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Liu Y, Bailey KE, Dyall-Smith M, Marenda MS, Hardefeldt LY, Browning GF, Gilkerson JR, Billman-Jacobe H. Faecal microbiota and antimicrobial resistance gene profiles of healthy foals. Equine Vet J 2020; 53:806-816. [PMID: 33030244 DOI: 10.1111/evj.13366] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 09/02/2020] [Accepted: 09/20/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND The human and domestic animal faecal microbiota can carry various antimicrobial resistance genes (ARGs), especially if they have been exposed to antimicrobials. However, little is known about the ARG profile of the faecal microbiota of healthy foals. A high-throughput qPCR array was used to detect ARGs in the faecal microbiota of healthy foals. OBJECTIVES To characterise the faecal microbiota and ARG profiles in healthy Australian foals aged less than 1 month. STUDY DESIGN Observational study. METHODS The faecal microbiota and ARG profiles of 37 Thoroughbred foals with no known gastrointestinal disease or antimicrobial treatment were determined using 16S rRNA gene sequencing and a high-throughput ARG qPCR array. Each foal was sampled on one occasion. RESULTS Firmicutes and Bacteroidetes were dominant in the faecal microbiota. Foals aged 1-2 weeks had significantly lower microbiota richness than older foals. Tetracycline resistance genes were the most common ARGs in the majority of foals, regardless of age. ARGs of high clinical concern were rarely detected in the faeces. The presence of ARGs was associated with the presence of class I integron genes. MAIN LIMITATIONS Samples were collected for a case-control study so foals were not sampled longitudinally, and thus the development of the microbiota as individual foals aged could not be proven. The history of antimicrobial treatment of the dams was not collected and may have affected the microbiota of the foals. CONCLUSION The ARGs in foal faeces varied concomitantly with age-related microbiota shifts. The high abundance of tetracycline resistance genes was likely due to the dominance of Bacteroides spp.
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Affiliation(s)
- Yuhong Liu
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, Australia
| | - Kirsten E Bailey
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, Australia.,National Centre for Antimicrobial Stewardship, Peter Doherty Institute, Melbourne, Australia
| | - Michael Dyall-Smith
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, Australia
| | - Marc S Marenda
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, Australia
| | - Laura Y Hardefeldt
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, Australia.,National Centre for Antimicrobial Stewardship, Peter Doherty Institute, Melbourne, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, Australia.,National Centre for Antimicrobial Stewardship, Peter Doherty Institute, Melbourne, Australia
| | - James R Gilkerson
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, Australia
| | - Helen Billman-Jacobe
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, Australia.,National Centre for Antimicrobial Stewardship, Peter Doherty Institute, Melbourne, Australia
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152
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Marano RBM, Fernandes T, Manaia CM, Nunes O, Morrison D, Berendonk TU, Kreuzinger N, Tenson T, Corno G, Fatta-Kassinos D, Merlin C, Topp E, Jurkevitch E, Henn L, Scott A, Heß S, Slipko K, Laht M, Kisand V, Di Cesare A, Karaolia P, Michael SG, Petre AL, Rosal R, Pruden A, Riquelme V, Agüera A, Esteban B, Luczkiewicz A, Kalinowska A, Leonard A, Gaze WH, Adegoke AA, Stenstrom TA, Pollice A, Salerno C, Schwermer CU, Krzeminski P, Guilloteau H, Donner E, Drigo B, Libralato G, Guida M, Bürgmann H, Beck K, Garelick H, Tacão M, Henriques I, Martínez-Alcalá I, Guillén-Navarro JM, Popowska M, Piotrowska M, Quintela-Baluja M, Bunce JT, Polo-López MI, Nahim-Granados S, Pons MN, Milakovic M, Udikovic-Kolic N, Ory J, Ousmane T, Caballero P, Oliver A, Rodriguez-Mozaz S, Balcazar JL, Jäger T, Schwartz T, Yang Y, Zou S, Lee Y, Yoon Y, Herzog B, Mayrhofer H, Prakash O, Nimonkar Y, Heath E, Baraniak A, Abreu-Silva J, Choudhury M, Munoz LP, Krizanovic S, Brunetti G, Maile-Moskowitz A, Brown C, Cytryn E. A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants. ENVIRONMENT INTERNATIONAL 2020; 144:106035. [PMID: 32835921 DOI: 10.1016/j.envint.2020.106035] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 05/29/2023]
Abstract
The World Health Organization Global Action Plan recommends integrated surveillance programs as crucial strategies for monitoring antibiotic resistance. Although several national surveillance programs are in place for clinical and veterinary settings, no such schemes exist for monitoring antibiotic-resistant bacteria in the environment. In this transnational study, we developed, validated, and tested a low-cost surveillance and easy to implement approach to evaluate antibiotic resistance in wastewater treatment plants (WWTPs) by targeting cefotaxime-resistant (CTX-R) coliforms as indicators. The rationale for this approach was: i) coliform quantification methods are internationally accepted as indicators of fecal contamination in recreational waters and are therefore routinely applied in analytical labs; ii) CTX-R coliforms are clinically relevant, associated with extended-spectrum β-lactamases (ESBLs), and are rare in pristine environments. We analyzed 57 WWTPs in 22 countries across Europe, Asia, Africa, Australia, and North America. CTX-R coliforms were ubiquitous in raw sewage and their relative abundance varied significantly (<0.1% to 38.3%), being positively correlated (p < 0.001) with regional atmospheric temperatures. Although most WWTPs removed large proportions of CTX-R coliforms, loads over 103 colony-forming units per mL were occasionally observed in final effluents. We demonstrate that CTX-R coliform monitoring is a feasible and affordable approach to assess wastewater antibiotic resistance status.
