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Wiesner-Friedman C, Beattie RE, Stewart JR, Hristova KR, Serre ML. Identifying sources of antibiotic resistance genes in the environment using the microbial Find, Inform, and Test framework. Front Microbiol 2023; 14:1223876. [PMID: 37731922 PMCID: PMC10508347 DOI: 10.3389/fmicb.2023.1223876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/07/2023] [Indexed: 09/22/2023] Open
Abstract
Introduction Antimicrobial resistance (AMR) is an increasing public health concern for humans, animals, and the environment. However, the contributions of spatially distributed sources of AMR in the environment are not well defined. Methods To identify the sources of environmental AMR, the novel microbial Find, Inform, and Test (FIT) model was applied to a panel of five antibiotic resistance-associated genes (ARGs), namely, erm(B), tet(W), qnrA, sul1, and intI1, quantified from riverbed sediment and surface water from a mixed-use region. Results A one standard deviation increase in the modeled contributions of elevated AMR from bovine sources or land-applied waste sources [land application of biosolids, sludge, and industrial wastewater (i.e., food processing) and domestic (i.e., municipal and septage)] was associated with 34-80% and 33-77% increases in the relative abundances of the ARGs in riverbed sediment and surface water, respectively. Sources influenced environmental AMR at overland distances of up to 13 km. Discussion Our study corroborates previous evidence of offsite migration of microbial pollution from bovine sources and newly suggests offsite migration from land-applied waste. With FIT, we estimated the distance-based influence range overland and downstream around sources to model the impact these sources may have on AMR at unsampled sites. This modeling supports targeted monitoring of AMR from sources for future exposure and risk mitigation efforts.
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Affiliation(s)
- Corinne Wiesner-Friedman
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, United States
| | - Rachelle E. Beattie
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, United States
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Jill R. Stewart
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | - Marc L. Serre
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Kim DY, Sharma SK, Rasool K, Koduru JR, Syed A, Ghodake G. Development of Novel Peptide-Modified Silver Nanoparticle-Based Rapid Biosensors for Detecting Aminoglycoside Antibiotics. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12883-12898. [PMID: 37603424 DOI: 10.1021/acs.jafc.3c03565] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The detection and monitoring of aminoglycoside antibiotics (AGAs) have become of utmost importance due to their widespread use in human and animal therapy, as well as the associated risks of exposure, toxicity, and the emergence of antimicrobial resistance. In this study, we successfully synthesized casein hydrolysate peptides-functionalized silver nanoparticles (CHPs@AgNPs) and employed them as a novel colorimetric analytical platform to demonstrate remarkable specificity and sensitivity toward AGAs. The colorimetric and spectral response of the CHPs@AgNPs was observed at 405 and 520 nm, showing a linear correlation with the concentration of streptomycin, a representative AGA. The color changes from yellow to orange provided a visual indication of the analyte concentration, enabling quantitative determination for real-world samples. The AgNP assay exhibited excellent sensitivity with dynamic ranges of approximately 200-650 and 100-700 nM for streptomycin-spiked tap water and dairy whey with limits of detection found to be ∼98 and 56 nM, respectively. The mechanism behind the selective aggregation of CHPs@AgNPs in the presence of AGAs involves the amine groups of the target analytes acting as molecular bridges for electrostatic coupling with hydroxyl or carboxyl functionalities of adjacent NPs, driving the formation of stable NP aggregates. The developed assay offers several advantages, making it suitable for various practical applications. It is characterized by its simplicity, rapidity, specificity, sensitivity, and cost-effectiveness. These unique features make the method a promising tool for monitoring water quality, ensuring food safety, and dealing with emergent issues of antibiotic resistance.
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Affiliation(s)
- Dae-Young Kim
- Department of Biological and Environmental Science, Dongguk University - Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Republic of Korea
| | - Sanjeev K Sharma
- Biomaterials and Sensors Laboratory, Department of Physics, CCS University, Meerut Campus, Meerut 250004, Uttar Pradesh, India
| | - Kashif Rasool
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Janardhan Reddy Koduru
- Department of Environmental Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Asad Syed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Gajanan Ghodake
- Department of Biological and Environmental Science, Dongguk University - Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang-si 10326, Gyeonggi-do, Republic of Korea
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Burch TR, Stokdyk JP, Firnstahl AD, Kieke BA, Cook RM, Opelt SA, Spencer SK, Durso LM, Borchardt MA. Microbial source tracking and land use associations for antibiotic resistance genes in private wells influenced by human and livestock fecal sources. JOURNAL OF ENVIRONMENTAL QUALITY 2023; 52:270-286. [PMID: 36479898 DOI: 10.1002/jeq2.20443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Antimicrobial resistance is a growing public health problem that requires an integrated approach among human, agricultural, and environmental sectors. However, few studies address all three components simultaneously. We investigated the occurrence of five antibiotic resistance genes (ARGs) and the class 1 integron gene (intI1) in private wells drawing water from a vulnerable aquifer influenced by residential septic systems and land-applied dairy manure. Samples (n = 138) were collected across four seasons from a randomized sample of private wells in Kewaunee County, Wisconsin. Measurements of ARGs and intI1 were related to microbial source tracking (MST) markers specific to human and bovine feces; they were also related to 54 risk factors for contamination representing land use, rainfall, hydrogeology, and well construction. ARGs and intI1 occurred in 5%-40% of samples depending on target. Detection frequencies for ARGs and intI1 were lowest in the absence of human and bovine MST markers (1%-30%), highest when co-occurring with human and bovine markers together (11%-78%), and intermediate when co-occurring with just one type of MST marker (4%-46%). Gene targets were associated with septic system density more often than agricultural land, potentially because of the variable presence of manure on the landscape. Determining ARG prevalence in a rural setting with mixed land use allowed an assessment of the relative contribution of human and bovine fecal sources. Because fecal sources co-occurred with ARGs at similar rates, interventions intended to reduce ARG occurrence may be most effective if both sources are considered.
