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Ma W, An B, Xu X, Huo M, Mi K, Tian X, Kou Z, Tang A, Cheng G, Huang L. Ceftiofur in swine manure contributes to reducing pathogens and antibiotic resistance genes during composting. ENVIRONMENTAL RESEARCH 2024; 252:119033. [PMID: 38685300 DOI: 10.1016/j.envres.2024.119033] [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: 06/14/2023] [Revised: 03/14/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Aerobic composting is a common way for the disposal of feces produced in animal husbandry, and can reduce the release of antibiotic resistance genes (ARGs) from feces into the environment. In this study, we collected samples from two distinct treatments of swine manure compost with and without ceftiofur (CEF), and identified the ARGs, mobile genetic elements (MGEs), and bacterial community by metagenomic sequencing. The impacts of CEF on the bacterial community composition and fate of ARGs and MGEs were investigated. With increasing composting temperature and pH, the concentration of CEF in the manure decreased rapidly, with a degradation half-life of 1.12 d and a 100% removal rate after 10 d of aerobic composting. Metagenomics demonstrated that CEF in the manure might inhibit the growth of Firmicutes and Proteobacteria, thereby reducing some ARGs and MGEs hosted by these two bacteria, which was further confirmed by the variations of ARGs and MGEs. A further redundancy analysis suggested that pH and temperature are key environmental factors affecting ARG removal during composting, and intI1 and bacterial communities also have significant influence on ARG abundance. These results are of great significance for promoting the removal of some ARGs from animal manure by controlling some key environmental factors and the type of antibiotics used in animals.
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Affiliation(s)
- Wenjin Ma
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Boyu An
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiangyue Xu
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Meixia Huo
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Kun Mi
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiaoyuan Tian
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Ziyan Kou
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Aoran Tang
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Guyue Cheng
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China.
| | - Lingli Huang
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China.
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Agga GE, Durso LM, Sistani KR. Effect of poultry litter soil amendment on antibiotic-resistant Escherichia coli. JOURNAL OF ENVIRONMENTAL QUALITY 2024; 53:300-313. [PMID: 38576271 DOI: 10.1002/jeq2.20560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/14/2024] [Indexed: 04/06/2024]
Abstract
Given the high cost and non-renewability of mineral-based fertilizers, there is increasing interest in the innovative use of manure-based materials, such as poultry litter (PL). However, manure-based fertilizers add both nutrients and microbes to the soil, including antibiotic-resistant Escherichia coli (AREc). PL soil amendment impact on AREc in corn fields was evaluated in a randomized field experiment (May-October 2017). Two winter cropping systems (fallow and cover crop) were assigned to whole plots, with three spring-applied fertilizer treatments (untreated control [UC], PL, and commercial fertilizer [CF]) assigned to subplots. Soil was collected from 0 to 15 cm on days 0, 7, 28, 70, 98, and 172 post-treatment applications. Samples were cultured for the enumeration and prevalence of generic, tetracycline-resistant (TETr), third-generation cephalosporin-resistant (3GCr) E. coli isolates, and extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae. PL soil amendment significantly (p < 0.05) increased the levels of generic E. coli, TETr E. coli, and 3GCr E. coli on days 7 and 28 compared to UC or CF. Beyond day 28, AREc did not significantly (p > 0.05) differ by fertilizer treatment and returned to baseline on day 70. ESBL-producing Enterobacteriaceae were detected from 16 samples, mostly on day 70. Cover crop significantly decreased TETr E. coli concentration on day 28, with no significant effects on the prevalence of 3GCr E. coli and ESBL-producing Enterobacteriaceae compared to no cover crop. All ESBL-producing Enterobacteriaceae and 79% of the 3GCr E. coli isolates were positive for blaCTX-M gene by polymerase chain reaction. Results show that PL soil amendment transiently increases the levels of AREc compared to mineral fertilizer.
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Affiliation(s)
- Getahun E Agga
- USDA-ARS, Food Animal Environmental Research Unit, Bowling Green, Kentucky, USA
| | - Lisa M Durso
- USDA-ARS, Agroecosystem Management Research Unit, Lincoln, Nebraska, USA
| | - Karamat R Sistani
- USDA-ARS, Food Animal Environmental Research Unit, Bowling Green, Kentucky, USA
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3
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Billet L, Pesce S, Martin-Laurent F, Devers-Lamrani M. Experimental Evidence for Manure-Borne Bacteria Invasion in Soil During a Coalescent Event: Influence of the Antibiotic Sulfamethazine. MICROBIAL ECOLOGY 2023; 85:1463-1472. [PMID: 35556154 PMCID: PMC10167166 DOI: 10.1007/s00248-022-02020-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/19/2022] [Indexed: 05/10/2023]
Abstract
The fertilization of agricultural soil by organic amendment that may contain antibiotics, like manure, can transfer bacterial pathogens and antibiotic-resistant bacteria to soil communities. However, the invasion by manure-borne bacteria in amended soil remains poorly understood. We hypothesized that this kind of process is both influenced by the soil properties (and those of its microbial communities) and by the presence of contaminants such as antibiotics used in veterinary care. To test that, we performed a microcosm experiment in which four different soils were amended or not with manure at an agronomical dose and exposed or not to the antibiotic sulfamethazine (SMZ). After 1 month of incubation, the diversity, structure, and composition of bacterial communities of the soils were assessed by 16S rDNA sequencing. The invasion of manure-borne bacteria was still perceptible 1 month after the soil amendment. The results obtained with the soil already amended in situ with manure 6 months prior to the experiment suggest that some of the bacterial invaders were established in the community over the long term. Even if differences were observed between soils, the invasion was mainly attributable to some of the most abundant OTUs of manure (mainly Firmicutes). SMZ exposure had a limited influence on soil microorganisms but our results suggest that this kind of contaminant can enhance the invasion ability of some manure-borne invaders.
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Affiliation(s)
- Loren Billet
- INRAE, UR RiverLy, Villeurbanne, France.
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne Franche-Comté, Dijon, France.
| | | | - Fabrice Martin-Laurent
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne Franche-Comté, Dijon, France
| | - Marion Devers-Lamrani
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne Franche-Comté, Dijon, France
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Dunn LL, Sharma V, Chapin TK, Friedrich LM, Larson CC, Rodrigues C, Jay-Russell M, Schneider KR, Danyluk MD. The prevalence and concentration of Salmonella enterica in poultry litter in the southern United States. PLoS One 2022; 17:e0268231. [PMID: 35617326 PMCID: PMC9135211 DOI: 10.1371/journal.pone.0268231] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/22/2022] [Indexed: 02/03/2023] Open
Abstract
Poultry litter is applied to crop production land in the southern United States as a waste management strategy as it is a nitrogen-rich fertilizer and plentiful throughout the region. While litter is a known reservoir for human enteric pathogens including Salmonella enterica, little is known regarding pathogen prevalence, concentration, and common serotypes within the material. Litter from thirteen farms across four southern states was examined for Salmonella. Samples (n = 490) from six of the thirteen (46.2%) farms tested positive. Thirty-three samples out of 490 (6.7%) were Salmonella positive. Salmonella was ca. 95% less likely to be collected from stacked litter piles than from the poultry house floor or pasture, and every day increase in litter age reduced the likelihood of recovering Salmonella by 5.1%. When present, concentrations of Salmonella in contaminated poultry litter were variable, ranging from <0.45 to >280,000 MPN/g. The most prevalent serotypes found were Kentucky (45.5%), Kiambu (18.2%), and Michigan (12.1%). Salmonella Kentucky also had the greatest distribution and was found on 4 of the 6 (66.7%) positive farms. Results from this survey demonstrated that Salmonella prevalence and concentration in poultry litter is highly variable, and good agricultural practices are critical to safely use poultry litter as a soil amendment on fresh produce fields.
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Affiliation(s)
- Laurel L. Dunn
- Department of Food Science and Technology, University of Georgia, Athens, GA, United States of America
- * E-mail:
| | - Vijendra Sharma
- Food Science and Human Nutrition Department, Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
| | - Travis K. Chapin
- Food Science and Human Nutrition Department, Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
| | - Loretta M. Friedrich
- Food Science and Human Nutrition Department, Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
| | - Colleen C. Larson
- Okeechobee County Cooperative Extension Service, Institute of Food and Human Nutrition University of Florida, Okeechobee, FL, United States of America
| | - Camila Rodrigues
- Department of Food Science and Technology, University of Georgia, Athens, GA, United States of America
| | - Michele Jay-Russell
- Western Center for Food Safety, University of California, Davis, Davis, CA, United States of America
| | - Keith R. Schneider
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL, United States of America
| | - Michelle D. Danyluk
- Food Science and Human Nutrition Department, Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States of America
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Burch TR, Firnstahl AD, Spencer SK, Larson RA, Borchardt MA. Fate and seasonality of antimicrobial resistance genes during full-scale anaerobic digestion of cattle manure across seven livestock production facilities. JOURNAL OF ENVIRONMENTAL QUALITY 2022; 51:352-363. [PMID: 35388483 DOI: 10.1002/jeq2.20350] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Anaerobic digestion has been suggested as an intervention to attenuate antibiotic resistance genes (ARGs) in livestock manure but supporting data have typically been collected at laboratory scale. Few studies have quantified ARG fate during full-scale digestion of livestock manure. We sampled untreated manure and digestate from seven full-scale mesophilic dairy manure digesters to assess ARG fate through each system. Samples were collected biweekly from December through August (i.e., winter, spring, and summer; n = 235 total) and analyzed by quantitative polymerase chain reaction for intI1, erm(B), sul1, tet(A), and tet(W). Concentrations of intI1, sul1, and tet(A) decreased during anaerobic digestion, but their removal was less extensive than expected based on previous laboratory studies. Removal for intI1 during anaerobic digestion equaled 0.28 ± 0.03 log10 units (mean ± SE), equivalent to only 48% removal and notable given intI1's role in horizontal gene transfer and multiple resistance. Furthermore, tet(W) concentrations were unchanged during anaerobic digestion (p > 0.05), and erm(B) concentrations increased by 0.52 ± 0.03 log10 units (3.3-fold), which is important given erythromycin's status as a critically important antibiotic for human medicine. Seasonal log10 changes in intI1, sul1, and tet(A) concentrations were ≥50% of corresponding log10 removals by anaerobic digestion, and variation in ARG and intI1 concentrations among digesters was quantitatively comparable to anaerobic digestion effects. These results suggest that mesophilic anaerobic digestion may be limited as an intervention for ARGs in livestock manure and emphasize the need for multiple farm-level interventions to attenuate antibiotic resistance.