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Affiliation(s)
- Roberto B M Marano
- Department of Agroecology and Plant Health, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel; Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel
| | - Telma Fernandes
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Olga Nunes
- LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Donald Morrison
- School Applied Sciences, Edinburgh Napier University, EH11 4BN, UK
| | | | - Norbert Kreuzinger
- Vienna University of Technology, Institute for Water Quality and Resources Management, Vienna, Austria
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Estonia
| | - Gianluca Corno
- CNR-IRSA Molecular Ecology Group, Largo Tonolli 50, 28922 Verbania, Italy
| | - Despo Fatta-Kassinos
- Civil and Environmental Engineering Department and Nireas International Water Research Center, University of Cyprus, P.O. Box 20537, CY-1678 Nicosia, Cyprus
| | | | - Edward Topp
- Agriculture and Agri-Food Canada, London Research and Development Centre (ON), Canada; Department of Biology, University of Western Ontario, London, ON, Canada
| | - Edouard Jurkevitch
- Department of Agroecology and Plant Health, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Leonie Henn
- School Applied Sciences, Edinburgh Napier University, EH11 4BN, UK
| | - Andrew Scott
- Agriculture and Agri-Food Canada, London Research and Development Centre (ON), Canada
| | - Stefanie Heß
- Institute of Hydrobiology, TU Dresden, Dresden, Germany; Institute of Microbiology, TU Dresden, Dresden, Germany
| | - Katarzyna Slipko
- Vienna University of Technology, Institute for Water Quality and Resources Management, Vienna, Austria
| | - Mailis Laht
- Institute of Technology, University of Tartu, Estonia; Estonian Environmental Research Centre, Estonia
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Estonia
| | - Andrea Di Cesare
- CNR-IRSA Molecular Ecology Group, Largo Tonolli 50, 28922 Verbania, Italy
| | - Popi Karaolia
- Civil and Environmental Engineering Department and Nireas International Water Research Center, University of Cyprus, P.O. Box 20537, CY-1678 Nicosia, Cyprus
| | - Stella G Michael
- Civil and Environmental Engineering Department and Nireas International Water Research Center, University of Cyprus, P.O. Box 20537, CY-1678 Nicosia, Cyprus
| | - Alice L Petre
- Department of Chemical Engineering, University of Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Roberto Rosal
- Department of Chemical Engineering, University of Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Virginia Riquelme
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ana Agüera
- Solar Energy Research Centre (CIESOL), Joint Centre University of Almería-CIEMAT, 04120 Almería, Spain
| | - Belen Esteban
- Solar Energy Research Centre (CIESOL), Joint Centre University of Almería-CIEMAT, 04120 Almería, Spain
| | - Aneta Luczkiewicz
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, G. Narutowicza 11/12 street, 80-233 Gdańsk, Poland
| | - Agnieszka Kalinowska
- Faculty of Civil and Environmental Engineering, Gdansk University of Technology, G. Narutowicza 11/12 street, 80-233 Gdańsk, Poland
| | - Anne Leonard
- University of Exeter Medical School, European Centre for Environment and Human Health, Environment and Sustainability Institute, University of Exeter, Penryn campus, TR10 9FE, UK
| | - William H Gaze
- University of Exeter Medical School, European Centre for Environment and Human Health, Environment and Sustainability Institute, University of Exeter, Penryn campus, TR10 9FE, UK
| | - Anthony A Adegoke
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban South Africa; Department of Microbiology, University of Uyo, Uyo, Nigeria
| | - Thor A Stenstrom
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban South Africa
| | | | | | - Carsten U Schwermer
- Norwegian Institute for Water Research, Gaustadalléen 21, N-0349 Oslo, Norway
| | - Pawel Krzeminski
- Norwegian Institute for Water Research, Gaustadalléen 21, N-0349 Oslo, Norway
| | | | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
| | - Giovanni Libralato
- Department of Biology, University of Naples Federico II, via Cinthia 21, 80126 Naples, Italy
| | - Marco Guida
- Department of Biology, University of Naples Federico II, via Cinthia 21, 80126 Naples, Italy
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Karin Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Hemda Garelick
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - Marta Tacão
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Portugal
| | - Isabel Henriques
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Portugal; University of Coimbra, Department of Life Sciences, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Isabel Martínez-Alcalá
- Department of Civil Engineering, Av. de los Jerónimos, 135, 30107 Guadalupe, Murcia, Spain
| | - Jose M Guillén-Navarro
- Department of Civil Engineering, Av. de los Jerónimos, 135, 30107 Guadalupe, Murcia, Spain
| | - Magdalena Popowska
- Institute of Microbiology, Department of Applied Microbiology, Faculty of Biology, University of Warsaw, Poland
| | - Marta Piotrowska
- Institute of Microbiology, Department of Applied Microbiology, Faculty of Biology, University of Warsaw, Poland
| | | | - Joshua T Bunce
- School of Engineering, Newcastle University, Newcastle Upon Tyne, UK
| | - Maria I Polo-López
- Solar Energy Research Centre (CIESOL), Joint Centre University of Almería-CIEMAT, 04120 Almería, Spain; Plataforma Solar de Almería - CIEMAT, P.O. Box 22, 04200 Tabernas, Almería, Spain
| | - Samira Nahim-Granados
- Solar Energy Research Centre (CIESOL), Joint Centre University of Almería-CIEMAT, 04120 Almería, Spain; Plataforma Solar de Almería - CIEMAT, P.O. Box 22, 04200 Tabernas, Almería, Spain
| | | | | | | | - Jérôme Ory
- Laboratoire "Microorganisme: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France; CNRS, UMR 6023, LMGE, F-63170 Campus Universitaire des Cézeaux, Clermont-Ferrand, France; Service d'hygiène hospitalière, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Traore Ousmane
- Laboratoire "Microorganisme: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France; CNRS, UMR 6023, LMGE, F-63170 Campus Universitaire des Cézeaux, Clermont-Ferrand, France; Service d'hygiène hospitalière, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | | | - Antoni Oliver
- Laboratori EMATSA, Ctra Valls Km 3, 43130 Tarragona, Spain
| | | | - Jose L Balcazar
- Catalan Institute for Water Research (ICRA), 17003 Girona, Spain
| | - Thomas Jäger
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Thomas Schwartz
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Ying Yang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shichun Zou
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yunho Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Younggun Yoon
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Bastian Herzog
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), Germany
| | - Heidrun Mayrhofer
- Chair of Urban Water Systems Engineering, Technical University of Munich (TUM), Germany
| | - Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Pune 411007, India
| | - Yogesh Nimonkar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Pune 411007, India
| | - Ester Heath
- Jozef Stefan Institute, Jamova 39 1000 Ljubljana, Slovenia
| | - Anna Baraniak
- National Medicines Institute, Department of Molecular Microbiology, Chelmska 30/34, 00-725 Warsaw, Poland
| | - Joana Abreu-Silva
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Manika Choudhury
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - Leonardo P Munoz
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | | | - Gianluca Brunetti
- Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
| | | | - Connor Brown
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Eddie Cytryn
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil Water and Environmental Sciences, Volcani Center, Agricultural Research Organization, Rishon Lezion, Israel.