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Affiliation(s)
- Tucker R Burch
- U.S. Department of Agriculture-Agricultural Research Service, Environmentally Integrated Dairy Management Research Unit, Marshfield, WI, USA
- U.S. Geological Survey and U.S. Department of Agriculture-Agricultural Research Service, Laboratory for Infectious Disease and the Environment, Marshfield, WI, USA
| | - Joel P Stokdyk
- U.S. Geological Survey and U.S. Department of Agriculture-Agricultural Research Service, Laboratory for Infectious Disease and the Environment, Marshfield, WI, USA
- U.S. Geological Survey, Upper Midwest Water Science Center, Marshfield, WI, USA
| | - Aaron D Firnstahl
- U.S. Geological Survey and U.S. Department of Agriculture-Agricultural Research Service, Laboratory for Infectious Disease and the Environment, Marshfield, WI, USA
- U.S. Geological Survey, Upper Midwest Water Science Center, Marshfield, WI, USA
| | - Burney A Kieke
- Marshfield Clinic Research Institute, Center for Clinical Epidemiology and Population Health, Marshfield, WI, USA
| | - Rachel M Cook
- U.S. Department of Agriculture-Agricultural Research Service, Environmentally Integrated Dairy Management Research Unit, Marshfield, WI, USA
- U.S. Geological Survey and U.S. Department of Agriculture-Agricultural Research Service, Laboratory for Infectious Disease and the Environment, Marshfield, WI, USA
| | - Sarah A Opelt
- U.S. Department of Agriculture-Agricultural Research Service, Environmentally Integrated Dairy Management Research Unit, Marshfield, WI, USA
- U.S. Geological Survey and U.S. Department of Agriculture-Agricultural Research Service, Laboratory for Infectious Disease and the Environment, Marshfield, WI, USA
| | - Susan K Spencer
- U.S. Department of Agriculture-Agricultural Research Service, Environmentally Integrated Dairy Management Research Unit, Marshfield, WI, USA
- U.S. Geological Survey and U.S. Department of Agriculture-Agricultural Research Service, Laboratory for Infectious Disease and the Environment, Marshfield, WI, USA
| | - Lisa M Durso
- U.S. Department of Agriculture-Agricultural Research Service, Agroecosystem Management Research Unit, Lincoln, NE, USA
| | - Mark A Borchardt
- U.S. Department of Agriculture-Agricultural Research Service, Environmentally Integrated Dairy Management Research Unit, Marshfield, WI, USA
- U.S. Geological Survey and U.S. Department of Agriculture-Agricultural Research Service, Laboratory for Infectious Disease and the Environment, Marshfield, WI, USA
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Wang J, Pan R, Dong P, Liu S, Chen Q, Borthwick AGL, Sun L, Xu N, Ni J. Supercarriers of antibiotic resistome in a world's large river. MICROBIOME 2022; 10:111. [PMID: 35897057 PMCID: PMC9331799 DOI: 10.1186/s40168-022-01294-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/15/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Antibiotic resistome has been found to strongly interact with the core microbiota in the human gut, yet little is known about how antibiotic resistance genes (ARGs) correlate with certain microbes in large rivers that are regarded as "terrestrial gut." RESULTS By creating the integral pattern for ARGs and antibiotic-resistant microbes in water and sediment along a 4300-km continuum of the Yangtze River, we found that human pathogen bacteria (HPB) share 13.4% and 5.9% of the ARG hosts in water and sediment but contribute 64% and 46% to the total number of planktonic and sedimentary ARGs, respectively. Moreover, the planktonic HPB harbored 79 ARG combinations that are dominated by "natural" supercarriers (e.g., Rheinheimera texasensis and Noviherbaspirillum sp. Root189) in river basins. CONCLUSIONS We confirmed that terrestrial HPB are the major ARG hosts in the river, rather than conventional supercarriers (e.g., Enterococcus spp. and other fecal indicator bacteria) that prevail in the human gut. The discovery of HPB as natural supercarriers in a world's large river not only interprets the inconsistency between the spatial dissimilarities in ARGs and their hosts, but also highlights the top priority of controlling terrestrial HPB in the future ARG-related risk management of riverine ecosystems globally. Video Abstract.
