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Congilosi JL, Aga DS. Review on the fate of antimicrobials, antimicrobial resistance genes, and other micropollutants in manure during enhanced anaerobic digestion and composting. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:123634. [PMID: 33153790 DOI: 10.1016/j.jhazmat.2020.123634] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/01/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
While manure has been used as nutrient-rich fertilizer for centuries, anaerobic digestion (AD) of manure has only been recognized recently as a promising renewable energy source for producing methane-rich biogas. Various forms of AD have been evaluated for the removal of manure contaminants, such as antimicrobials, antimicrobial resistance genes (ARGs), hormones, and pesticides that pose risks to human health and the environment. Increasing demand for cleaner energy prompts examination of the fate of manure contaminants in conventional and advanced AD techniques. This review reveals that removal of contaminants differs based on type (e.g. antimicrobials vs hormones) or class (e.g. tetracyclines vs sulfonamides) of chemicals being treated. Increasingly, pre-treatment techniques are incorporated into AD systems to enhance biogas production and degrade manure contaminants. For instance, activated carbon with microwave pretreatment removed 87-95% of ARGs. Advanced anaerobic digestion and solid-state anaerobic digestion reduced various ARGs associated with sulfonamides, macrolides, and tetracyclines. Further, total hormone reduction improved using high-temperature pretreatment prior to mesophilic AD. Finally, several studies revealed partial removal of antimicrobials and ARGs during managed composting. Although AD can independently decrease manure contaminants prior to use as fertilizer, augmenting AD with composting and other physical treatment processes can further enhance their removal.
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Affiliation(s)
- Jena L Congilosi
- Chemistry Department, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Diana S Aga
- Chemistry Department, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA.
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He Y, Zhou X, Chen Z, Deng X, Gehring A, Ou H, Zhang L, Shi X. PRAP: Pan Resistome analysis pipeline. BMC Bioinformatics 2020; 21:20. [PMID: 31941435 PMCID: PMC6964052 DOI: 10.1186/s12859-019-3335-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/23/2019] [Indexed: 01/01/2023] Open
Abstract
Background Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species. Therefore, a pan-genome approach to analyzing resistomes is necessary for thoroughly characterizing patterns of ARGs distribution within particular pathogen populations. Software tools are readily available for either ARGs identification or pan-genome analysis, but few exist to combine the two functions. Results We developed Pan Resistome Analysis Pipeline (PRAP) for the rapid identification of antibiotic resistance genes from various formats of whole genome sequences based on the CARD or ResFinder databases. Detailed annotations were used to analyze pan-resistome features and characterize distributions of ARGs. The contribution of different alleles to antibiotic resistance was predicted by a random forest classifier. Results of analysis were presented in browsable files along with a variety of visualization options. We demonstrated the performance of PRAP by analyzing the genomes of 26 Salmonella enterica isolates from Shanghai, China. Conclusions PRAP was effective for identifying ARGs and visualizing pan-resistome features, therefore facilitating pan-genomic investigation of ARGs. This tool has the ability to further excavate potential relationships between antibiotic resistance genes and their phenotypic traits.
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Affiliation(s)
- Yichen He
- Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xiujuan Zhou
- Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Ziyan Chen
- Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xiangyu Deng
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA, 30223, USA
| | - Andrew Gehring
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA
| | - Hongyu Ou
- Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Lida Zhang
- Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xianming Shi
- Department of Food Science and Technology, MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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Archaea, from obscurity to superhero microbes: 40 years of surprises and critical biological insights. Emerg Top Life Sci 2018; 2:453-458. [PMID: 33525822 PMCID: PMC7288999 DOI: 10.1042/etls20180022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/25/2018] [Accepted: 09/28/2018] [Indexed: 11/17/2022]
Abstract
This issue of Emerging Topics in the Life Sciences highlights current areas of research in the field of archaeal biology and the following introductory editorial sets the stage by considering some of the key developments over the last four decades since the initial identification of the archaea as a unique form of life. Emerging topics from this vibrant and rapidly expanding field of research are considered and detailed further in the articles within this issue.
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