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153
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Sun J, Jin L, He T, Wei Z, Liu X, Zhu L, Li X. Antibiotic resistance genes (ARGs) in agricultural soils from the Yangtze River Delta, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 740:140001. [PMID: 32569910 DOI: 10.1016/j.scitotenv.2020.140001] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/28/2020] [Accepted: 06/03/2020] [Indexed: 05/23/2023]
Abstract
As an important reservoir of intrinsic antimicrobial resistance, soil is subjected to increasing anthropogenic activities that creates sustained selection pressure for the prevalence of antibiotic resistance genes (ARGs), thus constituting an important environmental dissemination pathway to human exposure. This study investigated the levels and spatial distributions of three classes of ARGs in relation to a range of co-occurring chemical mixtures and soil properties at a regional scale of the Yangtze River Delta (YRD), China. The selected eight ARGs were all detected in 241 agricultural soil samples with relative abundances ranging from 1.01 × 10-7 to 2.31 × 10-1 normalized to the 16S rRNA gene. The sulII and tetG were the dominant ARGs with a mean relative abundance of 6.67 × 10-3 and 5.25 × 10-3, respectively. The ARGs were mainly present in agricultural soils alongside Taihu Lake and Shanghai municipality, the most agriculturally and economically vibrant area of the YRD region. Antibiotics, rather than other co-occurring pollutants and soil properties, remain to be the dominant correlate to the ARGs, suggesting their co-introduction into the soils via irrigation and manure application or the sustained selection pressure of antibiotics from these sources for the proliferation of ARGs in the soils. While the current dataset provided useful information to assess the ARGs pollution for mitigation, future studies are warranted to reveal the complete picture on the potential transfer of antimicrobial resistance from soil to agricultural produces to human consumption and associated health implications.
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Affiliation(s)
- Jianteng Sun
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China; Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China; Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Ling Jin
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Tangtian He
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Zi Wei
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Xinyi Liu
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Xiangdong Li
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
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154
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Fan K, Delgado-Baquerizo M, Guo X, Wang D, Zhu YG, Chu H. Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment. ISME JOURNAL 2020; 15:550-561. [PMID: 33028975 DOI: 10.1038/s41396-020-00796-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 12/13/2022]
Abstract
Cropping systems have fertilized soils for decades with undetermined consequences for the productivity and functioning of terrestrial ecosystems. One of the critical unknowns is the role of soil biodiversity in controlling crop production after decades of fertilization. This knowledge gap limits our capacity to assess how changes in soil biodiversity could alter crop production and soil health in changing environments. Here, we used multitrophic ecological networks to investigate the importance of soil biodiversity, in particular, the biodiversity of key-stone taxa in controlling soil functioning and wheat production in a 35-year field fertilization experiment. We found strong and positive associations between soil functional genes, crop production and the biodiversity of key-stone phylotypes; soils supporting a larger number of key-stone nematode, bacteria and fungi phylotypes yielded the highest wheat production. These key-stone phylotypes were also positively associated with plant growth (phototrophic bacteria, nitrogen fixers) and multiple functional genes related to nutrient cycling. The retrieved information on the genomes clustered with key-stone bacterial phylotypes indicated that the key-stone taxa had higher gene copies of oxidoreductases (participating most biogeochemical cycles of ecosystems and linking to microbial energetics) and 71 essential functional genes associated with carbon, nitrogen, phosphorus, and sulfur cycling. Altogether, our work highlights the fundamental role of the biodiversity of key-stone phylotypes in maintaining soil functioning and crop production after several decades of fertilization, and provides a list of key-stone phylotypes linking to crop production and soil nutrient cycling, which could give science-based guidance for sustainable food production.
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Affiliation(s)
- Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Xisheng Guo
- Institute of Soil and Fertilizer Research, Anhui Academy of Agricultural Sciences, South Nongke Road 40, Hefei, 230031, China
| | - Daozhong Wang
- Institute of Soil and Fertilizer Research, Anhui Academy of Agricultural Sciences, South Nongke Road 40, Hefei, 230031, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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155
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Liang Z, Yu Y, Ye Z, Li G, Wang W, An T. Pollution profiles of antibiotic resistance genes associated with airborne opportunistic pathogens from typical area, Pearl River Estuary and their exposure risk to human. ENVIRONMENT INTERNATIONAL 2020; 143:105934. [PMID: 32645489 DOI: 10.1016/j.envint.2020.105934] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/19/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
To reveal the selective pressures of near-shore human activities on marine and continental bioaerosols, the pollution profile and potential exposure risk of airborne pathogens and antibiotic-resistance genes (ARGs) in Pearl River Estuaries (113.52 oE, 22.69 oN), a transitional zone between marine and continental environments, were fully explored. The results showed that the total bacteria among bioaerosols varied largely with average pollution levels of 1.86 × 105 and 4.35 × 104 cfu m-3 in spring and summer, respectively, and were high than those of airborne fungi. The predominant aerodynamic diameters of bioaerosols were in respirable size range (<4.7 µm), and the microbes communities' diversity and abundance varied significantly. Besides, many opportunistic pathogenic bacteria (Burkholderia-Paraburkholderia, Staphylococcus and Acinetobacter) and fungi (Alternaria, Penicillium and Cladosporium) were dominant in bioaerosol samples. Of 21 ARGs subtypes detected, the tetracycline resistance gene tetA was the most abundant, followed by aminoglycoside resistance gene and mobile genetic elements. Correlation analysis revealed that the changes of pathogens community contributed significantly to the prevalence of ARGs in bioaerosol. Based on the average daily dose rates of microorganisms and human direct intake of ARGs, health risk of bioaerosols from the Pearl River Estuaries were also evaluated. In summary, the presence of opportunistic pathogens and diversity of ARGs strengthens the call to consider the bioaerosol in air quality monitoring and risk assessment in the future.
