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Zhang Z, Zhu X, Su JQ, Zhu S, Zhang L, Ju F. Metagenomic Insights into Potential Impacts of Antibacterial Biosynthesis and Anthropogenic Activity on Nationwide Soil Resistome. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134677. [PMID: 38795484 DOI: 10.1016/j.jhazmat.2024.134677] [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: 02/16/2024] [Revised: 04/25/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
The presence of antibiotic resistance genes (ARGs) in soils has received extensive attention regarding its impacts on environmental, animal, and human systems under One Health. However, the health risks of soil ARGs and microbial determinants of soil resistomes remain poorly understood. Here, a nationwide metagenomic investigation of ARGs in cropland and forest soils in China was conducted. The findings indicated that the abundance and richness of high-risk (i.e., mobilizable, pathogen-carriable and clinically relevant) ARGs in cropland soils were 25.7 times and 8.4 times higher, respectively, compared to those identified in forest soils, suggesting the contribution of agricultural practices to the elevated risk level of soil resistomes. The biosynthetic potential of antibacterials best explained the total ARG abundance (Mantel's r = 0.52, p < 0.001) when compared with environmental variables and anthropogenic disturbance. Both microbial producers' self-resistance and antagonistic interactions contributed to the ARG abundance, of which self-resistance ARGs account for 14.1 %- 35.1 % in abundance. With the increased biosynthetic potential of antibacterials, the antagonistic interactions within the microbial community were greatly enhanced, leading to a significant increase in ARG abundance. Overall, these findings advance our understanding of the emergence and dissemination of soil ARGs and provide critical implications for the risk control of soil resistomes.
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Affiliation(s)
- Zhiguo Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China; Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, Zhejiang Province, China; Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou 310030, Zhejiang Province, China
| | - Xinyu Zhu
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, Zhejiang Province, China; Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou 310030, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China; Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Sixi Zhu
- College of Eco-environment Engineering, Guizhou Minzu University, Guiyang 550025, China
| | - Lu Zhang
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, Zhejiang Province, China; Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou 310030, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China; Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China.
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Xu R, Zhang L, Huang FY, Zhu YG, Zhao Y, Guo H. Geogenic high arsenic elevates the groundwater antibiotic resistomes: A blind spot of resistance in Anthropocene. WATER RESEARCH 2024; 260:121957. [PMID: 38941868 DOI: 10.1016/j.watres.2024.121957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/08/2024] [Accepted: 06/17/2024] [Indexed: 06/30/2024]
Abstract
Metals/metalloids, being ubiquitous in the environment, can function as a co-selective pressure on antibiotic resistance genes (ARGs) threatening human health. However, the effect of geogenic arsenic (As) on groundwater antibiotic resistomes and their health risks remain largely unknown. Here, we systematically analyzed bacterial communities, pathogenic bacteria, antibiotic resistomes, and in-situ multidrug-resistant isolates with the assessment of the health risk of ARGs and the pathogenicity of their hosts in high As groundwater from the Hetao basin, Northwestern China. We found that long-term geogenic As exposure shifted the assembly of resistomes and resulted in a high abundance and diversity of ARGs in groundwater. Significantly positive associations among As, As cycling genes, ARGs, and mobile genetic elements (MGEs) revealed by network and pathway analyses, together with genetic evidence of As-tolerant multidrug-resistant isolates by whole genomic sequencing, robustly indicate the geogenic As-induced co-selection for antibiotic resistance in groundwater. Variance partitioning analysis further confirmed the determinative role of geogenic As in groundwater resistomes, with As species and As cycling genes as the core abiotic and biotic drivers, respectively. More seriously, geogenic As accelerated the prevalence of high-risk ARGs and multidrug-resistant bacteria. Our findings highlight the significance of geogenic As-induced co-selection for antibiotic resistance in groundwater and the hidden role of geogenic metals/metalloids in increasing antibiotic resistance. This study provides a basis for groundwater management of both high As and ARGs for human health.
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Affiliation(s)
- Rui Xu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Beijing), Beijing 100083, China; Key Laboratory of Groundwater Conservation of MWR & School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Lingzhi Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Beijing), Beijing 100083, China; Key Laboratory of Groundwater Conservation of MWR & School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Fu-Yi Huang
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yong-Guan Zhu
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yi Zhao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Beijing), Beijing 100083, China; Key Laboratory of Groundwater Conservation of MWR & School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China.
| | - Huaming Guo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Beijing), Beijing 100083, China; Key Laboratory of Groundwater Conservation of MWR & School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China.
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Jaafarzadeh N, Talepour N. Microplastics as carriers of antibiotic resistance genes and pathogens in municipal solid waste (MSW) landfill leachate and soil: a review. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2024; 22:1-12. [PMID: 38887766 PMCID: PMC11180052 DOI: 10.1007/s40201-023-00879-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/25/2023] [Indexed: 06/20/2024]
Abstract
Landfill leachate contains antibiotic resistance genes (ARGs) and microplastics (MPs), making it an important reservoir. However, little research has been conducted on how ARGs are enriched on MPs and how the presence of MPs affects pathogens and ARGs in leachates and soil. MPs possess the capacity to establish unique bacterial populations and assimilate contaminants from their immediate surroundings, generating a potential environment conducive to the growth of disease-causing microorganisms and antibiotic resistance genes (ARGs), thereby exerting selection pressure. Through a comprehensive analysis of scientific literature, we have carried out a practical assessment of this topic. The gathering of pollutants and the formation of dense bacterial communities on microplastics create advantageous circumstances for an increased frequency of ARG transfer and evolution. Additional investigations are necessary to acquire a more profound comprehension of how pathogens and ARGs are enriched, transported, and transferred on microplastics. This research is essential for evaluating the health risks associated with human exposure to these pollutants. Graphical Abstract
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Affiliation(s)
- Neamatollah Jaafarzadeh
- Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Environmental Health Engineering, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Nastaran Talepour
- Department of Environmental Health Engineering, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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4
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Wu J, Hu Y, Perlin MH, Danko D, Lu J, Oliveira M, Werner J, Zambrano MM, Sierra MA, Osuolale OO, Łabaj P, Rascovan N, Hazrin-Chong NH, Jang S, Suzuki H, Nieto-Caballero M, Prithiviraj B, Lee PKH, Chmielarczyk A, Różańska A, Zhao Y, Wang L, Mason CE, Shi T. Landscape of global urban environmental resistome and its association with local socioeconomic and medical status. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1292-1301. [PMID: 38489008 DOI: 10.1007/s11427-023-2504-1] [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: 10/10/2023] [Accepted: 12/06/2023] [Indexed: 03/17/2024]
Abstract
Antimicrobial resistance (AMR) poses a critical threat to global health and development, with environmental factors-particularly in urban areas-contributing significantly to the spread of antibiotic resistance genes (ARGs). However, most research to date has been conducted at a local level, leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments. To address this issue, we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples, which were collected by the MetaSUB International Consortium involving diverse urban environments in 60 cities of 27 countries, utilizing a deep-learning based methodology. Our findings demonstrated the strong geographical specificity of urban environmental resistome, and their correlation with various local socioeconomic and medical conditions. We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters (BGCs) across different countries, and discovered that the urban environment represents a rich source of novel antibiotics. Our study provides a comprehensive overview of the global urban environmental resistome, and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.
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Affiliation(s)
- Jun Wu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yige Hu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, 40292, USA
| | - David Danko
- Weill Cornell Medicine, New York, 10065, USA
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, 10065, USA
| | - Jun Lu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Manuela Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4050-290, Portugal
- Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, 4200-465, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, 4050-290, Portugal
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Wächterstraße 76, 72074, Tübingen, Germany
| | | | - Maria A Sierra
- Weill Cornell Medicine, New York, 10065, USA
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, 10065, USA
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, 340271, Nigeria
| | - Paweł Łabaj
- Maopolska Centre of Biotechnology, Jagiellonian University, Kraków, 30-005, Poland
| | - Nicolás Rascovan
- Aix-Marseille Université, Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, 83041, France
| | - Nur Hazlin Hazrin-Chong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia UKM, 43600, Bangi, Selangor, Malaysia
| | - Soojin Jang
- Institut Pasteur Korea, Seoul, 13488, Republic of Korea
| | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
| | - Marina Nieto-Caballero
- Civil, Environmental and Architectural Department, University of Colorado at Boulder, Boulder, 80303, USA
| | | | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, 999077, China
| | - Agnieszka Chmielarczyk
- Department of Microbiology, Faculty of Medicine, Jagiellonian University, Krakow, 30-005, Poland
| | - Anna Różańska
- Department of Microbiology, Faculty of Medicine, Jagiellonian University, Krakow, 30-005, Poland
| | - Yongxiang Zhao
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning, 530021, China.
| | - Lan Wang
- College of Architecture and Urban Planning, Tongji University, Shanghai, 200092, China.
| | - Christopher E Mason
- Weill Cornell Medicine, New York, 10065, USA.
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, 10065, USA.
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
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Chen J, Ren J, Wu Y, Hu N, Zhao F, Zhang L. Wet adhesive hydrogels based on niobium carbide for experimental research of oral mucosal impairment. RSC Adv 2024; 14:12935-12946. [PMID: 38650683 PMCID: PMC11033722 DOI: 10.1039/d4ra01352b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/13/2024] [Indexed: 04/25/2024] Open
Abstract
Oral mucosal impairment is a prevalent oral disease that frequently causes pain for patients. Conventional treatments have limited effectiveness and can cause adverse reactions. Furthermore, the moist and dynamic nature of the oral mucosal environment makes persistent adherence of conventional materials challenging, which can affect treatment efficacy. In this study, we investigated the potential of a NbC/TA-GelMA hydrogel system, where niobium carbide (NbC) and tannic acid (TA) were added to gelatin methacryloyl (GelMA), for repairing oral mucosal impairment. The wet adhesion properties of NbC/TA-GelMA hydrogels were confirmed by the inclusion of TA with a catechol-rich group. In addition, the photothermal effect of NbC/TA-GelMA hydrogel under near-infrared light, synergizing with TA, provided sustained antibacterial action. Furthermore, the NbC/TA-GelMA hydrogel effectively healed damaged oral mucosa of rats.
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Affiliation(s)
- Jiayuan Chen
- First Affiliated Hospital of Harbin Medical University, College of Stomatology, Harbin Medical University No. 143 Yiman Street, Nangang District Harbin 150001 China
| | - Junyu Ren
- Oral Implant Center, Second Affiliated Hospital of Harbin Medical University, Harbin Medical University Harbin Heilongjiang China
| | - Yingjie Wu
- Key Laboratory of Microsystems and Microstructures Manufacturing (Ministry of Education), School of Medicine and Health, Harbin Institute of Technology No. 92 XiDaZhi Street Harbin 150001 China
| | - Narisu Hu
- Oral Implant Center, Second Affiliated Hospital of Harbin Medical University, Harbin Medical University Harbin Heilongjiang China
| | - Fang Zhao
- Department of Dentistry, Second Affiliated Hospital of Harbin Medical University, Harbin Medical University Harbin Heilongjiang China
| | - Lin Zhang
- First Affiliated Hospital of Harbin Medical University, College of Stomatology, Harbin Medical University No. 143 Yiman Street, Nangang District Harbin 150001 China
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6
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Zhang S, Cui L, Zhao Y, Xie H, Song M, Wu H, Hu Z, Liang S, Zhang J. The critical role of microplastics in the fate and transformation of sulfamethoxazole and antibiotic resistance genes within vertical subsurface-flow constructed wetlands. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133222. [PMID: 38101014 DOI: 10.1016/j.jhazmat.2023.133222] [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: 09/20/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Constructed wetlands (CWs) are reservoirs of microplastics (MPs) in the environment. However, knowledge about the impact of MPs on antibiotic removal and the fate of antibiotic resistance genes (ARGs) is limited. We focused on sulfamethoxazole (SMX) as a representative compound to examine the effects of MPs on SMX removal and the proliferation and dissemination of two SMX-related ARGs (sul1 and sul2) in vertical subsurface-flow CW (VFCW) microcosm. The presence of MPs in the substrate was found to enhance the proliferation of microorganisms owing to the large specific surface area of the MPs and the release of dissolved organic carbon (DOC) on MP surfaces, which resulted in a high SMX removal ranging from 97.80 % to 99.80 %. However, the presence of MPs promoted microbial interactions and the horizontal gene transfer (HGT) of ARGs, which led to a significant increase in the abundances of sul1 and sul2 of 68.47 % and 17.20 %, respectively. It is thus imperative to implement rigorous monitoring strategies for MPs to mitigate their potential ecological hazards.
