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Liu W, Xie WY, Liu HJ, Chen C, Chen SY, Jiang GF, Zhao FJ. Assessing intracellular and extracellular distribution of antibiotic resistance genes in the commercial organic fertilizers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172558. [PMID: 38643884 DOI: 10.1016/j.scitotenv.2024.172558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/23/2024]
Abstract
Compost-based organic fertilizers often contain high levels of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Previous studies focused on quantification of total ARGs and MGEs. For a more accurate risk assessment of the dissemination risk of antibiotic resistance, it is necessary to quantify the intracellular and extracellular distribution of ARGs and MGEs. In the present study, extracellular ARGs and MGEs (eARGs and eMGEs) and intracellular ARGs and MGEs (iARGs and iMGEs) were separately analyzed in 51 commercial composts derived from different raw materials by quantitative polymerase chain reaction (qPCR) and metagenomic sequencing. Results showed that eARGs and eMGEs accounted for 11-56% and 4-45% of the total absolute abundance of ARGs and MGEs, respectively. Comparable diversity, host composition and association with MGEs were observed between eARGs and iARGs. Contents of high-risk ARGs were similar between eARGs and iARGs, with high-risk ARGs in the two forms accounting for 6.7% and 8.2% of the total abundances, respectively. Twenty-four percent of the overall ARGs were present in plasmids, while 56.7% of potentially mobile ARGs were found to be associated with plasmids. Variation partitioning analysis, null model and neutral community model indicated that the compositions of both eARGs and iARGs were largely driven by deterministic mechanisms. These results provide important insights into the cellular distribution of ARGs in manure composts that should be paid with specific attention in risk assessment and management.
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Affiliation(s)
- Wei Liu
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wan-Ying Xie
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Hong-Jun Liu
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuan Chen
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shu-Yao Chen
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Gao-Fei Jiang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang-Jie Zhao
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
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2
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Wang H, Wang X, Zhang L, Zhang X, Cao Y, Xiao R, Bai Z, Ma L. Meta-analysis addressing the potential of antibiotic resistance gene elimination through aerobic composting. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 182:197-206. [PMID: 38670003 DOI: 10.1016/j.wasman.2024.04.034] [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: 11/06/2023] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
The significant increase in antibiotic resistance genes (ARGs) in organic solid wastes (OSWs) has emerged as a major threat to the food chain. Aerobic composting is a widely used technology for OSW management, with the potential to influence the fate of AGRs. However, the variability of the ARG elimination effects reported in different studies has highlighted the uncertainty regarding the effects of composting on ARGs. To identify the potential of composting in reducing ARG and the factors (e.g., composting technologies and physiochemical properties) influence ARG changes, a meta-analysis was conducted with a database including 4,232 observations. The abundances of ARGs and mobile genetic elements (MGEs) can be substantially reduced by 74.3% and 78.8%, respectively, via aerobic composting. During composting, the ARG levels in chicken and swine manure tended to be reduced more significantly (81.7% and 78.0%) compared to those in cattle manure (52.3%) and sewage sludge (32.6%). The reduction rate of sulfonamide resistant genes was only 35.3%, which was much lower than those of other types. MGEs and composting duration (CD) were identified as the most important factors driving ARG changes during composting. These findings provide a comprehensive insight into the effects of composting on ARG reduction, which may help prevent the transmission in food systems.
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Affiliation(s)
- Hongge Wang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China; University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, PR China
| | - Xuan Wang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China
| | - Lu Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China; University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, PR China
| | - Xinyuan Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China; University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, PR China
| | - Yubo Cao
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China; University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, PR China
| | - Ran Xiao
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Zhaohai Bai
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China
| | - Lin Ma
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, Hebei, PR China.
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3
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Oladele P, Ngo J, Chang T, Johnson TA. Temporal dynamics of fecal microbiota community succession in broiler chickens, calves, and piglets under aerobic exposure. Microbiol Spectr 2024; 12:e0408423. [PMID: 38717193 DOI: 10.1128/spectrum.04084-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/16/2024] [Indexed: 06/06/2024] Open
Abstract
Researchers have extensively studied the effect of oxygen on the growth and survival of bacteria. However, the impact of oxygen on bacterial community structure, particularly its ability to select for taxa within the context of a complex microbial community, is still unclear. In a 21-day microcosm experiment, we investigated the effect of aerobic exposure on the fecal community structure and succession pattern in broiler, calf, and piglet feces (n = 10 for each feces type). Bacterial diversity decreased and community structure changed rapidly in the broiler microbiome (P < 0.001), while the fecal community of calves and piglets, which have higher initial diversity, was stable after initial exposure but decreased in diversity after 3 days (P < 0.001). The response to aerobic exposure was host animal specific, but in all three animals, the change in community structure was driven by a decrease in anaerobic species, primarily belonging to Firmicutes and Bacteroidetes (except in broilers where Bacteroidetes increased), along with an increase in aerobic species belonging to Proteobacteria and Actinobacteria. Using random forest regression, we identified microbial features that predict aerobic exposure. In all three animals, host-beneficial Prevotella-related ASVs decreased after exposure, while ASVs belonging to Acinetobacter, Corynbacterium, and Tissierella were increased. The decrease of Prevotella was rapid in broilers but delayed in calves and piglets. Knowing when these pathobionts increase in abundance after aerobic exposure could inform farm sanitation practices and could be important in designing animal experiments that modulate the microbiome.IMPORTANCEThe fecal microbial community is contained within a dynamic ecosystem of interacting microbes that varies in biotic and abiotic components across different animal species. Although oxygen affects bacterial growth, its specific impact on the structure of complex communities, such as those found in feces, and how these effects vary between different animal species are poorly understood. In this study, we demonstrate that the effect of aerobic exposure on the fecal microbiota was host-animal-specific, primarily driven by a decrease in Firmicutes and Bacteroidetes, but accompanied by an increase in Actinobacteria, Proteobacteria, and other pathobionts. Interestingly, we observed that more complex communities from pig and cattle exhibited initial resilience, while a less diverse community from broilers displayed a rapid response to aerobic exposure. Our findings offer insights that can inform farm sanitation practices, as well as experimental design, sample collection, and processing protocols for microbiome studies across various animal species.
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Affiliation(s)
- Paul Oladele
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Jennifer Ngo
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Tiffany Chang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Timothy A Johnson
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
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4
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Zhang Y, Hu Y, Li X, Gao L, Wang S, Jia S, Shi P, Li A. Prevalence of antibiotics, antibiotic resistance genes, and their associations in municipal wastewater treatment plants along the Yangtze River basin, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 348:123800. [PMID: 38518970 DOI: 10.1016/j.envpol.2024.123800] [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: 11/26/2023] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/24/2024]
Abstract
The overuse and misuse of antibiotics have resulted in the pollution of antibiotics and antibiotic resistance genes (ARGs) in municipal wastewater treatment plants (WWTPs), posing threats to ecological security and human health. Thus, a comprehensive investigation was conducted to assess the occurrence, removal efficiency, and ecological risk of antibiotics, along with the diversity, abundance, and co-occurrence of ARGs, and their correlations in 13 WWTPs along the Yangtze River Basin. Among 35 target antibiotics, 23 antibiotics within 6 categories were detected in all the samples. Amoxicillin (AMO), ofloxacin (OFL), and pefloxacin (PEF) were predominant in influents, while AMO exhibited dominance with the highest concentration of 1409 ng/L in effluents. Although antibiotic removal performance varied among different WWTPs, a significant decrease in each antibiotic category and overall antibiotics was observed in effluents compared with that in influents (p < 0.05). Remarkably, ecological risk assessment revealed high risks associated with AMO and ciprofloxacin (CIP) and medium risks linked to several antibiotics, notably including OFL, roxithromycin (ROX), clarithromycin (CLA), and tetracycline (TC). Furthermore, 96 ARG subtypes within 12 resistance types were detected in this study, and the total absolute abundance and diversity of ARGs were significantly decreased from influents to effluents (p < 0.05). Enrichment of 38 ARGs (e.g., blaNDM, ermA, vatA, mexA, and dfrA25) in effluents indicated potential health risks. Various mobile genetic elements (MGEs), exhibited significant correlations with a majority of ARGs in both influents and effluents, such as intⅠ1, tnpA1, tnpA5, and tp614, underscoring the important role of MGEs in contributing to the ARG dissemination. Many antibiotics displayed lower correlations with corresponding ARGs, but exhibited higher correlations with other ARGs, suggesting complex selective pressures influencing ARG propagation. Overall, the incomplete elimination of antibiotics and ARGs in WWTPs is likely to pose adverse impacts on aquatic ecosystems in the Yangtze River Basin.
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Affiliation(s)
- Yangyang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Yifan Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Xiuwen Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Linjun Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuya Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuyu Jia
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Peng Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China
| | - Aimin Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, China
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5
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Mahmud B, Vargas RC, Sukhum KV, Patel S, Liao J, Hall LR, Kesaraju A, Le T, Kitchner T, Kronholm E, Koshalek K, Bendixsen CG, VanWormer JJ, Shukla SK, Dantas G. Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes. Nat Microbiol 2024; 9:1007-1020. [PMID: 38570675 DOI: 10.1038/s41564-024-01639-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 02/14/2024] [Indexed: 04/05/2024]
Abstract
Globally, half a billion people are employed in animal agriculture and are directly exposed to the associated microorganisms. However, the extent to which such exposures affect resident human microbiomes is unclear. Here we conducted a longitudinal profiling of the nasal and faecal microbiomes of 66 dairy farmers and 166 dairy cows over a year-long period. We compare farmer microbiomes to those of 60 age-, sex- and ZIP code-matched people with no occupational exposures to farm animals (non-farmers). We show that farming is associated with microbiomes containing livestock-associated microbes; this is most apparent in the nasal bacterial community, with farmers harbouring a richer and more diverse nasal community than non-farmers. Similarly, in the gut microbial communities, we identify more shared microbial lineages between cows and farmers from the same farms. Additionally, we find that shared microbes are associated with antibiotic resistance genes. Overall, our study demonstrates the interconnectedness of human and animal microbiomes.
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Affiliation(s)
- Bejan Mahmud
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Rhiannon C Vargas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Kimberley V Sukhum
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Sanket Patel
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - James Liao
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Lindsey R Hall
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Akhil Kesaraju
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Thao Le
- Integrated Research Development Laboratory, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Terrie Kitchner
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Erik Kronholm
- Center for Clinical Epidemiology & Population Health, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Kyle Koshalek
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Casper G Bendixsen
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Jeffrey J VanWormer
- Center for Clinical Epidemiology & Population Health, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA.
- Computational Informatics in Biology and Medicine program, University of Wisconsin-Madison, Madison, WI, USA.
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
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6
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Hazra M, Watts JEM, Williams JB, Joshi H. An evaluation of conventional and nature-based technologies for controlling antibiotic-resistant bacteria and antibiotic-resistant genes in wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170433. [PMID: 38286289 DOI: 10.1016/j.scitotenv.2024.170433] [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: 08/27/2023] [Revised: 01/10/2024] [Accepted: 01/23/2024] [Indexed: 01/31/2024]
Abstract
Antibiotic resistance is a globally recognized health concern which leads to longer hospital stays, increased morbidity, increased mortality, and higher medical costs. Understanding how antibiotic resistance persists and exchanges in environmental systems like soil, water, and wastewater are critically important for understanding the emergence of pathogens with new resistance profiles and the subsequent exposure of people who indirectly/directly come in contact with these pathogens. There are concerns about the widespread application of prophylactic antibiotics in the clinical and agriculture sectors, as well as chemicals/detergents used in food and manufacturing industries, especially the quaternary ammonium compounds which have been found responsible for the generation of resistant genes in water and soil. The rates of horizontal gene transfer increase where there is a lack of proper water/wastewater infrastructure, high antibiotic manufacturing industries, or endpoint users - such as hospitals and intensive agriculture. Conventional wastewater treatment technologies are often inefficient in the reduction of ARB/ARGs and provide the perfect combination of conditions for the development of antibiotic resistance. The wastewater discharged from municipal facilities may therefore be enriched with bacterial communities/pathogens and provide a suitable environment (due to the presence of nutrients and other pollutants) to enhance the transfer of antibiotic resistance. However, facilities with tertiary treatment (either traditional/emerging technologies) provide higher rates of reduction. This review provides a synthesis of the current understanding of wastewater treatment and antibiotic resistance, examining the drivers that may accelerate their possible transmission to a different environment, and highlighting the need for tertiary technologies used in treatment plants for the reduction of resistant bacteria/genes.