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Affiliation(s)
- Jiawen Wang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, People's Republic of China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China
| | - Rui Pan
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, People's Republic of China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China
| | - Peiyan Dong
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China
| | - Shufeng Liu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, People's Republic of China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, People's Republic of China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Alistair G L Borthwick
- Institute of Infrastructure and Environment, School of Engineering, The University of Edinburgh, The King's Buildings, Edinburgh, EH9 3JL, UK
- School of Engineering, Computing and Mathematics, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK
| | - Liyu Sun
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, People's Republic of China
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, People's Republic of China
| | - Nan Xu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, People's Republic of China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, People's Republic of China.
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Beattie RE, Su B, Thill R, Hristova KR. Recycled concrete aggregates are an economic form of urban riparian erosion management with limited impacts on freshwater chemistry and microbial diversity. JOURNAL OF HAZARDOUS MATERIALS 2022; 434:128934. [PMID: 35461000 DOI: 10.1016/j.jhazmat.2022.128934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Urban streams are at high risk of riparian erosion which impacts adjacent infrastructure stability. Methods to prevent stream erosion have been proposed including using recycled concrete (RC) materials to help stabilize the streambed; however, little is known about the environmental and biological impacts of using RC in urban streams. RC, new concrete (NC), and river rock controls were evaluated for their impact on water chemistry, water quality, and microbial community composition over 6.5 months in controlled laboratory mesocosms. Concentrations of 19 metals, nutrients, and pH of mesocosms containing RC were not significantly different from the river rock mesocosm throughout the experiment; however, NC mesocosms contained significantly higher (p < 0.05) concentrations of Co, As, Al, and V in mesocosm water samples compared to both RC and the river rock control. Microbial community diversity was not significantly impacted by mesocosm treatment. Microbial sequences mapping to taxa including Rhodoferax, Acidovorax, Nitrosomonas, and Novosphingobium were significantly more abundant (p < 0.01) in RC and NC mesocosm samples; however, the overall microbial community structure was similar across treatment types. Results from this study suggest that RC does not significantly alter the stream environment including microbial community diversity and is a viable option for use in stream restoration projects.
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Affiliation(s)
- Rachelle E Beattie
- Department of Biological Sciences, Marquette University, 1428 W Clybourn Street, Milwaukee, WI 53233, USA.
| | - Bixia Su
- Department of Biological Sciences, Marquette University, 1428 W Clybourn Street, Milwaukee, WI 53233, USA.
| | - Rebecca Thill
- Department of Biological Sciences, Marquette University, 1428 W Clybourn Street, Milwaukee, WI 53233, USA.
| | - Krassimira R Hristova
- Department of Biological Sciences, Marquette University, 1428 W Clybourn Street, Milwaukee, WI 53233, USA.
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6
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Samanta P, Horn H, Saravia F. Removal of Diverse and Abundant ARGs by MF-NF Process from Pig Manure and Digestate. MEMBRANES 2022; 12:membranes12070661. [PMID: 35877864 PMCID: PMC9317629 DOI: 10.3390/membranes12070661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 02/05/2023]
Abstract
Antimicrobial resistances are emerging as one main threat to worldwide human health and are expected to kill 10 million people by 2050. Intensive livestock husbandry, along with biogas digestate, are considered as one of the biggest ARG reservoirs. Despite major concerns, little information is available on the diversity and abundance of various ARGs in small to large scale pig farms and biogas digestate slurry in Germany, followed by their consequent removal using microfiltration (MF)-nanofiltration (NF) process. Here, we report the identification and quantification of 189 ARGs in raw manure and digestate samples, out of which 66 ARGs were shared among manures and 53 ARGs were shared among both manure and digestate samples. The highest reported total ARG copy numbers in a single manure sampling site was 1.15 × 108 copies/100 µL. In addition, we found the absolute concentrations of 37 ARGs were above 105 copies/100 μL. Filtration results showed that the highly concentrated ARGs (except aminoglycoside resistance ARGs) in feed presented high log retention value (LRV) from 3 to as high as 5 after the MF-NF process. Additionally, LRV below 2 was noticed where the initial absolute ARG concentrations were ≤103 copies/100 μL. Therefore, ARG removal was found to be directly proportional to its initial concentration in the raw manure and in digestate samples. Consequently, some ARGs (tetH, strB) can still be found within the permeate of NF with up to 104 copies/100 μL.