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Affiliation(s)
- Shiwen Zhang
- Environmental Research Institute, Shandong University, Binhai Road 72, Qingdao 266237, China
| | - Lele Cui
- Environmental Research Institute, Shandong University, Binhai Road 72, Qingdao 266237, China
| | - Yanhui Zhao
- School of Environmental Science and Engineering, Shandong University, Binhai Road 72, Qingdao 266237, China
| | - Huijun Xie
- Environmental Research Institute, Shandong University, Binhai Road 72, Qingdao 266237, China.
| | - Maoyong Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Haiming Wu
- School of Environmental Science and Engineering, Shandong University, Binhai Road 72, Qingdao 266237, China
| | - Zhen Hu
- School of Environmental Science and Engineering, Shandong University, Binhai Road 72, Qingdao 266237, China
| | - Shuang Liang
- School of Environmental Science and Engineering, Shandong University, Binhai Road 72, Qingdao 266237, China
| | - Jian Zhang
- School of Environmental Science and Engineering, Shandong University, Binhai Road 72, Qingdao 266237, China; College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, China
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Gunarathne V, Phillips AJ, Zanoletti A, Rajapaksha AU, Vithanage M, Di Maria F, Pivato A, Korzeniewska E, Bontempi E. Environmental pitfalls and associated human health risks and ecological impacts from landfill leachate contaminants: Current evidence, recommended interventions and future directions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169026. [PMID: 38056656 DOI: 10.1016/j.scitotenv.2023.169026] [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: 08/03/2023] [Revised: 10/17/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
The improper management of solid waste, particularly the dumping of untreated municipal solid waste, poses a growing global challenge in both developed and developing nations. The generation of leachate is one of the significant issues that arise from this practice, and it can have harmful impacts on both the environment and public health. This paper presents an overview of the primary waste types that generate landfill leachate and their characteristics. This includes examining the distribution of waste types in landfills globally and how they have changed over time, which can provide valuable insights into potential pollutants in a given area and their trends. With a lack of specific regulations and growing concerns regarding environmental and health impacts, the paper also focuses on emerging contaminants. Furthermore, the environmental and ecological impacts of leachate, along with associated health risks, are analyzed. The potential applications of landfill leachate, suggested interventions and future directions are also discussed in the manuscript. Finally, this work addresses future research directions in landfill leachate studies, with attention, for the first time to the potentialities that artificial intelligence can offer for landfill leachate management, studies, and applications.
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Affiliation(s)
- Viraj Gunarathne
- Ecosphere Resilience Research Centre, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, CO 10250, Sri Lanka; University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water- and Waste-Management, Laboratory of Soil- and Groundwater-Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany
| | - Ankur J Phillips
- Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India
| | - Alessandra Zanoletti
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy
| | - Anushka Upamali Rajapaksha
- Ecosphere Resilience Research Centre, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, CO 10250, Sri Lanka; Instrument Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
| | - Meththika Vithanage
- Ecosphere Resilience Research Centre, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, CO 10250, Sri Lanka
| | - Francesco Di Maria
- LAR5 Laboratory, Dipartimento di Ingegneria, University of Perugia, via G. Duranti 93, 06125 Perugia, Italy
| | - Alberto Pivato
- DICEA - Department of Civil, Environmental and Architectural Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-719 Olsztyn, Poland
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy.
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Han Z, Luan X, Feng H, Deng Y, Yang M, Zhang Y. Metagenomic insights into microorganisms and antibiotic resistance genes of waste antibiotic fermentation residues along production, storage and treatment processes. J Environ Sci (China) 2024; 136:45-55. [PMID: 37923454 DOI: 10.1016/j.jes.2022.10.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2023]
Abstract
Antibiotic fermentation residue (AFR) is nutrient-rich solid waste generated from fermentative antibiotic production process. It is demonstrated that AFR contains high-concentration of remaining antibiotics, and thus may promote antibiotic resistance development in receiving environment or feeding farmed animals. However, the dominate microorganisms and antibiotic resistance genes (ARGs) in AFRs have not been adequately explored, hampering understanding on the potential antibiotic resistance risk development caused by AFRs. Herein, seven kinds of representative AFRs along their production, storage, and treatment processes were collected, and multiple methods including amplicon sequencing, metagenomic sequencing, and bioinformatic approaches were adopted to explore the biological characteristics of AFRs. As expected, antibiotic fermentation producer was found as the predominant species in raw AFRs, which were collected at the outlet of fermentation tanks. However, except for producer species, more environment-derived species persisted in stored AFRs, which were temporarily stored at a semi-open space. Lactobacillus genus, classified as Firmicutes phylum and Bacilli class, became predominant bacterial taxa in stored AFRs, which might attribute to its tolerance to high concentration of antibiotics. Results from metagenomic sequencing together with assembly and binning approaches showed that these newly-colonizing species (e.g., Lactobacillus genus) tended to carry ARGs conferring resistance to the remaining antibiotic. However, after thermal treatment, remaining antibiotic could be efficiently removed from AFRs, and microorganisms together with DNA could be strongly destroyed. In sum, the main risk from the AFRs was the remaining antibiotic, while environment-derived bacteria which tolerate extreme environment, survived in ARFs with high content antibiotics, and may carry ARGs. Thus, hydrothermal or other harmless treatment technologies are recommended to remove antibiotic content and inactivate bacteria before recycling of AFRs in pharmaceutical industry.
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Affiliation(s)
- Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Luan
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Haodi Feng
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yanqin Deng
- Wuhan Agricultural Inspection Center, Wuhan 430016, China
| | - Min Yang
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Zhang L, Adyari B, Hou L, Yang X, Gad M, Wang Y, Ma C, Sun Q, Tang Q, Zhang Y, Yu CP, Hu A. Mass-immigration shapes the antibiotic resistome of wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168193. [PMID: 37914134 DOI: 10.1016/j.scitotenv.2023.168193] [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: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
Wastewater treatment plants (WWTPs) are the hotspots for the spread of antibiotic resistance genes (ARGs) into the environment. Nevertheless, a comprehensive assessment of the city-level and short-term daily (inter-day) variations of ARG profiles in the whole process (influent-INF, activated sludge-AS and effluent-EF) of WWTPs is still lacking. Here, 285 ARGs and ten mobile gene elements were monitored in seven WWTPs in Xiamen for seven days via high-throughput qPCR. The average daily load of ARGs to WWTPs was about 1.32 × 1020 copies/d, and a total of 1.56 × 1018 copies/d was discharged to the environment across the entire city. Stochastic processes were the main force determining the assembly of ARG communities during sampling campaign, with their relative importance ranked in the order of INF > EFF > AS. There're little daily variations in ARG richness, abundance, β-diversity composition as well as assembly mechanisms. The results of SourceTracker, variation partitioning analysis, and hierarchical partitioning analysis indicated that bacteria and ARGs from upstream treatment processes played an increasingly dominant role in shaping ARG communities in AS and EFF, respectively, suggesting the importance of mass-immigration of bacteria and ARGs from the source on ARG transport in wastewater treatment processes. This emphasizes the need to revise the way we mitigate ARG contamination but focus on the source of ARGs in urban wastewater.
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Affiliation(s)
- Lanping Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Bob Adyari
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Department of Environmental Engineering, Universitas Pertamina, Jakarta 12220, Indonesia
| | - Liyuan Hou
- Department of Civil and Environmental Engineering, Utah State University, UT 84322, USA; Utah Water Research Laboratory, Utah State University, Logan, UT 84322, USA
| | - Xiaoyong Yang
- School of Environmental and Material Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Mahmoud Gad
- Water Pollution Research Department, National Research Centre, Giza 12622, Egypt
| | - Yuwen Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Cong Ma
- Xiamen Municipal Environmental Technology Co., Ltd., Xiamen 361001, China
| | - Qian Sun
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qiang Tang
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Yifeng Zhang
- Department of Environmental and Resource Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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10
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Qi Q, Ghaly TM, Rajabal V, Gillings MR, Tetu SG. Dissecting molecular evolution of class 1 integron gene cassettes and identifying their bacterial hosts in suburban creeks via epicPCR. J Antimicrob Chemother 2024; 79:100-111. [PMID: 37962091 DOI: 10.1093/jac/dkad353] [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: 08/22/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
OBJECTIVES Our study aimed to sequence class 1 integrons in uncultured environmental bacterial cells in freshwater from suburban creeks and uncover the taxonomy of their bacterial hosts. We also aimed to characterize integron gene cassettes with altered DNA sequences relative to those from databases or literature and identify key signatures of their molecular evolution. METHODS We applied a single-cell fusion PCR-based technique-emulsion, paired isolation and concatenation PCR (epicPCR)-to link class 1 integron gene cassette arrays to the phylogenetic markers of their bacterial hosts. The levels of streptomycin resistance conferred by the WT and altered aadA5 and aadA11 gene cassettes that encode aminoglycoside (3″) adenylyltransferases were experimentally quantified in an Escherichia coli host. RESULTS Class 1 integron gene cassette arrays were detected in Alphaproteobacteria and Gammaproteobacteria hosts. A subset of three gene cassettes displayed signatures of molecular evolution, namely the gain of a regulatory 5'-untranslated region (5'-UTR), the loss of attC recombination sites between adjacent gene cassettes, and the invasion of a 5'-UTR by an IS element. Notably, our experimental testing of a novel variant of the aadA11 gene cassette demonstrated that gaining the observed 5'-UTR contributed to a 3-fold increase in the MIC of streptomycin relative to the ancestral reference gene cassette in E. coli. CONCLUSIONS Dissecting the observed signatures of molecular evolution of class 1 integrons allowed us to explain their effects on antibiotic resistance phenotypes, while identifying their bacterial hosts enabled us to make better inferences on the likely origins of novel gene cassettes and IS that invade known gene cassettes.
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Affiliation(s)
- Qin Qi
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Timothy M Ghaly
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Vaheesan Rajabal
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Michael R Gillings
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Sasha G Tetu
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
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11
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Higuera‐Llantén S, Alcalde‐Rico M, Vasquez‐Ponce F, Ibacache‐Quiroga C, Blazquez J, Olivares‐Pacheco J. A whole-cell hypersensitive biosensor for beta-lactams based on the AmpR-AmpC regulatory circuit from the Antarctic Pseudomonas sp. IB20. Microb Biotechnol 2024; 17:e14385. [PMID: 38197486 PMCID: PMC10832568 DOI: 10.1111/1751-7915.14385] [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: 08/11/2023] [Revised: 10/25/2023] [Accepted: 11/26/2023] [Indexed: 01/11/2024] Open
Abstract
Detecting antibiotic residues is vital to minimize their impact. Yet, existing methods are complex and costly. Biosensors offer an alternative. While many biosensors detect various antibiotics, specific ones for beta-lactams are lacking. To address this gap, a biosensor based on the AmpC beta-lactamase regulation system (ampR-ampC) from Pseudomonas sp. IB20, an Antarctic isolate, was developed in this study. The AmpR-AmpC system is well-conserved in the genus Pseudomonas and has been extensively studied for its involvement in peptidoglycan recycling and beta-lactam resistance. To create the biosensor, the ampC coding sequence was replaced with the mCherry fluorescent protein as a reporter, resulting in a transcriptional fusion. This construct was then inserted into Escherichia coli SN0301, a beta-lactam hypersensitive strain, generating a whole-cell biosensor. The biosensor demonstrated dose-dependent detection of penicillins, cephalosporins and carbapenems. However, the most interesting aspect of this work is the high sensitivity presented by the biosensor in the detection of carbapenems, as it was able to detect 8 pg/mL of meropenem and 40 pg/mL of imipenem and reach levels of 1-10 ng/mL for penicillins and cephalosporins. This makes the biosensor a powerful tool for the detection of beta-lactam antibiotics, specifically carbapenems, in different matrices.
