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Sha G, Wu Z, Chen T, Zhang G, Shen J, Zhao X, Wang L. Mechanisms for more efficient antibiotics and antibiotic resistance genes removal during industrialized treatment of over 200 tons of tylosin and spectinomycin mycelial dregs by integrated meta-omics. BIORESOURCE TECHNOLOGY 2024; 401:130715. [PMID: 38641304 DOI: 10.1016/j.biortech.2024.130715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/29/2024] [Accepted: 04/17/2024] [Indexed: 04/21/2024]
Abstract
To mitigate the environmental risks posed by the accumulation of antibiotic mycelial dregs (AMDs), this study first attempted over 200 tons of mass production fermentation (MP) using tylosin and spectinomycin mycelial dregs alongside pilot-scale fermentation (PS) for comparison, utilizing the integrated-omics and qPCR approaches. Co-fermentation results showed that both antibiotics were effectively removed in all treatments, with an average removal rate of 92%. Antibiotic resistance gene (ARG)-related metabolic pathways showed that rapid degradation of antibiotics was associated with enzymes that inactivate macrolides and aminoglycosides (e.g., K06979, K07027, K05593). Interestingly, MP fermentations with optimized conditions had more efficient ARGs removal because homogenization permitted faster microbial succession, with more stable removal of antibiotic resistant bacteria and mobile genetic elements. Moreover, Bacillus reached 75% and secreted antioxidant enzymes that might inhibit horizontal gene transfer of ARGs. The findings confirmed the advantages of MP fermentation and provided a scientific basis for other AMDs.
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Affiliation(s)
- Guomeng Sha
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan 250033, China
| | - Zhengwen Wu
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan 250033, China
| | - Tong Chen
- Neutralization and Environmental Protection of Lukang Industrial Group Company, Jining, Shandong 272000, China
| | - Guangen Zhang
- Neutralization and Environmental Protection of Lukang Industrial Group Company, Jining, Shandong 272000, China
| | - Jianguo Shen
- Neutralization and Environmental Protection of Lukang Industrial Group Company, Jining, Shandong 272000, China
| | - Xiaogang Zhao
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan 250033, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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Huang B, Lv X, Zheng H, Yu H, Zhang Y, Zhang C, Wang J. Microbial organic fertilizer prepared by co-composting of Trichoderma dregs mitigates dissemination of resistance, virulence genes, and bacterial pathogens in soil and rhizosphere. ENVIRONMENTAL RESEARCH 2024; 241:117718. [PMID: 37995998 DOI: 10.1016/j.envres.2023.117718] [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: 10/08/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
The use of manure, mycelium dregs and other waste as organic fertilizer is the main source of antibiotic resistance genes (ARGs) and pathogens in farmland. Composting of waste may effectively remove ARGs and pathogens. However, the profiles and drivers of changes in metal resistance genes (MRGs), biocide resistance genes (BRGs), and virulence genes (VGs) in soil-crop rhizosphere systems after compost application remain largely unknown. Here, we prepared two kinds of microbial organic fertilizers (MOF) by using Trichoderma dregs (TDs) and organic fertilizer mixing method (MOF1) and TDs co-composting method (MOF2). The effects of different types and doses of MOF on resistance genes, VGs and pathogens in soil-rhizosphere system and their potential mechanisms were studied. The results showed that co-composting of TDs promoted the decomposition of organic carbon and decreased the absolute abundance of ARGs and mobile genetic elements (MGEs) by 53.4-65.0%. MOF1 application significantly increased the abundance and diversity of soil ARGs, BRGs, and VGs, while low and medium doses of MOF2 significantly decreased their abundance and diversity in soil and rhizosphere. Patterns of positive co-occurrence between MGEs and VGs/MRGs/BRGs/ARGs were observed through statistical analysis and gene arrangements. ARGs/MRGs reductions in MOF2 soil were directly driven by weakened horizontal gene transfer triggered by MGEs. Furthermore, MOF2 reduced soil BRGs/VGs levels by shifting bacterial communities (e.g., reduced bacterial host) or improving soil property. Our study provided new insights into the rational use of waste to minimize the spread of resistomes and VGs in soil.