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Affiliation(s)
- Prantik Samanta
- DVGW-Research Center at the Engler-Bunte-Institut, Water Chemistry and Water Technology, Karlsruhe Institute of Technology, Engler-Bunte-Ring 9, 76131 Karlsruhe, Germany; (H.H.); (F.S.)
- Karlsruhe Institute of Technology, Engler-Bunte-Institut, Water Chemistry and Water Technology, Engler-Bunte-Ring 9, 76131 Karlsruhe, Germany
- Correspondence:
| | - Harald Horn
- DVGW-Research Center at the Engler-Bunte-Institut, Water Chemistry and Water Technology, Karlsruhe Institute of Technology, Engler-Bunte-Ring 9, 76131 Karlsruhe, Germany; (H.H.); (F.S.)
- Karlsruhe Institute of Technology, Engler-Bunte-Institut, Water Chemistry and Water Technology, Engler-Bunte-Ring 9, 76131 Karlsruhe, Germany
| | - Florencia Saravia
- DVGW-Research Center at the Engler-Bunte-Institut, Water Chemistry and Water Technology, Karlsruhe Institute of Technology, Engler-Bunte-Ring 9, 76131 Karlsruhe, Germany; (H.H.); (F.S.)
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Wiesner-Friedman C, Beattie RE, Stewart JR, Hristova KR, Serre ML. Characterizing Differences in Sources of and Contributions to Fecal Contamination of Sediment and Surface Water with the Microbial FIT Framework. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4231-4240. [PMID: 35298143 DOI: 10.1021/acs.est.2c00224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Surface water monitoring and microbial source tracking (MST) are used to identify host sources of fecal pollution and protect public health. However, knowledge of the locations of spatial sources and their relative impacts on the environment is needed to effectively mitigate health risks. Additionally, sediment samples may offer time-integrated information compared to transient surface water. Thus, we implemented the newly developed microbial find, inform, and test framework to identify spatial sources and their impacts on human (HuBac) and bovine (BoBac) MST markers, quantified from both riverbed sediment and surface water in a bovine-dense region. Dairy feeding operations and low-intensity developed land-cover were associated with 99% (p-value < 0.05) and 108% (p-value < 0.05) increases, respectively, in the relative abundance of BoBac in sediment, and with 79% (p-value < 0.05) and 39% increases in surface water. Septic systems were associated with a 48% increase in the relative abundance of HuBac in sediment and a 56% increase in surface water. Stronger source signals were observed for sediment responses compared to water. By defining source locations, predicting river impacts, and estimating source influence ranges in a Great Lakes region, this work informs pollution mitigation strategies of local and global significance.
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Affiliation(s)
- Corinne Wiesner-Friedman
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7400, United States
| | - Rachelle E Beattie
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Jill R Stewart
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7400, United States
| | - Krassimira R Hristova
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Marc L Serre
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7400, United States
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Wiesner-Friedman C, Beattie RE, Stewart JR, Hristova KR, Serre ML. Microbial Find, Inform, and Test Model for Identifying Spatially Distributed Contamination Sources: Framework Foundation and Demonstration of Ruminant Bacteroides Abundance in River Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10451-10461. [PMID: 34291905 DOI: 10.1021/acs.est.1c01602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Microbial pollution in rivers poses known ecological and health risks, yet causal and mechanistic linkages to sources remain difficult to establish. Host-associated microbial source tracking (MST) markers help to assess the microbial risks by linking hosts to contamination but do not identify the source locations. Land-use regression (LUR) models have been used to screen the source locations using spatial predictors but could be improved by characterizing transport (i.e., hauling, decay overland, and downstream). We introduce the microbial Find, Inform, and Test (FIT) framework, which expands previous LUR approaches and develops novel spatial predictor models to characterize the transported contributions. We applied FIT to characterize the sources of BoBac, a ruminant Bacteroides MST marker, quantified in riverbed sediment samples from Kewaunee County, Wisconsin. A 1 standard deviation increase in contributions from land-applied manure hauled from animal feeding operations (AFOs) was associated with a 77% (p-value <0.05) increase in the relative abundance of ruminant Bacteroides (BoBac-copies-per-16S-rRNA-copies) in the sediment. This is the first work finding an association between the upstream land-applied manure and the offsite bovine-associated fecal markers. These findings have implications for the sediment as a reservoir for microbial pollution associated with AFOs (e.g., pathogens and antibiotic-resistant bacteria). This framework and application advance statistical analysis in MST and water quality modeling more broadly.