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Affiliation(s)
- Sebastián Higuera‐Llantén
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales, GRABPA, Instituto de BiologíaPontificia Universidad Católica de ValparaísoValparaísoChile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB‐R)ValparaísoChile
| | - Manuel Alcalde‐Rico
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales, GRABPA, Instituto de BiologíaPontificia Universidad Católica de ValparaísoValparaísoChile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB‐R)ValparaísoChile
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen Macarena, CSIC, Universidad de SevillaSevillaSpain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIIMadridSpain
| | - Felipe Vasquez‐Ponce
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales, GRABPA, Instituto de BiologíaPontificia Universidad Católica de ValparaísoValparaísoChile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB‐R)ValparaísoChile
- Department of Microbiology, Institute of Biomedical SciencesUniversidade de São PauloSão PauloBrazil
| | - Claudia Ibacache‐Quiroga
- Escuela de Nutrición y Dietética, Facultad de FarmaciaUniversidad de ValparaísoValparaísoChile
- Centro de Micro‐BioinnovaciónUniversidad de ValparaísoValparaísoChile
| | - Jesús Blazquez
- National Center for Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Jorge Olivares‐Pacheco
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales, GRABPA, Instituto de BiologíaPontificia Universidad Católica de ValparaísoValparaísoChile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB‐R)ValparaísoChile
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12
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Liu S, Han Z, Zhu D, Luan X, Deng L, Dong L, Yang M, Zhang Y. Field-based evidence for the enrichment of intrinsic antibiotic resistome stimulated by plant-derived fertilizer in agricultural soil. J Environ Sci (China) 2024; 135:728-740. [PMID: 37778843 DOI: 10.1016/j.jes.2022.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 10/03/2023]
Abstract
Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils. However, little is known about the effects of plant-derived fertilizer on soil antibiotic resistome. Herein, metagenomic sequencing was used to investigate the effects of a plant-derived fertilizer processed from sugarcane and beet on soil antibiotic resistance genes (ARGs) in a soybean field along crop growth stages. ARG profiles in the soils amended by plant-derived fertilizer were compared with those in the soils amended by chicken manure. The abundance and diversity of total ARGs in the soils amended by plant-derived fertilizer were significantly (P < 0.05) elevated at the sprout stage, to a level comparable to that in the manured soils. Whereas, unlike chicken manure mainly introducing manure-borne ARGs to soil, the plant-derived fertilizer was indicated to mainly enrich multidrug resistance genes in soil by nourishing indigenous bacteria. ARGs with abundances in amended soils significantly (P < 0.05) higher than in unamended soils at the sprout stage of soybean were considered as enriched ARGs. Decrease in the abundance of the enriched ARGs was observed in both the amended soils from the sprout to the harvest. Network analysis further identified Proteobacteria and Bacteroidetes as the primary bacterial taxa involved in the temporal variation of the enriched ARGs in the soils amended by plant-derived fertilizer, while in manured soils were Firmicutes and Actinobacteria. As revealed by multivariate statistical analyses, variation of the enriched ARGs in the soils amended by plant-derived fertilizer was majorly attributed to the response of co-occurred bacteria to depleting nutrients, which was different from the failed establishment of manure-borne bacteria in the manured soils. Our study provided field-based evidence that plant-derived fertilizer stimulated the intrinsic antibiotic resistome, and proposed attention to the un-perceived risk since some clinically relevant ARGs originate and evolve from natural resistome.
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Affiliation(s)
- Shihai Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, 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
| | - Xiao Luan
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Liujie Deng
- State Environmental Protection Engineering Center for Harmless Treatment and Resource Utilization of Antibiotic Residues, Khorgos 835007, China
| | - Liping Dong
- State Environmental Protection Engineering Center for Harmless Treatment and Resource Utilization of Antibiotic Residues, Khorgos 835007, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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13
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Givens CE, Kolpin DW, Hubbard LE, Meppelink SM, Cwiertny DM, Thompson DA, Lane RF, Wilson MC. Simultaneous stream assessment of antibiotics, bacteria, antibiotic resistant bacteria, and antibiotic resistance genes in an agricultural region of the United States. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166753. [PMID: 37673265 DOI: 10.1016/j.scitotenv.2023.166753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Antimicrobial resistance (AMR) is now recognized as a leading global threat to human health. Nevertheless, there currently is a limited understanding of the environment's role in the spread of AMR and antibiotic resistance genes (ARGs). In 2019, the U.S. Geological Survey conducted the first statewide assessment of antibiotic resistant bacteria (ARB) and ARGs in surface water and bed sediment collected from 34 stream locations across Iowa. Environmental samples were analyzed for a suite of 29 antibiotics and plated on selective media for 15 types of bacteria growth; DNA was extracted from culture growth and used in downstream polymerase chain reaction (PCR) assays for the detection of 24 ARGs. ARGs encoding resistance to antibiotics of clinical importance to human health and disease prevention were prioritized as their presence in stream systems has the potential for environmental significance. Total coliforms, Escherichia coli (E. coli), and staphylococci were nearly ubiquitous in both stream water and stream bed sediment samples, with enterococci present in 97 % of water samples, and Salmonella spp. growth present in 94 % and 67 % of water and bed sediment samples. Bacteria enumerations indicate that high bacteria loads are common in Iowa's streams, with 23 (68 %) streams exceeding state guidelines for primary contact for E. coli in recreational waters and 6 (18 %) streams exceeding the secondary contact advisory level. Although antibiotic-resistant E. coli growth was detected from 40 % of water samples, vancomycin-resistant enterococci (VRE) and penicillinase-resistant Staphylococcus aureus (MRSA) colony growth was detected from nearly all water samples. A total of 14 different ARGs were detected from viable bacteria cells from 30 Iowa streams (88 %, n = 34). Study results provide the first baseline understanding of the prevalence of ARB and ARGs throughout Iowa's waterways and health risk potential for humans, wildlife, and livestock using these waterways for drinking, irrigating, or recreating.
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Affiliation(s)
- Carrie E Givens
- U.S. Geological Survey, 5840 Enterprise Drive, Lansing, MI 48911, USA.
| | - Dana W Kolpin
- U.S. Geological Survey, 400 S. Clinton Street, Iowa City, Iowa 52240, USA
| | - Laura E Hubbard
- U.S. Geological Survey, 1 Gifford Pinchot Drive, Madison, WI 53726, USA
| | | | - David M Cwiertny
- University of Iowa Center for Health Effects of Environmental Contamination, The University of Iowa, 251 North Capitol Street, Chemistry Building - Room W195, Iowa City, Iowa 52242, USA
| | - Darrin A Thompson
- University of Iowa Center for Health Effects of Environmental Contamination, The University of Iowa, 251 North Capitol Street, Chemistry Building - Room W195, Iowa City, Iowa 52242, USA
| | - Rachael F Lane
- U.S. Geological Survey, 1217 Biltmore Drive, Lawrence, Kansas 66049, USA
| | - Michaelah C Wilson
- U.S. Geological Survey, 1217 Biltmore Drive, Lawrence, Kansas 66049, USA
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14
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Shintani M, Vestergaard G, Milaković M, Kublik S, Smalla K, Schloter M, Udiković-Kolić N. Integrons, transposons and IS elements promote diversification of multidrug resistance plasmids and adaptation of their hosts to antibiotic pollutants from pharmaceutical companies. Environ Microbiol 2023; 25:3035-3051. [PMID: 37655671 DOI: 10.1111/1462-2920.16481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/01/2023] [Indexed: 09/02/2023]
Abstract
Plasmids are important vehicles for the dissemination of antibiotic resistance genes (ARGs) among bacteria by conjugation. Here, we determined the complete nucleotide sequences of nine different plasmids previously obtained by exogenous plasmid isolation from river and creek sediments and wastewater from a pharmaceutical company. We identified six IncP/P-1ε plasmids and single members of IncL, IncN and IncFII-like plasmids. Genetic structures of the accessory regions of the IncP/P-1ε plasmids obtained implied that multiple insertions and deletions had occurred, mediated by different transposons and Class 1 integrons with various ARGs. Our study provides compelling evidence that Class 1 integrons, Tn402-like transposons, Tn3-like transposons and/or IS26 played important roles in the acquisition of ARGs across all investigated plasmids. Our plasmid sequencing data provide new insights into how these mobile genetic elements could mediate the acquisition and spread of ARGs in environmental bacteria.
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Affiliation(s)
- Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Ibaraki, Japan
| | | | - Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Croatia
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Zagreb, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Zagreb, Germany
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15
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Chukwu KB, Abafe OA, Amoako DG, Essack SY, Abia ALK. Environmental concentrations of antibiotics, biocides, and heavy metals fail to induce phenotypic antimicrobial resistance in Escherichia coli. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165721. [PMID: 37482346 DOI: 10.1016/j.scitotenv.2023.165721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
Most anthropogenically affected environments contain mixtures of pollutants from different sources. The impact of these pollutants is usually the combined effect of the individual polluting constituents. However, how these stressors contribute to the development of antimicrobial resistance in environmental microorganisms is poorly understood. Thus, a 30-day exposure experiment to environmental and sub-inhibitory concentrations of oxytetracycline, amoxicillin, zinc, copper, BAC (benzalkonium chloride) 10 and DADMAC (diallyldimethylammonium chloride) 12, was conducted using fully susceptible E. coli ATCC 25922 to ascertain any development of phenotypic or genotypic resistance. Furthermore, wild-type isolates were collected from the same aquatic environment as the stressors, analysed for phenotypic resistance using the disk diffusion method and genotypically through whole genome sequencing. Exposure to the various concentrations and combinations of the stressors did not trigger phenotypic resistance in the experimental bacteria. Furthermore, genotypic analysis of the WGS on the exposed isolates only found the macrolide resistance mdf(A) gene (also present in the control strain) and the disinfectant resistance gene sitABCD. With further analysis for single nucleotide variants (SNV), mutations were detected for 19 genes that encoded for oxidative stress, DNA repair, membrane proteins efflux systems, growth and persister formations except for the robA, a transcription protein subset of the ArcC/XylS family of proteins, which confer multidrug resistance in E. coli. This indicates that exposure to sub-inhibitory concentrations of antibiotics, heavy metals and biocide residues in the aquatic environmental concentrations of the stressors identified in the current study could not induce phenotypic or genotypic resistance but encoded for genes responsible for the development of persistence and tolerance in bacteria, which could be a precursor to the development of resistance in environmental bacteria.
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Affiliation(s)
- Kelechi B Chukwu
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ovokeroye A Abafe
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; Residue Laboratory, Agricultural Research Council - Onderstepoort Veterinary Research Campus, Onderstepoort 0110, South Africa
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Integrative Biology and Bioinformatics, University of Guelph, Ontario N1G 2W1, Canada
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Akebe L K Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Environmental Research Foundation, Westville 3630, Kwazulu-Natal, South Africa.
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16
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Shafi M, Jan R, Gani KM. Selection of priority emerging contaminants in surface waters of India, Pakistan, Bangladesh, and Sri Lanka. CHEMOSPHERE 2023; 341:139976. [PMID: 37657704 DOI: 10.1016/j.chemosphere.2023.139976] [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: 06/15/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/03/2023]
Abstract
The challenge of emerging contaminants (ECs) in global surface water bodies and particularly in low- and middle-income countries such as India, Pakistan, Bangladesh, and Sri Lanka, is evident from the literature. The complexity arises from the high costs involved in EC analysis and the extensive list of ECs, which complicates the selection of essential compounds for scientific and regulatory investigations. Consequently, monitoring programs often include ECs that may have minimal significance within a region and do not pose known or suspected ecological or human health risks. This study aims to address this issue by employing a multi-risk assessment approach to identify priority ECs in the surface waters of the aforementioned countries. Through an analysis of occurrence levels and frequency data gathered from published literature, an optimized risk quotient (RQ) was derived. The findings reveal a priority list of 38 compounds that exhibit potential environmental risks and merit consideration in future water quality monitoring programs. Furthermore, the majority of antibiotics in India (12 out of 17) and Pakistan (7 out of 17) exhibit a risk quotient for antimicrobial resistance selection (RQAMR) greater than 1, highlighting the need for devising effective strategies to mitigate the escalation of antibiotic resistance in the environment.
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Affiliation(s)
- Mozim Shafi
- Department of Civil Engineering, National Institute of Technology, Srinagar, Jammu, and Kashmir, 190006, India; Environmental Engineering and Management, Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India
| | - Ruby Jan
- Department of Civil Engineering, National Institute of Technology, Srinagar, Jammu, and Kashmir, 190006, India
| | - Khalid Muzamil Gani
- Department of Civil Engineering, National Institute of Technology, Srinagar, Jammu, and Kashmir, 190006, India.
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17
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Wu Y, Li S, Yu K, Hu J, Chen Q, Sun W. Wastewater treatment plant effluents exert different impacts on antibiotic resistome in water and sediment of the receiving river: Metagenomic analysis and risk assessment. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132528. [PMID: 37713776 DOI: 10.1016/j.jhazmat.2023.132528] [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: 04/22/2023] [Revised: 08/06/2023] [Accepted: 09/09/2023] [Indexed: 09/17/2023]
Abstract
Wastewater treatment plants (WWTPs) are considered as hotspots for the spread of antibiotic resistome into the environment. However, the differential contributions of WWTPs to the antibiotic resistome in the receiving river water and sediment are poorly understood. Here, based on metagenomic analysis, we found that the WWTP effluents significantly elevated the diversities and abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the receiving river water from the Qinghai-Tibet Plateau, but showed less interference with the antibiotic resistome in sediment. Estimated by SourceTracker, WWTPs contributed 60.691.8% of ARGs in downstream river water, much higher than those for sediment (7.7568.0%). A holistic comparison of ARG risks based on analysis of ARG combination, mobility risk, ARG hosts and ARG-carrying pathogens further revealed the great impacts of WWTP effluents on downstream river water rather than sediment. Among various MGEs, tnpA exhibited the greatest potential for the dissemination of ARGs, and displayed highest co-occurrence frequency with multiple ARGs. P. aeruginosa, E. cloacae, and E. coli were identified as the critical-priority pathogens of ARG hosts. This study demonstrated the much greater impacts of WWTP effluents on the downstream water compared with sediment, which is significant for developing effective strategies to mitigate ARG risks.