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Affiliation(s)
- Moushumi Hazra
- Department of Hydrology, Indian Institute of Technology, Roorkee, Uttarakhand, India; International Water Management Institute, New Delhi, India; Civil and Environmental Engineering, University of Nebraska Lincoln, United States.
| | - Joy E M Watts
- School of Biological Sciences, University of Portsmouth, United Kingdom
| | - John B Williams
- School of Civil Engineering and Surveying, University of Portsmouth, United Kingdom
| | - Himanshu Joshi
- Department of Hydrology, Indian Institute of Technology, Roorkee, Uttarakhand, India
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7
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Zhang Y, Qin K, Liu C. Low-density polyethylene enhances the disturbance of microbiome and antibiotic resistance genes transfer in soil-earthworm system induced by pyraclostrobin. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133459. [PMID: 38219581 DOI: 10.1016/j.jhazmat.2024.133459] [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: 11/06/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/16/2024]
Abstract
Non-antibiotic chemicals in farmlands, including microplastics (MPs) and pesticides, have the potential to influence the soil microbiome and the dissemination of antibiotic resistance genes (ARGs). Despite this, there is limited understanding of the combined effects of MPs and pesticides on microbial communities and ARGs transmission in soil ecosystems. In this study, we observed that low-density polyethylene (LDPE) microplastic enhance the accumulation of pyraclostrobin in earthworms, resulting in reduced weight and causing severe oxidative damage. Analysis of 16 S rRNA amplification revealed that exposure to pyraclostrobin and/or LDPE disrupts the microbial community structure at the phylum and genus levels, leading to reduced alpha diversity in both the soil and earthworm gut. Furthermore, co-exposure to LDPE and pyraclostrobin increased the relative abundance of ARGs in the soil and earthworm gut by 2.15 and 1.34 times, respectively, compared to exposure to pyraclostrobin alone. It correlated well with the increasing relative abundance of genera carrying ARGs. Our findings contribute novel insights into the impact of co-exposure to MPs and pesticides on soil and earthworm microbiomes, highlighting their role in promoting the transfer of ARGs. This knowledge is crucial for managing the risk associated with the dissemination of ARGs in soil ecosystems.
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Affiliation(s)
- Yirong Zhang
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Wushan Road 483, Tianhe District, Guangzhou 510642, China
| | - Kaikai Qin
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Wushan Road 483, Tianhe District, Guangzhou 510642, China
| | - Chenglan Liu
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Wushan Road 483, Tianhe District, Guangzhou 510642, China.
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8
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Jiang B, Zeng Q, Liu Q, Chai H, Xiang J, Li H, Shi S, Yang A, Chen Z, Cui Y, Hu D, Ge H, Yuan C, Dong J, Han F. Impacts of electric field-magnetic powder coupled membrane bioreactor on phenol wastewater treatment: Performance, synergistic mechanism, antibiotic resistance genes, and eco-environmental benefit evaluation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168607. [PMID: 37981150 DOI: 10.1016/j.scitotenv.2023.168607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/03/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
A novel electric field-magnetic powder coupled membrane bioreactor (EM-MBR) was constructed, which was superior on improvement of phenol treatment performance and sludge characteristics, and mitigation of membrane fouling. EM-MBR enhanced the phenol degradation via the improvement activity of phenol degrading enzymes. The EPS contents and SVI of EM-MBR were significantly reduced by 49.3 % and 58.7 % than that of the conventional MBR, respectively. Moreover, EM-MBR successfully reduced fouling rate by 57.0 %, delaying the membrane resistance. The EPS contents were positively correlated with the SVI and fouling rate, implying that the sludge settleability was strengthened by improving the properties of EPS with the assistance of electromagnetic, thus mitigating the membrane fouling. Microbial co-occurrence network demonstrated that EM-MBR enriched phenol-degrading and EPS-degrading genera correlated to Fe redox cycle. Furthermore, the activation of the antioxidant system in the EM-MBR resulted in the suppression of reactive oxygen species (ROS) generation, consequently impeding the dissemination of antibiotic resistance genes (ARGs). Co-occurrence patterns of MGEs and ARGs revealed that intercellular binding facilitated by ist and Integrase may account for the horizontal transfer of ARGs. The reduction of unit capital costs (15.63 %), running costs (53.00 %), and total average carbon emissions (15.18 %) indicated that EM-MBR was environmentally beneficial.
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Affiliation(s)
- Bei Jiang
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
| | - Qianzhi Zeng
- School of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Qiangwei Liu
- School of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Huiying Chai
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
| | - Jinxun Xiang
- School of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Hongxin Li
- School of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Shengnan Shi
- School of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Aifu Yang
- Technology Center of Dalian Customs District, Dalian 116001, China
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China.
| | - Yubo Cui
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
| | - Dongxue Hu
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
| | - Hui Ge
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
| | - Chang Yuan
- Southwest Guizhou Vocational and Technical College for Nationalities, Xingyi 562400, China
| | - Jian Dong
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
| | - Fei Han
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian Jinpu New District, Dalian 116600, China
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9
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Danov A, Segev O, Bograd A, Ben Eliyahu Y, Dotan N, Kaplan T, Levy A. Toxinome-the bacterial protein toxin database. mBio 2024; 15:e0191123. [PMID: 38117054 PMCID: PMC10790787 DOI: 10.1128/mbio.01911-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Microbes use protein toxins as important tools to attack neighboring cells, microbial or eukaryotic, and for self-killing when attacked by viruses. These toxins work through different mechanisms to inhibit cell growth or kill cells. Microbes also use antitoxin proteins to neutralize the toxin activities. Here, we developed a comprehensive database called Toxinome of nearly two million toxins and antitoxins that are encoded in 59,475 bacterial genomes. We described the distribution of bacterial toxins and identified that they are depleted by bacteria that live in hot and cold temperatures. We found 5,161 cases in which toxins and antitoxins are densely clustered in bacterial genomes and termed these areas "Toxin Islands." The Toxinome database is a useful resource for anyone interested in toxin biology and evolution, and it can guide the discovery of new toxins.
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Affiliation(s)
- Aleks Danov
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ofir Segev
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avi Bograd
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yedidya Ben Eliyahu
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Dotan
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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Yi X, Lu H, Liu X, He J, Li B, Wang Z, Zhao Y, Zhang X, Yu X. Unravelling the enigma of the human microbiome: Evolution and selection of sequencing technologies. Microb Biotechnol 2024; 17:e14364. [PMID: 37929823 PMCID: PMC10832515 DOI: 10.1111/1751-7915.14364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023] Open
Abstract
The human microbiome plays a crucial role in maintaining health, with advances in high-throughput sequencing technology and reduced sequencing costs triggering a surge in microbiome research. Microbiome studies generally incorporate five key phases: design, sampling, sequencing, analysis, and reporting, with sequencing strategy being a crucial step offering numerous options. Present mainstream sequencing strategies include Amplicon sequencing, Metagenomic Next-Generation Sequencing (mNGS), and Targeted Next-Generation Sequencing (tNGS). Two innovative technologies recently emerged, namely MobiMicrobe high-throughput microbial single-cell genome sequencing technology and 2bRAD-M simplified metagenomic sequencing technology, compensate for the limitations of mainstream technologies, each boasting unique core strengths. This paper reviews the basic principles and processes of these three mainstream and two novel microbiological technologies, aiding readers in understanding the benefits and drawbacks of different technologies, thereby guiding the selection of the most suitable method for their research endeavours.
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Affiliation(s)
- Xin Yi
- Department of PharmacyShanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Hong Lu
- Department of Clinical laboratoryThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xiang Liu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Junyi He
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Bing Li
- Department of Public HealthShanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Zhelong Wang
- Department of PharmacyGuangdong Pharmaceutical UniversityGuangzhouPeople's Republic of China
| | - Yujing Zhao
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xinri Zhang
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xiao Yu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
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Eiamsam-Ang T, Tadee P, Buddhasiri S, Chuammitri P, Kittiwan N, Pascoe B, Patchanee P. Commercial farmed swine harbour a variety of pathogenic bacteria and antimicrobial resistance genes. J Med Microbiol 2024; 73. [PMID: 38230911 DOI: 10.1099/jmm.0.001787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024] Open
Abstract
Introduction. The northern region of Thailand serves as a crucial area for swine production, contributing to the Thai community food supply. Previous studies have highlighted the presence of foodborne bacterial pathogens originating from swine farms in this region, posing a threat to both human and animal health.Gap statement. Multiple swine bacterial pathogens have been studied at a species level, but the distribution and co-occurrence of bacterial pathogens in agricultural swine has not been well established.Aim. Our study employed the intestinal scraping technique to directly examine the bacterial micro-organisms interacting with the swine host.Methodology. We used shotgun metagenomic sequencing to analyse the bacterial pathogens inhabiting the caecal microbiome of swine from five commercial farms in northern Thailand.Results. A variety of pathogenic and opportunistic bacteria were identified, including Escherichia coli, Clostridium botulinum, Staphylococcus aureus and the Corynebacterium genus. From a One Health perspective, these species are important foodborne and opportunistic pathogens in both humans and agricultural animals, making swine a critical pathogen reservoir that can cause illness in humans, especially farm workers. Additionally, the swine caecal microbiome contains commensal bacteria such as Bifidobacterium, Lactobacillus and Faecalibacterium, which are associated with normal physiology and feed utilization in healthy swine. Antimicrobial resistance genes were also detected in all samples, specifically conferring resistance to tetracycline and aminoglycosides, which have historically been used extensively in swine farming.Conclusion. The findings further support the need for improved sanitation standards in swine farms, and additional monitoring of agricultural animals and farm workers to reduce contamination and improved produce safety for human consumption.
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Affiliation(s)
- Thanaporn Eiamsam-Ang
- Graduate Program in Veterinary Science, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Pakpoom Tadee
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Songphon Buddhasiri
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Phongsakorn Chuammitri
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Nattinee Kittiwan
- Veterinary Research and Development Center (Upper Northern Region), Hang Chat, Lampang, Thailand
| | - Ben Pascoe
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
- Centre for Genomic Pathogen Surveillance, Pandemic Sciences Institute, University of Oxford, Oxford, UK
- Ineos Oxford Istitute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Prapas Patchanee
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
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12
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Męcik M, Buta-Hubeny M, Paukszto Ł, Maździarz M, Wolak I, Harnisz M, Korzeniewska E. Poultry manure-derived microorganisms as a reservoir and source of antibiotic resistance genes transferred to soil autochthonous microorganisms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 348:119303. [PMID: 37832303 DOI: 10.1016/j.jenvman.2023.119303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023]
Abstract
Animal husbandry is increasing yearly due to the growing demand for meat and livestock products, among other reasons. To meet these demands, prophylactic antibiotics are used in the livestock industry (i.e., poultry farming) to promote health and stimulate animal growth. However, antibiotics are not fully metabolized by animals, and they are evacuated to the environment with excreta. Animal manure is used as fertilizer to reduce the volume of waste generated in the livestock sector. However, manure often contains microorganisms harboring antibiotic resistance genes (ARGs). Then, the microbiome of manure applicate to the soil may contribute to the spread of antibiotic resistance in the environment, including autochthonous soil-dwelling microorganisms. The present study was conducted during the crops growing season in Poland (May to September 2019) to determine the influence of poultry manure as well as poultry manure supplemented with selected antibiotics on the diversity of the soil microbiome in treatments that had not been previously fertilized with manure and the ability of antibiotic-resistant bacteria to transfer ARGs to other soil bacteria. Antibiotic concentrations were elevated at the beginning of the study and decreased over time. Poultry manure induced significant changes in the structure of microbial communities in soil; the diversity of the soil microbiome decreased, and the abundance of bacterial genera Bradyrhizobium, Streptomyces, and Pseudomonas, which are characteristic of the analyzed manure, increased. Over time, soil microbial diversity was restored to the state observed before the application of manure. Genes conferring resistance to multiple drugs as well as genes encoding resistance to bacitracin and aminoglycosides were the most frequently identified ARGs in the analyzed bacteria, including on mobile genetic elements. Multidrug resistance was observed in 17 bacterial taxa, whereas ARGs were identified in 32 bacterial taxa identified in the soil microbiome. The results of the study conclude that the application of poultry manure supplemented with antibiotics initially affects soil microbiome and resistome diversity but finally, the soil shows resilience and returns to its original state after time, with most antibiotic resistance genes disappearing. This phenomenon is of great importance in sustainable soil health after manure application.
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Affiliation(s)
- Magdalena Męcik
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Martyna Buta-Hubeny
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-721, Olsztyn, Poland
| | - Mateusz Maździarz
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-721, Olsztyn, Poland
| | - Izabela Wolak
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Monika Harnisz
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland.
