiMedia; read at 80% (MIC80%) and 100% inhibition (MIC100%)) and disk diffusion (Rosco, Oxoid, BD, Liofilchem) for 161 wild and 198 non-wild type iNTS. RESULTS Azithromycin MIC ECOFF was 16 mg/l corresponding to a 12mm zone diameter; mphA was detected in 192/197 non-wild and 0/47 wild type iNTS. Categorical agreement was excellent (≥98%) for all methods. Essential agreement was very good for agar dilution (>90%), but moderate for gradient tests (MIC80%: 52 - 71% and MIC100%: 72 - 91%). Repeatability was good for all methods/brands. Interreader agreement was high for broth microdilution and agar dilution (all ≤1 twofold dilution difference) and disk diffusion (>96% ≤3mm difference), but lower for gradient tests (MIC80% & MIC100%: 83 - 94% ≤1 twofold dilution difference). CONCLUSIONS Azithromycin ECOFF of iNTS was 16 mg/l, i.e. equal to Salmonella Typhi. Disk diffusion is an accurate, precise, and user-friendly alternatives for agar dilution and broth microdilution. Reading gradient tests at 100% instead of 80% inhibition improved accuracy and precision.
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Affiliation(s)
- Bieke Tack
- Department of Clinical Sciences, Institute of Tropical Medicine - Antwerp Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven - Leuven Belgium.
| | - Marie-France Phoba
- Department of Microbiology, National Institute for Biomedical Research - Kinshasa Democratic Republic of the Congo; Department of Microbiology, University Teaching Hospital of Kinshasa - Kinshasa Democratic Republic of the Congo
| | - Phe Thong
- Sihanouk Hospital Center of Hope - Phnom Penh Cambodia
| | | | | | - Stefanie Desmet
- Department of Microbiology, Immunology and Transplantation, KU Leuven - Leuven Belgium; Clinical Department of Laboratory Medicine, University Hospitals Leuven - Leuven Belgium
| | - Delphine Martiny
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires de Bruxelles - Universitaire Laboratorium Brussel (LHUB-ULB) - Bruxelles Belgium; Faculté de Médecine et Pharmacie, Université de Mons (UMONS), Mons, Belgium
| | - Wesley Mattheus
- Division of Human Bacterial Diseases, Sciensano - Uccle Belgium
| | - Maria Pardos De La Gandara
- Institut Pasteur, Université de Paris, Unité des Bactéries pathogènes entériques, Centre National de Référence des E. coli,Shigella et Salmonella - Paris France
| | - Lisette Mbuyi-Kalonji
- Department of Microbiology, National Institute for Biomedical Research - Kinshasa Democratic Republic of the Congo; Department of Microbiology, University Teaching Hospital of Kinshasa - Kinshasa Democratic Republic of the Congo
| | - Laura Kuijpers
- Department of Infectious Diseases, Leiden University Medical Center - Leiden The Netherlands
| | - Benoit Prevost
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires de Bruxelles - Universitaire Laboratorium Brussel (LHUB-ULB) - Bruxelles Belgium
| | - Barbara Barbé
- Department of Clinical Sciences, Institute of Tropical Medicine - Antwerp Belgium
| | - Olivier Vandenberg
- Center for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles - Brussels Belgium; Innovation and Business Development Unit, Laboratoire des Hôpitaux Universitaires de Bruxelles - Universitaire Laboratorium Brussel (LHUB-ULB) - Bruxelles Belgium; Division of Infection and Immunity, Faculty of Medical Sciences, University College London - London United Kingdom
| | - Octavie Lunguya
- Department of Microbiology, National Institute for Biomedical Research - Kinshasa Democratic Republic of the Congo; Department of Microbiology, University Teaching Hospital of Kinshasa - Kinshasa Democratic Republic of the Congo
| | - Joaquim Ruiz
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Cientifica del Sur - Lima Peru
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine - Antwerp Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven - Leuven Belgium
| | - Liselotte Hardy
- Department of Clinical Sciences, Institute of Tropical Medicine - Antwerp Belgium
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Black Z, Balta I, Black L, Naughton PJ, Dooley JSG, Corcionivoschi N. The Fate of Foodborne Pathogens in Manure Treated Soil. Front Microbiol 2021; 12:781357. [PMID: 34956145 PMCID: PMC8702830 DOI: 10.3389/fmicb.2021.781357] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/22/2021] [Indexed: 12/25/2022] Open
Abstract
The aim of this review was to provide an update on the complex relationship between manure application, altered pathogen levels and antibiotic resistance. This is necessary to protect health and improve the sustainability of this major farming practice in agricultural systems based on high levels of manure production. It is important to consider soil health in relation to environment and land management practices in the context of the soil microflora and the introduction of pathogens on the health of the soil microbiome. Viable pathogens in manure spread on agricultural land may be distributed by leaching, surface run-off, water source contamination and contaminated crop removal. Thus it is important to understand how multiple pathogens can persist in manures and on soil at farm-scale and how crops produced under these conditions could be a potential transfer route for zoonotic pathogens. The management of pathogen load within livestock manure is a potential mechanism for the reduction and prevention of outbreaks infection with Escherichia coli, Listeria Salmonella, and Campylobacter. The ability of Campylobacter, E. coli, Listeria and Salmonella to combat environmental stress coupled with their survival on food crops and vegetables post-harvest emphasizes the need for further study of these pathogens along with the emerging pathogen Providencia given its link to disease in the immunocompromised and its’ high levels of antibiotic resistance. The management of pathogen load within livestock manure has been widely recognized as a potential mechanism for the reduction and prevention of outbreaks infection but any studies undertaken should be considered as region specific due to the variable nature of the factors influencing pathogen content and survival in manures and soil. Mediocre soils that require nutrients could be one template for research on manure inputs and their influence on soil health and on pathogen survival on grassland and in food crops.