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Affiliation(s)
- Tucker R Burch
- USDA-ARS, Environmentally Integrated Dairy Management Research Unit, 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
- Laboratory for Infectious Disease and the Environment (an interagency laboratory supported by USDA-ARS and USGS), 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
| | - Aaron D Firnstahl
- Laboratory for Infectious Disease and the Environment (an interagency laboratory supported by USDA-ARS and USGS), 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
- USGS, Upper Midwest Water Science Center, 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
| | - Susan K Spencer
- USDA-ARS, Environmentally Integrated Dairy Management Research Unit, 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
- Laboratory for Infectious Disease and the Environment (an interagency laboratory supported by USDA-ARS and USGS), 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
| | - Rebecca A Larson
- Dep. of Biological Systems Engineering, Univ. of Wisconsin-Madison, 232C Agricultural Engineering Building, 460 Henry Mall, Madison, WI, 53706, USA
| | - Mark A Borchardt
- USDA-ARS, Environmentally Integrated Dairy Management Research Unit, 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
- Laboratory for Infectious Disease and the Environment (an interagency laboratory supported by USDA-ARS and USGS), 2615 Yellowstone Dr., Marshfield, WI, 54449, USA
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Junior SFS, da Silva EO, de Farias Araujo G, Soares LOS, Parente CET, Malm O, Saggioro EM, Correia FV. Antioxidant system alterations and biological health status of earthworms following long-term exposure to antibiotic-contaminated poultry litter. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:23607-23618. [PMID: 34811610 DOI: 10.1007/s11356-021-17599-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Poultry litter is widely applied as a fertilizer even though it is one of the main antibiotic sources to agricultural soils. Long-term sublethal effects (56 days) on the antioxidant system of Eisenia andrei earthworms following exposure to fluoroquinolone-contaminated poultry litter (enrofloxacin + ciprofloxacin) at 5.0, 10, and 20 g kg-1 were evaluated. The following biomarkers were assessed: superoxide dismutase (SOD), catalase (CAT), glutathione-S-transferase (GST), reduced glutathione (GSH), and a lipid peroxidation (LPO) proxy. Significant CAT and SOD increases, and a moderate positive correlation (ρ = 0.67, p < 0.05) between these enzymes was observed. Glutathione-S-transferase levels increased significantly at 10 g kg-1, while GSH exhibited a dose-dependent response at 5.0 mg kg-1 (4-106%), 10 mg kg-1 (28-330 %), and 20 mg kg-1 (45-472%). LPO levels exhibited a decreasing trend with increasing poultry litter concentrations of 8-170% (5.0 g kg-1), 7-104% (10 mg kg-1), and 3-6% (20 mg kg-1). A principal component analysis (PCA) highlighted increased SOD and CAT activities, possibly due to increased reactive oxygen species (ROS) concentrations. Biological health status assessments based on the biomarker response index indicate major alterations in the first month of exposure and becoming moderate in the second month. These findings indicate an antioxidant system attenuation trend. It is possible, however, that successive poultry litter applications may reduce the long-term recovery capacity of the evaluated biomarkers.
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Affiliation(s)
- Sidney Fernandes Sales Junior
- Programa de Pós-Graduação em Saúde Pública e Meio Ambiente, Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Evelyn Oliveira da Silva
- Programa de Pós-Graduação em Saúde Pública e Meio Ambiente, Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Gabriel de Farias Araujo
- Programa de Pós-Graduação em Saúde Pública e Meio Ambiente, Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Lorena Oliveira Souza Soares
- Programa de Pós-Graduação em Saúde Pública e Meio Ambiente, Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Radioisótopos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho s/n, bloco G0, sala 60, subsolo, Rio de Janeiro, 21941-902, Brazil
| | - Cláudio Ernesto Taveira Parente
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, 21040-360, Brazil
| | - Olaf Malm
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, 21040-360, Brazil
| | - Enrico Mendes Saggioro
- Programa de Pós-Graduação em Saúde Pública e Meio Ambiente, Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
- UNIRIO, Departamento de Ciências Naturais, Av. Pasteur, 458, Urca, Rio de Janeiro, 22290-20, Brazil.
| | - Fábio Veríssimo Correia
- Laboratório de Radioisótopos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho s/n, bloco G0, sala 60, subsolo, Rio de Janeiro, 21941-902, Brazil
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Hilaire SS, Chen C, Radolinski J, Leventhal T, Preisendanz H, Kleinman PJA, Maguire R, Stewart RD, Saporito LS, Xia K. Culturable antibiotic-resistant fecal coliform bacteria in soil and surface runoff after liquid dairy manure surface application and subsurface injection. JOURNAL OF ENVIRONMENTAL QUALITY 2022; 51:288-300. [PMID: 35122692 DOI: 10.1002/jeq2.20332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Land application of manure, while beneficial to soil health and plant growth, can lead to an overabundance of nutrients and introduction of emerging contaminants into agricultural fields. Compared with surface application of manure, subsurface injection has been shown to reduce nutrients and antibiotics in surface runoff. However, less is known about the influence of subsurface injection on the transport and persistence of antibiotic-resistant microorganisms. We simulated rainfall to field plots at two sites (one in Virginia and one in Pennsylvania) 1 or 7 d after liquid dairy manure surface and subsurface application (56 Mg ha-1 ) and monitored the abundance of culturable antibiotic-resistant fecal coliform bacteria (ARFCB) in surface runoff and soils for 45 d. We performed these tests at both sites in spring 2018 and repeated the test at the Virginia site in fall 2019. Manure subsurface injection, compared with surface application, resulted in less ARFCB in surface runoff, and this reduction was greater at Day 1 after application compared with Day 7. The reductions of ARFCB in surface runoff because of manure subsurface injection were 2.5-593 times at the Virginia site in spring 2018 and fall 2019 and 4-5 times at the Pennsylvania site in spring 2018. The ARFCB were only detectable in the 0-to-5-cm soil depth within 14 d of manure surface application but remained detectable in the injection slits of manure subsurface-injected plots even at Day 45. This study demonstrated that subsurface injection can significantly reduce surface runoff of ARFCB from manure-applied fields.
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Affiliation(s)
| | - Chaoqi Chen
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
- School of Resource and Environmental Sciences, Wuhan, 430079, China
| | - Jesse Radolinski
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
- Dep. of Ecology, Univ. of Innsbruck, Innsbruck, 6020, Austria
| | - Talia Leventhal
- Agricultural and Biological Engineering, Penn State, State College, PA, 16802, USA
| | - Heather Preisendanz
- Agricultural and Biological Engineering, Penn State, State College, PA, 16802, USA
| | - Peter J A Kleinman
- Pasture Systems and Watershed Management Research Unit, USDA-ARS, University Park, PA, 16802, USA
| | - Rory Maguire
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Ryan D Stewart
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Lou S Saporito
- Pasture Systems and Watershed Management Research Unit, USDA-ARS, University Park, PA, 16802, USA
| | - Kang Xia
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
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8
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Subirats J, Murray R, Yin X, Zhang T, Topp E. Impact of chicken litter pre-application treatment on the abundance, field persistence, and transfer of antibiotic resistant bacteria and antibiotic resistance genes to vegetables. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149718. [PMID: 34425441 DOI: 10.1016/j.scitotenv.2021.149718] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Treatment of manures prior to land application can potentially reduce the abundance of antibiotic resistance genes and thus the risk of contaminating crops or water resources. In this study, raw and composted chicken litter were applied to field plots that were cropped to carrots, lettuce and radishes. Vegetables were washed per normal culinary practice before downstream analysis. The impact of composting on manure microbial composition, persistence of antibiotic resistant bacteria in soil following application, and distribution of antibiotic resistance genes and bacteria on washed vegetables were determined. A subset of samples that were thought likely to reveal the most significant effects were chosen for shotgun sequencing. The absolute abundance of all target genes detected by qPCR decreased after composting except sul1, intI1, incW and erm(F) that remained stable. The shotgun sequencing revealed that some integron integrases were enriched by composting. Composting significantly reduced the abundance of enteric bacteria, including those carrying antibiotic resistance. Manure-amended soil showed significantly higher abundances of sul1, str(A), str(B), erm(B), aad(A), intI1 and incW compared to unmanured soil. At harvest, those genes that were detected in soil samples before the application of manure (intI1, sul1, strA and strB) were quantifiable by qPCR on vegetables, with a larger number of gene targets detected on the radishes than in the carrots or lettuce. Shotgun metagenomic sequencing suggested that the increase of antibiotic resistance genes on radishes produced in soil receiving raw manure may be due to changes to soil microbial communities following manure application, rather than transfer to the radishes of enteric bacteria. Overall, under field conditions there was limited evidence for transfer of antibiotic resistance genes from composted or raw manure to vegetables that then persisted through washing.