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Affiliation(s)
- Bin Huang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Xiaolin Lv
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Hao Zheng
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Haitao Yu
- Institute of Plant Protection, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Yu Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Chengsheng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Jie Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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Feng M, Liu Y, Yang L, Li Z. Antibiotics and antibiotic resistance gene dynamics in the composting of antibiotic fermentation waste - A review. BIORESOURCE TECHNOLOGY 2023; 390:129861. [PMID: 37863331 DOI: 10.1016/j.biortech.2023.129861] [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: 07/16/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/22/2023]
Abstract
Fate of antibiotics and antibiotic resistance genes (ARGs) during composting of antibiotic fermentation waste (AFW) is a major concern. This review article focuses on recent literature published on this subject. The key findings are that antibiotics can be removed effectively during AFW composting, with higher temperatures, appropriate bulking agents, and suitable pretreatments improving their degradation. ARGs dynamics during composting are related to bacteria and mobile genetic elements (MGEs). Higher temperatures, suitable bulking agents and an appropriate C/N ratio (30:1) lead to more efficient removal of ARGs/MGEs by shaping the bacterial composition. Keeping materials dry (moisture less than 30%) and maintaining pH stable around 7.5 after composting could inhibit the rebound of ARGs. Overall, safer utilization of AFW can be realized by optimizing composting conditions. However, further removal of antibiotics and ARGs at low levels, degradation mechanism of antibiotics, and spread mechanism of ARGs during AFW composting require further investigation.
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Affiliation(s)
- Minmin Feng
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Yuanwang Liu
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China.
| | - Lie Yang
- Wuhan University of Technology, School of Resources & Environmental Engineering, Wuhan 430070, China
| | - Zhaojun Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Liu Y, Feng M, Johansen A, Cheng D, Xue J, Feng Y, Fan S, Li Z. Composting reduces the risks of antibiotic resistance genes in maize seeds posed by gentamicin fermentation waste. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 870:161785. [PMID: 36736399 DOI: 10.1016/j.scitotenv.2023.161785] [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: 11/15/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Using high-throughput quantitative PCR and next generation sequencing, the impact of land application of raw and composted gentamicin fermentation waste (GFW) on antibiotic resistance genes (ARGs) in maize seeds was studied in a three-year field trial. The raw and composted GFW changed both the bacterial community composition and the ARGs diversity in the maize seeds compared to non-amended controls and chemical fertilizer. The abundance of ARGs after raw GFW amendment was significantly higher than other treatments because of a high abundance of aadA1, qacEdeltal and aph(2')-Id-02; probably induced by gentamicin selection pressure in maize tissues. Meanwhile, the potential host of these three ARGs, pathogenic bacteria Tenacibaculum, also increased significantly in maize seeds after the application of raw GFW. But our result proved that composting could weaken the risk posed by GFW. We further reveal that the key biotic driver for shaping the ARG profiles in maize seeds is bacterial community followed by heavy metal resistance genes, and ARGs are more likely located on bacterial chromosomes. Our findings provide new insight into ARGs dispersal mechanism in maize seeds after long-term GFW application, demonstrate the potential benefits of composting the GFW to reduce risks as well as the potential efficient management method to GFW.
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Affiliation(s)
- Yuanwang Liu
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China; Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Minmin Feng
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Anders Johansen
- Department of Environmental Science, Faculty of Technical Sciences, Aarhus University, Roskilde 4000, Denmark
| | - Dengmiao Cheng
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan 523808, China
| | - Jianming Xue
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; Scion, Private Bag 29237, Christchurch 8440, New Zealand
| | - Yao Feng
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuanghu Fan
- College of Life Science, Langfang Normal University, Langfang 065000, China
| | - Zhaojun Li
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, China-New Zealand Joint Laboratory for Soil Molecular Ecology, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Fatimazahra S, Latifa M, Laila S, Monsif K. Review of hospital effluents: special emphasis on characterization, impact, and treatment of pollutants and antibiotic resistance. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:393. [PMID: 36780024 PMCID: PMC9923651 DOI: 10.1007/s10661-023-11002-5] [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: 09/23/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Health care institutions generate large volumes of liquid effluents from specific activities related to healthcare, analysis, and research. Their direct discharge into the environment has various negative effects on aquatic environments and human health, due to their high organic matter charges and the presence of various emerging contaminants such as disinfectants, drugs, bacteria, viruses, and parasites. Moreover, hospital effluents, by carrying antibiotics, contribute to the development of antibiotic-resistant microorganisms in the environment. This resistance has become a global issue that manifests itself variously in different countries, causing the transmission of different infections. In this respect, an effort is provided to protect water resources by current treatment methods that imply physical-chemical processes such as adsorption and advanced oxidation processes, biological processes such as activated sludge and membrane bioreactors and other hybrid techniques. The purpose of this review is to improve the knowledge on the composition and impact of hospital wastewater on man and the environment, highlighting the different treatment techniques appropriate to this type of disposal before discharge into the environment.