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Affiliation(s)
- Zoe Black
- Grassland and Plant Sciences Branch, AFBI Crossnacreevy, Sustainable Agri-Food Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, United Kingdom
| | - Igori Balta
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Faculty of Bioengineering of Animal Resources, Banat University of Animal Sciences and Veterinary Medicine, King Michael I of Romania, Timisoara, Romania
| | - Lisa Black
- Grassland and Plant Sciences Branch, AFBI Crossnacreevy, Sustainable Agri-Food Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Patrick J Naughton
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, United Kingdom
| | - James S G Dooley
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, United Kingdom
| | - Nicolae Corcionivoschi
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Faculty of Bioengineering of Animal Resources, Banat University of Animal Sciences and Veterinary Medicine, King Michael I of Romania, Timisoara, Romania
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Tian X, Han B, Liang J, Yang F, Zhang K. Tracking antibiotic resistance genes (ARGs) during earthworm conversion of cow dung in northern China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 222:112538. [PMID: 34325199 DOI: 10.1016/j.ecoenv.2021.112538] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 06/19/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Using cow dung to breed earthworms poses a risk of environmental transmission of antibiotic resistance genes (ARGs). The purpose of this study was to address the occurrence, persistence and environmental fate of ARGs during earthworm conversion of cow dung. The results showed that ARGs persisted through the whole process. Notably, earthworm conversion effectively reduced some ARGs in cow dung, but a definite concentration of ARGs still remained in earthworms and vermicompost (up to 10-1 and 10-2 copies/16S copies, respectively). We found that tet-ARGs were the most abundant in 15 earthworm farms (10-6~10-1 copies/16S copies) and some high-risk ARGs (i.e., blaampC, blaOXA-1 and blaTEM-1) were even prevalent in these farms. Interestingly, although ARGs differ widely in cow dung (10-10~10-1 copies/16S copies), the ARGs levels were comparable in vermicompost samples from different farms (10-8~10-2 copies/16S copies). Notably, earthworm conversion effectively reduced some ARGs in cow dung, but significant level of ARGs still remained in earthworms and vermicompost (up to 10-1 and 10-2 copies/16S copies, respectively). Nevertheless, the concentrations of some heavy metals (Cu, Zn and Ni), the abundance of mobile genetic elements (MGEs) and total nitrogen content were confirmed to be correlated to the enrichment of some ARGs. Overall, this study demonstrated the high prevalence of ARGs contamination in earthworm farms, and also highlighted the dissemination risk of ARGs during the earthworm conversion of cow dung.