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13
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Fishbein SRS, Mahmud B, Dantas G. Antibiotic perturbations to the gut microbiome. Nat Rev Microbiol 2023; 21:772-788. [PMID: 37491458 DOI: 10.1038/s41579-023-00933-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
Antibiotic-mediated perturbation of the gut microbiome is associated with numerous infectious and autoimmune diseases of the gastrointestinal tract. Yet, as the gut microbiome is a complex ecological network of microorganisms, the effects of antibiotics can be highly variable. With the advent of multi-omic approaches for systems-level profiling of microbial communities, we are beginning to identify microbiome-intrinsic and microbiome-extrinsic factors that affect microbiome dynamics during antibiotic exposure and subsequent recovery. In this Review, we discuss factors that influence restructuring of the gut microbiome on antibiotic exposure. We present an overview of the currently complex picture of treatment-induced changes to the microbial community and highlight essential considerations for future investigations of antibiotic-specific outcomes. Finally, we provide a synopsis of available strategies to minimize antibiotic-induced damage or to restore the pretreatment architectures of the gut microbial community.
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Affiliation(s)
- Skye R S Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bejan Mahmud
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
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14
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Okonkwo V, Cholet F, Ijaz UZ, Koottatep T, Pussayanavin T, Polpraset C, Sloan WT, Connelly S, Smith CJ. intI1 gene abundance from septic tanks in Thailand using validated intI1 primers. Appl Environ Microbiol 2023; 89:e0107123. [PMID: 37874304 PMCID: PMC10686061 DOI: 10.1128/aem.01071-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/22/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Antimicrobial resistance is a global crisis, and wastewater treatment, including septic tanks, remains an important source of antimicrobial resistance (AMR) genes. The role of septic tanks in disseminating class 1 integron, and by extension AMR genes, in Thailand, where antibiotic use is unregulated remains understudied. We aimed to monitor gene abundance as a proxy to infer potential AMR from septic tanks in Thailand. We evaluated published intI1 primers due to the lack of consensus on optimal Q-PCR primers and the absence of standardization. Our findings confirmed septic tanks are a source of class 1 integron to the environment. We highlighted the significance of intI1 primer choice, in the context of interpretation of risk associated with AMR spread from septic tanks. We recommend the validated set (F3-R3) for optimal intI1 quantification toward the goal of achieving standardization across studies.
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Affiliation(s)
- Valentine Okonkwo
- Department of Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Fabien Cholet
- Department of Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Umer Z. Ijaz
- Department of Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Thammarat Koottatep
- School of Environment, Resources and Development, Asian Institute of Technology, Khlong Nueng, Thailand
| | | | - Chongrak Polpraset
- Thammasat School of Engineering, Thammasat University, Bangkok, Thailand
| | - William T. Sloan
- Department of Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Stephanie Connelly
- Department of Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Cindy J. Smith
- Department of Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
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15
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Tams KW, Larsen I, Hansen JE, Spiegelhauer H, Strøm-Hansen AD, Rasmussen S, Ingham AC, Kalmar L, Kean IRL, Angen Ø, Holmes MA, Pedersen K, Jelsbak L, Folkesson A, Larsen AR, Strube ML. The effects of antibiotic use on the dynamics of the microbiome and resistome in pigs. Anim Microbiome 2023; 5:39. [PMID: 37605221 PMCID: PMC10440943 DOI: 10.1186/s42523-023-00258-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/25/2023] [Indexed: 08/23/2023] Open
Abstract
Antibiotics are widely used in pig farming across the world which has led to concerns about the potential impact on human health through the selection of antibiotic resistant pathogenic bacteria. This worry has resulted in the development of a production scheme known as pigs Raised Without Antibiotics (RWA), in which pigs are produced in commercial farms, but are ear-tagged as RWA until slaughter unless they receive treatment, thus allowing the farmer to sell the pigs either as premium priced RWA or as conventional meat. Development of antibiotic resistance in pig farming has been studied in national surveys of antibiotic usage and resistance, as well as in experimental studies of groups of pigs, but not in individual pigs followed longitudinally in a commercial pig farm. In this study, a cohort of RWA designated pigs were sampled at 10 time points from birth until slaughter along with pen-mates treated with antibiotics at the same farm. From these samples, the microbiome, determined using 16S sequencing, and the resistome, as determined using qPCR for 82 resistance genes, was investigated, allowing us to examine the difference between RWA pigs and antibiotic treated pigs. We furthermore included 176 additional pigs from six different RWA farms which were sampled at the slaughterhouse as an endpoint to substantiate the cohort as well as for evaluation of intra-farm variability. The results showed a clear effect of age in both the microbiome and resistome composition from early life up until slaughter. As a function of antibiotic treatment, however, we observed a small but significant divergence between treated and untreated animals in their microbiome composition immediately following treatment, which disappeared before 8 weeks of age. The effect on the resistome was evident and an effect of treatment could still be detected at week 8. In animals sampled at the slaughterhouse, we observed no difference in the microbiome or the resistome as a result of treatment status but did see a strong effect of farm origin. Network analysis of co-occurrence of microbiome and resistome data suggested that some resistance genes may be transferred through mobile genetic elements, so we used Hi-C metagenomics on a subset of samples to investigate this. We conclude that antibiotic treatment has a differential effect on the microbiome vs. the resistome and that although resistance gene load is increased by antibiotic treatment load, this effect disappears before slaughter. More studies are needed to elucidate the optimal way to rear pigs without antibiotics.
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Affiliation(s)
- Katrine Wegener Tams
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Inge Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1871, Copenhagen, Denmark
| | - Julie Elvekjær Hansen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Henrik Spiegelhauer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | | | - Sophia Rasmussen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300, Copenhagen, Denmark
| | - Lajos Kalmar
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Øystein Angen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300, Copenhagen, Denmark
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Karl Pedersen
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute, 751 89, Uppsala, Sweden
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Anders Folkesson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300, Copenhagen, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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16
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Fan Q, Zhang J, Shi H, Chang S, Hou F. Metagenomic Profiles of Yak and Cattle Manure Resistomes in Different Feeding Patterns before and after Composting. Appl Environ Microbiol 2023; 89:e0064523. [PMID: 37409977 PMCID: PMC10370317 DOI: 10.1128/aem.00645-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/04/2023] [Indexed: 07/07/2023] Open
Abstract
Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants; furthermore, animal manure is an important reservoir of biocide resistance genes (BRGs) and metal resistance genes (MRGs). However, few studies have reported differences in the abundance and diversity of BRGs and MRGs between different types of animal manure and the changes in BRGs and MRGs before and after composting. This study employed a metagenomics-based approach to investigate ARGs, BRGs, MRGs, and mobile genetic elements (MGEs) of yak and cattle manure before and after composting under grazing and intensive feeding patterns. The total abundances of ARGs, clinical ARGs, BRGs, MRGs, and MGEs were lower in the manure of grazing livestock than in the manure of the intensively fed group. After composting, the total abundances of ARGs, clinical ARGs, and MGEs in intensively fed livestock manure decreased, whereas those of ARGs, clinical ARGs, MRGs, and MGEs increased in grazing livestock manure. The synergy between MGEs mediated horizontal gene transfer and vertical gene transmission via host bacteria proliferation, which was the main driver that altered the abundance and diversity of ARGs, BRGs, and MRGs in livestock manure and compost. Additionally, tetQ, IS91, mdtF, and fabK were potential indicators for estimating the total abundance of clinical ARGs, BRGs, MRGs, and MGEs in livestock manure and compost. These findings suggest that grazing livestock manure can be directly discharged into the fields, whereas intensively fed livestock manure should be composted before returning to the field. IMPORTANCE The recent increase in the prevalence of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and metal resistance genes (MRGs) in livestock manure poses risks to human health. Composting is known to be a promising technology for reducing the abundance of resistance genes. This study investigated the differences and changes in the abundances of ARGs, BRGs, and MRGs between yak and cattle manure under grazing and intensive feeding patterns before and after composting. The results indicate that the feeding pattern significantly affected the abundances of resistance genes in livestock manure. Manure in intensive farming should be composted before being discharged into the field, while grazing livestock manure is not suitable for composting due to an increased number of resistance genes.
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Affiliation(s)
- Qingshan Fan
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jing Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Hairen Shi
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Shenghua Chang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Fujiang Hou
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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17
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Sun J, Yuan Y, Cai L, Zeng M, Li X, Yao F, Chen W, Huang Y, Shafiq M, Xie Q, Zhang Q, Wong N, Wang Z, Jiao X. Metagenomic evidence for antibiotics-driven co-evolution of microbial community, resistome and mobilome in hospital sewage. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121539. [PMID: 37019259 DOI: 10.1016/j.envpol.2023.121539] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/11/2023] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
Overconsumption of antibiotics is an immediate cause for the emergence of antimicrobial resistance (AMR) and antibiotic resistant bacteria (ARB), though its environmental impact remains inadequately clarified. There is an urgent need to dissect the complex links underpinning the dynamic co-evolution of ARB and their resistome and mobilome in hospital sewage. Metagenomic and bioinformatic methods were employed to analyze the microbial community, resistome and mobilome in hospital sewage, in relation to data on clinical antibiotic use collected from a tertiary-care hospital. In this study, resistome (1,568 antibiotic resistance genes, ARGs, corresponding to 29 antibiotic types/subtypes) and mobilome (247 types of mobile genetic elements, MGEs) were identified. Networks connecting co-occurring ARGs with MGEs encompass 176 nodes and 578 edges, in which over 19 types of ARGs had significant correlations with MGEs. Prescribed dosage and time-dependent antibiotic consumption were associated with the abundance and distributions of ARGs, and conjugative transfer of ARGs via MGEs. Variation partitioning analyses show that effects of conjugative transfer were most likely the main contributors to transient propagation and persistence of AMR. We have presented the first evidence supporting idea that use of clinical antibiotics is a potent driving force for the development of co-evolving resistome and mobilome, which in turn supports the growth and evolution of ARB in hospital sewage. The use of clinical antibiotics calls for greater attention in antibiotic stewardship and management.
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Affiliation(s)
- Jiayu Sun
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China; Guangdong Province Center for Disease Control and Prevention, Guangzhou, 511400, China
| | - Yumeng Yuan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Leshan Cai
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China; Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, 515041, China
| | - Mi Zeng
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Xin Li
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Fen Yao
- Department of Pharmacology, Shantou University Medical College, Shantou, 515041, China
| | - Weidong Chen
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Yuanchun Huang
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Muhammad Shafiq
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Qingdong Xie
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Qiaoxin Zhang
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Naikei Wong
- Department of Pharmacology, Shantou University Medical College, Shantou, 515041, China
| | - Zhen Wang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515041, China
| | - Xiaoyang Jiao
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China; Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, 515041, China.
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18
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Li Z, Wang X, Zhang B, Li B, Du H, Wu Z, Rashid A, Mensah CO, Lei M. Transmission mechanisms of antibiotic resistance genes in arsenic-contaminated soil under sulfamethoxazole stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 326:121488. [PMID: 36958659 DOI: 10.1016/j.envpol.2023.121488] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/02/2023] [Accepted: 03/21/2023] [Indexed: 06/18/2023]
Abstract
Numerous studies have revealed the spread mechanism of antibiotic resistance genes (ARGs) in single antibiotic-contaminated soils. However, the comprehensive impacts of heavy metals and antibiotics on ARGs and the underlying mechanisms are still unknown. Here, high-throughput quantitative PCR and high-throughput sequencing were used to investigate changes in ARGs and bacterial communities under various sulfamethoxazole (SMX) regimes (0, 1, 10, 50 mg kg-1) in arsenic (As) contaminated soils. The study found that the abundances of ARGs, mobile genetic elements (MGEs), and heavy metal resistance genes (HMRGs) significantly increased in the soil fortified at 10 and 50 mg kg-1 SMX concentrations. The ARGs abundance increased with the increase in the MGEs abundance. Many significant positive correlations between various ARGs subtypes and HMRGs subtypes were found. These results indicate that the HMRGs and MGEs positively contributed to the enrichment of ARGs in As-contaminated soils under SMX stress. Meanwhile, the abundance of copiotrophic (Actinobacteriota) reduced and oligotrophic (Gemmatimonadota) increased, indicating that the life history strategy of the community changed. In addition, Gemmatimonadota was positively correlated to ARGs, HMRGs, and MGEs, suggesting that Gemmatimonadota, which can cope with As and SMX stress, was the host for resistance genes in the soil. Finally, the study found that MGEs play a determinant role in ARGs proliferation due to the direct utilization of HGT, and the indirect effect for ARGs spread under a co-selection mechanism of ARGs and HMRGs, while the bacterial community showed indirect influences by altering environmental factors to act on MGEs. Collectively, this study revealed new insights into the mechanisms of resistance gene transmission under combined SMX and As contamination in soil ecosystems.