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Affiliation(s)
- Corinne Wiesner-Friedman
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7400, United States
| | - Rachelle E Beattie
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Jill R Stewart
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7400, United States
| | - Krassimira R Hristova
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - Marc L Serre
- Gillings School of Global Public Health, Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7400, United States
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Beattie RE, Hristova KR. Manure derived nutrients alter microbial community composition and increase the presence of potential pathogens in freshwater sediment. J Appl Microbiol 2021; 132:747-757. [PMID: 34312944 DOI: 10.1111/jam.15232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/01/2022]
Abstract
AIM To determine the impact of an acute, pulse disturbance of nutrients from manure on freshwater sediment microbiomes in an experimental system. METHODS AND RESULTS A controlled freshwater mesocosm experiment was designed to compare the effect of disturbance from nutrients derived from sterile manure (SM), disturbance from equivalent concentrations of laboratory-derived nutrients, and a nondisturbed control on freshwater sediment microbial community composition and function using 16S rRNA amplicon sequencing. Sediment microbiomes impacted by nutrients from SM showed no sign of compositional recovery after 28 days but those impacted by laboratory-derived chemicals lead to a new steady-state (p < 0.05). Carbon and nitrate sources within disturbed mesocosms were the primary drivers of altered microbial community composition. Additionally, multiple potential pathogens (based on exact sequence matching at the species level) were enriched in mesocosms treated with SM. CONCLUSIONS Nutrient disturbance from SM, in the absence of the manure microbial community, alters the microbiome of sediments without recovery after 28 days and enriches potential pathogens. SIGNIFICANCE AND IMPACT OF THE STUDY These results suggest manure land application practices should be re-evaluated to account for impact of nutrient disturbance on environmental microbiomes in addition to the impact of the manure microbial community.
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Affiliation(s)
- Rachelle E Beattie
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
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10
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Congilosi JL, Aga DS. Review on the fate of antimicrobials, antimicrobial resistance genes, and other micropollutants in manure during enhanced anaerobic digestion and composting. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:123634. [PMID: 33153790 DOI: 10.1016/j.jhazmat.2020.123634] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/01/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
While manure has been used as nutrient-rich fertilizer for centuries, anaerobic digestion (AD) of manure has only been recognized recently as a promising renewable energy source for producing methane-rich biogas. Various forms of AD have been evaluated for the removal of manure contaminants, such as antimicrobials, antimicrobial resistance genes (ARGs), hormones, and pesticides that pose risks to human health and the environment. Increasing demand for cleaner energy prompts examination of the fate of manure contaminants in conventional and advanced AD techniques. This review reveals that removal of contaminants differs based on type (e.g. antimicrobials vs hormones) or class (e.g. tetracyclines vs sulfonamides) of chemicals being treated. Increasingly, pre-treatment techniques are incorporated into AD systems to enhance biogas production and degrade manure contaminants. For instance, activated carbon with microwave pretreatment removed 87-95% of ARGs. Advanced anaerobic digestion and solid-state anaerobic digestion reduced various ARGs associated with sulfonamides, macrolides, and tetracyclines. Further, total hormone reduction improved using high-temperature pretreatment prior to mesophilic AD. Finally, several studies revealed partial removal of antimicrobials and ARGs during managed composting. Although AD can independently decrease manure contaminants prior to use as fertilizer, augmenting AD with composting and other physical treatment processes can further enhance their removal.
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Affiliation(s)
- Jena L Congilosi
- Chemistry Department, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Diana S Aga
- Chemistry Department, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA.
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11
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Imchen M, Kumavath R. Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment. FEMS Microbiol Ecol 2021; 96:5897355. [PMID: 32845305 DOI: 10.1093/femsec/fiaa173] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 08/18/2020] [Indexed: 12/20/2022] Open
Abstract
Saline tolerant mangrove forests partake in vital biogeochemical cycles. However, they are endangered due to deforestation as a result of urbanization. In this study, we have carried out a metagenomic snapshot of the mangrove ecosystem from five countries to assess its taxonomic, functional and antibiotic resistome structure. Chao1 alpha diversity varied significantly (P < 0.001) between the countries (Brazil, Saudi Arabia, China, India and Malaysia). All datasets were composed of 33 phyla dominated by eight major phyla covering >90% relative abundance. Comparative analysis of mangrove with terrestrial and marine ecosystems revealed the strongest heterogeneity in the mangrove microbial community. We also observed that the mangrove community shared similarities to both the terrestrial and marine microbiome, forming a link between the two contrasting ecosystems. The antibiotic resistant genes (ARG) resistome was comprised of nineteen level 3 classifications dominated by multidrug resistance efflux pumps (46.7 ± 4.3%) and BlaR1 family regulatory sensor-transducer disambiguation (25.2 ± 4.8%). ARG relative abundance was significantly higher in Asian countries and in human intervention datasets at a global scale. Our study shows that the mangrove microbial community and its antibiotic resistance are affected by geography as well as human intervention and are unique to the mangrove ecosystem. Understanding changes in the mangrove microbiome and its ARG is significant for sustainable development and public health.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (P.O) Kasaragod, Kerala-671320, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (P.O) Kasaragod, Kerala-671320, India
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12