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Affiliation(s)
- Xueli Tian
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Junfeng Liang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
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Alt LM, Iverson AN, Soupir ML, Moorman TB, Howe A. Antibiotic resistance gene dissipation in soil microcosms amended with antibiotics and swine manure. JOURNAL OF ENVIRONMENTAL QUALITY 2021; 50:911-922. [PMID: 33982299 DOI: 10.1002/jeq2.20240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
The use of antibiotics in animal agriculture has exacerbated the presence of both antibiotic resistance genes (ARGs) and residual antibiotics excreted in animal manure. Field application of this manure is a common practice because its nutrient rich material can benefit crop growth. However, this practice can also introduce antibiotics and ARGs into nonagricultural settings. The integration of prairie buffer strips within and at the edge of crop fields is a potential management solution to reduce concentrations of ARGs commonly transported via water runoff and infiltration. An incubation experiment was conducted to investigate the fate of ARGs in directly manured crop field soils and the surrounding affected prairie strip soils. Row crop and prairie strip soils sampled from three sites received either an antibiotic spike and swine manure addition or a control water addition. The concentrations of select ARGs were then monitored over a 72-d period. Although soil vegetation and site location were not observed to influence ARG dissipation, the select genes did display different half-lives from one another. For example, tetM demonstrated the fastest dissipation of the genes quantified (average half-life, 5.18 d). Conversely, sul1 did not conform to the first-order linear regression kinetics used to describe the other investigated genes and was highly abundant in control prairie strip soils. The quantified half-lives of these select ARGs are comparable to previous studies and can inform monitoring and mitigative efforts aimed at reducing the spread of ARGs in the environment.
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Affiliation(s)
- Laura M Alt
- Dep. of Agricultural and Biosystems Engineering, IA State Univ., Elings Hall, 605 Bissell Rd., Ames, IA, 50011, USA
| | - Alyssa N Iverson
- Dep. of Agricultural and Biosystems Engineering, IA State Univ., Elings Hall, 605 Bissell Rd., Ames, IA, 50011, USA
| | - Michelle L Soupir
- Dep. of Agricultural and Biosystems Engineering, IA State Univ., Elings Hall, 605 Bissell Rd., Ames, IA, 50011, USA
| | - Thomas B Moorman
- National Lab. for Agriculture and the Environment, USDA-ARS, 1015 N University Blvd., Ames, IA, 50011, USA
| | - Adina Howe
- Dep. of Agricultural and Biosystems Engineering, IA State Univ., Elings Hall, 605 Bissell Rd., Ames, IA, 50011, USA
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9
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Macedo G, Hernandez-Leal L, van der Maas P, Heederik D, Mevius D, Schmitt H. The impact of manure and soil texture on antimicrobial resistance gene levels in farmlands and adjacent ditches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 737:139563. [PMID: 32512295 DOI: 10.1016/j.scitotenv.2020.139563] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 05/26/2023]
Abstract
Manure application can spread antimicrobial resistance (AMR) from manure to soil and surface water. This study evaluated the role of the soil texture on the dynamics of antimicrobial resistance genes (ARGs) in soils and surrounding surface waters. Six dairy farms with distinct soil textures (clay, sand, and peat) were sampled at different time points after the application of manure, and three representative ARGs sul1, erm(B), and tet(W) were quantified with qPCR. Manuring initially increased levels of erm(B) by 1.5 ± 0.5 log copies/kg of soil and tet(W) by 0.8 ± 0.4 log copies/kg across soil textures, after which levels gradually declined. In surface waters from clay environments, regardless of the ARG, the gene levels initially increased by 2.6 ± 1.6 log copies/L, after which levels gradually declined. The gene decay in soils was strongly dependent on the type of ARG (erm(B) < tet(W) < sul1; half-lives of 7, 11, and 75 days, respectively), while in water, the decay was primarily dependent on the soil texture adjacent to the sampled surface water (clay < peat < sand; half-lives of 2, 6, and 10 days, respectively). Finally, recovery of ARG levels was predicted after 29-42 days. The results thus showed that there was not a complete restoration of ARGs in soils between rounds of manure application. In conclusion, this study demonstrates that rather than showing similar dynamics of decay, factors such as the type of ARG and soil texture drive the ARG persistence in the environment.
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Affiliation(s)
- Gonçalo Macedo
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands.