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Affiliation(s)
- Jessica Subirats
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada; Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Roger Murray
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
| | - Xiaole Yin
- Environmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Tong Zhang
- Environmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Edward Topp
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada; Department of Biology, University of Western Ontario, London, Ontario, Canada.
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Bindari YR, Moore RJ, Van TTH, Hilliar M, Wu SB, Walkden-Brown SW, Gerber PF. Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum. PLoS One 2021; 16:e0255633. [PMID: 34351989 PMCID: PMC8341621 DOI: 10.1371/journal.pone.0255633] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/20/2021] [Indexed: 12/26/2022] Open
Abstract
Traditional sampling methods for the study of poultry gut microbiota preclude longitudinal studies as they require euthanasia of birds for the collection of caecal and ileal contents. Some recent research has investigated alternative sampling methods to overcome this issue. The main goal of this study was to assess to what extent the microbial composition of non-invasive samples (excreta, litter and poultry dust) are representative of invasive samples (caecal and ileal contents). The microbiota of excreta, dust, litter, caecal and ileal contents (n = 110) was assessed using 16S ribosomal RNA gene amplicon sequencing. Of the operational taxonomic units (OTUs) detected in caecal contents, 99.7% were also detected in dust, 98.6% in litter and 100% in excreta. Of the OTUs detected in ileal contents, 99.8% were detected in dust, 99.3% in litter and 95.3% in excreta. Although the majority of the OTUs found in invasive samples were detected in non-invasive samples, the relative abundance of members of the microbial communities of these groups were different, as shown by beta diversity measures. Under the conditions of this study, correlation analysis showed that dust could be used as a proxy for ileal and caecal contents to detect the abundance of the phylum Firmicutes, and excreta as a proxy of caecal contents for the detection of Tenericutes. Similarly, litter could be used as a proxy for caecal contents to detect the abundance of Firmicutes and Tenericutes. However, none of the non-invasive samples could be used to infer the overall abundance of OTUs observed in invasive samples. In conclusion, non-invasive samples could be used to detect the presence and absence of the majority of the OTUs found in invasive samples, but could not accurately reflect the microbial community structure of invasive samples.
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Affiliation(s)
- Yugal R. Bindari
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Robert J. Moore
- School of Science, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora West Campus, Bundoora, Victoria, Australia
| | - Matthew Hilliar
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Shu-Biao Wu
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Stephen W. Walkden-Brown
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Priscilla F. Gerber
- Animal Science, School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
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10
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Zalewska M, Błażejewska A, Czapko A, Popowska M. Antibiotics and Antibiotic Resistance Genes in Animal Manure - Consequences of Its Application in Agriculture. Front Microbiol 2021; 12:610656. [PMID: 33854486 PMCID: PMC8039466 DOI: 10.3389/fmicb.2021.610656] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 03/03/2021] [Indexed: 02/06/2023] Open
Abstract
Antibiotic resistance genes (ARGs) are a relatively new type of pollutant. The rise in antibiotic resistance observed recently is closely correlated with the uncontrolled and widespread use of antibiotics in agriculture and the treatment of humans and animals. Resistant bacteria have been identified in soil, animal feces, animal housing (e.g., pens, barns, or pastures), the areas around farms, manure storage facilities, and the guts of farm animals. The selection pressure caused by the irrational use of antibiotics in animal production sectors not only promotes the survival of existing antibiotic-resistant bacteria but also the development of new resistant forms. One of the most critical hot-spots related to the development and dissemination of ARGs is livestock and poultry production. Manure is widely used as a fertilizer thanks to its rich nutrient and organic matter content. However, research indicates that its application may pose a severe threat to human and animal health by facilitating the dissemination of ARGs to arable soil and edible crops. This review examines the pathogens, potentially pathogenic microorganisms and ARGs which may be found in animal manure, and evaluates their effect on human health through their exposure to soil and plant resistomes. It takes a broader view than previous studies of this topic, discussing recent data on antibiotic use in farm animals and the effect of these practices on the composition of animal manure; it also examines how fertilization with animal manure may alter soil and crop microbiomes, and proposes the drivers of such changes and their consequences for human health.
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Affiliation(s)
- Magdalena Zalewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Aleksandra Błażejewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agnieszka Czapko
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Magdalena Popowska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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11
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Overcoming bacterial resistance to antibiotics: the urgent need – a review. ANNALS OF ANIMAL SCIENCE 2021. [DOI: 10.2478/aoas-2020-0098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The discovery of antibiotics is considered one of the most crucial breakthroughs in medicine and veterinary science in the 20th century. From the very beginning, this type of drug was used as a ‘miraculous cure’ for every type of infection. In addition to their therapeutic uses, antibiotics were also used for disease prevention and growth promotion in livestock. Though this application was banned in the European Union in 2006, antibiotics are still used in this way in countries all over the world. The unlimited and unregulated use of antibiotics has increased the speed of antibiotic resistance’s spread in different types of organisms. This phenomenon requires searching for new strategies to deal with hard-to-treat infections. The antimicrobial activity of some plant derivatives and animal products has been known since ancient times. At the beginning of this century, even more substances, such as antimicrobial peptides, were considered very promising candidates for becoming new alternatives to commonly used antimicrobials. However, many preclinical and clinical trials ended without positive results. A variety of strategies to fight microbes exist, but we are a long way from approving them as therapies. This review begins with the discovery of antibiotics, covers the modes of action of select antimicrobials, and ends with a literature review of the newest potential alternative approaches to overcoming the drug resistance phenomenon.
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12
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Miller DN, Jurgens ME, Durso LM, Schmidt AM. Simulated Winter Incubation of Soil With Swine Manure Differentially Affects Multiple Antimicrobial Resistance Elements. Front Microbiol 2020; 11:611912. [PMID: 33391241 PMCID: PMC7772212 DOI: 10.3389/fmicb.2020.611912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/25/2020] [Indexed: 11/29/2022] Open
Abstract
Gastrointestinal bacteria that harbor antibiotic resistance genes (ARG) become enriched with antibiotic use. Livestock manure application to cropland for soil fertility presents a concern that ARG and bacteria may proliferate and be transported in the environment. In the United States, manure applications typically occur during autumn with slow mineralization until spring planting season. A laboratory soil incubation study was conducted mimicking autumn swine manure application to soils with concentrations of selected ARG monitored during simulated 120-day winter incubation with multiple freeze-thaw events. Additionally, the effects of two soil moistures [10 and 30% water holding capacity (WHC)] and two manure treatments [raw versus hydrated lime alkaline stabilization (HLAS)] were assessed. Fourteen tetracycline resistance genes were evaluated; tet(D), tet(G), and tet(L) were detected in background soil while swine manure contained tet(A), tet(B), tet(C), tet(G), tet(M), tet(O), tet(Q), and tet(X). By day 120, the manure-borne tet(M) and tet(O) were still detected while tet(C), tet(D), tet(L), and tet(X) genes were detected less frequently. Other tet resistance genes were detected rarely, if at all. The sum of unique tet resistance genes among all treatments decreased during the incubation from an average of 8.9 to 3.8 unique tet resistance genes. Four resistance elements, intI1, blactx–m–32, sul(I), erm(B), and 16s rRNA genes were measured using quantitative PCR. ARG abundances relative to 16S abundance were initially greater in the raw manure compared to background soil (−1.53 to −3.92 log abundance in manure; −4.02 to <−6.7 log abundance in soil). In the mixed manure/soil, relative abundance of the four resistance elements decreased (0.87 to 1.94 log abundance) during the incubation largely because 16S rRNA genes increased by 1.21 log abundance. Throughout the incubation, the abundance of intI1, blactx–m–32, sul(I), and erm(B) per gram in soil amended with HLAS-treated manure was lower than in soil amended with raw manure. Under low initial soil moisture conditions, HLAS treatment reduced the abundance of intI1 and resulted in loss of blactx–m–32, sul(I), and erm(B)] compared to other treatment-moisture combinations. Although one might expect antibiotic resistance to be relatively unchanged after simulated winter manure application to soil, a variety of changes in diversity and relative abundance can be expected.
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Affiliation(s)
- Daniel N Miller
- USDA-ARS, Agroecosystem Management Research Unit, Lincoln, NE, United States
| | | | - Lisa M Durso
- USDA-ARS, Agroecosystem Management Research Unit, Lincoln, NE, United States
| | - Amy M Schmidt
- Department of Biological Systems Engineering, University of Nebraska, Lincoln, NE, United States
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13
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Subirats J, Murray R, Scott A, Lau CHF, Topp E. Composting of chicken litter from commercial broiler farms reduces the abundance of viable enteric bacteria, Firmicutes, and selected antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:141113. [PMID: 32768779 DOI: 10.1016/j.scitotenv.2020.141113] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 06/11/2023]
Abstract
We examined the ability of composting to remove ARGs and enteric bacteria in litter obtained from broiler chickens fed with a diet supplemented with Bacitracin methylene disalicylate (BDM) (conventional chicken litter), or an antibiotic-free diet (raised without antibiotic (RWA) chicken litter). This was done by evaluating the litter before and after composting for the abundance of ten gene targets associated with antibiotic resistance or horizontal gene transfer, the composition of the bacterial communities, and the abundance of viable enteric bacteria. The abundance of gene targets was determined by qPCR and the microbial community composition of chicken litter determined by 16S rRNA gene amplicon sequencing. Enteric bacteria were enumerated by viable plate count. A majority of the gene targets were more abundant in conventional than in RWA litter. In both litter types, the absolute abundance of all of the target genes decreased after composting except sul1, intI1, incW and erm(F) that remained stable. Composting significantly reduced the abundance of enteric bacteria, including those carrying antibiotic resistance. The major difference in bacterial community composition between conventional and RWA litter was due to members affiliated to the genus Pseudomonas, which were 28% more abundant in conventional than in RWA litter. Composting favoured the presence of thermophilic bacteria, such as those affiliated with the genus Truepera, but decreased the abundance of those bacterial genera associated with cold-adapted species, such as Carnobacterium, Psychrobacter and Oceanisphaera. The present study shows that chicken litter from broilers fed with a diet supplemented with antibiotic has an increased abundance of some ARGs, even after composting. However, we can conclude that fertilization with composted litter represents a reduced risk of transmission of antibiotic resistance genes and enteric bacteria of poultry origin to soil and crops than will fertilization with raw litter.