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Affiliation(s)
- Zhuoqing Li
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410128, PR China
| | - Xinqi Wang
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410128, PR China
| | - Beibei Zhang
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410128, PR China
| | - Bingyu Li
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410128, PR China
| | - Huihui Du
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410128, PR China
| | - Zhibin Wu
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410128, PR China
| | - Azhar Rashid
- Department of Environmental Sciences, The University of Haripur, Haripur, Pakistan
| | - Caleb Oppong Mensah
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410128, PR China
| | - Ming Lei
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410128, PR China.
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19
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Li B, Yan T. Metagenomic next generation sequencing for studying antibiotic resistance genes in the environment. ADVANCES IN APPLIED MICROBIOLOGY 2023; 123:41-89. [PMID: 37400174 DOI: 10.1016/bs.aambs.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Bacterial antimicrobial resistance (AMR) is a persisting and growing threat to human health. Characterization of antibiotic resistance genes (ARGs) in the environment is important to understand and control ARG-associated microbial risks. Numerous challenges exist in monitoring ARGs in the environment, due to the extraordinary diversity of ARGs, low abundance of ARGs with respect to the complex environmental microbiomes, difficulties in linking ARGs with bacterial hosts by molecular methods, difficulties in achieving quantification and high throughput simultaneously, difficulties in assessing mobility potential of ARGs, and difficulties in determining the specific AMR determinant genes. Advances in the next generation sequencing (NGS) technologies and related computational and bioinformatic tools are facilitating rapid identification and characterization ARGs in genomes and metagenomes from environmental samples. This chapter discusses NGS-based strategies, including amplicon-based sequencing, whole genome sequencing, bacterial population-targeted metagenome sequencing, metagenomic NGS, quantitative metagenomic sequencing, and functional/phenotypic metagenomic sequencing. Current bioinformatic tools for analyzing sequencing data for studying environmental ARGs are also discussed.
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Affiliation(s)
- Bo Li
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Tao Yan
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI, United States.
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20
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Gao FZ, He LY, Chen X, Chen JL, Yi X, He LX, Huang XY, Chen ZY, Bai H, Zhang M, Liu YS, Ying GG. Swine farm groundwater is a hidden hotspot for antibiotic-resistant pathogenic Acinetobacter. ISME COMMUNICATIONS 2023; 3:34. [PMID: 37081217 PMCID: PMC10119254 DOI: 10.1038/s43705-023-00240-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/28/2023] [Accepted: 04/05/2023] [Indexed: 04/22/2023]
Abstract
Acinetobacter is present in the livestock environment, but little is known about their antibiotic resistance and pathogenic species in the farm groundwater. Here we investigated antibiotic resistance of Acinetobacter in the swine farm groundwater (JZPG) and residential groundwater (JZG) of a swine farming village, in comparison to a nearby (3.5 km) non-farming village (WTG) using metagenomic and culture-based approaches. Results showed that the abundance of antibiotic resistome in some JZG and all JZPG (~3.4 copies/16S rRNA gene) was higher than that in WTG (~0.7 copies/16S rRNA gene), indicating the influence of farming activities on both groundwater types. Acinetobacter accounted for ~95.7% of the bacteria in JZG and JZPG, but only ~8.0% in WTG. They were potential hosts of ~95.6% of the resistome in farm affected groundwater, which includes 99 ARG subtypes against 23 antibiotic classes. These ARGs were associated with diverse intrinsic and acquired resistance mechanisms, and the predominant ARGs were tetracyclines and fluoroquinolones resistance genes. Metagenomic binning analysis elucidated that non-baumannii Acinetobacter including A. oleivorans, A. beijerinckii, A. seifertii, A. bereziniae and A. modestus might pose environmental risks because of multidrug resistance, pathogenicity and massive existence in the groundwater. Antibiotic susceptibility tests showed that the isolated strains were resistant to multiple antibiotics including sulfamethoxazole (resistance ratio: 96.2%), levofloxacin (42.5%), gatifloxacin (39.0%), ciprofloxacin (32.6%), tetracycline (32.0%), doxycycline (29.0%) and ampicillin (12.0%) as well as last-resort polymyxin B (31.7%), colistin (24.1%) and tigecycline (4.1%). The findings highlight potential prevalence of groundwater-borne antibiotic-resistant pathogenic Acinetobacter in the livestock environment.
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Affiliation(s)
- Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, PR China
- School of Environment, South China Normal University, University Town, Guangzhou, 510006, PR China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, PR China.
- School of Environment, South China Normal University, University Town, Guangzhou, 510006, PR China.
| | - Xin Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, PR China
| | - Jing-Liang Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, PR China
| | - Xinzhu Yi
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Lu-Xi He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, PR China
- School of Environment, South China Normal University, University Town, Guangzhou, 510006, PR China
| | - Xin-Yi Huang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, PR China
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Zi-Yin Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, PR China
- School of Environment, South China Normal University, University Town, Guangzhou, 510006, PR China
| | - Hong Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, PR China
- School of Environment, South China Normal University, University Town, Guangzhou, 510006, PR China
| | - Min Zhang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, PR China
- School of Environment, South China Normal University, University Town, Guangzhou, 510006, PR China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, PR China
- School of Environment, South China Normal University, University Town, Guangzhou, 510006, PR China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, PR China.
- School of Environment, South China Normal University, University Town, Guangzhou, 510006, PR China.
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21
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Hochhauser D, Millman A, Sorek R. The defense island repertoire of the Escherichia coli pan-genome. PLoS Genet 2023; 19:e1010694. [PMID: 37023146 PMCID: PMC10121019 DOI: 10.1371/journal.pgen.1010694] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/21/2023] [Accepted: 03/06/2023] [Indexed: 04/08/2023] Open
Abstract
It has become clear in recent years that anti-phage defense systems cluster non-randomly within bacterial genomes in so-called "defense islands". Despite serving as a valuable tool for the discovery of novel defense systems, the nature and distribution of defense islands themselves remain poorly understood. In this study, we comprehensively mapped the defense system repertoire of >1,300 strains of Escherichia coli, the most widely studied organism for phage-bacteria interactions. We found that defense systems are usually carried on mobile genetic elements including prophages, integrative conjugative elements and transposons, which preferentially integrate at several dozens of dedicated hotspots in the E. coli genome. Each mobile genetic element type has a preferred integration position but can carry a diverse variety of defensive cargo. On average, an E. coli genome has 4.7 hotspots occupied by defense system-containing mobile elements, with some strains possessing up to eight defensively occupied hotspots. Defense systems frequently co-localize with other systems on the same mobile genetic element, in agreement with the observed defense island phenomenon. Our data show that the overwhelming majority of the E. coli pan-immune system is carried on mobile genetic elements, explaining why the immune repertoire varies substantially between different strains of the same species.
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Affiliation(s)
- Dina Hochhauser
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Millman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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22
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Guajardo-Leiva S, Mendez KN, Meneses C, Díez B, Castro-Nallar E. A First Insight into the Microbial and Viral Communities of Comau Fjord—A Unique Human-Impacted Ecosystem in Patagonia (42∘ S). Microorganisms 2023; 11:microorganisms11040904. [PMID: 37110327 PMCID: PMC10143455 DOI: 10.3390/microorganisms11040904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
While progress has been made in surveying the oceans to understand microbial and viral communities, the coastal ocean and, specifically, estuarine waters, where the effects of anthropogenic activity are greatest, remain partially understudied. The coastal waters of Northern Patagonia are of interest since this region experiences high-density salmon farming as well as other disturbances such as maritime transport of humans and cargo. Here, we hypothesized that viral and microbial communities from the Comau Fjord would be distinct from those collected in global surveys yet would have the distinctive features of microbes from coastal and temperate regions. We further hypothesized that microbial communities will be functionally enriched in antibiotic resistance genes (ARGs) in general and in those related to salmon farming in particular. Here, the analysis of metagenomes and viromes obtained for three surface water sites showed that the structure of the microbial communities was distinct in comparison to global surveys such as the Tara Ocean, though their composition converges with that of cosmopolitan marine microbes belonging to Proteobacteria, Bacteroidetes, and Actinobacteria. Similarly, viral communities were also divergent in structure and composition but matched known viral members from North America and the southern oceans. Microbial communities were functionally enriched in ARGs dominated by beta-lactams and tetracyclines, bacitracin, and the group macrolide–lincosamide–streptogramin (MLS) but were not different from other communities from the South Atlantic, South Pacific, and Southern Oceans. Similarly, viral communities were characterized by exhibiting protein clusters similar to those described globally (Tara Oceans Virome); however, Comau Fjord viromes displayed up to 50% uniqueness in their protein content. Altogether, our results indicate that microbial and viral communities from the Comau Fjord are a reservoir of untapped diversity and that, given the increasing anthropogenic impacts in the region, they warrant further study, specifically regarding resilience and resistance against antimicrobials and hydrocarbons.
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Affiliation(s)
- Sergio Guajardo-Leiva
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
- Centro de Ecología Integrativa, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
| | - Katterinne N. Mendez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
| | - Claudio Meneses
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- ANID—Millennium Science Initiative Program—Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8370186, Chile
| | - Beatriz Díez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Center for Climate and Resilience Research (CR)2, Santiago 8370449, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago 7800003, Chile
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
- Centro de Ecología Integrativa, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
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23
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Cui H, Zhu D, Ding L, Wang Y, Su J, Duan G, Zhu Y. Co-occurrence of genes for antibiotic resistance and arsenic biotransformation in paddy soils. J Environ Sci (China) 2023; 125:701-711. [PMID: 36375951 DOI: 10.1016/j.jes.2022.02.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 06/16/2023]
Abstract
Paddy soils are potential hotspots of combined contamination with arsenic (As) and antibiotics, which may induce co-selection of antibiotic resistance genes (ARGs) and As biotransformation genes (ABGs), resulting in dissemination of antimicrobial resistance and modification in As biogeochemical cycling. So far, little information is available for these co-selection processes and specific patterns between ABGs and ARGs in paddy soils. Here, the 16S rRNA amplicon sequencing and high-throughput quantitative PCR and network analysis were employed to investigate the dynamic response of ABGs and ARGs to As stress and manure application. The results showed that As stress increased the abundance of ARGs and mobile genetic elements (MGEs), resulting in dissemination risk of antimicrobial resistance. Manure amendment increased the abundance of ABGs, enhanced As mobilization and methylation in paddy soil, posing risk to food safety. The frequency of the co-occurrence between ABGs and ARGs, the host bacteria carrying both ARGs and ABGs were increased by As or manure treatment, and remarkably boosted in soils amended with both As and manure. Multidrug resistance genes were found to have the preference to be co-selected with ABGs, which was one of the dominant co-occurring ARGs in all treatments, and manure amendment increased the frequency of Macrolide-Lincosamide-Streptogramin B resistance (MLSB) to co-occur with ABGs. Bacillus and Clostridium of Firmicutes are the dominant host bacteria carrying both ABGs and ARGs in paddy soils. This study would extend our understanding on the co-selection between genes for antibiotics and metals, also unveil the hidden environmental effects of combined pollution.
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Affiliation(s)
- Huiling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longjun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifei Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianqiang Su
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guilan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yongguan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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24
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Rovira P. Short-Term Impact of Oxytetracycline Administration on the Fecal Microbiome, Resistome and Virulome of Grazing Cattle. Antibiotics (Basel) 2023; 12:antibiotics12030470. [PMID: 36978337 PMCID: PMC10044027 DOI: 10.3390/antibiotics12030470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/14/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
Antimicrobial resistance (AMR) is an important public health concern around the world. Limited information exists about AMR in grasslands-based systems where antibiotics are seldom used in beef cattle. The present study investigated the impacts of oxytetracycline (OTC) on the microbiome, antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) in grazing steers with no previous exposure to antibiotic treatments. Four steers were injected with a single dose of OTC (TREAT), and four steers were kept as control (CONT). The effects of OTC on fecal microbiome, ARGs, and VFGs were assessed for 14 days using 16S rRNA sequencing and shotgun metagenomics. Alpha and beta microbiome diversities were significantly affected by OTC. Following treatment, less than 8% of bacterial genera had differential abundance between CONT and TREAT samples. Seven ARGs conferring resistance to tetracycline (tet32, tet40, tet44, tetO, tetQ, tetW, and tetW/N/W) increased their abundance in the post-TREAT samples compared to CONT samples. In addition, OTC use was associated with the enrichment of macrolide and lincosamide ARGs (mel and lnuC, respectively). The use of OTC had no significant effect on VFGs. In conclusion, OTC induced short-term alterations of the fecal microbiome and enrichment of ARGs in the feces of grazing beef cattle.