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Affiliation(s)
- Yang Wu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Si Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Ke Yu
- Shenzhen Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jingrun Hu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Qian Chen
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Weiling Sun
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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18
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Li H, Cao H, Li T, He Z, Zhao J, Zhang Y, Song HL. Biofilm electrode reactor coupled manganese ore substrate up-flow microbial fuel cell-constructed wetland system: High removal efficiencies of antibiotic, zinc (II), and the corresponding antibiotic resistance genes. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132394. [PMID: 37657329 DOI: 10.1016/j.jhazmat.2023.132394] [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: 06/24/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023]
Abstract
A coupled system comprised of a biofilm electrode reactor (BER) and a manganese ore substrate microbial fuel cell-constructed wetland (MFC-CW) system was used to remove co-exposed antibiotic and Zn (II), as well as simultaneously reduce copies of antibiotic resistance genes (ARGs) in the current study. In this system, BER primarily reduced the concentrations of antibiotics and Zn (II), and the effluent was used as the input to the MFC-CW, thereby providing electricity to BER. Co-exposure to a high concentration of Zn (II) decreased the relative abundances (RAs) of ARGs in the BER effluent, whereas the remaining sub-lethal concentration of Zn (II) increased the RAs of ARGs in the MFC-CW effluent. Even though the absolute copies of ARGs in the effluents increased during co-exposure, the total number of target ARG copies in the effluent of MFC-CW was significantly lower than that of BER. Moreover, BER pre-treatment eliminated most of Zn (II), which improved the electrical power generation characteristic of the MFC-CW unit. Correspondingly, the bacterial community and the ARGs hosts were analyzed to demonstrate the mechanism. In conclusion, the coupled system demonstrates significant potential to reduce antibiotics, Zn (II) and environmental risks posed by ARGs.
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Affiliation(s)
- Hua Li
- College of Urban Construction, Nanjing Tech University, Nanjing 211816, China
| | - Haipeng Cao
- College of Urban Construction, Nanjing Tech University, Nanjing 211816, China
| | - Tao Li
- College of Urban Construction, Nanjing Tech University, Nanjing 211816, China
| | - Zhiming He
- Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Jinhui Zhao
- College of Urban Construction, Nanjing Tech University, Nanjing 211816, China
| | - Yifeng Zhang
- Department of Environmental Engineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Hai-Liang Song
- School of Environment, Jiangsu Engineering Lab of Water and Soil Eco-remediation, Jiangsu Province Engineering Research Center of Environmental Risk Prevention and Emergency Response Technology, Nanjing Normal University, Wenyuan Road 1, Nanjing 210023, China.
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Liu JL, Yao J, Zhou DL, Liu B, Liu H, Li M, Zhao C, Sunahara G, Duran R. Mining-related multi-resistance genes in sulfate-reducing bacteria treatment of typical karst nonferrous metal(loid) mine tailings in China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:104753-104766. [PMID: 37707732 DOI: 10.1007/s11356-023-29203-3] [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: 05/08/2023] [Accepted: 08/02/2023] [Indexed: 09/15/2023]
Abstract
Management of tailings at metal mine smelter sites can reduce the potential hazards associated with exposure to toxic metal(loid)s and residual organic flotation reagents. In addition, microbes in the tailings harboring multi-resistance genes (e.g., tolerance to multiple antimicrobial agents) can cause high rates of morbidity and global economic problems. The potential co-selection mechanisms of antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) during tailings sulfate-reducing bacteria (SRB) treatment have been poorly investigated. Samples were collected from a nonferrous metal mine tailing site treated with an established SRB protocol and were analyzed for selected geochemical properties and high throughput sequencing of 16S rRNA gene barcoding. Based on the shotgun metagenomic analysis, the bacterial domain was dominant in nonferrous metal(loid)-rich tailings treated with SRB for 12 months. KEGGs related to ARGs and MRGs were detected. Thiobacillus and Sphingomonas were the main genera carrying the bacA and mexEF resistance operons, along with Sulfuricella which were also found as the main genera carrying MRGs. The SRB treatment may mediate the distribution of numerous resistance genes. KOs based on the metagenomic database indicated that ARGs (mexNW, merD, sul, and bla) and MRGs (czcABCR and copRS genes) were found on the same contig. The SRB strains (Desulfosporosinus and Desulfotomaculum), and the acidophilic strain Acidiphilium significantly contributed to the distribution of sul genes. The functional metabolic pathways related to siderophores metabolism were largely from anaerobic genera of Streptomyces and Microbacterium. The presence of arsenate reductase, metal efflux pump, and Fe transport genes indicated that SRB treatment plays a key role in the metal(loid)s transformation. Overall, our findings show that bio-treatment is an effective tool for managing ARGs/MRGs and metals in tailings that contain numerous metal(loid) contaminants.
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Affiliation(s)
- Jian-Li Liu
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Jun Yao
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - De-Liang Zhou
- Beijing Zhongdianyida Technology Co., Ltd, Beijing, 100190, China
| | - Bang Liu
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Houquan Liu
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Miaomiao Li
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Chenchen Zhao
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Geoffrey Sunahara
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
- Department of Natural Resource Sciences, McGill University, Montreal, Quebec, H9X3V9, Canada
| | - Robert Duran
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
- Université de Pau et des Pays de l'Adour/E2S UPPA, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
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20
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Kyung SM, Lee J, Lee ES, Hwang CY, Yoo HS. Genomic molecular epidemiology of carbapenemase-producing Escherichia coli ST410 isolates by complete genome analysis. Vet Res 2023; 54:72. [PMID: 37658425 PMCID: PMC10472685 DOI: 10.1186/s13567-023-01205-6] [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: 04/16/2023] [Accepted: 07/04/2023] [Indexed: 09/03/2023] Open
Abstract
The circulation of carbapenemase-producing Escherichia coli (CPEC) in our society is a serious concern for vulnerable patients in nosocomial environments. However, the genomic epidemiology of the circulation of CPEC bacteria among companion animals remains largely unknown. In this study, epidemiological analysis was conducted using complete genome identification of CPEC ST410 isolates obtained from companion animals. To estimate the genomic distance and relatedness of the isolates, a total of 37 whole-genome datasets of E. coli ST410 strains were downloaded and comparatively analysed. As a result of the analysis, the genomic structure of the chromosomes and plasmids was identified, revealing the genomic positions of multiple resistance and virulence genes. The isolates in this study were grouped into the subclade H24/RxC, with fimH24, and substituted quinolone resistance-determining regions (QRDRs) and multiple beta-lactamases, including extended-spectrum β-lactamase (ESBL) and carbapenemase. In addition, the in silico comparison of the whole-genome datasets revealed unidentified ST410 H24/Rx subgroups, including either high pathogenicity islands (HPIs) or H21 serotypes. Considering the genetic variations and resistance gene dissemination of the isolates carried by companion animals, future approaches for preventive measurement must include the "One Health" perspective for public health in our society.
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Affiliation(s)
- Su Min Kyung
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Junho Lee
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Eun-Seo Lee
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Cheol-Yong Hwang
- Department of Veterinary Dermatology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Han Sang Yoo
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
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21
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Zhang Z, Zhang Q, Gao S, Xu H, Guo J, Yan F. Antibacterial, anti-inflammatory and wet-adhesive poly(ionic liquid)-based oral patch for the treatment of oral ulcers with bacterial infection. Acta Biomater 2023; 166:254-265. [PMID: 37187300 DOI: 10.1016/j.actbio.2023.05.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/21/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023]
Abstract
Oral aphthous ulcers are a common inflammatory efflorescence of oral mucosa, presenting as inflammation and oral mucosal damage and manifesting as pain. The moist and highly dynamic environment of the oral cavity makes the local treatment of oral aphthous ulcers challenging. Herein, a poly(ionic liquid)-based diclofenac sodium (DS)-loaded (PIL-DS) buccal tissue adhesive patch fabricated with intrinsically antimicrobial, highly wet environment adhesive properties and anti-inflammatory activities to treat oral aphthous ulcers was developed. The PIL-DS patch was prepared via polymerization of a catechol-containing ionic liquid, acrylic acid, and butyl acrylate, followed by anion exchange with DS-. The PIL-DS can adhere to wet tissues, including mucosa muscles and organs, and efficiently deliver the carried DS- at wound sites, exerting remarkable synergistic antimicrobial (bacteria and fungi) properties. Accordingly, the PIL-DS elicited dual therapeutic effects on oral aphthous ulcers with Staphylococcus aureus infection through antibacterial and anti-inflammatory activities, significantly accelerating oral aphthous ulcer healing as an oral mucosa patch. The results indicated that the PIL-DS patch, with inherently antimicrobial and wet adhesion properties, is promising for treating oral aphthous ulcers in clinical practice. STATEMENT OF SIGNIFICANCE: Oral aphthous ulcers are a common oral mucosal disease, which could lead to bacterial infection and inflammation in severe cases, especially for people with large ulcers or low immunity. However, moist oral mucosa and highly dynamic oral environment make it challenging to maintain therapeutic agents and physical barriers at the wound surface. Therefore, an innovative drug carrier with wet adhesion is urgently needed. Herein, a poly(ionic liquid)-based diclofenac sodium (DS)-loaded (PIL-DS) buccal tissue adhesive patch was developed to treat oral aphthous ulcers showing intrinsically antimicrobial and highly wet environment adhesive properties due to the presence of catechol-containing ionic liquid monomer. Additionally, the PIL-DS showed significantly therapeutic effects on oral aphthous ulcers with S. aureus infection through antibacterial and anti-inflammatory activities. We expect that our work can provide inspiration for the development of treatment for microbially infected oral ulcers.
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Affiliation(s)
- Zijun Zhang
- Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Negative Carbon Technologies College of Chemistry, Suzhou Key Laboratory of Soft Material and New Energy, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Qiuyang Zhang
- Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Negative Carbon Technologies College of Chemistry, Suzhou Key Laboratory of Soft Material and New Energy, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Shuna Gao
- Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Negative Carbon Technologies College of Chemistry, Suzhou Key Laboratory of Soft Material and New Energy, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Hui Xu
- Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Negative Carbon Technologies College of Chemistry, Suzhou Key Laboratory of Soft Material and New Energy, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Jiangna Guo
- Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Negative Carbon Technologies College of Chemistry, Suzhou Key Laboratory of Soft Material and New Energy, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China.
| | - Feng Yan
- Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Negative Carbon Technologies College of Chemistry, Suzhou Key Laboratory of Soft Material and New Energy, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China.
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22
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Abramova A, Berendonk TU, Bengtsson-Palme J. A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments. ENVIRONMENT INTERNATIONAL 2023; 178:108084. [PMID: 37421899 DOI: 10.1016/j.envint.2023.108084] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/23/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023]
Abstract
The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, little effort has been made to monitor AMR outside of clinical and veterinary settings. Partially, this is caused by a lack of comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish a baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey, identifying 150 scientific papers containing relevant qPCR data on antimicrobial resistance genes (ARGs) in environments associated with potential routes for AMR dissemination. The collected data included 1594 samples distributed across 30 different countries and 12 sample types, in a time span from 2001 to 2020. We found that for most ARGs, the typically reported abundances in human impacted environments fell in an interval from 10-5 to 10-3 copies per 16S rRNA, roughly corresponding to one ARG copy in a thousand bacteria. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.
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Affiliation(s)
- Anna Abramova
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance research (CARe) in Gothenburg, Sweden; Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Thomas U Berendonk
- Institute for Hydrobiology, Technische Universität Dresden, Dresden 01062, Germany
| | - Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10A, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance research (CARe) in Gothenburg, Sweden; Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.
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23
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Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Forslund SK, Gschwind R, Heikinheimo A, Jarquín-Díaz VH, Khan AA, Klümper U, Löber U, Nekoro M, Osińska AD, Ugarcina Perovic S, Pitkänen T, Rødland EK, Ruppé E, Wasteson Y, Wester AL, Zahra R. Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs? ENVIRONMENT INTERNATIONAL 2023; 178:108089. [PMID: 37441817 DOI: 10.1016/j.envint.2023.108089] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Antimicrobial resistance (AMR) is a global threat to human and animal health and well-being. To understand AMR dynamics, it is important to monitor resistant bacteria and resistance genes in all relevant settings. However, while monitoring of AMR has been implemented in clinical and veterinary settings, comprehensive monitoring of AMR in the environment is almost completely lacking. Yet, the environmental dimension of AMR is critical for understanding the dissemination routes and selection of resistant microorganisms, as well as the human health risks related to environmental AMR. Here, we outline important knowledge gaps that impede implementation of environmental AMR monitoring. These include lack of knowledge of the 'normal' background levels of environmental AMR, definition of high-risk environments for transmission, and a poor understanding of the concentrations of antibiotics and other chemical agents that promote resistance selection. Furthermore, there is a lack of methods to detect resistance genes that are not already circulating among pathogens. We conclude that these knowledge gaps need to be addressed before routine monitoring for AMR in the environment can be implemented on a large scale. Yet, AMR monitoring data bridging different sectors is needed in order to fill these knowledge gaps, which means that some level of national, regional and global AMR surveillance in the environment must happen even without all scientific questions answered. With the possibilities opened up by rapidly advancing technologies, it is time to fill these knowledge gaps. Doing so will allow for specific actions against environmental AMR development and spread to pathogens and thereby safeguard the health and wellbeing of humans and animals.