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Beattie RE, Bandla A, Swarup S, Hristova KR. Freshwater Sediment Microbial Communities Are Not Resilient to Disturbance From Agricultural Land Runoff. Front Microbiol 2020; 11:539921. [PMID: 33178143 PMCID: PMC7593329 DOI: 10.3389/fmicb.2020.539921] [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: 03/03/2020] [Accepted: 09/22/2020] [Indexed: 01/02/2023] Open
Abstract
Microorganisms are critically important for the function of surface water ecosystems but are frequently subjected to anthropogenic disturbances at either acute (pulse) or long-term (press) scales. Response and recovery of microbial community composition and function following pulse disturbance is well-studied in controlled, laboratory scale experiments but is less well-understood in natural environments undergoing continual press disturbance. The objectives of this study were to determine the drivers of sediment microbial compositional and functional changes in freshwaters receiving continual press disturbance from agricultural land runoff and to evaluate the ability of the native microbial community to resist disturbance related changes as a proxy for freshwater ecosystem health. Freshwater sediments were collected seasonally over 1 year in Kewaunee County, Wisconsin, a region impacted by concentrated dairy cattle farming, manure fertilization, and associated agricultural runoff which together serve as a press disturbance. Using 16S rRNA gene amplicon sequencing, we found that sediments in locations strongly impacted by intensive agriculture contain significantly higher abundances (p < 0.01) of the genera Thiobacillus, Methylotenera, Crenotrhix, Nitrospira, and Rhodoferax compared to reference sediments, and functions including nitrate reduction, nitrite reduction, and nitrogen respiration are significantly higher (p < 0.05) at locations in close proximity to large farms. Nine species-level potential human pathogens were identified in riverine sediments including Acinetobacer lwoffi and Arcobacter skirrowii, two pathogens associated with the cattle microbiome. Microbial community composition at locations in close proximity to intensive agriculture was not resistant nor resilient to agricultural runoff disturbance within 5 months post-disturbance but did reach a new, stable microbial composition. From this data, we conclude that sediment microbial community composition is sensitive and shifts in response to chemical and microbial pollution from intensive agriculture, has a low capacity to resist infiltration by non-native, harmful bacteria and, overall, the natural buffering capacity of freshwater ecosystems is unable to fully resist the impacts from agricultural press disturbance.
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Affiliation(s)
- Rachelle E. Beattie
- Department of Biological Sciences, Marquette University, Milwaukee, WI, United States
| | - Aditya Bandla
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sanjay Swarup
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Department of Biological Science, National University of Singapore, Singapore, Singapore
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13
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Elder FCT, Feil EJ, Snape J, Gaze WH, Kasprzyk-Hordern B. The role of stereochemistry of antibiotic agents in the development of antibiotic resistance in the environment. ENVIRONMENT INTERNATIONAL 2020; 139:105681. [PMID: 32251898 DOI: 10.1016/j.envint.2020.105681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/28/2020] [Accepted: 03/21/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance (ABR) is now recognised as a serious global health and economic threat that is most efficiently managed via a 'one health' approach incorporating environmental risk assessment. Although the environmental dimension of ABR has been largely overlooked, recent studies have underlined the importance of non-clinical settings in the emergence and spread of resistant strains. Despite this, several research gaps remain in regard to the development of a robust and fit-for-purpose environmental risk assessment for ABR drivers such as antibiotics (ABs). Here we explore the role the environment plays in the dissemination of ABR within the context of stereochemistry and its particular form, enantiomerism. Taking chloramphenicol as a proof of principle, we argue that stereoisomerism of ABs impacts on biological properties and the mechanisms of resistance and we discuss more broadly the importance of stereochemistry (enantiomerism in particular) with respect to antimicrobial potency and range of action.
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Affiliation(s)
- Felicity C T Elder
- Department of Chemistry, University of Bath, BA27AY Bath, United Kingdom
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA27AY Bath, United Kingdom
| | - JasoN Snape
- AstraZeneca Global Safety, Health and Environment, Mereside, Macclesfield SK10, 4TG, United Kingdom
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, Truro, Cornwall TR1 3HD, United Kingdom
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14
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Beattie RE, Bakke E, Konopek N, Thill R, Munson E, Hristova KR. Antimicrobial Resistance Traits of Escherichia coli Isolated from Dairy Manure and Freshwater Ecosystems Are Similar to One Another but Differ from Associated Clinical Isolates. Microorganisms 2020; 8:microorganisms8050747. [PMID: 32429352 PMCID: PMC7284991 DOI: 10.3390/microorganisms8050747] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) is a prevalent global health problem across human and veterinary medicine. The One Health approach to AMR is necessary to mitigate transmission between sources of resistance and decrease the spread of resistant bacteria among humans, animals, and the environment. Our primary goal was to identify associations in resistance traits between Escherichia coli isolated from clinical (n = 103), dairy manure (n = 65), and freshwater ecosystem (n = 64) environments within the same geographic location and timeframe. Clinical E. coli isolates showed the most phenotypic resistance (47.5%), followed by environmental isolates (15.6%) and manure isolates (7.7%), with the most common resistances to ampicillin, ampicillin-sulbactam, and cefotaxime antibiotics. An isolate subset was screened for extended spectrum beta-lactamase (ESBL) production resulting in the identification of 35 ESBL producers. The most common ESBL gene identified was blaTEM-1. Additionally, we found nine different plasmid replicon types including IncFIA-FIB, which were frequently associated with ESBL producer isolates. Molecular phylotyping revealed a significant portion of clinical E. coli were associated with phylotype B2, whereas manure and environmental isolates were more diverse. Manure and environmental isolates were significantly different from clinical isolates based on analyzed traits, suggesting more transmission occurs between these two sources in the sampled environment.