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Affiliation(s)
- Pablo Rovira
- Instituto Nacional de Investigación Agropecuaria (INIA Uruguay), Treinta y Tres 33000, Uruguay
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25
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Brinck JE, Lassen SB, Forouzandeh A, Pan T, Wang YZ, Monteiro A, Blavi L, Solà-Oriol D, Stein HH, Su JQ, Brandt KK. Impacts of dietary copper on the swine gut microbiome and antibiotic resistome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159609. [PMID: 36273560 DOI: 10.1016/j.scitotenv.2022.159609] [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: 07/23/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Restrictions on antibiotic growth promoters have prompted livestock producers to use alternative growth promoters, and dietary copper (Cu) supplementation is currently being widely used in pig production. However, elevated doses of dietary Cu constitute a risk for co-selection of antibiotic resistance and the risk may depend on the type of Cu-based feed additives being used. We here report the first controlled experiment investigating the impact of two contrasting Cu-based feed additives on the overall swine gut microbiome and antibiotic resistome. DNA was extracted from fecal samples (n = 96) collected at four time points during 116 days from 120 pigs allotted to three dietary treatments: control, divalent copper sulfate (CuSO4; 250 μg Cu g-1 feed), and monovalent copper oxide (Cu2O; 250 μg Cu g-1 feed). Bacterial community composition, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) were assessed, and bioavailable Cu ([Cu]bio) was determined using whole-cell bacterial bioreporters. Cu supplementation to feed increased total Cu concentrations ([Cu]total) and [Cu]bio in feces 8-10 fold and at least 670-1000 fold, respectively, but with no significant differences between the two Cu sources. The swine gut microbiome harbored highly abundant and diverse ARGs and MGEs irrespective of the treatments throughout the experiment. Microbiomes differed significantly between pig growth stages and tended to converge over time, but only minor changes in the bacterial community composition and resistome could be linked to Cu supplementation. A significant correlation between bacterial community composition (i.e., bacterial taxa present) and ARG prevalence patterns were observed by Procrustes analysis. Overall, results of the experiment did not provide evidence for Cu-induced co-selection of ARGs or MGEs even at a Cu concentration level exceeding the maximal permitted level for pig diets in the EU (25 to 150 μg Cu g-1 feed depending on pig age).
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Affiliation(s)
- Julius Emil Brinck
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Simon Bo Lassen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Beijing, China
| | - Asal Forouzandeh
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Animal Nutrition and Welfare Service (SNiBA), Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Ting Pan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yan-Zi Wang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | | | - Laia Blavi
- Animal Nutrition and Welfare Service (SNiBA), Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - David Solà-Oriol
- Animal Nutrition and Welfare Service (SNiBA), Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Hans H Stein
- Department of Animal Sciences, University of Illinois, Urbana 61801, USA
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Kristian K Brandt
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Beijing, China.
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26
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Chen X, Wang J, Pan C, Feng L, Chen S, Xie S. Metagenomic insights into the influence of thallium spill on sediment microbial community. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120660. [PMID: 36436665 DOI: 10.1016/j.envpol.2022.120660] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/03/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Thallium (Tl) is an extremely toxic metal. The release of Tl into the natural environment can pose a potential threat to organisms. So far, information about the impact of Tl on indigenous microorganisms is still very limited. In addition, there has been no report on how sudden Tl spill influences the structure and function of the microbial community. Therefore, this study explored the response of river sediment microbiome to a Tl spill. Residual T1 in the sediment significantly decreased bacterial community diversity. The increase in the abundance of Bacteroidetes in all Tl- impacted sediments suggested the advantage of Bacteroidetes to resist Tl pressure. Under T1 stress, microbial genes related to carbon fixation and gene cysH participating in assimilatory sulfate reduction were down-regulated, while genes related to nitrogen cycling were up-regulated. After T1 spill, increase in both metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) was observed in Tl-impacted sediments. Moreover, the abundance of MRGs and ARGs was significantly correlated with sediment Tl concentration, implying the positive effect of Tl contamination on the proliferation of these resistance genes. Procrustes analysis suggested a significant congruence between profiles of MRGs and bacterial communities. Through LEfSe and co-occurrence network analysis, Trichococcus, Polaromonas, and Arenimonas were identified to be tolerant and resistant to Tl pollution. The colocalization analysis of contigs indicated the co-effects of selection and transfer for MRGs/ARGs were important reasons for the increase in the microbial resistance in Tl-impacted sediments. This study added new insights into the effect of Tl spill on microbial community and highlighted the role of heavy metal spill in the increase of both heavy metal and antibiotic resistance genes.
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Affiliation(s)
- Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Ji Wang
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou, 510655, China
| | - Chaoyi Pan
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou, 510655, China
| | - Lishi Feng
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou, 510655, China
| | - Sili Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou, 510655, China.
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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27
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Lin Y, Zhang L, Wu J, Yang K. Wild birds-the sentinel of antibiotic resistance for urban river: Study on egrets and Jinjiang river in Chengdu, China. ENVIRONMENTAL RESEARCH 2023; 216:114566. [PMID: 36273597 DOI: 10.1016/j.envres.2022.114566] [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: 07/05/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic resistance has become a comprehensive and complicated environmental problem. It is of great importance to effectively determine the abundance of various antibiotic resistance genes (ARGs) in the environment. Here, we attempted to find a practical method for monitoring environmental antibiotic resistance. The results of culture-based analysis of antibiotic resistance and metagenomic sequencing indicate that egrets inhabiting along the urban river (Jinjiang River) can be used as the sentinel of environmental antibiotic resistance. The antibiotic resistance in the environment fluctuated with time, while that in the wild bird was relatively stable. The network analysis based on metagenomic sequencing data gave the co-occurrence pattern of ARGs. The overall situation of the antibiotic resistance in the river was determined by quantifying several module hub genes of the co-occurrence network in river sediments. The temporal and spatial distribution of ARGs in Jinjiang River is highly correlated with that of human gut-specific bacteriophage (crAssphage), which indicates that one main source of the antibiotic resistance in the river is likely to be municipal sewage. The mobility potential of ARGs varying among different niches suggests the transmission direction of antibiotic resistance in the environment.
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Affiliation(s)
- Yufei Lin
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China; Patent Examination Cooperation Sichuan Center of the Patent Office, Chengdu, 610213, China
| | - Lihua Zhang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Jinyong Wu
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Kun Yang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China.
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28
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Abstract
The prevalence and propagation of antimicrobial resistance (AMR) are serious global public health concerns. The large and the ever-increasing use of antibiotics in livestock is also considered a great concern. The extent of the similarity of acquired antibiotic resistance genes (ARGs) between humans and food animals and the driving factors underlying AMR transfer between them are not clear, although a link between ARGs in both hosts was proposed. To address this question, with swine and chicken as examples of food animals, we analyzed over 1,000 gut metagenomes of humans and food animals from over the world. A relatively high abundance and diversity of ARGs were observed in swine compared with those in humans as a whole. Commensal bacteria, particularly species from Clostridiales, contribute the most ARGs associated with mobile genetic elements (MGEs) and were found in both humans and food animals. Further studies demonstrate that overrepresented MGEs, namely, Tn4451/Tn4453 and TnAs3, are attributed mainly to the sharing between humans and food animals. A member of large resolvase family site-specific recombinases, TnpX, is found in Tn4451/Tn4453 which facilitates the insertions of the transient circular molecule. Although the variance in the transferability of ARGs in humans is higher than that in swine, a higher average transferability was observed in swine than that in humans. In conclusion, the potential antibiotic resistance hot spots with higher transferability in food animals observed in the present study emphasize the importance of surveillance for emerging resistance threats before they spread. IMPORTANCE Antimicrobial resistance (AMR) has proven to be a global public health concern. To conquer this increasingly worrying trend, an overarching, One Health approach has been used that brings together different sectors, but the fundamental knowledge of the relationship between humans, food animals, and their environments is not mature yet or is lacking in some aspect. With swine and chicken as examples of food animals, a large global data set of over 1,000 human and food animal gut metagenomes was analyzed with a focus on acquired antibiotic resistance genes (ARGs) associated with mobile genetic elements (MGEs) to answer this question. Outputs from this work open a new avenue to further our understanding of ARG transferability in food animals. It is a necessary milestone to better equip governmental agencies to monitor and pre-empt antibiotic resistance hot spots. This work will assist and give guidance on how to decipher other links within any One Health initiatives with expected positive feedback to human health.
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Xiong S, Wang K, Yan H, Hou D, Wang Y, Li M, Zhang D. Geographic patterns and determinants of antibiotic resistomes in coastal sediments across complex ecological gradients. Front Microbiol 2022; 13:922580. [PMID: 36406438 PMCID: PMC9669582 DOI: 10.3389/fmicb.2022.922580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/29/2022] [Indexed: 09/17/2023] Open
Abstract
Coastal areas are highly influenced by terrestrial runoffs and anthropogenic disturbances, commonly leading to ecological gradients from bay, nearshore, to offshore areas. Although the occurrence and distribution of sediment antibiotic resistome are explored in various coastal environments, little information is available regarding geographic patterns and determinants of coastal sediment antibiotic resistomes across ecological gradients at the regional scale. Here, using high-throughput quantitative PCR, we investigated the geographic patterns of 285 antibiotic resistance genes (ARGs) in coastal sediments across a ~ 200 km scale in the East China Sea. Sediment bacterial communities and physicochemical properties were characterized to identify the determinants of sediments antibiotic resistome. Higher richness and abundance of ARGs were detected in the bay samples compared with those in nearshore and offshore samples, and significant negative correlations between the richness and/or abundance of ARGs and the distance to coastline (DTC) were identified, whereas different types of ARGs showed inconsistency in their relationships with DTC. The composition of antibiotic resistome showed significant correlations with nutrition-related variables (including NH4 +-N, NO3 --N, and total phosphorus) and metals/metalloid (including As, Cu, Ni, and Zn), suggesting that terrestrial disturbances largely shape the antibiotic resistome. The Bipartite network showed strong associations between ARGs and mobile genetic elements (MGEs), and Partial Least Squares Path Modeling further revealed that terrestrial disturbance strength (as indicated by DTC) directly affected abiotic environmental conditions and bacterial community composition, and indirectly affected antibiotic resistome via MGEs. These findings provide insights into regional variability of sediment antibiotic resistome and its shaping path across complex ecological gradients, highlighting terrestrial disturbances as determinative forces in shaping coastal sediment antibiotic resistomes.
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Affiliation(s)
- Shangling Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Kai Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China
| | - Huizhen Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Dandi Hou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
| | - Yanting Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Meng Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China
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Lin D, Huang D, Zhang J, Yao Y, Zhang G, Ju F, Xu B, Wang M. Reduction of antibiotic resistance genes (ARGs) in swine manure-fertilized soil via fermentation broth from fruit and vegetable waste. ENVIRONMENTAL RESEARCH 2022; 214:113835. [PMID: 35810807 DOI: 10.1016/j.envres.2022.113835] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The issue of growing increase of antibiotic resistance genes (ARGs) in manure-fertilized soil needs urgently addressing. In this study, fermentation broth from fruit and vegetable waste was prepared to reduce ARG abundance in swine manure-fertilized soils. With a six-month field experiment, we found that swine manure-fertilized soil had significantly higher ARG abundance than soil applied with chemical fertilizer. As expected, the homemade fermentation broth significantly reduced ARG abundance in swine manure-fertilized soil, possibly through the decrease of abundance of Actinomyces, in which there was a 48.0%, 51.9%, and 66.7% decrease in the abundance of Nocardioides, Streptomyces, and Nonomuraea, respectively. With the bacteriostatic experiment, we observed that fermentation broth (5 mL/L) significantly inhibited the growth and metabolism in Actinomycetes spp. and Nocardioides sp., in terms of ATPase and PDH activity. These findings confirmed that the inhibition of Actinobacteria, some of the most dominant ARG hosts, was one of the main mechanisms responsible for the decrease in ARG abundance in fermentation broth-treated soil. This study provides field-scale evidence of a feasible strategy for controlling farmland ARG pollution, which is of utmost importance for soil health in the context of sustainable agriculture.
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Affiliation(s)
- Da Lin
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Dan Huang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Jinghan Zhang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Yanlai Yao
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Guoqing Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024, China
| | - Baile Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environment and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China.