| | - Lucia Hernandez-Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands
| | - Peter van der Maas
- Van Hall Larenstein, University of Applied Sciences, Agora 1, 8901 BV Leeuwarden, the Netherlands
| | - Dick Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Dik Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands; Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands
| | - Heike Schmitt
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands; Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
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10
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Esperón F, Albero B, Ugarte-Ruíz M, Domínguez L, Carballo M, Tadeo JL, Del Mar Delgado M, Moreno MÁ, de la Torre A. Assessing the benefits of composting poultry manure in reducing antimicrobial residues, pathogenic bacteria, and antimicrobial resistance genes: a field-scale study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:27738-27749. [PMID: 32399873 DOI: 10.1007/s11356-020-09097-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
The poultry industry in the European Union produces 13 million tons of manure annually, which represents a major health and environmental challenge. Composting is an environmental-friendly technique for the management of manure, but there are few studies about antibiotic residues and antimicrobial resistances at a field scale. The goal of this study was to determine if the composting of poultry manure at a field scale would result in the reduction of antibiotic residues, pathogenic bacteria, and antibiotic resistance genes (ARGs) in the final fertilizer product. A 10-week composting of poultry manure spiked with enrofloxacin, doxycycline, and ciprofloxacin was performed. The determination of antibiotics residues and 22 selected ARGs was carried out together with the identification of bacteria by metagenomics. In the case of ciprofloxacin and doxycycline, a 90% decrease was observed after composting for 3 weeks. Sixteen ARGs were detected at the beginning of the experiment; 12 of them decreased from week 0 to week 10 (reduction of 73.7-99.99%). The presence of potentially pathogenic bacteria, such as, Campylobacter coli or commensal bacteria such as Escherichia coli decreases along the composting process. In conclusion, 10-week composting of poultry manure promotes the reduction of antibiotic residues and most of the ARGs and pathogenic bacteria.
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Affiliation(s)
- Fernando Esperón
- Animal Health Research Center (INIA-CISA), Ctra Algete a El Casar s/n, 28130, Valdeolmos, Madrid, Spain.
| | - Beatriz Albero
- Department of Environment and Agronomy (INIA), Ctra La Coruña Km. 7.5, 28040, Madrid, Spain
| | - María Ugarte-Ruíz
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Avda. Puerta de Hierro, s/n, 28040, Madrid, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Avda. Puerta de Hierro, s/n, 28040, Madrid, Spain
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Ada. Puerta de Hierro, s/n, Madrid, Spain
| | - Matilde Carballo
- Animal Health Research Center (INIA-CISA), Ctra Algete a El Casar s/n, 28130, Valdeolmos, Madrid, Spain
| | - José Luis Tadeo
- Department of Environment and Agronomy (INIA), Ctra La Coruña Km. 7.5, 28040, Madrid, Spain
| | - María Del Mar Delgado
- Department of Environment and Agronomy (INIA), Ctra La Coruña Km. 7.5, 28040, Madrid, Spain
| | - Miguel Ángel Moreno
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Avda. Puerta de Hierro, s/n, 28040, Madrid, Spain
- Department of Animal Health, Veterinary Faculty, Complutense University of Madrid, Ada. Puerta de Hierro, s/n, Madrid, Spain
| | - Ana de la Torre
- Animal Health Research Center (INIA-CISA), Ctra Algete a El Casar s/n, 28130, Valdeolmos, Madrid, Spain
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11
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Lopatto E, Choi J, Colina A, Ma L, Howe A, Hinsa-Leasure S. Characterizing the soil microbiome and quantifying antibiotic resistance gene dynamics in agricultural soil following swine CAFO manure application. PLoS One 2019; 14:e0220770. [PMID: 31425534 PMCID: PMC6699696 DOI: 10.1371/journal.pone.0220770] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/23/2019] [Indexed: 12/16/2022] Open
Abstract
As agriculture industrializes, concentrated animal feeding operations (CAFOs) are becoming more common. Feces from CAFOs is often used as fertilizer on fields. However, little is known about the effects manure has on the soil microbiome, which is an important aspect of soil health and fertility. In addition, due to the subtherapeutic levels of antibiotics necessary to keep the animals healthy, CAFO manure has elevated levels of antibiotic resistant bacteria. Using 16s rRNA high-throughput sequencing and qPCR, this study sought to determine the impact of swine CAFO manure application on both the soil microbiome and abundance of select antibiotic resistance genes (ARGs) and mobile element genes (erm(B), erm(C), sul1, str(B), intI1, IncW repA) in agricultural soil over the fall and spring seasons. We found the manure community to be distinct from the soil community, with a majority of bacteria belonging to Bacteroidetes and Firmicutes. The soil samples had more diverse communities dominated by Acidobacteria, Actinobacteria, Proteobacteria, Verrucomicrobia, and unclassified bacteria. We observed significant differences in the soil microbiome between all time points, except between the spring samples. However, by tracking manure associated taxa, we found the addition of the manure microbiome to be a minor driver of the shift. Of the measured genes, manure application only significantly increased the abundance of erm(B) and erm(C) which remained elevated in the spring. These results suggest bacteria in the manure do not survive well in soil and that ARG dynamics in soil following manure application vary by resistance gene.