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Affiliation(s)
- Johan Bengtsson-Palme
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) in Gothenburg, Sweden.
| | - Anna Abramova
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) in Gothenburg, Sweden
| | - Thomas U Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Zellescher Weg 40, 01217 Dresden, Germany
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rémi Gschwind
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME F-75018 Paris, France
| | - Annamari Heikinheimo
- University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O.Box 66, FI-00014, Finland; Finnish Food Authority, P.O.Box 100, 00027 Seinäjoki, Finland
| | - Víctor Hugo Jarquín-Díaz
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Ayaz Ali Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Department of Biotechnology, University of Malakand, Chakdara, Dir (Lower), Khyber Pakhtunkhwa, Pakistan
| | - Uli Klümper
- Institute of Hydrobiology, Technische Universität Dresden, Zellescher Weg 40, 01217 Dresden, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Marmar Nekoro
- Swedish Knowledge Centre on Pharmaceuticals in the Environment, Swedish Medical Products Agency, P.O Box 26, 751 03 Uppsala, Sweden
| | - Adriana D Osińska
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, P.O.Box 5003 NMBU, N-1432 Ås, Norway
| | - Svetlana Ugarcina Perovic
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Tarja Pitkänen
- University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O.Box 66, FI-00014, Finland; Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O.Box 95, FI-70701 Kuopio, Finland
| | | | - Etienne Ruppé
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME F-75018 Paris, France
| | - Yngvild Wasteson
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, P.O.Box 5003 NMBU, N-1432 Ås, Norway
| | | | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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24
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Wang J, Xu S, Zhao K, Song G, Zhao S, Liu R. Risk control of antibiotics, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) during sewage sludge treatment and disposal: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162772. [PMID: 36933744 DOI: 10.1016/j.scitotenv.2023.162772] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/14/2023] [Accepted: 03/06/2023] [Indexed: 05/06/2023]
Abstract
Sewage sludge is an important reservoir of antibiotics, antibiotic resistance genes (ARGs), and antibiotic resistant bacteria (ARB) in wastewater treatment plants (WWTPs), and the reclamation of sewage sludge potentially threats human health and environmental safety. Sludge treatment and disposal are expected to control these risks, and this review summarizes the fate and controlling efficiency of antibiotics, ARGs, and ARB in sludge involved in different processes, i.e., disintegration, anaerobic digestion, aerobic composting, drying, pyrolysis, constructed wetland, and land application. Additionally, the analysis and characterization methods of antibiotics, ARGs, and ARB in complicate sludge are reviewed, and the quantitative risk assessment approaches involved in land application are comprehensively discussed. This review benefits process optimization of sludge treatment and disposal, with regard to environmental risks control of antibiotics, ARGs, and ARB in sludge. Furthermore, current research limitations and gaps, e.g., the antibiotic resistance risk assessment in sludge-amended soil, are proposed to advance the future studies.
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Affiliation(s)
- Jiaqi Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Yangze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siqi Xu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Kai Zhao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ge Song
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shunan Zhao
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruiping Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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25
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Marutescu LG, Popa M, Gheorghe-Barbu I, Barbu IC, Rodríguez-Molina D, Berglund F, Blaak H, Flach CF, Kemper MA, Spießberger B, Wengenroth L, Larsson DGJ, Nowak D, Radon K, de Roda Husman AM, Wieser A, Schmitt H, Pircalabioru Gradisteanu G, Vrancianu CO, Chifiriuc MC. Wastewater treatment plants, an "escape gate" for ESCAPE pathogens. Front Microbiol 2023; 14:1193907. [PMID: 37293232 PMCID: PMC10244645 DOI: 10.3389/fmicb.2023.1193907] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
Abstract
Antibiotics are an essential tool of modern medicine, contributing to significantly decreasing mortality and morbidity rates from infectious diseases. However, persistent misuse of these drugs has accelerated the evolution of antibiotic resistance, negatively impacting clinical practice. The environment contributes to both the evolution and transmission of resistance. From all anthropically polluted aquatic environments, wastewater treatment plants (WWTPs) are probably the main reservoirs of resistant pathogens. They should be regarded as critical control points for preventing or reducing the release of antibiotics, antibiotic-resistant bacteria (ARB), and antibiotic-resistance genes (ARGs) into the natural environment. This review focuses on the fate of the pathogens Enterococcus faecium, Staphylococcus aureus, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae spp. (ESCAPE) in WWTPs. All ESCAPE pathogen species, including high-risk clones and resistance determinants to last-resort antibiotics such as carbapenems, colistin, and multi-drug resistance platforms, were detected in wastewater. The whole genome sequencing studies demonstrate the clonal relationships and dissemination of Gram-negative ESCAPE species into the wastewater via hospital effluents and the enrichment of virulence and resistance determinants of S. aureus and enterococci in WWTPs. Therefore, the efficiency of different wastewater treatment processes regarding the removal of clinically relevant ARB species and ARGs, as well as the influence of water quality factors on their performance, should be explored and monitored, along with the development of more effective treatments and appropriate indicators (ESCAPE bacteria and/or ARGs). This knowledge will allow the development of quality standards for point sources and effluents to consolidate the WWTP barrier role against the environmental and public health AR threats.
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Affiliation(s)
- Luminita Gabriela Marutescu
- Department of Microbiology and Immunology, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Marcela Popa
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Irina Gheorghe-Barbu
- Department of Microbiology and Immunology, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Ilda Czobor Barbu
- Department of Microbiology and Immunology, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Daloha Rodríguez-Molina
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology – IBE, LMU Munich, Munich, Germany
- Pettenkofer School of Public Health, Munich, Germany
| | - Fanny Berglund
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Hetty Blaak
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Merel Aurora Kemper
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Beate Spießberger
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
- Department of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Munich, Germany
| | - Laura Wengenroth
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
| | - D. G. Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Dennis Nowak
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research (DZL), Munich, Germany
| | - Katja Radon
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Ana Maria de Roda Husman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Andreas Wieser
- German Centre for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, Munich, Germany
- Department of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Munich, Germany
| | - Heike Schmitt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Gratiela Pircalabioru Gradisteanu
- Department of Microbiology and Immunology, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Romanian Academy of Sciences, Bucharest, Romania
| | - Corneliu Ovidiu Vrancianu
- Department of Microbiology and Immunology, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Department of Microbiology and Immunology, Faculty of Biology, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- Earth, Environmental and Life Sciences Section, Research Institute of the University of Bucharest, University of Bucharest, Bucharest, Romania
- The Romanian Academy, Bucharest, Romania
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Liang J, Lin H, Singh B, Wang A, Yan Z. A global perspective on compositions, risks, and ecological genesis of antibiotic resistance genes in biofilters of drinking water treatment plants. WATER RESEARCH 2023; 233:119822. [PMID: 36871385 DOI: 10.1016/j.watres.2023.119822] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/16/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
Antibiotic resistance genes (ARGs) in biofilters of drinking water treatment plants (DWTPs) are regarded to be a remarkable potential health risk to human. A global survey on ARGs in biofilters may help evaluate their risk features as a whole. This study aims to explore the compositions, risks, and ecological genesis of ARGs in the biofilters of DWTPs. In total, 98 metagenomes of DWTP biofilters were collected from Sequence Read Archive (SRA) of National center for Biotechnology Information (NCBI), and the main ARG types were recognized, with multidrug, bacitracin, and beta-lactam as the first three types. Source water types (surface water vs. groundwater) were found to significantly influence antibiotic resistome, overpassing biofilter media and locations. Although ARG abundances of surface water biofilters were approximately five times higher than that of groundwater biofilters, the risk pattern of ARGs was highly similar between surface water biofilters and groundwater biofilters, and up to 99.61% of the ARGs on average belong to the least risk and unassessed ranks, and only 0.23% the highest risk rank. Monobactam biosynthesis pathway and prodigiosin biosynthesis pathway, two antibiotics biosynthesis pathways, were observed to be positively correlated with several ARG types and total ARG abundance in samples of surface water and groundwater biofilters, respectively, suggesting their potential roles in ecological genesis of ARGs. Overall, the results of this study would deepen our understanding of the ARG risks in biofilters of DWTPs and shed light on their ecological genesis inside.
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Affiliation(s)
- Jinsong Liang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China.
| | - Huan Lin
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, 2751, NSW Australia; Global Centre for Land-Based Innovation, Western Sydney University, Penrith, 2751, NSW Australia
| | - Aijie Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Zhenzhen Yan
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, 2751, NSW Australia
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Rasmussen JA, Chua PYS. Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community. Microbiol Res 2023; 271:127372. [PMID: 37018898 DOI: 10.1016/j.micres.2023.127372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/04/2023]
Abstract
The gut microbiome is a critical component of avian health, influencing nutrient uptake and immune functions. While the gut microbiomes of agriculturally important birds have been studied, the microbiomes of wild birds still need to be explored. Filling this knowledge gap could have implications for the microbial rewilding of captive birds and managing avian hosts for antibiotic-resistant bacteria (ARB). Using genome-resolved metagenomics, we recovered 112 metagenome-assembled genomes (MAGs) from the faeces of wild and captive western capercaillies (Tetrao urogallus) (n = 8). Comparisons of bacterial diversity between the wild and captive capercaillies suggest that the reduced diversity in the captive individual could be due to differences in diet. This was further substantiated through the analyses of 517,657 clusters of orthologous groups (COGs), which revealed that gene functions related to amino acids and carbohydrate metabolisms were more abundant in wild capercaillies. Metagenomics mining of resistome identified 751 antibiotic resistance genes (ARGs), of which 40.7 % were specific to wild capercaillies suggesting that capercaillies could be potential reservoirs for hosting ARG-associated bacteria. Additionally, the core resistome shared between wild and captive capercaillies indicates that birds can acquire these ARG-associated bacteria naturally from the environment (43.1 % of ARGs). The association of 26 MAGs with 120 ARGs and 378 virus operational taxonomic units (vOTUs) also suggests a possible interplay between these elements, where putative phages could have roles in modulating the gut microbiota of avian hosts. These findings can have important implications for conservation and human health, such as avian gut microbiota rewilding, identifying the emerging threats or opportunities due to phage-microbe interactions, and monitoring the potential spread of ARG-associated bacteria from wild avian populations.
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Inda-Díaz JS, Lund D, Parras-Moltó M, Johnning A, Bengtsson-Palme J, Kristiansson E. Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes. MICROBIOME 2023; 11:44. [PMID: 36882798 PMCID: PMC9993715 DOI: 10.1186/s40168-023-01479-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Bacterial communities in humans, animals, and the external environment maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs are well-characterized and thus established in existing resistance gene databases. In contrast, the remaining latent ARGs are typically unknown and overlooked in most sequencing-based studies. Our view of the resistome and its diversity is therefore incomplete, which hampers our ability to assess risk for promotion and spread of yet undiscovered resistance determinants. RESULTS A reference database consisting of both established and latent ARGs (ARGs not present in current resistance gene repositories) was created. By analyzing more than 10,000 metagenomic samples, we showed that latent ARGs were more abundant and diverse than established ARGs in all studied environments, including the human- and animal-associated microbiomes. The pan-resistomes, i.e., all ARGs present in an environment, were heavily dominated by latent ARGs. In comparison, the core-resistome, i.e., ARGs that were commonly encountered, comprised both latent and established ARGs. We identified several latent ARGs shared between environments and/or present in human pathogens. Context analysis of these genes showed that they were located on mobile genetic elements, including conjugative elements. We, furthermore, identified that wastewater microbiomes had a surprisingly large pan- and core-resistome, which makes it a potentially high-risk environment for the mobilization and promotion of latent ARGs. CONCLUSIONS Our results show that latent ARGs are ubiquitously present in all environments and constitute a diverse reservoir from which new resistance determinants can be recruited to pathogens. Several latent ARGs already had high mobile potential and were present in human pathogens, suggesting that they may constitute emerging threats to human health. We conclude that the full resistome-including both latent and established ARGs-needs to be considered to properly assess the risks associated with antibiotic selection pressures. Video Abstract.