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31
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Muurinen J, Muziasari WI, Hultman J, Pärnänen K, Narita V, Lyra C, Fadlillah LN, Rizki LP, Nurmi W, Tiedje JM, Dwiprahasto I, Hadi P, Virta MPJ. Antibiotic Resistomes and Microbiomes in the Surface Water along the Code River in Indonesia Reflect Drainage Basin Anthropogenic Activities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14994-15006. [PMID: 35775832 PMCID: PMC9631996 DOI: 10.1021/acs.est.2c01570] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Water and sanitation are important factors in the emergence of antimicrobial resistance in low- and middle-income countries. Drug residues, metals, and various wastes foster the spread of antibiotic resistance genes (ARGs) with the help of mobile genetic elements (MGEs), and therefore, rivers receiving contaminants and effluents from multiple sources are of special interest. We followed both the microbiome and resistome of the Code River in Indonesia from its pristine origin at the Merapi volcano through rural and then city areas to the coast of the Indian Ocean. We used a SmartChip quantitative PCR with 382 primer pairs for profiling the resistome and MGEs and 16S rRNA gene amplicon sequencing to analyze the bacterial communities. The community structure explained the resistome composition in rural areas, while the city sampling sites had lower bacterial diversity and more ARGs, which correlated with MGEs, suggesting increased mobility potential in response to pressures from human activities. Importantly, the vast majority of ARGs and MGEs were no longer detectable in marine waters at the ocean entrance. Our work provides information on the impact of different influents on river health as well as sheds light on how land use contributes to the river resistome and microbiome.
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Affiliation(s)
- Johanna Muurinen
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Windi I. Muziasari
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
- Resistomap
Oy, Viikinkaari 4, 00790 Helsinki, Finland
| | - Jenni Hultman
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Katariina Pärnänen
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Vanny Narita
- PT.
AmonRa, Jalan Panti Asuhan
37, 13330 Jakarta
Timur, Indonesia
| | - Christina Lyra
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Lintang N. Fadlillah
- Center
for Environmental Studies (PSLH), Universitas
Gadjah Mada, Jalan Kuningan, 55281 Yogyakarta, Indonesia
- Faculty
of Geography, Universitas Gadjah Mada, Jalan Kaliurang, 55281 Yogyakarta, Indonesia
| | - Ludhang P. Rizki
- Center
for Environmental Studies (PSLH), Universitas
Gadjah Mada, Jalan Kuningan, 55281 Yogyakarta, Indonesia
- Faculty of
Medicine, Universitas Gadjah Mada, Jalan Farmako, 55281 Yogyakarta, Indonesia
| | - William Nurmi
- Resistomap
Oy, Viikinkaari 4, 00790 Helsinki, Finland
| | - James M. Tiedje
- Center
for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, United States
| | - Iwan Dwiprahasto
- Faculty of
Medicine, Universitas Gadjah Mada, Jalan Farmako, 55281 Yogyakarta, Indonesia
| | - Pramono Hadi
- Center
for Environmental Studies (PSLH), Universitas
Gadjah Mada, Jalan Kuningan, 55281 Yogyakarta, Indonesia
- Faculty
of Geography, Universitas Gadjah Mada, Jalan Kaliurang, 55281 Yogyakarta, Indonesia
| | - Marko P. J. Virta
- Department
of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
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32
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Liu L, Zhang Y, Chen H, Teng Y. Fate of resistome components and characteristics of microbial communities in constructed wetlands and their receiving river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:157226. [PMID: 35809723 DOI: 10.1016/j.scitotenv.2022.157226] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Currently, most researches focus on that constructed wetlands (CWs) achieve desirable removal of antibiotics, antibiotic resistance genes (ARGs) and human pathogens. However, few studies have assessed the fate of resistome components, especially the behavior and cooccurrence of ARGs, mobile genetic elements (MGEs) and virulence factors (VFs). Therefore, characteristics of microbial communities (MCs) in CWs and their receiving rivers also deserve attention. These factors are critical to water ecological security. This study used two CWs to explore the fate of resistome components and characteristics of MCs in the CWs and their receiving river. Eleven samples were collected from the two CWs and their receiving river. High-throughput profiles of ARGs and microbial taxa in the samples were characterized. 31 ARG types consisting of 400 subtypes with total relative abundance 42.63-84.94× /Gb of sequence were detected in CWs, and 62.07-88.08× /Gb of sequence in river, evidencing that ARG pollution covered CWs and the river, and implying huge potential risks from ARGs. MGEs and VFs were detected, and tnpA, IS91 and intI1 were the three dominant MGEs, while Flagella. Type IV pili and peritrichous flagella were main VFs. Both CWs can remove ARGs, MGEs and VFs efficiently. However, some ARGs were difficult to remove, such as sul1 and sul2, and certain ARGs remained in the effluent of the CWs. The co-occurrence of ARGs, MGEs, and VFs implies the risk of antibiotic resistance and dissemination of ARGs. Eighty-five types of human pathogen were detected in the river samples, particularly Pseudomonas aeruginosa, Bordetella bronchiseptica, Aeromonas hydrophila and Helicobacter pylori. Correlation analysis indicated that MCs had significant effects on the profiles of ARGs in the water environment. This study reveals potential risks of the reuse of reclaimed water, and illustrates the removal ability of ARGs and related elements by CWs. This study will be helpful for monitoring and managing resistomes in water environments.
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Affiliation(s)
- Linmei Liu
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Yuxin Zhang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Haiyang Chen
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Yanguo Teng
- College of Water Sciences, Beijing Normal University, Beijing 100875, China.
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Han B, Ma L, Yu Q, Yang J, Su W, Hilal MG, Li X, Zhang S, Li H. The source, fate and prospect of antibiotic resistance genes in soil: A review. Front Microbiol 2022; 13:976657. [PMID: 36212863 PMCID: PMC9539525 DOI: 10.3389/fmicb.2022.976657] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022] Open
Abstract
Antibiotic resistance genes (ARGs), environmental pollutants of emerging concern, have posed a potential threat to the public health. Soil is one of the huge reservoirs and propagation hotspot of ARGs. To alleviate the potential risk of ARGs, it is necessary to figure out the source and fate of ARGs in the soil. This paper mainly reviewed recent studies on the association of ARGs with the microbiome and the transmission mechanism of ARGs in soil. The compositions and abundance of ARGs can be changed by modulating microbiome, soil physicochemical properties, such as pH and moisture. The relationships of ARGs with antibiotics, heavy metals, polycyclic aromatic hydrocarbons and pesticides were discussed in this review. Among the various factors mentioned above, microbial community structure, mobile genetic elements, pH and heavy metals have a relatively more important impact on ARGs profiles. Moreover, human health could be impacted by soil ARGs through plants and animals. Understanding the dynamic changes of ARGs with influencing factors promotes us to develop strategies for mitigating the occurrence and dissemination of ARGs to reduce health risks.
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Affiliation(s)
- Binghua Han
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - Li Ma
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
| | - Jiawei Yang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - Wanghong Su
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - Mian Gul Hilal
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - Xiaoshan Li
- Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Faculty of Basic Medical Sciences, Chongqing Three Gorges Medical College, Wanzhou, China
| | - Shiheng Zhang
- Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Faculty of Basic Medical Sciences, Chongqing Three Gorges Medical College, Wanzhou, China
- *Correspondence: Shiheng Zhang, ; Huan Li,
| | - Huan Li
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou, China
- *Correspondence: Shiheng Zhang, ; Huan Li,
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Zhang Y, Cheng D, Xie J, Zhang Y, Wan Y, Zhang Y, Shi X. Impacts of farmland application of antibiotic-contaminated manures on the occurrence of antibiotic residues and antibiotic resistance genes in soil: A meta-analysis study. CHEMOSPHERE 2022; 300:134529. [PMID: 35395269 DOI: 10.1016/j.chemosphere.2022.134529] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/23/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
A meta-analysis of 94 published studies was conducted to explore the impacts of farmland application of antibiotic-contaminated manures on antibiotic concentrations and ARG abundances in manure-amended soil. Forty-nine antibiotics were reported, in which chlortetracycline, oxytetracycline, doxycycline, tetracycline, enrofloxacin, ciprofloxacin and norfloxacin were the most prevalent and had relatively high concentrations. The responses of ARG and mobile genetic element (MGE) abundances to farmland application of antibiotic-contaminated manures varied considerably under different management strategies and environmental settings. On average, compared to unamended treatments, farmland application of antibiotic-contaminated manures significantly increased the total ARG and MGE abundances by 591% and 351%, respectively (P < 0.05). Of all the included ARG classes, the largest increase was found for sulfonamide resistance genes (1121%), followed by aminoglycoside (852%) and tetracycline (763%) resistance genes. Correlation analysis suggested that soil organic carbon (SOC) was significantly negatively correlated with antibiotic concentrations in manured soil (P < 0.05) due to the formation of covalent bonds and nonextractable residues. Soil silt content was significantly positively correlated with antibiotic concentration (P < 0.05), which was attributed to greater sorption capacities. The ARG abundances were significantly positively correlated with soil silt content, antibiotic concentrations, mean annual temperature, SOC, MGEs and soil pH (P < 0.05), suggesting that changes in these factors may shape the ARG profiles. Collectively, these findings advanced our understanding of the occurrence of antibiotics and ARGs in manure-amended soil and potential factors affecting them and will contribute to better management of these contaminants in future agricultural production.
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Affiliation(s)
- Yu Zhang
- College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Dengmiao Cheng
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Jun Xie
- College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Yuting Zhang
- College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Yu Wan
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing, 400074, China
| | - Yueqiang Zhang
- College of Resources and Environment, Southwest University, Chongqing, 400716, China
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing, 400716, China.
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35
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Qin Y, Guo Z, Huang H, Zhu L, Dong S, Zhu YG, Cui L, Huang Q. Widespread of Potential Pathogen-Derived Extracellular Vesicles Carrying Antibiotic Resistance Genes in Indoor Dust. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:5653-5663. [PMID: 35438977 DOI: 10.1021/acs.est.1c08654] [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] [Indexed: 06/14/2023]
Abstract
Extracellular vesicles (EVs) are newly recognized as important vectors for carrying and spreading antibiotic resistance genes (ARGs). However, the ARGs harbored by EVs in ambient environments and the transfer potential are still unclear. In this study, the prevalence of ARGs and mobile genetic elements (MGEs) in EVs and their microbial origins were studied in indoor dust from restaurants, kindergarten, dormitories, and vehicles. The amount of EVs ranged from 3.40 × 107 to 1.09 × 1011 particles/g dust. The length of EV-associated DNA fragments was between 21 bp and 9.7 kb. Metagenomic sequencing showed that a total of 241 antibiotic ARG subtypes encoding resistance to 16 common classes were detected in the EVs from all four fields. Multidrug, quinolone, and macrolide resistance genes were the dominant types. 15 ARG subtypes were exclusively carried and even enriched in EVs compared to the indoor microbiome. Moreover, several ARGs showed co-occurrence with MGEs. The EVs showed distinct taxonomic composition with their original dust microbiota. 30.23% of EV-associated DNA was predicted to originate from potential pathogens. Our results indicated the widespread of EVs carrying ARGs and virulence genes in daily life indoor dust, provided new insights into the status of extracellular DNA, and raised risk concerns on their gene transfer potential.
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Affiliation(s)
- Yifei Qin
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zihan Guo
- Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Haining Huang
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Liting Zhu
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sijun Dong
- Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Yong-Guan Zhu
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Li Cui
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qiansheng Huang
- Xiamen Key Laboratory of Indoor Air and Health, Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- National Basic Science Data Center, Beijing 100190, China
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36
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Evolution of the murine gut resistome following broad-spectrum antibiotic treatment. Nat Commun 2022; 13:2296. [PMID: 35484157 PMCID: PMC9051133 DOI: 10.1038/s41467-022-29919-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/06/2022] [Indexed: 12/29/2022] Open
Abstract
The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and timescales shaping this resistome remain elusive. Using an antibiotic cocktail administered to a murine model along with a longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire antimicrobial resistance genes (ARGs) after a single antibiotic course. While most of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Enterobacteriaceae, Enterococcaceae, and Lactobacillaceae families acquire resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotics in the corresponding metagenome-assembled genomes (MAGs) and trace their origins within each genome. Here we show that, while mobile genetic elements (MGEs), including bacteriophages and plasmids, contribute to the spread of ARGs, integrons represent key factors mediating AMR in the antibiotic-treated mice. Our findings suggest that a single course of antibiotics alone may act as the selective sweep driving ARG acquisition and incidence in gut commensals over a single mammalian lifespan. Antimicrobial resistance represents an ongoing silent pandemic. Here, de Nies et al. show that a single antibiotic treatment leads to resistance in bacteria such as Akkermansia muciniphila and that integrons play a key role in mediating this resistance.