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Affiliation(s)
- Jessica Subirats
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada; Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Roger Murray
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
| | - Andrew Scott
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
| | - Calvin Ho-Fung Lau
- Canadian Food Inspection Agency, 960 Carling Avenue, Ottawa, Ontario, Canada
| | - Edward Topp
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada; Department of Biology, University of Western Ontario, London, Ontario, Canada.
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14
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Yang Y, Ashworth AJ, DeBruyn JM, Durso LM, Savin M, Cook K, Moore Jr. PA, Owens PR. Antimicrobial resistant gene prevalence in soils due to animal manure deposition and long-term pasture management. PeerJ 2020; 8:e10258. [PMID: 33194426 PMCID: PMC7646296 DOI: 10.7717/peerj.10258] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/06/2020] [Indexed: 02/01/2023] Open
Abstract
The persistence of antimicrobial resistant (AMR) genes in the soil-environment is a concern, yet practices that mitigate AMR are poorly understood, especially in grasslands. Animal manures are widely deposited on grasslands, which are the largest agricultural land-use in the United States. These nutrient-rich manures may contain AMR genes. The aim of this study was to enumerate AMR genes in grassland soils following 14-years of poultry litter and cattle manure deposition and evaluate if best management practices (rotationally grazed with a riparian (RBR) area and a fenced riparian buffer strip (RBS), which excluded cattle grazing and poultry litter applications) relative to standard pasture management (continuously grazed (CG) and hayed (H)) minimize the presence and amount of AMR genes. Quantitative PCR (Q-PCR) was performed to enumerate four AMR genes (ermB, sulI, intlI, and blactx-m-32 ) in soil, cattle manure, and poultry litter environments. Six soil samples were additionally subjected to metagenomic sequencing and resistance genes were identified from assembled sequences. Following 14-years of continuous management, ermB, sulI, and intlI genes in soil were greatest (P < 0.05) in samples collected under long-term continuous grazing (relative to conservation best management practices), under suggesting overgrazing and continuous cattle manure deposition may increase AMR gene presence. In general, AMR gene prevalence increased downslope, suggesting potential lateral movement and accumulation based on landscape position. Poultry litter had lower abundance of AMR genes (ermB, sulI, and intlI) relative to cattle manure. Long-term applications of poultry litter increased the abundance of sulI and intlI genes in soil (P < 0.05). Similarly, metagenomic shotgun sequencing revealed a greater total number of AMR genes under long-term CG, while fewer AMR genes were found in H (no cattle manure) and RBS (no animal manure or poultry litter). Results indicate long-term conservation pasture management practices (e.g., RBS and RBR) and select animal manure (poultry litter inputs) may minimize the presence and abundance of AMR genes in grassland soils.
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Affiliation(s)
- Yichao Yang
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America
| | - Amanda J. Ashworth
- Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Fayetteville, AR, United States of America
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering & Soil Science, University of Tennessee - Knoxville, Knoxville, TN, United States of America
| | - Lisa M. Durso
- Agroecosystem Management Research Unit, United States Department of Agriculture, Agricultural Research Service, Lincoln, NE, United States of America
| | - Mary Savin
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America
| | - Kim Cook
- United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States of America
| | - Philip A. Moore Jr.
- Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Fayetteville, AR, United States of America
| | - Phillip R. Owens
- Dale Bumpers Small Farms Research Center, United States Department of Agriculture, Agricultural Research Service, Booneville, AR, United States of America
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15
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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: 6.3] [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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16
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Hubbard LE, Givens CE, Griffin DW, Iwanowicz LR, Meyer MT, Kolpin DW. Poultry litter as potential source of pathogens and other contaminants in groundwater and surface water proximal to large-scale confined poultry feeding operations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 735:139459. [PMID: 32485450 DOI: 10.1016/j.scitotenv.2020.139459] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 05/24/2023]
Abstract
Manure from livestock production has been associated with the contamination of water resources. To date, research has primarily focused on runoff of these contaminants from animal operations into surface water, and the introduction of poultry-derived pathogenic zoonoses and other contaminants into groundwater is under-investigated. We characterized pathogens and other microbial and chemical contaminants in poultry litter, groundwater, and surface water near confined poultry feeding operations (chicken layer, turkey) at 9 locations in Iowa and one in Wisconsin from May and June 2016. Results indicate that poultry litter from large-scale poultry confined feeding operations is a likely source of environmental contamination and that groundwater is also susceptible to such poultry-derived contamination. Poultry litter, groundwater, and surface water samples had detections of viable bacteria growth (Salmonella spp., enterococci, staphylococci, lactobacilli), multi-drug resistant Salmonella DT104 flost and int genes, F+ RNA coliphage (group I and IV), antibiotic resistance genes (ARGs; blaDHA, blaOXA-48, blaTEM, blaCMY-2, tetM), phytoestrogens (biochanin A, daidzein, formononetin), and a progestin (progesterone). In addition, mcr-1 (a colistin ARG), was detected in a groundwater sample and in another groundwater sample, antibiotic resistant isolates were positive for Brevibacterium spp., a potential signature of poultry in the environment. Detectable estrogenicity was not measured in poultry litter, but was observed in 67% of the surface water samples and 22% were above the U.S. Environmental Protection Agency trigger level of 1 ng/L. The transport of microbial pathogens to groundwater was significantly greater (p < 0.001) than the transport of trace organic contaminants to groundwater in this study. In addition to viable pathogens, several clinically important ARGs were detected in litter, groundwater, and surface water, highlighting the need for additional research on sources of these contaminants in livestock dominated areas.
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Affiliation(s)
- L E Hubbard
- U.S. Geological Survey, Upper Midwest Water Science Center, 8505 Research Way, Middleton, WI 53562, USA.
| | - C E Givens
- U.S. Geological Survey, Upper Midwest Water Science Center, 5840 Enterprise Drive, Lansing, MI 48911, USA
| | - D W Griffin
- U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, 600 4th Street South, St. Petersburg, FL 33701, USA
| | - L R Iwanowicz
- U.S. Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV 25430, USA
| | - M T Meyer
- U.S. Geological Survey, Kansas Water Science Center, 1217 Biltmore Drive, Lawrence, KS 66049, USA
| | - D W Kolpin
- U.S. Geological Survey, Central Midwest Science Center, 400 South Clinton Street Suite 269, Iowa City, IA 52240, USA
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17
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Elicitor and Receptor Molecules: Orchestrators of Plant Defense and Immunity. Int J Mol Sci 2020; 21:ijms21030963. [PMID: 32024003 PMCID: PMC7037962 DOI: 10.3390/ijms21030963] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/11/2020] [Accepted: 01/13/2020] [Indexed: 02/07/2023] Open
Abstract
Pathogen-associated molecular patterns (PAMPs), microbe-associated molecular patterns (MAMPs), herbivore-associated molecular patterns (HAMPs), and damage-associated molecular patterns (DAMPs) are molecules produced by microorganisms and insects in the event of infection, microbial priming, and insect predation. These molecules are then recognized by receptor molecules on or within the plant, which activates the defense signaling pathways, resulting in plant’s ability to overcome pathogenic invasion, induce systemic resistance, and protect against insect predation and damage. These small molecular motifs are conserved in all organisms. Fungi, bacteria, and insects have their own specific molecular patterns that induce defenses in plants. Most of the molecular patterns are either present as part of the pathogen’s structure or exudates (in bacteria and fungi), or insect saliva and honeydew. Since biotic stresses such as pathogens and insects can impair crop yield and production, understanding the interaction between these organisms and the host via the elicitor–receptor interaction is essential to equip us with the knowledge necessary to design durable resistance in plants. In addition, it is also important to look into the role played by beneficial microbes and synthetic elicitors in activating plants’ defense and protection against disease and predation. This review addresses receptors, elicitors, and the receptor–elicitor interactions where these components in fungi, bacteria, and insects will be elaborated, giving special emphasis to the molecules, responses, and mechanisms at play, variations between organisms where applicable, and applications and prospects.
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18
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Yang Y, Ashworth AJ, Willett C, Cook K, Upadhyay A, Owens PR, Ricke SC, DeBruyn JM, Moore Jr. PA. Review of Antibiotic Resistance, Ecology, Dissemination, and Mitigation in U.S. Broiler Poultry Systems. Front Microbiol 2019; 10:2639. [PMID: 31803164 PMCID: PMC6872647 DOI: 10.3389/fmicb.2019.02639] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 10/30/2019] [Indexed: 12/24/2022] Open
Abstract
Since the onset of land application of poultry litter, transportation of microorganisms, antibiotics, and disinfectants to new locations has occurred. While some studies provide evidence that antimicrobial resistance (AMR), an evolutionary phenomenon, could be influenced by animal production systems, other research suggests AMR originates in the environment from non-anthropogenic sources. In addition, AMR impacts the effective prevention and treatment of poultry illnesses and is increasingly a threat to global public health. Therefore, there is a need to understand the dissemination of AMR genes to the environment, particularly those directly relevant to animal health using the One Health Approach. This review focuses on the potential movement of resistance genes to the soil via land application of poultry litter. Additionally, we highlight impacts of AMR on microbial ecology and explore hypotheses explaining gene movement pathways from U.S. broiler operations to the environment. Current approaches for decreasing antibiotic use in U.S. poultry operations are also described in this review.