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Affiliation(s)
- Juan Salvador Inda-Díaz
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - David Lund
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Marcos Parras-Moltó
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
- Department of Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, Sweden
| | - Johan Bengtsson-Palme
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, SE-412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
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Ju H, Liu L, Liu X, Wu Y, Li L, Gin KYH, Zhang G, Zhang J. A comprehensive study of the source, occurrence, and spatio-seasonal dynamics of 12 target antibiotics and their potential risks in a cold semi-arid catchment. WATER RESEARCH 2023; 229:119433. [PMID: 36493699 DOI: 10.1016/j.watres.2022.119433] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 11/06/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Antibiotics are widely consumed and are ubiquitous in aquatic ecosystems, such as in agricultural and fishery lake catchments, for prophylactic treatment. However, there are very few comprehensive studies reporting all seasonal occurrences, spatiotemporal dynamics, and risk assessments of antibiotics in agricultural lake catchments, especially in cold regions during the winter season. This study measured seasonality in the concentrations of 12 antibiotics belonging to seven different classes in the surface waters (tributary rivers and lakes) of the Chagan lake catchment in northeast China. All antibiotics were detected in most of the water samples across most seasons, with concentrations varying for different compounds, locations, and seasons. These levels were discussed in terms of the main sources at different sampling sites, including agriculture, fish farming, municipal wastewater, and others. In general, the highest concentrations of most compounds were observed during the freeze-thaw periods. The number of antibiotic resistance genes (ARGs) correlated with compound lipophilicity and half-life. Based on the ecological risks of antibiotics and the relative abundance of ARGs, a hierarchical control priority list (HCPL) of antibiotics was determined, considering four levels (critical, high, medium, and low). To further strengthen the control and effectively manage antibiotics, we highly recommend the reduction and selective use of veterinary antibiotics in winter and spring during the freeze-thaw periods in the Chagan lake catchment.
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Affiliation(s)
- Hanyu Ju
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Xuemei Liu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yao Wu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Lei Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Karina Yew-Hoong Gin
- Department of Civil & Environmental Engineering, National University of Singapore, E1A-07-03, 1 Engineering Drive 2, Singapore 117576, Singapore; NUS Environmental Research Institute, National University of Singapore, 1 Create way, Create Tower, #15-02, Singapore 138602, Singapore
| | - Guangxin Zhang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Jingjie Zhang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; Department of Civil & Environmental Engineering, National University of Singapore, E1A-07-03, 1 Engineering Drive 2, Singapore 117576, Singapore; NUS Environmental Research Institute, National University of Singapore, 1 Create way, Create Tower, #15-02, Singapore 138602, Singapore; Shenzhen Municipal Engineering Lab of Environmental IoT Technologies, Southern University of Science and Technology, Shenzhen 518055, China.
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30
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Xin H, Gao M, Wang X, Qiu T, Guo Y, Zhang L. Animal farms are hot spots for airborne antimicrobial resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158050. [PMID: 35985594 DOI: 10.1016/j.scitotenv.2022.158050] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Animal farms are known reservoirs for environmental antimicrobial resistance (AMR). However, knowledge of AMR burden in the air around animal farms remains disproportionately limited. In this study, we characterized the airborne AMR based on the quantitative information of 30 antimicrobial resistance genes (ARGs), four mobile genetic elements (MGEs), and four human pathogenic bacteria (HPBs) involving four animal species from 20 farms. By comparing these genes with those in animal feces, the distinguishing features of airborne AMR were revealed, which included high enrichment of ARGs and their potential mobility to host HPBs. We found that depending on the antimicrobial class, the mean concentration of airborne ARGs in the animal farms ranged from 102 to 104 copies/m3 and was accompanied by a considerable intensity of MGEs and HPBs (approximately 103 copies/m3). Although significant correlations were observed between the ARGs and bacterial communities of air and fecal samples, the abundance of target genes was generally high in fine inhalable particles (PM2.5), with an enrichment ratio of up to 102 in swine and cattle farms. The potential transferability of airborne ARGs was universally strengthened, embodied by a pronounced co-occurrence of ARGs-MGEs in air compared with that in feces. Exposure analysis showed that animal farmworkers may inhale approximately 104 copies of human pathogenic bacteria-associated genera per day potentially carrying highly transferable ARGs, including multidrug resistant Staphylococcus aureus. Moreover, PM2.5 inhalation posed higher human daily intake burdens of some ARGs than those associated with drinking water intake. Overall, our findings highlight the severity of animal-related airborne AMR and the subsequent inhalation exposure, thus improving our understanding of the airborne flow of AMR genes from animals to humans. These findings could help develop strategies to mitigate the human exposure and dissemination of ARGs across different media.
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Affiliation(s)
- Huibo Xin
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing 100083, China; Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Min Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xuming Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Tianlei Qiu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yajie Guo
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Liqiu Zhang
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing 100083, China.
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31
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Huang Y, Wang F, Li Y, Yue C, Zhang Y, Zhou P, Mu J. Influence of anthropogenic disturbances on antibiotic resistance gene distributions along the Minjiang River in Southeast China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 323:116154. [PMID: 36095989 DOI: 10.1016/j.jenvman.2022.116154] [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: 06/06/2022] [Revised: 08/03/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
River-reservoir systems have become ubiquitous among modern global aquatic environments due to the widespread construction of dams. However, little is known of antibiotic resistance gene (ARG) distributions in reservoir-river systems experiencing varying degrees of anthropogenic impacts. Here, the diversity, abundance, and spatial distribution of ARGs were comprehensively characterized along the main stem of the Minjiang River, a typical subtropic reservoir-river system in Southeast China using high-throughput quantitative PCR. A total of 252 ARG subtypes were detected from twelve sampling sites that were dominated by aac(3)-Via, followed by czcA, blaTEM, and sul1. Urban river waters (sites S9-S12) harbored more diverse ARGs than did the reservoir waters (sites S1-S7), indicating more serious antibiotic resistance pollution in areas with larger population densities. Dam construction could reduce the richness and absolute abundance of ARGs from upstream (site S7) to downstream (site S8). Urban river waters also harbored a higher proportion of mobile genetic elements (MGEs), suggesting that intensive human activities may promote ARG horizontal gene transfers. The mean relative abundance of Proteobacteria that could promote antibiotic resistance within microbial communities was also highest in urban river waters. Variance partitioning analysis indicated that MGEs and bacterial communities could explain 67.33%, 44.7%, and 90.29% of variation in selected ARGs for the entire watershed, aquaculture waters, and urban river waters, respectively. These results further suggest that urban rivers are ideal media for the acquisition and spread of ARGs. These findings provide new insights into the occurrence and potential mechanisms determining the distributions of ARGs in a reservoir-river system experiencing various anthropogenic disturbances at the watershed scale.
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Affiliation(s)
- Yaling Huang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Feipeng Wang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Yue Li
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China; College Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Yue
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China; College Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuting Zhang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Pei Zhou
- Xiamen Urban Planning & Design Institute Co, LTD, Xiamen, 361012, China
| | - Jingli Mu
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
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32
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Ren Z, Luo W. Metagenomic analysis reveals the diversity and distribution of antibiotic resistance genes in thermokarst lakes of the Yellow River Source Area. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 313:120102. [PMID: 36075331 DOI: 10.1016/j.envpol.2022.120102] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/27/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Thermokarst lakes form as the results of ice-rich permafrost thawing and act as important water resources in cold regions. However, the distributions of antibiotic resistance genes (ARGs) in thermokarst lakes are far less studied. Using metagenomic sequencing approach, we provided the first study to document ARGs in thermokarst lakes of the Yellow River Source Area on the Qinghai-Tibet Plateau (QTP). The results revealed that both sediment and water of the thermokarst lakes harbor diverse ARGs. Multidrug resistance genes were the most diverse, while rifamycin resistance genes were the most abundant with rpoB2 and rpoB genes having the highest proportion. Sediment samples contained more ARGs than water samples, but their composition differed between the two types of samples. However, the composition variations of sediment and water ARGs were closely correlated. The Sorensen dissimilarities of ARGs were controlled by strong turnover processes in sediment samples, and by turnover and nestedness in water samples. High contributions of nestedness were found between sediment and water samples. Moreover, ARGs in water had more significant relationships with environmental variables than that in sediment. Given the role of thermokarst lakes as important water resources in permafrost landscape, as well as intensifying influences of climate change and anthropogenetic activities, thermokarst lakes could bring potential ARG risks, warranting further investigation and evaluation.
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Affiliation(s)
- Ze Ren
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, 519087, China; School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Wei Luo
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, 200136, China; School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China.
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33
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Gao W, Li A, Ding G, Zhang K, Zhi S. Investigating changes in the characteristics of antibiotic resistance genes at different reaction stages of high solid anaerobic digestion with pig manure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 312:120032. [PMID: 36030955 DOI: 10.1016/j.envpol.2022.120032] [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: 02/22/2022] [Revised: 07/20/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Contamination of antibiotic resistance genes (ARGs) from animals is a serious issue as they may spread to human pathogenic bacteria. The reduction of ARG contamination from livestock waste is thus essential. High solid anaerobic digestion (HSAD) is a new and effective technology although some aspects, such as change characteristics of ARGs at different reaction stages, have not been fully investigated. This study focused firstly on the variations in ARGs at different reaction stages in HSAD systems with five different starting methods: 1 natural start (the control) and 4 rapid starts by changing leachate reflux forms. The results showed that the rapid starting methods could accelerate start-up and increase biogas production by 312.5%. The starting and acidification stages showed higher microbial richness and diversity compared with the other stages. ARGs found to be reduced at acidification stage. Variation in ARGs at the starting and acidification stages was mainly driven by a combination of microbial community, mobile genetic elements (MGEs), and environmental factors; while the main contributory factors at the gas production stage were biomass and several unexplained factors. At the ending stage, the main driving factors were biomass and microbial communities. Most of the potential hosts (16/20) of the ARGs belonged to the Firmicutes phylum, which showed the lowest connections with the ARGs at the gas production stage.
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Affiliation(s)
- Wenxuan Gao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Ao Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Gongyao Ding
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Suli Zhi
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
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Shi J, Dang Q, Zhang C, Zhao X. Insight into effects of polyethylene microplastics in anaerobic digestion systems of waste activated sludge: Interactions of digestion performance, microbial communities and antibiotic resistance genes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 310:119859. [PMID: 35944782 DOI: 10.1016/j.envpol.2022.119859] [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: 04/30/2022] [Revised: 07/19/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
The environmental risks of microplastics (MPs) have raised an increasing concern. However, the effects of MPs in anaerobic digestion (AD) systems of waste activated sludge (WAS), especially on the fate of antibiotic resistance genes (ARGs), have not been clearly understood. Herein, the variation and interaction of digestion performance, microbial communities and ARGs during AD process of WAS in the presence of polyethylene (PE) MPs with two sizes, PE MPs-180μm and PE MPs-1mm, were investigated. The results showed that the presence of PE MPs, especially PE MPs-1mm, led to the increased hydrolysis of soluble polysaccharides and proteins and the accumulation of volatile fatty acids. The methane production decreased by 6.1% and 13.8% in the presence of PE MPs-180μm and PE MPs-1mm, respectively. Together with this process, hydrolytic bacteria and acidogens were enriched, and methanogens participating in acetoclastic methanogenesis were reduced. Meanwhile, ARGs were enriched obviously by the presence of PE MPs, the abundances of which in PE MPs-180μm and PE MPs-1mm groups were 1.2-3.0 times and 1.5-4.0 times higher than that in the control by the end of AD. That was associated with different co-occurrence patterns between ARGs and bacterial taxa and the enrichment of ARG-hosting bacteria caused by the presence of PE MPs. Together these results suggested the adverse effects of PE MPs on performance and ARGs removal during AD process of WAS through inducing the changes of microbial populations.
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Affiliation(s)
- Jianhong Shi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai, 201306, China
| | - Qiuling Dang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Chuanyan Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xinyu Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
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Liu S, Zhao H, Zheng M, Wang H, Jing C, Zhang W, Hu F. The physiological, biochemical and transcriptional responses to sulfamethoxazole in the Asian clam, Corbicula fluminea (O. F. Müller, 1774). Comp Biochem Physiol C Toxicol Pharmacol 2022; 260:109406. [PMID: 35793736 DOI: 10.1016/j.cbpc.2022.109406] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/24/2022] [Accepted: 06/30/2022] [Indexed: 12/27/2022]
Abstract
Sulfamethoxazole (SMX), a broad-spectrum antibiotic, has been widely used in the treatment and prevention of infection caused by bacteria in recent years. The present study was aimed to evaluate the response mechanisms to SMX stress in gills and digestive gland of Corbicula fluminea (O. F. Müller, 1774). To this end, clams were exposed to environmentally relevant concentrations of SMX (0, 1, 10 and 100 μg/L) for 7 and 28 days, and siphon behavior, tissue-specific enzymatic and transcriptional changes were assayed. Our results showed that exposure to SMX significantly suppressed filtration rate and acetylcholinesterase (AChE) activity, activated antioxidant defense system and elevated transcription of several genes related to cell apoptosis in gills and digestive gland of clams. In general, SMX at environmentally relevant concentrations exhibited a negative impact on siphon behavior and induced neurotoxicology, oxidative stress and cell apoptosis in C. fluminea. The current study will help broaden our understanding of the ecotoxicity of SMX on freshwater bivalves.