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Affiliation(s)
- Rachelle E. Beattie
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (R.E.B.); (N.K.); (R.T.)
| | - Ellen Bakke
- Driskill Life Sciences, Northwestern Medicine Feinberg School of Medicine, Chicago, IL 60611, USA;
| | - Nicholas Konopek
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (R.E.B.); (N.K.); (R.T.)
| | - Rebecca Thill
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (R.E.B.); (N.K.); (R.T.)
| | - Erik Munson
- Department of Clinical Laboratory Science, Marquette University, Milwaukee, WI 53233, USA;
| | - Krassimira R. Hristova
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (R.E.B.); (N.K.); (R.T.)
- Correspondence:
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15
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Herrig I, Fleischmann S, Regnery J, Wesp J, Reifferscheid G, Manz W. Prevalence and seasonal dynamics of blaCTX-M antibiotic resistance genes and fecal indicator organisms in the lower Lahn River, Germany. PLoS One 2020; 15:e0232289. [PMID: 32353007 PMCID: PMC7192499 DOI: 10.1371/journal.pone.0232289] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/11/2020] [Indexed: 12/19/2022] Open
Abstract
Antibiotic-resistant bacteria represent an emerging global health problem and are frequently detected in riverine environments. Analyzing the occurrence of corresponding antibiotic-resistant genes in rivers is of public interest as it contributes towards understanding the origin and dissemination of these emerging microbial contaminants via surface water. This is critical for devising strategies to mitigate the spread of resistances in the environment. Concentrations of blaCTX-M antibiotic resistance genes were quantified weekly over a 12-month period in Lahn River surface water at two sampling sites using quantitative real-time PCR. Gene abundances were statistically assessed with regard to previously determined concentrations of fecal indicator organisms Escherichia coli, intestinal enterococci and somatic coliphages, as well as influential environmental factors. Similar seasonal patterns and strong positive correlations between fecal indicators and blaCTX-M genes indicated identical sources. Accordingly, linear regression analyses showed that blaCTX-M concentrations could largely be explained by fecal pollution. E. coli provided the best estimates (75% explained variance) at the upstream site, where proportions of blaCTX-M genes in relation to fecal indicator organisms were highest. At this site, rainfall proved to be more influential, hinting at surface runoff as an emission source. The level of agricultural impact increased from downstream to upstream, linking increasing blaCTX-M concentrations after rainfall events to the degree of agricultural land use. Exposure assessment revealed that even participants in non-swimming recreational activities were at risk of incidentally ingesting blaCTX-M genes and thus potentially antibiotic resistant bacteria. Considering that blaCTX-M genes are ubiquitous in Lahn River and participants in bathing and non-bathing water sports are at risk of exposure, results highlight the importance of microbial water quality monitoring with an emphasis on antibiotic resistance not only in designated bathing waters. Moreover, E. coli might serve as a suitable estimate for the presence of respective antibiotic resistant strains.