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Affiliation(s)
- Yichao Yang
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Amanda J. Ashworth
- Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Fayetteville, AR, United States
| | - Cammy Willett
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Kimberly Cook
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Athens, GA, United States
| | - Abhinav Upadhyay
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Phillip R. Owens
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Dale Bumpers Small Farms Research Center, Booneville, AR, United States
| | - Steven C. Ricke
- Department of Food Science and Center for Food Safety, University of Arkansas, Fayetteville, AR, United States
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Philip A. Moore Jr.
- Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Fayetteville, AR, United States
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19
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Durso LM, Cook KL. One Health and Antibiotic Resistance in Agroecosystems. ECOHEALTH 2019; 16:414-419. [PMID: 29541967 PMCID: PMC6858902 DOI: 10.1007/s10393-018-1324-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 05/23/2023]
Abstract
Agriculture reflects One Health principals, with the job of the farmer being to sustainably balance human, animal, and soil health. It is imperative to include an agricultural perspective when addressing antibiotic resistance (AR) from a One Health perspective, as the farmers, ranchers, and agricultural professionals have an intimate working knowledge of these complex systems, and they will be on the front lines of implementing on-farm control measures. Currently, communication across the One Health triad (humans, animals, environment) regarding agricultural AR is hindered by ambiguous language, complicated by cultural and linguistic differences that can lead to the conclusion that the other participant is not aware of the facts, or has ulterior motives. This work explores and identifies the language and vocabulary of AR in the context of supporting strategic short- and long-term problem solving in a One Health context.
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Affiliation(s)
- Lisa M Durso
- USDA, ARS, Agroecosystem Management Research Unit, 251 Filley Hall, UNL East Campus, Lincoln, NE, 68583, USA.
| | - Kimberly L Cook
- USDA, ARS, Bacterial Epidemiology and Antimicrobial Resistance Research Unit, 950 College Station Rd., Athens, GA, 30605, USA
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20
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Evaluation of Factors Affecting Antimicrobial Activity of Bacteriocin from Lactobacillus plantarum Microencapsulated in Alginate-Gelatin Capsules and Its Application on Pork Meat as a Bio-Preservative. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16061017. [PMID: 30897806 PMCID: PMC6466082 DOI: 10.3390/ijerph16061017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 11/17/2022]
Abstract
Antimicrobial compounds from traditional fermented foods have shown activity against a wide range of pathogen and spoilage microorganisms for several years. In this study, a Lactic acid bacteria (LAB), isolated from Vietnamese traditional fermented yogurt (Lactobacillus plantarum SC01), was encapsulated in alginate-gelatin (ALG-GEL) and the effect of incubation temperature, medium pH and surfactants were assessed. The aims of this research were to evaluate antimicrobial activity of bacteriocin produced by L. plantarum SC01. Another aim the research was to study the quality of pork meat treated with its Bacteriocin in 2 h as a bio-preservative at different storage times (0 h, 12 h, 24 h and 48 h) in room temperature, compared to control (treated with salt 40.0%). The antimicrobial activity of L. plantarum SC01 was identified through the inhibition rate of five indicator organisms, including Escherichia coli, Salmonella sp., Staphylococcus aureus, Listeria monocytogenes, and Bacillus subtilis by co-culture method. The results showed that L. plantarum SC01 microencapsulated in ALG-GEL (2.5% alginate and 6.0% gelatin, w/v) and 3.0% bacteria supplied into modified MRS medium (MRSOPTSC01) produced highly active compound inhibited the growth of indicator organisms at a density of 10⁴⁻10⁸ CFU/mL. Antibacterial compounds were highly active in a treatment at 80 °C; not to be affected by pH; affected by surfactant as Ethylenediaminetetraacetic acid (EDTA), Sodium dodecyl sulfate (SDS), and Tween. Moreover, LAB obtained from this study show the potent Bacteriocin in its usage as a preservative in food.
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Agga GE, Cook KL, Netthisinghe AMP, Gilfillen RA, Woosley PB, Sistani KR. Persistence of antibiotic resistance genes in beef cattle backgrounding environment over two years after cessation of operation. PLoS One 2019; 14:e0212510. [PMID: 30768641 PMCID: PMC6377141 DOI: 10.1371/journal.pone.0212510] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/04/2019] [Indexed: 11/18/2022] Open
Abstract
Confined animal feeding operations can facilitate the spread of genes associated with antibiotic resistance. It is not known how cattle removal from beef cattle backgrounding operation affects the persistence of antibiotic resistance genes (ARGs) in the environment. We investigated the effect of cessation of beef cattle backgrounding operation on the persistence and distribution of ARGs in the beef cattle backgrounding environment. The study was conducted at a pasture-feedlot type beef cattle backgrounding operation which consisted of feeding and grazing areas that were separated by a fence with an access gate. Backgrounding occurred for seven years before cattle were removed from the facility. Soil samples (n = 78) from 26 georeferenced locations were collected at the baseline before cattle were removed, and then one year and two years after cattle were removed. Metagenomic DNA was extracted from the soil samples and total bacterial population (16S rRNA), total Enterococcus species and class 1 integrons (intI1), and erythromycin (ermB and ermF), sulfonamide (sul1 and sul2) and tetracycline (tetO, tetW and tetQ) resistance genes were quantified. Concentrations of total bacteria, Enterococcus spp., class 1 integrons, and ARGs were higher in the feeding area and its immediate vicinity (around the fence and the gate) followed by a gradient decline along the grazing area. Although the concentrations of total bacteria, Enterococcus spp., class 1 integrons and ARGs in the feeding area significantly decreased two years after cattle removal, their concentrations were still higher than that observed in the grazing area. Higher concentrations over two years in the feeding area when compared to the grazing area suggest a lasting effect of confined beef cattle production system on the persistence of bacteria and ARGs in the soil.
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Affiliation(s)
- Getahun E. Agga
- Food Animal Environmental Systems Research Unit, Agricultural Research Service, United States Department of Agriculture, Bowling Green, Kentucky, United States of America
- * E-mail:
| | - Kimberly L. Cook
- Food Animal Environmental Systems Research Unit, Agricultural Research Service, United States Department of Agriculture, Bowling Green, Kentucky, United States of America
| | - Annesly M. P. Netthisinghe
- Department of Agriculture, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Rebecca A. Gilfillen
- Department of Agriculture, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Paul B. Woosley
- Department of Agriculture, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Karamat R. Sistani
- Food Animal Environmental Systems Research Unit, Agricultural Research Service, United States Department of Agriculture, Bowling Green, Kentucky, United States of America
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Couch M, Agga GE, Kasumba J, Parekh RR, Loughrin JH, Conte ED. Abundances of Tetracycline Resistance Genes and Tetracycline Antibiotics during Anaerobic Digestion of Swine Waste. JOURNAL OF ENVIRONMENTAL QUALITY 2019; 48:171-178. [PMID: 30640349 DOI: 10.2134/jeq2018.09.0331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The impact of anaerobic digestion of animal waste on the persistence of antibiotic resistance genes (ARGs) and antibiotics is not widely studied. Two identical, 800-L digesters seeded with swine slurry were followed up to 100 d in three separate trials. The trials received varying amounts of antibiotic-free corn ( L.) mixed with water to maintain the digestion process. Biogas production, seven tetracycline resistance () genes, and three tetracyclines and their transformation products were measured. Biogas production proportionally increased as the feeding loads increased between trials. In Trial 1, log gene copies showed small but statistically significant ( < 0.01) increases during digestion. In Trial 2, anaerobic digestion did not have a significant ( > 0.05) effect except for significant reductions in B ( < 0.0001) and G ( = 0.0335) log gene copies. In Trial 3, which received the highest amount of corn mix, log copies of the 16S ribosomal RNA and the genes significantly ( < 0.0001) reduced over time during digestion. Up to 36 μg L tetracycline, 112 μg L chlortetracycline, 11.9 mg L isochlortetracycline, and 30 μg L 4-epitetracycline were detected both in the liquid and solid digestates. Results of this study revealed that although anaerobic digestion of swine waste can produce useful biogas, it does not result in complete removal of bacteria, ARGs, and antibiotics regardless of differences in the feeding loads between trials. Further effluent and sludge treatments are required prior to their downstream use in crop production to minimize emergence and environmental dissemination of antimicrobial-resistant bacteria through animal manure.
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Netthisinghe AMP, Cook KL, Gilfillen RA, Woosley PB, Kingery T, Sistani KR. Managing Beef Backgrounding Residual Soil Contaminants by Alum and Biochar Amendments. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:1275-1283. [PMID: 30272780 DOI: 10.2134/jeq2018.02.0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Heavy manure-derived contamination of soils can make animal congregating areas nonpoint sources for environmental pollution. In situ soil stabilization is a cost-effective management strategy with a focus on lowering contaminant availability and limiting release to the environment. Soil stabilizing amendments can help mitigate the negative environmental impacts of contaminated soils. In this 2-yr study, we examined the effects of adding no amendment (control) or treating with alum [Al (SO)⋅18HO] or biochar as soil amendments on Mehlich-3 extractable soil P, Cu, and Zn contents, antimicrobial monensin concentrations, total bacteria (16S ribosomal RNA [rRNA] gene), antibiotic resistance genes (1 and B), and Class 1 integrons (1) in an abandoned beef backgrounding setting. The alum reduced soil P (1374 to 1060 mg kg), Cu (7.7 to 3.2 mg kg), and Zn (52.4 to 19.6 mg kg) contents. Both alum and biochar reduced monesin concentrations (1.8 to 0.7 and 2.1 to 1.1 ng g, respectively). All the treatments harbored consistent 16 rRNA concentrations (10 copies g) throughout. The B gene concentration (10 copies g) was lower than either the 1 or the 1 genes (10 copies g), regardless of treatments. However, concentrations of all genes in the soils of animal congregation areas were higher than those in background soils with the least animal impact. In contrast with the effect on other contaminants, the effect of soil amendments on bacteria with antibiotic resistance genes was not biologically significant. Future research should be directed toward evaluating effective alternative methods to mitigate these bacterial populations.