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Affiliation(s)
- Shangshu Liu
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haocheng Zhao
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengyan Zheng
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongkai Wang
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chen Jing
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weini Zhang
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fengxiao Hu
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Mao H, Guo J, Zhou J, Shi J, Cui H, Shi R, Yao J, Fang X, Wang B, Yan F. Antimicrobial poly(ionic liquid)-induced bacterial nanotube formation and drug-resistance spread. Biomater Sci 2022; 10:6460-6471. [PMID: 36155673 DOI: 10.1039/d2bm01130a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial nanotubes are tubular membranous structures bulging from the cell surface that can connect neighboring bacteria for the exchange of intercellular substances. However, little is known about the formation and function of bacterial nanotubes under the stress of antimicrobial materials. Herein, an imidazolium-type cationic poly(ionic liquid) (PIL) and corresponding PIL membranes with antimicrobial properties were synthesized. The effects of these cationic polymers on the formation of bacterial nanotubes between Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) or Vibrio fischeri (V. fischeri), followed by intraspecies and interspecies exchange of antibiotic resistance genes (ARGs) were investigated. The results showed that bacteria tend to produce more nanotubes accompanied by drug-resistance trade, which can even make the ARGs of pathogens spread to the environmental microbes of V. fischeri. Given the unique antimicrobial sustainability toward bacteria after they acquire ARGs via bacterial nanotubes, antimicrobial PILs demonstrate bright prospects in the battle against resistant bacteria.
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Affiliation(s)
- Hailei Mao
- Department of Anesthesiology and Critical Care Medicine, Zhongshan Hospital, Fudan, University, Shanghai 200032, China.
| | - Jiangna Guo
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China.
| | - Jiamei Zhou
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China.
| | - Jie Shi
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China.
| | - Hengqing Cui
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
| | - Rongwei Shi
- School of Material and Chemical Engineering, Tongren University, Tongren 554300, Guizhou, China
| | - Jieran Yao
- Department of Anesthesiology and Critical Care Medicine, Zhongshan Hospital, Fudan, University, Shanghai 200032, China.
| | - Xia Fang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
| | - Bin Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
| | - Feng Yan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China.
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Zhang J, Ge H, Shi J, Tao H, Li B, Yu X, Zhang M, Xu Z, Xiao R, Li X. A tiered probabilistic approach to assess antibiotic ecological and resistance development risks in the fresh surface waters of China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 243:114018. [PMID: 36037634 DOI: 10.1016/j.ecoenv.2022.114018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/23/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Exposure to antibiotics can result in not only ecotoxicity on aquatic organisms but also the development of antibiotic resistance. In the study, the ecotoxicity data and minimum inhibitory concentrations of the antibiotics were screened to derive predicted no-effect concentrations of ecological (PNECeco) and resistance development risks (PNECres) for 36 antibiotics in fresh surface waters of China. The derived PNECeco and PNECres values were ranged from 0.00175 to 2351 μg/L and 0.037-50 μg/L, respectively. Antibiotic ecological and resistance development risks were geographically widespread, especially in the Yongding River, Daqing River, and Ziya River basins of China. Based on the risk quotients, 11 and 14 of 36 target antibiotics were at high ecological risks and high resistance development risks in at least one basin, respectively. The higher tiered assessments provided more detailed risk descriptions by probability values and β-lactams (penicillin and amoxicillin) were present at the highest levels for ecological and resistance development risks. Although there was uncertainty based on the limited data and existing methods, this study can indicate the overall situation of the existing risk levels and provide essential insights and data supporting antibiotic management.
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Affiliation(s)
- Jiawei Zhang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Department of Civil Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong, China
| | - Hui Ge
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jianghong Shi
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Huanyu Tao
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Department of Civil Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong, China
| | - Bin Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiangyi Yu
- Solid Waste and Chemicals Management Center of Ministry of Ecology and Environment, Beijing 100029, China
| | - Mengtao Zhang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zonglin Xu
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijie Xiao
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiaoyan Li
- Department of Civil Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong, China.
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38
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Premke K, Wurzbacher C, Felsmann K, Fabian J, Taube R, Bodmer P, Attermeyer K, Nitzsche KN, Schroer S, Koschorreck M, Hübner E, Mahmoudinejad TH, Kyba CCM, Monaghan MT, Hölker F. Large-scale sampling of the freshwater microbiome suggests pollution-driven ecosystem changes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119627. [PMID: 35714791 DOI: 10.1016/j.envpol.2022.119627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
Freshwater microbes play a crucial role in the global carbon cycle. Anthropogenic stressors that lead to changes in these microbial communities are likely to have profound consequences for freshwater ecosystems. Using field data from the coordinated sampling of 617 lakes, ponds, rivers, and streams by citizen scientists, we observed linkages between microbial community composition, light and chemical pollution, and greenhouse gas concentration. All sampled water bodies were net emitters of CO2, with higher concentrations in running waters, and increasing concentrations at higher latitudes. Light pollution occurred at 75% of sites, was higher in urban areas and along rivers, and had a measurable effect on the microbial alpha diversity. Genetic elements suggestive of chemical stress and antimicrobial resistances (IntI1, blaOX58) were found in 85% of sites, and were also more prevalent in urban streams and rivers. Light pollution and CO2 were significantly related to microbial community composition, with CO2 inversely related to microbial phototrophy. Results of synchronous nationwide sampling indicate that pollution-driven alterations to the freshwater microbiome lead to changes in CO2 production in natural waters and highlight the vulnerability of running waters to anthropogenic stressors.
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Affiliation(s)
- Katrin Premke
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | | | - Katja Felsmann
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Jenny Fabian
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Germany
| | - Robert Taube
- City University of Applied Science, Bremen, Germany
| | | | - Katrin Attermeyer
- WasserCluster Lunz - Biologische Station, Lunz am See, Austria; Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Kai Nils Nitzsche
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Sibylle Schroer
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | | | - Eric Hübner
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | | | - Christopher C M Kyba
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; GFZ German Research Centre for Geosciences, Helmholtz Centre, Potsdam, Germany
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Institute für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Franz Hölker
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Institute für Biologie, Freie Universität Berlin, Berlin, Germany
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Li W, Zhang G. Detection and various environmental factors of antibiotic resistance gene horizontal transfer. ENVIRONMENTAL RESEARCH 2022; 212:113267. [PMID: 35413299 DOI: 10.1016/j.envres.2022.113267] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 05/25/2023]
Abstract
Bacterial antibiotic resistance in water environments is becoming increasingly severe, and new antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have also attracted the attention of researchers. The horizontal transfer of ARGs in water environments is considered one of the main sources of bacterial resistance in the natural environment. Horizontal gene transfer (HGT) mainly includes conjugation, natural transformation, and transduction, and conjugation has been investigated most. Several studies have shown that there are a large number of environmental factors that might affect the horizontal transfer of ARGs in water environments, such as nanomaterials, various oxidants, and light; however, there is still a lack of systematic and comprehensive reviews on the detection and the effects of the influence factors of on ARG horizontal transfer. Therefore, this study introduced three HGT modes, analysed the advantages and disadvantages of current methods for monitoring HGT, and then summarized the influence and mechanism of various factors on ARG horizontal transfer, and the possible reasons for the different effects caused by similar factors were mainly critically discussed. Finally, existing research deficiencies and future research directions of ARG horizontal transfer in water environments were discussed.
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Affiliation(s)
- Weiying Li
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, China.
| | - Guosheng Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, China
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40
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Development of a simple and sensitive method for the determination of virginiamycin M1 antibiotic by capillary electrophoresis. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02412-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Nielsen TK, Browne PD, Hansen LH. Antibiotic resistance genes are differentially mobilized according to resistance mechanism. Gigascience 2022; 11:6652189. [PMID: 35906888 PMCID: PMC9338424 DOI: 10.1093/gigascience/giac072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/16/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Screening for antibiotic resistance genes (ARGs) in especially environmental samples with (meta)genomic sequencing is associated with false-positive predictions of phenotypic resistance. This stems from the fact that most acquired ARGs require being overexpressed before conferring resistance, which is often caused by decontextualization of putative ARGs by mobile genetic elements (MGEs). Consequent overexpression of ARGs can be caused by strong promoters often present in insertion sequence (IS) elements and integrons and the copy number effect of plasmids, which may contribute to high expression of accessory genes. RESULTS Here, we screen all complete bacterial RefSeq genomes for ARGs. The genetic contexts of detected ARGs are investigated for IS elements, integrons, plasmids, and phylogenetic dispersion. The ARG-MOB scale is proposed, which indicates how mobilized detected ARGs are in bacterial genomes. It is concluded that antibiotic efflux genes are rarely mobilized and even 80% of β-lactamases have never, or very rarely, been mobilized in the 15,790 studied genomes. However, some ARGs are indeed mobilized and co-occur with IS elements, plasmids, and integrons. CONCLUSIONS In this study, ARGs in all complete bacterial genomes are classified by their association with MGEs, using the proposed ARG-MOB scale. These results have consequences for the design and interpretation of studies screening for resistance determinants, as mobilized ARGs pose a more concrete risk to human health. An interactive table of all results is provided for future studies targeting highly mobilized ARGs.
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Affiliation(s)
- Tue Kjærgaard Nielsen
- Department of Plant and Environmental Sciences, Section for Environmental Microbiology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Patrick Denis Browne
- Department of Plant and Environmental Sciences, Section for Environmental Microbiology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, Section for Environmental Microbiology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
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Liu Y, Cai Y, Li G, Wang W, Wong PK, An T. Response mechanisms of different antibiotic-resistant bacteria with different resistance action targets to the stress from photocatalytic oxidation. WATER RESEARCH 2022; 218:118407. [PMID: 35453030 DOI: 10.1016/j.watres.2022.118407] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/18/2022] [Accepted: 04/02/2022] [Indexed: 06/14/2023]
Abstract
The stress response of antibiotic-resistant bacteria (ARB) and the spread of antibiotic resistance genes (ARGs) pose a serious threat to the aquatic environment and human beings. This study mainly explored the effect of the heterogeneous photocatalytic oxidation (UVA-TiO2 system) on the stress response mechanism of ARB with different antibiotic resistance action targets, including the cell wall, proteins, DNA, RNA, folate and the cell membrane. Results indicate that the stress response mechanism of tetracycline- and sulfamethoxazole-resistant E. coli DH5α, which targets the synthesis of protein and folate, could rapidly induce global regulators by the overexpression of relative antibiotic resistance action target genes. Different stress response systems were mediated via cross-protection mechanism, causing stronger tolerance to an adverse environment than other ARB. Moreover, the photocatalytic inactivation mechanism of bacterial cells and a graded response of cellular stress mechanism caused differences in the intensity of the stress mechanism of antibiotic resistance action targets. E. coli DH5α resistant to cefotaxime and polymyxin, targeting synthesis of the cell wall and cell membrane, respectively, could confer greater advantages to bacterial survival and higher conjugative transfer frequency than E. coli DH5α resistant to nalidixic acid and rifampicin, which target the synthesis of DNA and RNA, respectively. This new perspective provides detailed information on the practical application of photocatalytic oxidation for inactivating ARB and hampering the spreading of ARGs in the aquatic environment.