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37
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Xie WY, Wang YT, Yuan J, Hong WD, Niu GQ, Zou X, Yang XP, Shen Q, Zhao FJ. Prevalent and highly mobile antibiotic resistance genes in commercial organic fertilizers. ENVIRONMENT INTERNATIONAL 2022; 162:107157. [PMID: 35219935 DOI: 10.1016/j.envint.2022.107157] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/19/2022] [Accepted: 02/19/2022] [Indexed: 06/14/2023]
Abstract
Compost-based organic fertilizers made from animal manures may contain high levels of antibiotic resistance genes (ARGs). However, the factors affecting the abundance and profile of ARGs in organic fertilizers remain unclear. We conducted a national-wide survey in China to investigate the effect of material type and composting process on ARG abundance in commercial organic fertilizers and quantified the contributions of bacterial composition and mobile genetic elements (MGEs) to the structuring of ARGs, using quantitative PCR and Illumina sequencing of 16S rRNA gene amplicons. The tetracycline, sulfonamide, aminoglycoside and macrolide resistance genes were present at high levels in all organic fertilizers. Seven ARGs that confer resistance to clinically important antibiotics, including three β-lactam resistance genes, three quinolone resistance genes and the colistin resistance gene mcr-1, were detected in 8 - 50% the compost samples, whereas the vancomycin resistance gene vanC was not detected. Raw material type had a significant (p < 0.001) effect on the ARG abundance, with composts made from animal feces except some cattle feces generally having higher loads of ARGs than those from non-animal raw materials. Composting process type showed no significant (p > 0.05) effect on ARG abundance in the organic fertilizers. MGEs exerted a greater influence on ARG composition than bacterial community, suggesting a strong mobility of ARGs in the organic fertilizers. Our study highlights the need to manage the risk of ARG dissemination from agricultural wastes.
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Affiliation(s)
- Wan-Ying Xie
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ya-Ting Wang
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Yuan
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen-Dan Hong
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guo-Qing Niu
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi Zou
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin-Ping Yang
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang-Jie Zhao
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Chen X, Wang J, Pan C, Feng L, Guo Q, Chen S, Xie S. Metagenomic analysis reveals the response of microbial community in river sediment to accidental antimony contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152484. [PMID: 34923019 DOI: 10.1016/j.scitotenv.2021.152484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
The mining of deposits containing metals like antimony (Sb) causes serious environmental issues that threaten human health and ecological systems. However, information on the effect of Sb on freshwater sediment microorganisms and the mechanism of microbial Sb resistance is still very limited. This was the first attempt to explore microbial communities in river sediments impacted by accidental Sb spill. Metagenomic analysis revealed the high relative abundance of Proteobacteria and Actinobacteria in all the studied river sediments, showing their advantage in resistance to Sb pollution. Under Sb stress, microbial functions related to DNA repair and ion transport were enhanced. Increase in heavy metal resistance genes (HMRGs), particularly Sb transport-related arsB gene, was observed at Sb spill-impacted sites. HMRGs were significantly correlated with ARGs and MGEs, and the abundant MGEs at Sb spill-impacted sites might contribute to the increase in HMRGs and ARGs via horizontal gene transfer. Deinococcus, Sphingopyxis and Paracoccus were identified as potential tolerant genera under Sb pressure and might be related to the transmission of HMRGs and ARGs. This study can add new insights towards the effect of accidental metal spill on sediment microbial community.
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Affiliation(s)
- Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Ji Wang
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China
| | - Chaoyi Pan
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China
| | - Lishi Feng
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China
| | - Qingwei Guo
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China
| | - Sili Chen
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou 510655, China.
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
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Zhao X, Wang Z, Xu T, Feng Z, Liu J, Luo L, He Y, Xiao Y, Peng H, Zhang Y, Deng O, Zhou W. The fate of antibiotic resistance genes and their influential factors during excess sludge composting in a full-scale plant. BIORESOURCE TECHNOLOGY 2021; 342:126049. [PMID: 34592456 DOI: 10.1016/j.biortech.2021.126049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
The alteration of antibiotic resistance genes (ARGs) during sludge composting has been less studied in a full-scale plant, causing the miss of practical implications for understanding/managing ARGs. Therefore, this study tracked the changes of ARGs and microbial communities in a full-scale plant engaged in excess sludge composting and then explored the key factors regulating ARGs through a series of analyses. After composting, the absolute and relative abundance of ARGs decreased by 91.90% and 66.57%, respectively. Additionally, pathway analysis showed that MGEs, composting physicochemical properties were the most vital factors directly influencing ARGs. Finally, network analysis indicated that Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the main hosts of ARGs. Based on these findings, it can be known that full-scale composting could reduce ARGs risk to an extent.
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Affiliation(s)
- Xin Zhao
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Zimu Wang
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Tao Xu
- Hangzhou Chunlai Technology Co., Ltd., Hangzhou 310052, PR China
| | - Zhihan Feng
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Jie Liu
- Chengdu Lvshan Biotechnology Co., Ltd., Chengdu 611139, PR China
| | - Ling Luo
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu 611130, PR China.
| | - Yan He
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Yinlong Xiao
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Hong Peng
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Yanzong Zhang
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Ouping Deng
- College of Resources, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Wei Zhou
- College of Resources, Sichuan Agricultural University, Chengdu 611130, PR China
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Fernández Rivas C, Porphyre T, Chase-Topping ME, Knapp CW, Williamson H, Barraud O, Tongue SC, Silva N, Currie C, Elsby DT, Hoyle DV. High Prevalence and Factors Associated With the Distribution of the Integron intI1 and intI2 Genes in Scottish Cattle Herds. Front Vet Sci 2021; 8:755833. [PMID: 34778436 PMCID: PMC8585936 DOI: 10.3389/fvets.2021.755833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
Integrons are genetic elements that capture and express antimicrobial resistance genes within arrays, facilitating horizontal spread of multiple drug resistance in a range of bacterial species. The aim of this study was to estimate prevalence for class 1, 2, and 3 integrons in Scottish cattle and examine whether spatial, seasonal or herd management factors influenced integron herd status. We used fecal samples collected from 108 Scottish cattle herds in a national, cross-sectional survey between 2014 and 2015, and screened fecal DNA extracts by multiplex PCR for the integrase genes intI1, intI2, and intI3. Herd-level prevalence was estimated [95% confidence interval (CI)] for intI1 as 76.9% (67.8-84.0%) and intI2 as 82.4% (73.9-88.6%). We did not detect intI3 in any of the herd samples tested. A regional effect was observed for intI1, highest in the North East (OR 11.5, 95% CI: 1.0-130.9, P = 0.05) and South East (OR 8.7, 95% CI: 1.1-20.9, P = 0.04), lowest in the Highlands. A generalized linear mixed model was used to test for potential associations between herd status and cattle management, soil type and regional livestock density variables. Within the final multivariable model, factors associated with herd positivity for intI1 included spring season of the year (OR 6.3, 95% CI: 1.1-36.4, P = 0.04) and watering cattle from a natural spring source (OR 4.4, 95% CI: 1.3-14.8, P = 0.017), and cattle being housed at the time of sampling for intI2 (OR 75.0, 95% CI: 10.4-540.5, P < 0.001). This study provides baseline estimates for integron prevalence in Scottish cattle and identifies factors that may be associated with carriage that warrant future investigation.
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Affiliation(s)
- Cristina Fernández Rivas
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom
| | - Thibaud Porphyre
- Laboratoire de Biométrie et Biologie Évolutive, UMR5558, CNRS, VetAgro Sup, Université de Lyon, Villeurbanne Cedex, France
| | - Margo E Chase-Topping
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom
| | - Charles W Knapp
- Centre for Water, Environment, Sustainability and Public Health, Department of Civil & Environmental Engineering, University of Strathclyde, Glasgow, United Kingdom
| | - Helen Williamson
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom
| | - Olivier Barraud
- INSERM, CHU Limoges, UMR1092, Université de Limoges, Limoges, France
| | - Sue C Tongue
- Epidemiology Research Unit, Scotland's Rural College (SRUC), An Lòchran, Inverness Campus, Inverness, United Kingdom
| | - Nuno Silva
- Moredun Research Institute, Edinburgh, United Kingdom
| | - Carol Currie
- Moredun Research Institute, Edinburgh, United Kingdom
| | - Derek T Elsby
- Environmental Research Institute, University of the Highlands and Islands, Thurso, United Kingdom
| | - Deborah V Hoyle
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland, United Kingdom
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Lu J, Zhang X, Wang C, Li M, Chen J, Xiong J. Responses of sediment resistome, virulence factors and potential pathogens to decades of antibiotics pollution in a shrimp aquafarm. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 794:148760. [PMID: 34323773 DOI: 10.1016/j.scitotenv.2021.148760] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/18/2021] [Accepted: 06/26/2021] [Indexed: 05/28/2023]
Abstract
Aquaculture ecosystem has become a hotspot of antibiotics resistance genes (ARGs) dissemination, owing to the abuse of prophylactic antibiotics. However, it is still unclear how and to what extent ARGs respond to the increasing antibiotic pollution, a trend as expected and as has occurred. Herein, a significant sediment antibiotic pollution gradient was detected along a drainage ditch after decades of shrimp aquaculture. The increasing antibiotic pollution evidently promoted the diversities and tailored the community structures of ARGs, mobile genetic elements (MGEs), virulence factors and pathogens. The profiles of ARGs and MGEs were directly altered by the concentrations of terramycin and sulphadimidine. By contrast, virulence factors were primarily affected by nutrient variables in sediment. The pathogens potentially hosted diverse virulence factors and ARGs. More than half of the detected ARGs subtypes non-linearly responded to increasing antibiotic pollution, as supported by significant tipping points. However, we screened seven antibiotic concentration discriminatory ARGs that could serve as independent variable for quantitatively diagnosing total antibiotic concentration. Co-occurrence analysis depicted that notorious aquaculture pathogens of Vibrio harveyi and V. parahaemolyticus potentially hosted ARGs that confer resistance to multiple antibiotics, while priority pathogens for humankind, e.g., Helicobacter pylori and Staphylococcus aureus, could have harbored redundant virulence factors. Collectively, the significant tipping points and antibiotic concentration-discriminatory ARGs may translate into warning index and diagnostic approach for diagnosing antibiotic pollution. Our findings provided novel insights into the interplay among ARGs, MGEs, pathogens, virulence factors and geochemical variables under the scenario of increasing antibiotic pollution.
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Affiliation(s)
- Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Xinxu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Chaohua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China.
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Danofloxacin Treatment Alters the Diversity and Resistome Profile of Gut Microbiota in Calves. Microorganisms 2021; 9:microorganisms9102023. [PMID: 34683343 PMCID: PMC8538188 DOI: 10.3390/microorganisms9102023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/18/2021] [Accepted: 09/23/2021] [Indexed: 12/25/2022] Open
Abstract
Fluoroquinolones, such as danofloxacin, are used to control bovine respiratory disease complex in beef cattle; however, little is known about their effects on gut microbiota and resistome. The objectives were to evaluate the effect of subcutaneously administered danofloxacin on gut microbiota and resistome, and the composition of Campylobacter in calves. Twenty calves were injected with a single dose of danofloxacin, and ten calves were kept as a control. The effects of danofloxacin on microbiota and the resistome were assessed using 16S rRNA sequencing, quantitative real-time PCR, and metagenomic Hi-C ProxiMeta. Alpha and beta diversities were significantly different (p < 0.05) between pre-and post-treatment samples, and the compositions of several bacterial taxa shifted. The patterns of association between the compositions of Campylobacter and other genera were affected by danofloxacin. Antimicrobial resistance genes (ARGs) conferring resistance to five antibiotics were identified with their respective reservoirs. Following the treatment, some ARGs (e.g., ant9, tet40, tetW) increased in frequencies and host ranges, suggesting initiation of horizontal gene transfer, and new ARGs (aac6, ermF, tetL, tetX) were detected in the post-treatment samples. In conclusion, danofloxacin induced alterations of gut microbiota and selection and enrichment of resistance genes even against antibiotics that are unrelated to danofloxacin.
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Guo X, Akram S, Stedtfeld R, Johnson M, Chabrelie A, Yin D, Mitchell J. Distribution of antimicrobial resistance across the overall environment of dairy farms - A case study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147489. [PMID: 34134353 DOI: 10.1016/j.scitotenv.2021.147489] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 05/12/2023]
Abstract
The environmental implications of antimicrobial resistance arising from food animal farm practice are still a knowledge gap. This study investigates the fate and transport of antimicrobial resistance genes related to the use of antibiotics on a dairy farm in Michigan. Manure, soil, animal feed, animal drinking water, surface and groundwater samples were taken and the abundance of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) were subsequently measured using high parallel quantitative PCR targeting 136 genes. The total abundance and detected numbers of ARGs were found to be highest in the stagnant lagoon. Up to 44 ARG subtypes with high abundance were found in drinking water in pen which was very close to those in manure compost. The ARGs pattern clustered by soil depth although they were treated by different manure. ARGs and MGEs were detected in surface and groundwater surrounded by dairy farmlands, with the occurrence of carbapenemase-encoding KPC gene in two waters, which may be due to transport of ARGs through runoff or other sources. Overall, the results of the study suggest high prevalence of ARGs both inside and outside the animal raising area and their potential contribution to environmental ARGs.