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Affiliation(s)
- Sayerh Fatimazahra
- Process Engineering and Environment Laboratory, Faculty of Science and Technology of Mohammedia, Hassan II University, Casablanca, Morocco
| | - Mouhir Latifa
- Process Engineering and Environment Laboratory, Faculty of Science and Technology of Mohammedia, Hassan II University, Casablanca, Morocco
| | - Saafadi Laila
- Process Engineering and Environment Laboratory, Faculty of Science and Technology of Mohammedia, Hassan II University, Casablanca, Morocco
| | - Khazraji Monsif
- Process Engineering and Environment Laboratory, Faculty of Science and Technology of Mohammedia, Hassan II University, Casablanca, Morocco
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Elmes K, Heywood A, Huang Z, Gavryushkin A. A fast lasso-based method for inferring higher-order interactions. PLoS Comput Biol 2022; 18:e1010730. [PMID: 36580499 PMCID: PMC9833600 DOI: 10.1371/journal.pcbi.1010730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/11/2023] [Accepted: 11/11/2022] [Indexed: 12/30/2022] Open
Abstract
Large-scale genotype-phenotype screens provide a wealth of data for identifying molecular alterations associated with a phenotype. Epistatic effects play an important role in such association studies. For example, siRNA perturbation screens can be used to identify combinatorial gene-silencing effects. In bacteria, epistasis has practical consequences in determining antimicrobial resistance as the genetic background of a strain plays an important role in determining resistance. Recently developed tools scale to human exome-wide screens for pairwise interactions, but none to date have included the possibility of three-way interactions. Expanding upon recent state-of-the-art methods, we make a number of improvements to the performance on large-scale data, making consideration of three-way interactions possible. We demonstrate our proposed method, Pint, on both simulated and real data sets, including antibiotic resistance testing and siRNA perturbation screens. Pint outperforms known methods in simulated data, and identifies a number of biologically plausible gene effects in both the antibiotic and siRNA models. For example, we have identified a combination of known tumour suppressor genes that is predicted (using Pint) to cause a significant increase in cell proliferation.
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Affiliation(s)
- Kieran Elmes
- Department of Computer Science, University of Otago, Dunedin, New Zealand
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
| | - Astra Heywood
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Zhiyi Huang
- Department of Computer Science, University of Otago, Dunedin, New Zealand
| | - Alex Gavryushkin
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
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Zuo X, Suo P. Distribution of typical antibiotic resistance genes in underlying surface sediments from urban commercial public squares and their potential hosts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155730. [PMID: 35525346 DOI: 10.1016/j.scitotenv.2022.155730] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Increasing attention has been paid to antibiotic resistance genes (ARGs) in environments. However, no available literature could be found on ARGs contamination in urban underlying surface sediments. In this study, sediments from commercial public squares around Nanjing (China) were selected for the investigation of target ARGs distribution, showing that intracellular ARGs (iARGs) in particles were the dominant with their relative abundances in descending order of 4.82 × 10-2 copies/16S rRNA (<0.063 mm), 4.18 × 10-2 copies/16S rRNA (0.063-0.125 mm), 3.70 × 10-2 copies/16S rRNA (0.25-0.5 mm), 3.44 × 10-2 copies/16S rRNA (0.5-1 mm), 3.20 × 10-2 copies/16S rRNA (0.125-0.25 mm) and 9.53 × 10-3 copies/16S rRNA (1-2 mm), which was different with that of extracellular ARGs (eARGs). The influence of street sweeping on ARGs levels indicated that the species and relative abundances for both iARGs and eARGs in sediments from different sites were not consistent with the corresponding population densities. The correlation between ARGs and dominant bacterial communities implied that both Firmicutes and Bacteroidetes were positively correlated with ARGs (P < 0.01). The role of solar UV disinfection demonstrated that UV irradiation could inactivate antibiotic resistance bacteria (ARB) slightly with 0.5-1.0 log reduction, implying a considerable risk of ARB after solar irradiation. Our results suggested that it would need the more effective sweeping modes for the cleaning of small particles (<0.25 mm) and the higher disinfection to ARGs potential hosts (like Firmicutes and Blastocatella).
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Affiliation(s)
- XiaoJun Zuo
- Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing 210044, China.
| | - PengCheng Suo
- Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing 210044, China
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