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Affiliation(s)
- Edward Lopatto
- Department of Biology, Grinnell College, Grinnell, Iowa, United States of America
| | - Jinlyung Choi
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Alfredo Colina
- Department of Biology, Grinnell College, Grinnell, Iowa, United States of America
| | - Lanying Ma
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Shannon Hinsa-Leasure
- Department of Biology, Grinnell College, Grinnell, Iowa, United States of America
- * E-mail:
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12
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Wang M, Xiong W, Zou Y, Lin M, Zhou Q, Xie X, Sun Y. Evaluating the net effect of sulfadimidine on nitrogen removal in an aquatic microcosm environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 248:1010-1019. [PMID: 31091633 DOI: 10.1016/j.envpol.2019.02.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/22/2019] [Accepted: 02/15/2019] [Indexed: 06/09/2023]
Abstract
Antibiotics enter into aquatic pond sediments by wastewater and could make detrimental effects on microbial communities. In this study, we examined the effects of sulfadimidine on nitrogen removal when added to experimental pond sediments. We found that sulfadimidine increased the number of sulfadimidine resistant bacteria and significantly increased the abundance of sul2 at the end of the incubation time (ANOVA test at Tukey HSD, P < 0.05). In addition, sulfadimidine decreased the N2O reduction rate as well as the amount of nitrate reduction. Pearson correlation analysis revealed that the N2O reduction rate was significantly and negatively correlated with narG (r = -0.679, P < 0.05). In contrast, we found a significant positive correlation between the amount of nitrate reduction and the abundance of narG (r = 0.609, P < 0.05) and nirK (r = 0.611, P < 0.05). High-throughput sequencing demonstrated that Actinobacteria, Euryarchaeota, Gemmatimonadetes, Nitrospirae, Burkholderiaceae (a family of Proteobacteria), and Thermoanaerobaculaceae (a family of Firmicutes) decreased with sulfadimidine exposure. In sediments, Actinobacteria, Bacteroidetes, Cyanobacteria, Epsilonbacteraeota, Euryarchaeota, Firmicutes, Gemmatimonadetes, and Spirochaetesat may play key roles in nitrogen transformation. Overall, the study exhibited a net effect of antibiotic exposure regarding nitrogen removal in an aquatic microcosm environment through a combination of biochemical pathways and molecular pathways, and draws attention to controlling antibiotic pollution in aquatic ecosystems.
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Affiliation(s)
- Mei Wang
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Wenguang Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Yong Zou
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Manxia Lin
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Qin Zhou
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Xiying Xie
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.
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13
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Wang M, Chen SY, Zhang JX, He XX, Xiong WG, Sun YX. Variations of antibiotic resistance profiles in chickens during administration of amoxicillin, chlortetracycline and florfenicol. J Appl Microbiol 2018; 125:1692-1701. [PMID: 30091825 DOI: 10.1111/jam.14065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 01/11/2023]
Abstract
AIM To assess the effect of antibiotics administered in feed on the resistance phenotypes and genotypes of Escherichia coli in the chicken intestine. METHOD AND RESULTS Chickens were administered amoxicillin, chlortetracycline and florfenicol in feed and 203 intestinal E. coli were examined for their susceptibility to 11 antimicrobial agents and for the presence of antibiotic resistance genes (ARG) using PCR. DNA was extracted from chicken stool samples in 15, 20, 30 and 40 day old chickens. We found that while antibiotic resistance rates increased with time, the relative gene abundance of tet(W), tet(A), cmlA, cfr and sul1 decreased. In contrast, the relative abundance of gene blaTEM and mcr-1 increased over the experimental period. Pearson correlation analysis indicated that sul1 was correlated with tet(W) (R = 0·630, P < 0·01) and cmlA was correlated with cfr (R = 0·587, P < 0·01). Interestingly, mcr-1 correlated with tet(W) (R = -0·546, P < 0·05). CONCLUSIONS Administration of different antibiotic reduced the relative abundance of ARG in chickens but did not halt the expansion of antibiotic resistance. SIGNIFICANCE AND IMPACT OF THE STUDY Changing the pattern of antibiotic types used to prevent antibiotic resistance in chickens is not a viable method to prevent the spread of ARG.
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Affiliation(s)
- M Wang
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU), South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bactria, South China Agricultural University, Guangzhou, China
| | - S-Y Chen
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU), South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bactria, South China Agricultural University, Guangzhou, China
| | - J-X Zhang
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU), South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bactria, South China Agricultural University, Guangzhou, China
| | - X-X He
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU), South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bactria, South China Agricultural University, Guangzhou, China
| | - W-G Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU), South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bactria, South China Agricultural University, Guangzhou, China
| | - Y-X Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU), South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bactria, South China Agricultural University, Guangzhou, China
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