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Impact of Vegetative Treatment Systems on Multiple Measures of Antibiotic Resistance in Agricultural Wastewater. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15071295. [PMID: 29933547 PMCID: PMC6069364 DOI: 10.3390/ijerph15071295] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/15/2018] [Accepted: 06/17/2018] [Indexed: 12/13/2022]
Abstract
Wastewater is an important vector of antibiotic resistant bacteria and antibiotic resistance genes (ARB/G). While there is broad agreement that ARB/G from agricultural (ag) wastewaters can be transported through the environment and may contribute to untreatable infectious disease in humans and animals, there remain large knowledge gaps surrounding applied details on the types and amounts of ARB/G associated with different agricultural wastewater treatment options and different ag production systems. This study evaluates a vegetative treatment system (VTS) built to treat the wastewater from a beef cattle feedlot. Samples were collected for three years, and plated on multiple media types to enumerate tetracycline and cefotaxime-resistant bacteria. Enterobacteriaceae isolates (n = 822) were characterized for carriage of tetracycline resistance genes, and E. coli isolates (n = 673) were phenotyped to determine multi-drug resistance (MDR) profiles. Tetracycline resistance in feedlot runoff wastewater was 2-to-3 orders of magnitude higher compared to rainfall runoff from the VTS fields, indicating efficacy of the VTA for reducing ARB over time following wastewater application. Clear differences in MDR profiles were observed based on the specific media on which a sample was plated. This result highlights the importance of method, especially in the context of isolate-based surveillance and monitoring of ARB in agricultural wastewaters.
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Wind L, Krometis LA, Hession WC, Chen C, Du P, Jacobs K, Xia K, Pruden A. Fate of Pirlimycin and Antibiotic-Resistant Fecal Coliforms in Field Plots Amended with Dairy Manure or Compost during Vegetable Cultivation. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:436-444. [PMID: 29864178 DOI: 10.2134/jeq2017.12.0491] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Identification of agricultural practices that mitigate the environmental dissemination of antibiotics is a key need in reducing the prevalence of antibiotic-resistant bacteria of human health concern. Here, we aimed to compare the effects of crop (lettuce [ L.] or radish [ L.]), soil amendment type (inorganic fertilizer, raw dairy manure, composted dairy manure, or no amendment), and prior antibiotic use history (no antibiotics during previous lactation cycles vs. manure mixed from cows administered pirlimycin or cephapirin) of manure-derived amendments on the incidence of culturable antibiotic-resistant fecal coliforms in agricultural soils through a controlled field-plot experiment. Antibiotic-resistant culturable fecal coliforms were recoverable from soils across all treatments immediately after application, although persistence throughout the experiment varied by antibiotic class and time. The magnitude of observed coliform counts differed by soil amendment type. Compost-amended soils had the highest levels of cephalosporin-resistant fecal coliforms, regardless of whether the cows from which the manure was derived were administered antibiotics. Samples from control plots or those treated with inorganic fertilizer trended toward lower counts of resistant coliforms, although these differences were not statistically significant. No statistical differences were observed between soils that grew leafy (lettuce) versus rooted (radish) crops. Only pirlimycin was detectable past amendment application in raw manure-amended soils, dissipating 12 to 25% by Day 28. Consequently, no quantifiable correlations between coliform count and antibiotic magnitude could be identified. This study demonstrates that antibiotic-resistant fecal coliforms can become elevated in soils receiving manure-derived amendments, but that a variety of factors likely contribute to their long-term persistence under typical field conditions.
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Brooks JP, Tewolde H, Adeli A, Shankle MW, Way TR, Smith RK, Pepper IL. Effects of Subsurface Banding and Broadcast of Poultry Litter and Cover Crop on Soil Microbial Populations. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:427-435. [PMID: 29864187 DOI: 10.2134/jeq2017.09.0382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Agronomic management is aimed at managing the crop environment to maximize crop yield, but soil biology is often ignored. This study aimed to compare the application of poultry litter via broadcast and subsurface banding versus standard inorganic fertilizer to cotton ( L.) and their effects on soil bacterial populations and fecal indicator bacteria. The study comprised a randomized complete block design, with fertilizer and time of application as treatment effects and cover crop as a main effect. Soil cores were collected and analyzed from 2008 to 2014. Fecal indicator bacteria were at detection limits for all treatments, where the integron 1 gene was significantly elevated in litter plots. There were few differences between litter application approaches, but both significantly increased key biogeochemical genes over control plots, whereas a cover crop only increased soil moisture and urease C. Data suggested a positive residual effect of litter application with 16S, phosphatase A, and urease C genes elevated over controls, but similar to standard fertilizer plots. High-throughput 16S ribosomal RNA analysis suggested increased diversity and enrichment indices in litter and standard fertilizer over untreated control plots. Litter and standard fertilizer effects persisted 4 and 2 yr after application, respectively, as evidenced by residual library community structures. This study demonstrated the positive effects of litter application on the soil bacterial community when compared with untreated control plots. Some differences between standard fertilization and litter practices were noted and suggest that there is a positive residual effect on soil microbial populations associated with both practices.
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Scott A, Tien YC, Drury CF, Reynolds WD, Topp E. Enrichment of antibiotic resistance genes in soil receiving composts derived from swine manure, yard wastes, or food wastes, and evidence for multiyear persistence of swine Clostridium spp. Can J Microbiol 2018; 64:201-208. [DOI: 10.1139/cjm-2017-0642] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The impact of amendment with swine manure compost (SMC), yard waste compost (YWC), or food waste compost (FWC) on the abundance of antibiotic resistance genes in soil was evaluated. Following a commercial-scale application of the composts in a field experiment, soils were sampled periodically for a decade, and archived air-dried. Soil DNA was extracted and gene targets quantified by qPCR. Compared with untreated control soil, all 3 amendment types increased the abundance of gene targets for up to 4 years postapplication. The abundance of several gene targets was much higher in soil amended with SMC than in soil receiving either YWC or FWC. The gene target ermB remained higher in the SMC treatment for a decade postapplication. Clostridia were significantly more abundant in the SMC-amended soil throughout the decade following application. Eight percent of Clostridium spp. isolates from the SMC treatment carried ermB. Overall, addition of organic amendments to soils has the potential to increase the abundance of antibiotic resistance genes. Amendments of fecal origin, such as SMC, will in addition entrain bacteria carrying antibiotic resistance genes. Environmentally recalcitrant clostridia, and the antibiotic resistance genes that they carry, will persist for many years under field conditions following the application of SMC.
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Affiliation(s)
- Andrew Scott
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Yuan-Ching Tien
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Craig F. Drury
- Agriculture and Agri-Food Canada, 2585 County Road 20, Harrow, ON N0R 1G0, Canada
| | - W. Daniel Reynolds
- Agriculture and Agri-Food Canada, 2585 County Road 20, Harrow, ON N0R 1G0, Canada
| | - Edward Topp
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
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Poulsen MN, Pollak J, Sills DL, Casey JA, Rasmussen SG, Nachman KE, Cosgrove SE, Stewart D, Schwartz BS. Residential proximity to high-density poultry operations associated with campylobacteriosis and infectious diarrhea. Int J Hyg Environ Health 2017; 221:323-333. [PMID: 29268955 DOI: 10.1016/j.ijheh.2017.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 12/13/2017] [Accepted: 12/13/2017] [Indexed: 12/31/2022]
Abstract
Poultry carry zoonotic bacteria that can cause gastroenteritis in humans. Environmental transmission of pathogens from poultry operations may increase gastrointestinal infection risk in surrounding communities. To evaluate associations between residential proximity to high-density poultry operations and individual-level diarrheal illnesses, we conducted a nested case-control study among 514,488 patients in Pennsylvania (2006-2015). Using electronic health records, we identified cases of five gastrointestinal outcomes: three pathogen-specific infections, including Escherichia coli (n = 1425), Campylobacter (n = 567), and Salmonella (n = 781); infectious diarrhea (n = 781); and non-specific diarrhea (2012-2015; n = 28,201). We estimated an inverse-distance squared activity metric for poultry operations based on farm and patient addresses. Patients in the second and fourth (versus first) quartiles of the poultry operation activity metric had increased odds of Campylobacter (AOR [CI], Q2: 1.36 [1.01, 1.82]; Q3: 1.38 [0.98, 1.96]; Q4: 1.75 [1.31, 2.33]). Patients in the second, third, and fourth quartiles had increased odds of infectious diarrhea (Q2: 1.76 [1.29, 2.39]; Q3: 1.76 [1.09, 2.85]; Q4: 1.60 [1.12, 2.30]). Stratification revealed stronger relations of fourth quartile and both Campylobacter and infectious diarrhea in townships, the most rural community type in the study geography. Increasing extreme rainfall in the week prior to diagnosis strengthened fourth quartile Campylobacter associations. The poultry operation activity metric was largely unassociated with E. coli, Salmonella, and non-specific diarrhea. Findings suggest high-density poultry operations may be associated with campylobacteriosis and infectious diarrhea in nearby communities, highlighting additional public health concerns of industrial agriculture.