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Affiliation(s)
- Xueping Guo
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
| | - Sina Akram
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Robert Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Martina Johnson
- Division of Public Health, College of Medicine, Michigan State University, East University, MI 48824, USA
| | - Alexandre Chabrelie
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Daqiang Yin
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Jade Mitchell
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA.
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Mohammadi-Aragh MK, Stokes CE. Assessing Class 1 Integron Presence in Poultry Litter Amended with Wood Biochar and Wood Vinegar. Curr Microbiol 2021; 78:3733-3740. [PMID: 34459936 DOI: 10.1007/s00284-021-02640-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 08/20/2021] [Indexed: 11/26/2022]
Abstract
Class 1 integrons are mobile genetic elements that facilitate the spread of antibiotic resistance genes among bacteria. The use of prophylactic antibiotics has resulted in the rise of antibiotic resistance genes accumulating in a wide range of settings, including poultry houses and the agricultural fields where poultry litter is applied as a fertilizer. Biochar and wood vinegar are forest products wastes that have generated increasing attention as additives to agricultural soils. The objectives of this study were to observe the prevalence of class 1 integrons in poultry litter blended with biochar and wood vinegar over time and to verify a modified class 1 integron screening assay. Poultry litter blends were sampled and screened for class 1 integrons using polymerase chain reaction, and 80 products, 79 of which showed positive, were sent for DNA sequencing. The GenBank® BLAST database was used to verify the presence of the class 1 integron-integrase gene (intI1). There was no change in prevalence over time in poultry litter blends. Out of 79 PCR products that were intI1 positive, 78 showed at least 95% sequence identity to intI1 encoding bacteria and 64 showed at least 97% sequence identity. This indicates that this method was effective for conducting baseline surveillance of class 1 integrons in poultry litter and poultry litter-blended biochar and/or wood vinegar. Most significantly, class 1 integron prevalence did not decrease over time, further supporting the recalcitrance of these elements and the need for improved monitoring systems.
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Affiliation(s)
- Maryam K Mohammadi-Aragh
- Department of Agricultural and Biological Engineering, Mississippi State University, Starkville, MS, USA.
| | - C Elizabeth Stokes
- Department of Sustainable Bioproducts, Mississippi State University, Starkville, MS, USA
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Nguyen AQ, Vu HP, Nguyen LN, Wang Q, Djordjevic SP, Donner E, Yin H, Nghiem LD. Monitoring antibiotic resistance genes in wastewater treatment: Current strategies and future challenges. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 783:146964. [PMID: 33866168 DOI: 10.1016/j.scitotenv.2021.146964] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 04/01/2021] [Accepted: 04/01/2021] [Indexed: 05/29/2023]
Abstract
Antimicrobial resistance (AMR) is a growing threat to human and animal health. Progress in molecular biology has revealed new and significant challenges for AMR mitigation given the immense diversity of antibiotic resistance genes (ARGs), the complexity of ARG transfer, and the broad range of omnipresent factors contributing to AMR. Municipal, hospital and abattoir wastewater are collected and treated in wastewater treatment plants (WWTPs), where the presence of diverse selection pressures together with a highly concentrated consortium of pathogenic/commensal microbes create favourable conditions for the transfer of ARGs and proliferation of antibiotic resistant bacteria (ARB). The rapid emergence of antibiotic resistant pathogens of clinical and veterinary significance over the past 80 years has re-defined the role of WWTPs as a focal point in the fight against AMR. By reviewing the occurrence of ARGs in wastewater and sludge and the current technologies used to quantify ARGs and identify ARB, this paper provides a research roadmap to address existing challenges in AMR control via wastewater treatment. Wastewater treatment is a double-edged sword that can act as either a pathway for AMR spread or as a barrier to reduce the environmental release of anthropogenic AMR. State of the art ARB identification technologies, such as metagenomic sequencing and fluorescence-activated cell sorting, have enriched ARG/ARB databases, unveiled keystone species in AMR networks, and improved the resolution of AMR dissemination models. Data and information provided in this review highlight significant knowledge gaps. These include inconsistencies in ARG reporting units, lack of ARG/ARB monitoring surrogates, lack of a standardised protocol for determining ARG removal via wastewater treatments, and the inability to support appropriate risk assessment. This is due to a lack of standard monitoring targets and agreed threshold values, and paucity of information on the ARG-pathogen host relationship and risk management. These research gaps need to be addressed and research findings need to be transformed into practical guidance for WWTP operators to enable effective progress towards mitigating the evolution and spread of AMR.
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Affiliation(s)
- Anh Q Nguyen
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Hang P Vu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Luong N Nguyen
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Steven P Djordjevic
- Institute of Infection, Immunity and Innovation, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Huabing Yin
- School of Engineering, University of Glasgow, Glasgow G12 8LT, UK
| | - Long D Nghiem
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia; Institute of Environmental Sciences, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam.
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Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces. Proc Natl Acad Sci U S A 2021; 118:2024464118. [PMID: 34161269 DOI: 10.1073/pnas.2024464118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While it is well recognized that the environmental resistome is global, diverse, and augmented by human activities, it has been difficult to assess risk because of the inability to culture many environmental organisms, and it is difficult to evaluate risk from current sequence-based environmental methods. The four most important criteria to determine risk are whether the antibiotic-resistance genes (ARGs) are a complete, potentially functional complement; if they are linked with other resistances; whether they are mobile; and the identity of their host. Long-read sequencing fills this important gap between culture and short sequence-based methods. To address these criteria, we collected feces from a ceftiofur-treated cow, enriched the samples in the presence of antibiotics to favor ARG functionality, and sequenced long reads using Nanopore and PacBio technologies. Multidrug-resistance genes comprised 58% of resistome abundance, but only 0.8% of them were plasmid associated; fluroquinolone-, aminoglycoside-, macrolide-lincosamide-streptogramin (MLS)-, and β-lactam-resistance genes accounted for 2.7 to 12.3% of resistome abundance but with 19 to 78% located on plasmids. A variety of plasmid types were assembled, some of which share low similarity to plasmids in current databases. Enterobacteriaceae were dominant hosts of antibiotic-resistant plasmids; physical linkage of extended-spectrum β-lactamase genes (CTX-M, TEM, CMY, and CARB) was largely found with aminoglycoside-, MLS-, tetracycline-, trimethoprim-, phenicol-, sulfonamide-, and mercury-resistance genes. A draft circular chromosome of Vagococcus lutrae was assembled; it carries MLS-, tetracycline- (including tetM and tetL on an integrative conjugative element), and trimethoprim-resistance genes flanked by many transposase genes and insertion sequences, implying that they remain transferrable.
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47
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Wang J, Gu J, Wang X, Song Z, Dai X, Guo H, Yu J, Zhao W, Lei L. Enhanced removal of antibiotic resistance genes and mobile genetic elements during swine manure composting inoculated with mature compost. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:125135. [PMID: 33858100 DOI: 10.1016/j.jhazmat.2021.125135] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/08/2021] [Accepted: 01/10/2021] [Indexed: 06/12/2023]
Abstract
Livestock manure is a major source of antibiotic resistance genes (ARGs) that enter the environment. This study assessed the effects of inoculation with mature compost (MC) on the fates of ARGs and the bacterial community during swine manure composting. The results showed that MC prolonged the thermophilic period and promoted the decomposition of organic matter, which was due to the rapid growth and reproduction of thermophilic bacteria (Bacillus, Thermobifida, and Thermobacillus). MC significantly reduced the relative abundances of ARGs (1.02 logs) and mobile genetic elements (MGEs) (1.70 logs) after composting, especially sulfanilamide resistance genes. The total ARGs removal rate was 1.11 times higher in MC than the control. Redundancy analysis and structural equation modeling showed that horizontal gene transfer mediated by MGEs (ISCR1 and intI1) was the main direct factor related to the changes in ARGs during composting, whereas the C/N ratio and pH were the two most important indirect factors. Network analysis showed that members of Firmicutes comprising Romboutsia, Clostridisensu_stricto_1, and Terrisporobacter were the main bacterial hosts of ARGs and MGEs. MC reduced the risk of ARGs transmission by decreasing the abundances of bacterial hosts. Thus, MC is a promising strategy for reducing the proliferation risk of ARGs.
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Affiliation(s)
- Jia Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zilin Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoxia Dai
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Honghong Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Yu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenya Zhao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Liusheng Lei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
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Qian X, Gunturu S, Guo J, Chai B, Cole JR, Gu J, Tiedje JM. Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems. MICROBIOME 2021; 9:108. [PMID: 33990222 PMCID: PMC8122544 DOI: 10.1186/s40168-021-01047-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/11/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic approach and datasets with well-characterized metadata to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively. RESULTS High diversity (242 ARG subtypes) and abundance (0.184-0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance and efflux pump the dominant class and mechanism. Ten regulatory genes were identified and they accounted for 13-35% of resistome abundances in soils, among them arlR, cpxR, ompR, vanR, and vanS were dominant and observed in all studied soils. We identified 55 non-regulatory ARGs shared by all 26 soil metagenomes of the three ecosystems, which accounted for more than 81% of non-regulatory resistome abundance. Proteobacteria, Firmicutes, and Actinobacteria were primary ARG hosts, 7 of 10 most abundant ARGs were found in all of them. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition. CONCLUSIONS Our results identify candidate background ARGs (shared in all 26 soils), classify ARG hosts, quantify resistance classes, and provide quantitative and sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future. Video abstract.
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Affiliation(s)
- Xun Qian
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Santosh Gunturu
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - Jiarong Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - James R. Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
| | - Jie Gu
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - James M. Tiedje
- Interdisciplinary Research Center for Soil Microbial Ecology and Land Sustainable Productivity in Dry Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824 USA
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Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil. mBio 2021; 12:mBio.00798-21. [PMID: 33975936 PMCID: PMC8262906 DOI: 10.1128/mbio.00798-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In agricultural settings, microbes and antimicrobial resistance genes (ARGs) have the potential to be transferred across diverse environments and ecosystems. The consequences of these microbial transfers are unclear and understudied. On dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. To determine the extent of both taxonomic and resistance similarity during these transitions, we collected fresh manure, manure from pits, and field soil across 15 different dairy farms for three consecutive seasons. We used a combination of shotgun metagenomic sequencing and functional metagenomics to quantitatively interrogate taxonomic and ARG compositional variation on farms. We found that as the microbiome transitions from fresh dairy cow manure to manure pits, microbial taxonomic compositions and resistance profiles experience distinct restructuring, including decreases in alpha diversity and shifts in specific ARG abundances that potentially correspond to fresh manure going from a gut-structured community to an environment-structured community. Further, we did not find evidence of shared microbial community or a transfer of ARGs between manure and field soil microbiomes. Our results suggest that fresh manure experiences a compositional change in manure pits during storage and that the storage of manure in manure pits does not result in a depletion of ARGs. We did not find evidence of taxonomic or ARG restructuring of soil microbiota with the application of manure to field soils, as soil communities remained resilient to manure-induced perturbation.
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Comparison of bacterial communities and antibiotic resistance genes in oxidation ditches and membrane bioreactors. Sci Rep 2021; 11:8955. [PMID: 33903636 PMCID: PMC8076264 DOI: 10.1038/s41598-021-88335-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/08/2021] [Indexed: 12/23/2022] Open
Abstract
Oxidation ditches (ODs) and membrane bioreactors (MBRs) are widely used in wastewater treatment plants (WWTPs) with bacteria and antibiotic resistance genes (ARGs) running through the whole system. In this study, metagenomic sequencing was used to compare the bacterial communities and ARGs in the OD and MBR systems, which received the same influent in a WWTP located in Xinjiang, China. The results showed that the removal efficiency of pollutants by the MBR process was better than that by the OD process. The composition and the relative abundance of bacteria in activated sludge were similar at the phylum and genus levels and were not affected by process type. Multidrug, fluoroquinolones and peptides were the main ARG types for the two processes, with macB being the main ARG subtype, and the relative abundance of ARG subtypes in MBR effluent was much higher than that in the OD effluent. The mobile genetic elements (MGEs) in the activated sludge were mainly transposons (tnpA) and insertion sequences (ISs; IS91). These results provide a theoretical basis for process selection and controlling the spread of ARGs.
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