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Affiliation(s)
- Ilona Herrig
- Department G3 Biochemistry, Ecotoxicology, Federal Institute of Hydrology, Koblenz, Germany
- Department of Biology, Institute for Integrated Natural Sciences, University of Koblenz-Landau, Koblenz, Germany
- * E-mail:
| | - Susanne Fleischmann
- Department G3 Biochemistry, Ecotoxicology, Federal Institute of Hydrology, Koblenz, Germany
| | - Julia Regnery
- Department G3 Biochemistry, Ecotoxicology, Federal Institute of Hydrology, Koblenz, Germany
| | - Jessica Wesp
- Department G3 Biochemistry, Ecotoxicology, Federal Institute of Hydrology, Koblenz, Germany
| | - Georg Reifferscheid
- Department G3 Biochemistry, Ecotoxicology, Federal Institute of Hydrology, Koblenz, Germany
| | - Werner Manz
- Department of Biology, Institute for Integrated Natural Sciences, University of Koblenz-Landau, Koblenz, Germany
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16
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Ducey TF, Durso LM, Ibekwe AM, Dungan RS, Jackson CR, Frye JG, Castleberry BL, Rashash DMC, Rothrock MJ, Boykin D, Whitehead TR, Ramos Z, McManus M, Cook KL. A newly developed Escherichia coli isolate panel from a cross section of U.S. animal production systems reveals geographic and commodity-based differences in antibiotic resistance gene carriage. JOURNAL OF HAZARDOUS MATERIALS 2020; 382:120991. [PMID: 31446353 DOI: 10.1016/j.jhazmat.2019.120991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
There are limited numbers of Escherichia coli isolate panels that represent United States food animal production. The majority of existing Escherichia coli isolate panels are typically designed: (i) to optimize genetic and/or phenotypic diversity; or (ii) focus on human isolates. To address this shortfall in agriculturally-related resources, we have assembled a publicly-available isolate panel (AgEc) from the four major animal production commodities in the United States, including beef, dairy, poultry, and swine, as well as isolates from agriculturally-impacted environments, and other commodity groups. Diversity analyses by phylotyping and Pulsed-field Gel Electrophoresis revealed a highly diverse composition, with the 300 isolates clustered into 71 PFGE sub-types based upon an 80% similarity cutoff. To demonstrate the panel's utility, tetracycline and sulfonamide resistance genes were assayed, which identified 131 isolates harboring genes involved in tetracycline resistance, and 41 isolates containing sulfonamide resistance genes. There was strong overlap in the two pools of isolates, 38 of the 41 isolates harboring sulfonamide resistance genes also contained tetracycline resistance genes. Analysis of antimicrobial resistance gene patterns revealed significant differences along commodity and geographical lines. This panel therefore provides the research community an E. coli isolate panel for study of issues pertinent to U.S. food animal production.
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Affiliation(s)
- Thomas F Ducey
- Coastal Plains Soil, Water, and Plant Research Center, Agricultural Research Service, Department of Agriculture, Florence, SC, United States.
| | - Lisa M Durso
- Agroecosystem Management Research Unit, Agricultural Research Service, Department of Agriculture, Lincoln, NE, United States
| | - Abasiofiok M Ibekwe
- U.S. Salinity Laboratory, Agricultural Research Service, Department of Agriculture, Riverside, CA, United States
| | - Robert S Dungan
- Northwest Irrigation and Soils Research Laboratory, Agricultural Research Service, Department of Agriculture, Kimberly, ID, United States
| | - Charlene R Jackson
- Bacterial Epidemiology & Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
| | - Jonathan G Frye
- Bacterial Epidemiology & Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
| | - B Lana Castleberry
- Livestock Nutrient Management Research Unit, Agricultural Research Service, Department of Agriculture, Bushland, TX, United States
| | - Diana M C Rashash
- North Carolina Cooperative Extension Service, Jacksonville, NC, United States
| | - Michael J Rothrock
- Egg Safety & Quality Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
| | - Debbie Boykin
- Jamie Whitten Delta States Research Center, Agricultural Research Service, Department of Agriculture, Stoneville, MS, United States
| | - Terence R Whitehead
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, Department of Agriculture, Peoria, IL, United States
| | - Zeanmarj Ramos
- South Carolina Governor's School for Science and Mathematics, Hartsville, SC, United States
| | - Morgan McManus
- South Carolina Governor's School for Science and Mathematics, Hartsville, SC, United States
| | - Kimberly L Cook
- Bacterial Epidemiology & Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, Department of Agriculture, Athens, GA, United States
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17
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Tiedje JM. Editorial: Environmental aspects of antibiotic resistance. FEMS Microbiol Ecol 2019; 95:5421059. [PMID: 30923814 DOI: 10.1093/femsec/fiz019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
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18
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Impact of Wuyiencin Application on the Soil Microbial Community and Fate of Typical Antibiotic Resistance Genes. Sci Rep 2019; 9:4016. [PMID: 30850695 PMCID: PMC6408571 DOI: 10.1038/s41598-019-40389-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/11/2019] [Indexed: 11/08/2022] Open
Abstract
Antibiotic resistance genes (ARGs) have raised numerous concerns in recent years as emerging environmental contaminants. At present, research on environmental contamination by antibiotics focuses on medical, animal husbandry, and aquaculture fields, with few studies on environmental contamination by agricultural antibiotics in the field of plant protection. Wuyiencin is a low toxicity, high efficiency, and broad-spectrum agricultural antibiotic. It has been widely used in agricultural production and it effectively controls crop fungal diseases. In the present study, pot experiments with four soil treatments (A, B, C and D) were set up in a greenhouse to investigate the effect of the application of wuyiencin on the fate of typical ARGs and microbial community. Eight typical ARGs were detected by real-time PCR and the microbial communities were analyzed using high-throughput sequencing. The results showed that wuyiencin neither significantly influenced ARG abundance and absolute gene copy numbers, nor significantly varied microbial community among treatments. Since it only was short-term results, and the detection number of ARGs was limited, whether wuyiencin is safe or not to ecological environment when using for long-term will need further deep research.
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