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Affiliation(s)
- Melissa N Poulsen
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Epidemiology and Health Services Research, Geisinger, Danville, PA, USA.
| | - Jonathan Pollak
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Deborah L Sills
- Department of Civil and Environmental Engineering, Bucknell University, Lewisburg, PA, USA
| | - Joan A Casey
- Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, USA
| | - Sara G Rasmussen
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Keeve E Nachman
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Risk Sciences and Public Policy Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Sara E Cosgrove
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Dalton Stewart
- Department of Civil and Environmental Engineering, Bucknell University, Lewisburg, PA, USA
| | - Brian S Schwartz
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Epidemiology and Health Services Research, Geisinger, Danville, PA, USA; Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Cook KL, Givan EC, Mayton HM, Parekh RR, Taylor R, Walker SL. Using the agricultural environment to select better surrogates for foodborne pathogens associated with fresh produce. Int J Food Microbiol 2017; 262:80-88. [PMID: 28968533 DOI: 10.1016/j.ijfoodmicro.2017.09.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 08/25/2017] [Accepted: 09/24/2017] [Indexed: 01/26/2023]
Abstract
Despite continuing efforts to reduce foodborne pathogen contamination of fresh produce, significant outbreaks continue to occur. Identification of appropriate surrogates for foodborne pathogens facilitates relevant research to identify reservoirs and amplifiers of these contaminants in production and processing environments. Therefore, the objective of this study was to identify environmental Escherichia coli isolates from manures (poultry, swine and dairy) and surface water sources with properties similar to those of the produce associated foodborne pathogens E. coli O157:H7 and Salmonella enterica serotype Typhimurium. The most similar environmental E. coli isolates were from poultry (n=3) and surface water (n=1) sources. The best environmental E. coli surrogates had cell surface characteristics (zeta potential, hydrophobicity and exopolysaccharide composition) that were similar (i.e., within 15%) to those of S. Typhimurium and/or formed biofilms more often when grown in low nutrient media prepared from lettuce lysates (24%) than when grown on high nutrient broth (7%). The rate of attachment of environmental isolates to lettuce leaves was also similar to that of S. Typhimurium. In contrast, E. coli O157:H7, a commonly used E. coli quality control strain and swine isolates behaved similarly; all were in the lowest 10% of isolates for biofilm formation and leaf attachment. These data suggest that the environment may provide a valuable resource for selection of surrogates for foodborne pathogens.
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Affiliation(s)
- Kimberly L Cook
- USDA-ARS, Food Animal Environmental Systems Research Unit, Bowling Green, KY, USA.
| | - Ethan C Givan
- Western Kentucky University, Department of Public Health, Bowling Green, KY, USA.
| | - Holly M Mayton
- University of California, Bourns College of Engineering, Riverside, CA, USA.
| | - Rohan R Parekh
- USDA-ARS, Food Animal Environmental Systems Research Unit, Bowling Green, KY, USA.
| | - Ritchie Taylor
- Western Kentucky University, Department of Public Health, Bowling Green, KY, USA.
| | - Sharon L Walker
- University of California, Bourns College of Engineering, Riverside, CA, USA.
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Locatelli A, Hiett KL, Caudill AC, Rothrock MJ. Do fecal and litter microbiomes vary within the major areas of a commercial poultry house, and does this affect sampling strategies for whole-house microbiomic studies? J APPL POULTRY RES 2017. [DOI: 10.3382/japr/pfw076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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31
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Tien YC, Li B, Zhang T, Scott A, Murray R, Sabourin L, Marti R, Topp E. Impact of dairy manure pre-application treatment on manure composition, soil dynamics of antibiotic resistance genes, and abundance of antibiotic-resistance genes on vegetables at harvest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 581-582:32-39. [PMID: 28076772 DOI: 10.1016/j.scitotenv.2016.12.138] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 06/06/2023]
Abstract
Manuring ground used for crop production is an important agricultural practice. Should antibiotic-resistant enteric bacteria carried in the manure be transferred to crops that are consumed raw, their consumption by humans or animals will represent a route of exposure to antibiotic resistance genes. Treatment of manures prior to land application is a potential management option to reduce the abundance of antibiotic resistance genes entrained with manure application. In this study, dairy manure that was untreated, anaerobically digested, mechanically dewatered or composted was applied to field plots that were then cropped to lettuce, carrots and radishes. The impact of treatment on manure composition, persistence of antibiotic resistance gene targets in soil following application, and distribution of antibiotic resistance genes and bacteria on vegetables at harvest was determined. Composted manure had the lowest abundance of antibiotic resistance gene targets compared to the other manures. There was no significant difference in the persistence characteristics of antibiotic resistance genes following land application of the various manures. Compared to unmanured soil, antibiotic resistance genes were detected more frequently in soil receiving raw or digested manure, whereas they were not in soil receiving composted manure. The present study suggests that vegetables grown in ground receiving raw or digested manure are at risk of contamination with manure-borne antibiotic resistant bacteria, whereas vegetables grown in ground receiving composted manure are less so.
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Affiliation(s)
- Yuan-Ching Tien
- Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Bing Li
- Graduate School at Shenzhen, Tsinghua University, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, University of Hong Kong, Hong Kong
| | - Andrew Scott
- Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Roger Murray
- Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Lyne Sabourin
- Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Romain Marti
- Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Edward Topp
- Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada; University of Western Ontario, London, Ontario, Canada.
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Hruby CE, Soupir ML, Moorman TB, Shelley M, Kanwar RS. Effects of tillage and poultry manure application rates on Salmonella and fecal indicator bacteria concentrations in tiles draining Des Moines Lobe soils. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2016; 171:60-69. [PMID: 26874615 DOI: 10.1016/j.jenvman.2016.01.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 01/28/2016] [Accepted: 01/30/2016] [Indexed: 06/05/2023]
Abstract
Application of poultry manure (PM) to cropland as fertilizer is a common practice in artificially drained regions of the Upper Midwest United States. Tile-waters have the potential to contribute pathogenic bacteria to downstream waters. This 3-year study (2010-2012) was designed to evaluate the impacts of manure management and tillage practices on bacteria losses to drainage tiles under a wide range of field conditions. PM was applied annually in spring, prior to planting corn, at application rates ranging from 5 to 40 kg/ha to achieve target rates of 112 and 224 kg/ha nitrogen (PM1 and PM2). Control plots received no manure (PM0). Each treatment was replicated on three chisel-plowed (CP) plots and one no-till (NT) plot. Tile-water grab samples were collected weekly when tiles were flowing beginning 30 days before manure application to 100 days post application, and additional grab samples were obtained to target the full spectrum of flow conditions. Manure and tile-water samples were analyzed for the pathogen, Salmonella spp. (SALM), and fecal indicator bacteria (FIB), Escherichia coli (EC), and enterococci (ENT). All three bacterial genera were detected more frequently, and at significantly higher concentrations, in tile-waters draining NT plots compared to CP plots. Transport of bacteria to NT tiles was most likely facilitated by macropores, which were significantly more numerous above tiles in NT plots in 2012 as determined by smoke-testing. While post-manure samples contained higher concentrations of bacteria than pre-manure samples, significant differences were not seen between low (PM1) and high (PM2) rates of PM application. The highest concentrations were observed under the NT PM2 plot in 2010 (6.6 × 10(3) cfu/100 mL EC, 6.6 × 10(5) cfu/100 mL ENT, and 2.8 × 10(3) cfu/100 mL SALM). Individual and 30-day geometric mean ENT concentrations correlated more strongly to SALM than EC; however, SALM were present in samples with little or no FIB.
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Affiliation(s)
- C E Hruby
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA
| | - M L Soupir
- Department of Agricultural and Biosystems Engineering, 3358 Elings Hall, Iowa State University, Ames, IA 50011, USA.
| | - T B Moorman
- National Laboratory for Agriculture and the Environment, USDA ARS, 2110 University Boulevard, Ames, IA 50011, USA
| | - M Shelley
- Departments of Statistics and Political Science, 509 Ross Hall, Iowa State University, Ames, IA 50011, USA
| | - R S Kanwar
- Department of Agricultural and Biosystems Engineering, 4358 Elings Hall, Iowa State University, Ames, IA 50011, USA
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Durso LM, Wedin DA, Gilley JE, Miller DN, Marx DB. Assessment of Selected Antibiotic Resistances in Ungrazed Native Nebraska Prairie Soils. JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:454-62. [PMID: 27065391 DOI: 10.2134/jeq2015.06.0280] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The inherent spatial heterogeneity and complexity of antibiotic-resistant bacteria and antibiotic resistance (AR) genes in manure-affected soils makes it difficult to sort out resistance that can be attributed to human antibiotic use from resistance that occurs naturally in the soil. This study characterizes native Nebraska prairie soils that have not been affected by human or food-animal waste products to provide data on background levels of resistance in southeastern Nebraskan soils. Soil samples were collected from 20 sites enumerated on tetracycline and cefotaxime media; screened for tetracycline-, sulfonamide-, β-lactamase-, and macrolide-resistance genes; and characterized for soil physical and chemical parameters. All prairies contained tetracycline- and cefotaxime-resistant bacteria, and 48% of isolates collected were resistant to two or more antibiotics. Most (98%) of the soil samples and all 20 prairies had at least one tetracycline gene. Most frequently detected were (D), (A) (O), (L), and (B). Sulfonamide genes, which are considered a marker of human or animal activity, were detected in 91% of the samples, despite the lack of human inputs at these sites. No correlations were found between either phenotypic or genotypic resistance and soil physical or chemical parameters. Heterogeneity was observed in AR within and between prairies. Therefore, multiple samples are necessary to overcome heterogeneity and to accurately assess AR. Conclusions regarding AR depend on the gene target measured. To determine the impacts of food-animal antibiotic use on resistance, it is essential that background and/or baseline levels be considered, and where appropriate subtracted out, when evaluating AR in agroecosystems.