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Affiliation(s)
- Yongjie Liu
- Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Technology Research Center for Photocatalytic Technology Integration and Equipment Engineering, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yiwei Cai
- Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Technology Research Center for Photocatalytic Technology Integration and Equipment Engineering, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Guiying Li
- Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Technology Research Center for Photocatalytic Technology Integration and Equipment Engineering, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Wanjun Wang
- Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Technology Research Center for Photocatalytic Technology Integration and Equipment Engineering, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Po Keung Wong
- Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Technology Research Center for Photocatalytic Technology Integration and Equipment Engineering, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
| | - Taicheng An
- Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Technology Research Center for Photocatalytic Technology Integration and Equipment Engineering, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
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Das S, Bombaywala S, Srivastava S, Kapley A, Dhodapkar R, Dafale NA. Genome plasticity as a paradigm of antibiotic resistance spread in ESKAPE pathogens. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:40507-40519. [PMID: 35349073 DOI: 10.1007/s11356-022-19840-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The major reason behind the spread of antibiotic resistance genes (ARGs) is persistent selective pressure in the environment encountered by bacteria. Genome plasticity plays a crucial role in dissemination of antibiotic resistance among bacterial pathogens. Mobile genetic elements harboring ARGs are reported to dodge bacterial immune system and mediate horizontal gene transfer (HGT) under selective pressure. Residual antibiotic pollutants develop selective pressures that force the bacteria to lose their defense mechanisms (CRISPR-cas) and acquire resistance. The present study targets the ESKAPE organisms (namely, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) causing various nosocomial infections and emerging multidrug-resistant species. The role of CRISPR-cas systems in inhibition of HGT in prokaryotes and its loss due to presence of various stressors in the environment is also focused in the study. IncF and IncH plasmids were identified in all strains of E. faecalis and K. pneumoniae, carrying Beta-lactam and fluoroquinolone resistance genes, whereas sal3, phiCTX, and SEN34 prophages harbored aminoglycoside resistance genes (aadA, aac). Various MGEs present in selected environmental niches that aid the bacterial genome plasticity and transfer of ARGs contributing to its spread are also identified.
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Affiliation(s)
- Sanchita Das
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Sakina Bombaywala
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 2010 20, India
| | - Shweta Srivastava
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 2010 20, India
| | - Atya Kapley
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Rita Dhodapkar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 2010 20, India.
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Wu X, Liu Z, Li M, Bartlam M, Wang Y. Integrated metagenomic and metatranscriptomic analysis reveals actively expressed antibiotic resistomes in the plastisphere. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128418. [PMID: 35144012 DOI: 10.1016/j.jhazmat.2022.128418] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/03/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
The plastisphere is viewed as a reservoir for the antibiotic resistome in water environments and may pose health concerns. However, the expression profiles of the resistome in the plastisphere are largely unknown. Here, we profiled the occurrence, abundance, and transcriptional level of antibiotic resistance genes (ARGs), plasmid associated ARGs, microbial composition and ARG bacterial hosts in the plastisphere and urban river water using 16S rRNA gene sequencing, metagenomic sequencing, and metatranscriptomic sequencing methods. A total of 173 ARGs conferring resistance to 24 major classes of antibiotics commonly prescribed to humans and animals were detected in the plastisphere. Of these, 75 genes were observed with transcriptional activity, indicating that the antibiotic resistome in the plastisphere was not only present, but also actively expressed. Human pathogens belonging to family Enterobacteriaceae were identified as bacterial hosts of ARGs in the plastisphere. The opportunistic and multidrug resistant human pathogen Enterobacter cloacae was found to actively express tetG and confer tetracycline resistance to the plastisphere. Furthermore, 39 genes were identified as "plasmid associated ARGs" in the plastisphere, displaying a higher proportion of transcript abundance compared with water. The above results suggest that the plastisphere is a hotspot for antibiotic resistome acquisition, expression, and dissemination.
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Affiliation(s)
- Xiaojian Wu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China
| | - Zongbao Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Mark Bartlam
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300071, China.
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China.
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45
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Gao M, Zhang X, Yue Y, Qiu T, Wang J, Wang X. Air path of antimicrobial resistance related genes from layer farms: Emission inventory, atmospheric transport, and human exposure. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128417. [PMID: 35183825 DOI: 10.1016/j.jhazmat.2022.128417] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/26/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Animal husbandry is a significant contributor to increased environmental antimicrobial resistance (AMR), but little is known regarding the dissemination of AMR from animal farms via airborne transmission. Here, we connected the air path of AMR related genes tailored to layer poultry farms from source of escape to end of sedimentation. The emission inventories of 8 AMR related genes from all 163-layer poultry farms around Beijing city were quantified. We developed the atmospheric transport model with a gene degradation module to estimate the spatiotemporal distribution of airborne AMR, and also assessed their corresponding regional exposure and sedimentation. Total emissions of 16 S rDNA and AMR related genes from layer houses ranged from 1015 to 1016 copies year-1. Those layer-sourced genes contributed 1-14.6% of antimicrobial resistant genes, 4.9% of Staphylococcus spp. and 2.2% of CintI1 to the corresponding annual genetic burden of Beijing's urban air. The average exposure of the Beijing residents to layer-sourced airborne 16 S rDNA was 1.39 × 104 copies year-1 person-1, approximately 87% of them would be deposited in the upper respiratory tract. The findings highlight that air medium represents an important dissemination pathway of animal-sourced genes to AMR burden in humans and environment.
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Affiliation(s)
- Min Gao
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaole Zhang
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland
| | - Yang Yue
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland
| | - Tianlei Qiu
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jing Wang
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland.
| | - Xuming Wang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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Crits-Christoph A, Hallowell HA, Koutouvalis K, Suez J. Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome. Gut Microbes 2022; 14:2055944. [PMID: 35332832 PMCID: PMC8959533 DOI: 10.1080/19490976.2022.2055944] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.
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Affiliation(s)
- Alexander Crits-Christoph
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Haley Anne Hallowell
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Kalia Koutouvalis
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jotham Suez
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA,CONTACT Jotham Suez Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, Maryland, USA, 21205
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47
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Evaluation of the Correspondence between the Concentration of Antimicrobials Entering Sewage Treatment Plant Influent and the Predicted Concentration of Antimicrobials Using Annual Sales, Shipping, and Prescriptions Data. Antibiotics (Basel) 2022; 11:antibiotics11040472. [PMID: 35453223 PMCID: PMC9027251 DOI: 10.3390/antibiotics11040472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 02/05/2023] Open
Abstract
The accuracy and correspondence between the measured concentrations from the survey and predicted concentrations on the basis of the three types of statistical antimicrobial use in Japan was evaluated. A monitoring survey of ten representative antimicrobials: ampicillin (APL), cefdinir (CDN), cefpodoxime proxetil (CPXP), ciprofloxacin (CFX), clarithromycin (CTM), doxycycline (DCL), levofloxacin (LFX), minocycline (MCL), tetracycline (TCL), and vancomycin (VMC), in the influent of sewage treatment plant (STP) located in urban areas of Japan, was conducted. Then, the measured values were verified in comparison with the predicted values estimated from the shipping volumes, sales volumes, and prescription volumes based on the National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB). The results indicate that the correspondence ratios between the predicted concentrations calculated on the basis of shipping and NDB volumes and the measured concentrations (predicted concentration/measured concentration) generally agreed for the detected concentration of antimicrobials in the STP influent. The correspondence ratio on the basis of shipping volume was, for CFX, 0.1; CTM, 2.9; LFX, 0.5; MCL, 1.9; and VMC, 1.7, and on the basis of NDB volume the measured concentration was CFX, 0.1; CTM, 3.7; DCL, 0.4; LFX, 0.7; MCL, 1.9; TCL, 0.6; and VMC, 1.6. To our knowledge, this is the first report to evaluate the accuracy of predicted concentrations based on sales, shipping, NDB statistics and measured concentrations for antimicrobials in the STP influent.
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Oxytetracycline Degrading Potential of Lysinibacillus sp. Strain 3+I Isolated from Poultry Manure. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:2750009. [PMID: 35368761 PMCID: PMC8970894 DOI: 10.1155/2022/2750009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/18/2022] [Indexed: 11/18/2022]
Abstract
Oxytetracycline (OTC) which is a broad-spectrum veterinary tetracycline antibiotic is extensively used in poultry farms as a prophylactic, therapeutic, and growth stimulator. Upon administration, unmetabolized OTC is excreted from the animal body through droppings and accumulated in litter in the poultry industry. This study aimed at investigating the OTC degradation potential of an-OTC tolerant bacterial strain, isolated from poultry manure. The isolated strain's morphology, biochemical properties, and 16S ribosomal RNA (rRNA) gene sequence confirmed that it belonged to the Lysinibacillus genus. To measure the residual OTC concentration, a high-performance liquid chromatography method was used. OTC degradation rates were 2.579 mg L−1d−1 with Lysinibacillus strain 3+I and 1.149 mg L−1d−1 without Lysinibacillus strain 3+I. In the presence of strain 3+I, the half-life significantly reduced to 2.68 days, compared to 6.03 days without strain 3+I. The strain demonstrated 85% removal with the OTC concentration of 10 μg/ml. The influence of pH, temperature, carbon sources, and nitrogen source, which influence degradation, were also investigated. The optimum condition favouring degradation was pH 6 at a temperature of 30°C. In addition, Lysinibacillus sp. strain 3+I's ability to degrade OTC in poultry litter offers a promising approach to treat poultry manure and effluent containing OTC, preventing its contamination in the environment.
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Hutinel M, Larsson DGJ, Flach CF. Antibiotic resistance genes of emerging concern in municipal and hospital wastewater from a major Swedish city. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:151433. [PMID: 34748849 DOI: 10.1016/j.scitotenv.2021.151433] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
Abstract
The spread of antibiotic resistance among bacterial pathogens is to a large extent mediated by mobile antibiotic resistance genes (ARGs). The prevalence and geographic distribution of several newly discovered ARGs, as well as some clinically important ARGs conferring resistance to last resort antibiotics, are largely unknown. Targeted analysis of wastewater samples could allow estimations of carriage in the population connected to the sewers as well as release to the environment. Here we quantified ARGs conferring resistance to linezolid (optrA and cfr(A)) and colistin (mcr-1, -2, -3, -4 and -5) and the recently discovered gar (aminoglycoside ARG) and sul4 (sulphonamide ARG) in raw hospital and municipal wastewater as well as treated municipal wastewater during five years in a low antibiotic resistance prevalence setting (Gothenburg, Sweden). Additionally, variations in bacterial composition of the wastewaters characterized by 16S rRNA sequencing were related to the variations of the ARGs in an attempt to reveal if the presence of known or suspected bacterial host taxa could explain the presence of the ARGs in wastewater. The mcr-1, mcr-3, mcr-4, mcr-5, sul4 and gar genes were detected regularly in all types of wastewater samples while optrA and cfr(A) were detected only in hospital wastewater. The most abundant genes were mcr-3 and mcr-5, especially in municipal wastewater. The detection of optrA was restricted to a peak during one year. Most of the ARGs correlated with taxa previously described as bacterial hosts and associated with humans. Although some of the tentative hosts may include bacteria also thriving in wastewater environments, detection of the ARGs in the wastewaters could reflect their presence in the gut flora of the contributing populations. If so, they could already today or in the near future hinder treatment of bacterial infections in a setting where they currently are rarely targeted/detected during clinical surveillance.
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Affiliation(s)
- Marion Hutinel
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden.
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50
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Ma N, Tong L, Li Y, Yang C, Tan Q, He J. Distribution of antibiotics in lake water-groundwater - Sediment system in Chenhu Lake area. ENVIRONMENTAL RESEARCH 2022; 204:112343. [PMID: 34748778 DOI: 10.1016/j.envres.2021.112343] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 10/01/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Antibiotics pollution in lakes has been widely reported worldwide, however rare studies were concerned about antibiotics distribution in lake water - groundwater - sediment system. Here, a total of 22 antibiotics and 4 sulfonamides metabolites were detected in lake water, sediments, and different depth of groundwater surrounding Chenhu Lake during the wet and dry seasons. N4-acetylsulfonamides (Ac-SAs), fluoroquinolones (FQs), and tetracyclines (TCs) were the main groups of antibiotics in the study area. In the whole lake environment, there were more types of antibiotics in the aquatic environments than in the sediments, and the antibiotics distribution was closely related to geographical location. Specifically, the average concentration of antibiotics in groundwater decreased with an increase in sampling site distance from the lake. All antibiotics, except oxytetracycline (OTC), showed a significant decline during the dry season that could be due to the implementation of lake conservation policies, which significantly helped reducing lake pollution. There were obvious differences in the distribution of antibiotics in distinct sedimentary environments. In the surface sediments, the antibiotics content in the reclamation and the perennially flooded areas was higher than in the lakeshore area. The hydraulic interactions in the perennial flooded area facilitated the deep migration of antibiotics into lake sediments. Correlation analysis revealed a good relevance between the distribution of antibiotics in lake water and groundwater. Redundancy analysis shows that dissolved oxygen and temperature were the main factors affecting the distribution of antibiotics.
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Affiliation(s)
- Naijin Ma
- School of Environmental Studies, China University of Geosciences, 430074, Wuhan, PR China
| | - Lei Tong
- School of Environmental Studies, China University of Geosciences, 430074, Wuhan, PR China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, PR China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, PR China.
| | - Yuqiong Li
- School of Environmental Studies, China University of Geosciences, 430074, Wuhan, PR China
| | - Cong Yang
- School of Environmental Studies, China University of Geosciences, 430074, Wuhan, PR China
| | - Qin Tan
- School of Environmental Studies, China University of Geosciences, 430074, Wuhan, PR China
| | - Jun He
- Wuhan Geological Survey Center, China Geological Survey, Wuhan, PR China
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