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Nordenholt RM, Goyne KW, Kremer RJ, Lin CH, Lerch RN, Veum KS. Veterinary Antibiotic Effects on Atrazine Degradation and Soil Microorganisms. JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:565-575. [PMID: 27065404 DOI: 10.2134/jeq2015.05.0235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Veterinary antibiotics (VAs) in manure applied to agricultural lands may change agrichemical degradation by altering soil microbial community structure or function. The objectives of this study were to investigate the influence of two VAs, sulfamethazine (SMZ) and oxytetracycline (OTC), on atrazine (ATZ) degradation, soil microbial enzymatic activity, and phospholipid fatty acid (PLFA) markers. Sandy loam soil with and without 5% swine manure (w/w) was amended with 0 or 500 μg kgC radiolabeled ATZ and with 0, 100, or 1000 μg kg SMZ or OTC and incubated at 25°C in the dark for 96 d. The half-life of ATZ was not significantly affected by VA treatment in the presence or absence of manure; however, the VAs significantly ( < 0.05) inhibited ATZ mineralization in soil without manure (25-50% reduction). Manure amendment decreased ATZ degradation by 22%, reduced ATZ mineralization by 50%, and increased the half-life of ATZ by >10 d. The VAs had limited adverse effects on the microbial enzymes β-glucosidase and dehydrogenase in soils with and without manure. In contrast, manure application stimulated dehydrogenase activity and altered chlorinated ATZ metabolite profiles. Concentrations of PLFA markers were reduced by additions of ATZ, manure, OTC, and SMZ; adverse additive effects of combined treatments were noted for arbuscular mycorrhizal fungi and actinobacteria. In this work, the VAs did not influence persistence of the ATZ parent compound or chlorinated ATZ metabolite formation and degradation. However, reduced CO evolved from VA-treated soil suggests an inhibition to the degradation of other ATZ metabolites due to an altered soil microbial community structure.
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Baker M, Hobman JL, Dodd CER, Ramsden SJ, Stekel DJ. Mathematical modelling of antimicrobial resistance in agricultural waste highlights importance of gene transfer rate. FEMS Microbiol Ecol 2016; 92:fiw040. [PMID: 26906100 DOI: 10.1093/femsec/fiw040] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2016] [Indexed: 01/19/2023] Open
Abstract
Antimicrobial resistance is of global concern. Most antimicrobial use is in agriculture; manures and slurry are especially important because they contain a mix of bacteria, including potential pathogens, antimicrobial resistance genes and antimicrobials. In many countries, manures and slurry are stored, especially over winter, before spreading onto fields as organic fertilizer. Thus, these are a potential location for gene exchange and selection for resistance. We develop and analyse a mathematical model to quantify the spread of antimicrobial resistance in stored agricultural waste. We use parameters from a slurry tank on a UK dairy farm as an exemplar. We show that the spread of resistance depends in a subtle way on the rates of gene transfer and antibiotic inflow. If the gene transfer rate is high, then its reduction controls resistance, while cutting antibiotic inflow has little impact. If the gene transfer rate is low, then reducing antibiotic inflow controls resistance. Reducing length of storage can also control spread of resistance. Bacterial growth rate, fitness costs of carrying antimicrobial resistance and proportion of resistant bacteria in animal faeces have little impact on spread of resistance. Therefore, effective treatment strategies depend critically on knowledge of gene transfer rates.
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Affiliation(s)
- Michelle Baker
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Christine E R Dodd
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Stephen J Ramsden
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
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Netthisinghe AMP, Cook KL, Gilfillen RA, Sistani KR, Woosley PB. Management Practices Affect Soil Nutrients and Bacterial Populations in Backgrounding Beef Feedlot. JOURNAL OF ENVIRONMENTAL QUALITY 2015; 44:1892-1902. [PMID: 26641341 DOI: 10.2134/jeq2014.11.0483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Contaminants associated with manure in animal production sites are of significant concern. Unless properly managed, manure-derived soil nutrients in livestock production sites can deteriorate soil and water quality. This 3-yr study evaluated a soil nutrient management strategy with four sequentially imposed management practices: 12-mo backgrounding (BG), manure removal from the feeder area (FD), 12-mo destocking (DS), and 12-mo grass hay harvesting (H) in a small backgrounding feedlot. Resulting soil nutrient levels, total (), and N cycling bacterial ( and ) populations after each management practice in feedlot feeder and grazing (GR) areas and in crop grown at the control location (CT) were measured. Irrespective of management practice, FD contained greater soil nutrient concentrations than the GR and CT. Regardless of management practice, total bacteria cells (1.4 × 10 cells g soil) and nitrate reducers (5.2 × 10 cells g soil) were an order of magnitude higher in the FD than in the GR and CT, whereas nitrifying bacteria concentrations (1.4 × 10 cells g soil) were higher in the GR. Manure removal from the feeder area reduced M3-P (39%), total C (21%), total N (23%), NH-N (47%), and NO-N (93%) levels established in the FD during BG. Destocking lowered total C and N (45%) in the FD and NH-N (47%), NO-N (76%), and Zn (16%) in the GR. Hay harvesting reduced all soil nutrients in the FD and GR marginally. The management strategy has potential to lower soil nutrient concentrations, control soil nutrient buildup, and limit nutrient spread within the feedlot.
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Cook KL, Ritchey EL, Loughrin JH, Haley M, Sistani KR, Bolster CH. Effect of turning frequency and season on composting materials from swine high-rise facilities. WASTE MANAGEMENT (NEW YORK, N.Y.) 2015; 39:86-95. [PMID: 25752584 DOI: 10.1016/j.wasman.2015.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 01/09/2015] [Accepted: 02/10/2015] [Indexed: 06/04/2023]
Abstract
Composting swine slurries has several advantages, liquid slurries are converted to solids at lower moisture, the total volume and weight of material is reduced and the stabilized product is more easily transported off-site. Despite this, swine waste is generally stored, treated and applied in its liquid form. High-rise finishing facilities (HRFF) permit liquid slurries to be converted to solids which are partially decomposed underneath the HRFF and then finished in compost windrows. The purpose of this study was to evaluate the effect of turning frequency and ambient weather conditions on biological, physical and chemical properties of composted slurry-woodchip mixtures from HRFF. Compost trials were conducted in either fall (FT) or spring (ST) and piles were turned once or three times per week or upon compost temperature reaching 65°C. Physical, chemical and microbiological characteristics were measured over the course of 112 (FT) or 143 (ST) days of composting. Total carbon, total nitrogen (N) and inorganic N decreased in all piles. Ammonium decreased while nitrate increased in all piles (including unturned), but total N losses were greatest in piles turned more frequently during the ST. Microbial populations of nitrifiers were dominated by ammonia-oxidizing archaea (3.0×10(3)-4.2×10(6)cellsg(-1) compost) but ammonia oxidizing bacteria (below detection to 6.0×10(5)cellsg(-1) compost) varied in response to turning and compost temperature; denitrifiers were present in high concentrations throughout the process. Swine HRFF materials composted well in windrows regardless of turning frequency and despite significant differences in starting materials and low initial C/N. Volume reduction, low moisture and low readily degradable organic matter suggest that the finished compost would have lower transportation costs and should provide value as a soil conditioner.
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Affiliation(s)
- K L Cook
- USDA-ARS, Food Animal Environmental Systems Research Unit, Bowling Green, KY, USA.
| | - E L Ritchey
- University of Kentucky, Plant and Soil Sciences, Lexington, KY, USA.
| | - J H Loughrin
- USDA-ARS, Food Animal Environmental Systems Research Unit, Bowling Green, KY, USA.
| | - M Haley
- USDA-ARS, Food Animal Environmental Systems Research Unit, Bowling Green, KY, USA.
| | - K R Sistani
- USDA-ARS, Food Animal Environmental Systems Research Unit, Bowling Green, KY, USA.
| | - C H Bolster
- USDA-ARS, Food Animal Environmental Systems Research Unit, Bowling Green, KY, USA.
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Fang H, Wang H, Cai L, Yu Y. Prevalence of antibiotic resistance genes and bacterial pathogens in long-term manured greenhouse soils as revealed by metagenomic survey. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:1095-104. [PMID: 25514174 DOI: 10.1021/es504157v] [Citation(s) in RCA: 222] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Antibiotic resistance genes (ARGs), human pathogenic bacteria (HPB), and HPB carrying ARGs pose a high risk to soil ecology and public health. Here, we used a metagenomic approach to investigate their diversity and abundance in chicken manures and greenhouse soils collected from Guli, Pulangke, and Hushu vegetable bases with different greenhouse planting years in Nanjing, Eastern China. There was a positive correlation between the levels of antibiotics, ARGs, HPB, and HPB carrying ARGs in manures and greenhouse soils. In total, 156.2–5001.4 μg/kg of antibiotic residues, 22 classes of ARGs, 32 HPB species, and 46 species of HPB carrying ARGs were found. The highest relative abundance was tetracycline resistance genes (manures) and multidrug resistance genes (greenhouse soils). The dominant HPB and HPB carrying ARGs in the manures were Bacillus anthracis, Bordetella pertussis, and B. anthracis (sulfonamide resistance gene, sul1), respectively. The corresponding findings in greenhouse soils were Mycobacterium tuberculosis and M. ulcerans, M. tuberculosis (macrolide-lincosamide-streptogramin resistance protein, MLSRP), and B. anthracis (sul1), respectively. Our findings confirmed high levels of antibiotics, ARGs, HPB, and HPB carrying ARGs in the manured greenhouse soils compared with those in the field soils, and their relative abundance increased with the extension of greenhouse planting years.
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Impacts of antibiotic use in agriculture: what are the benefits and risks? Curr Opin Microbiol 2014; 19:37-44. [DOI: 10.1016/j.mib.2014.05.019] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 05/14/2014] [Accepted: 05/28/2014] [Indexed: 11/20/2022]
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