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Affiliation(s)
- Zhishu Liang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Yun Yu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Zikai Ye
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Guiying Li
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Wanjun Wang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Taicheng An
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
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156
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Shi Y, Delgado-Baquerizo M, Li Y, Yang Y, Zhu YG, Peñuelas J, Chu H. Abundance of kinless hubs within soil microbial networks are associated with high functional potential in agricultural ecosystems. ENVIRONMENT INTERNATIONAL 2020; 142:105869. [PMID: 32593837 DOI: 10.1016/j.envint.2020.105869] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/22/2020] [Accepted: 05/16/2020] [Indexed: 05/14/2023]
Abstract
Microbial taxa within complex ecological networks can be classified by their universal roles based on their level of connectivity with other taxa. Highly connected taxa within an ecological network (kinless hubs) are theoretically expected to support higher levels of ecosystem functions than less connected taxa (peripherals). Empirical evidence of the role of kinless hubs in regulating the functional potential of soil microbial communities, however, is largely unexplored and poorly understood in agricultural ecosystems. Here, we built a correlation network of fungal and bacterial taxa using a large-scale survey consisting of 243 soil samples across functionally and economically important agricultural ecosystems (wheat and maize); and found that the relative abundance of taxa classified as kinless hubs within the ecological network are positively and significantly correlated with the abundance of functional genes including genes for C fixation, C degradation, C methanol, N cycling, P cycling and S cycling. Structural equation modeling of multiple soil properties further indicated that kinless hubs, but not provincial, connector or peripheral taxa, had direct significant and positive relationships with the abundance of multiple functional genes. Our findings provide novel evidence that the relative abundance of soil taxa classified as kinless hubs within microbial networks are associated with high functional potential, with implications for understanding and managing (through manipulating microbial key species) agricultural ecosystems at a large spatial scale.
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Affiliation(s)
- Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Yuntao Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Lab of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Catalonia E-08193, Spain; CREAF, Cerdanyola del Vallès, Catalonia E-08193, Spain
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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157
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Xu L, Campos LC, Canales M, Ciric L. Drinking water biofiltration: Behaviour of antibiotic resistance genes and the association with bacterial community. WATER RESEARCH 2020; 182:115954. [PMID: 32650149 DOI: 10.1016/j.watres.2020.115954] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 05/07/2020] [Accepted: 05/15/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance genes (ARGs) are being detected in drinking water frequently, constituting a major public health issue. As a typical drinking water treatment process, the biofilter may harbour various ARGs due to the filter biofilms established during the filtration process. The objective of this study was to investigate the behaviour of ARGs (blaCTX-M, blaOXA-1, blaTEM, ermB, tetA, tetG, tetQ, tetW, tetX, sul 1, sul 2, dfrA1 and dfrA12) and their possible association with bacteria in a bench-scale biofiltration system. The impact of filter media on horizontal gene transfer (HGT) was also explored using a model conjugative plasmid, RP1. The biofiltration system comprised four types of biofilters, including sand, granular activated carbon (GAC), GAC sandwich, and anthracite-sand biofilters. Results showed that although the absolute abundance of ARGs decreased (0.97-log reduction on average), the ARGs' abundance normalised to bacterial numbers showed an increasing trend in the filtered water. Biofilms collected from the surface layer revealed the lowest relative abundance of ARGs (p < 0.01) compared to the deeper layer biofilms, indicating that the proportion of ARG-carrying bacteria was greater in the lower position. Most chosen ARG numbers correlated to Proteobacteria, Acidobacteria and Nitrospirae phyla, which accounted for 51.9%, 5.2% and 2.0% of the biofilm communities, respectively. GAC media revealed the highest transfer frequency (2.60 × 10-5), followed by anthracite (5.31 × 10-6) and sand (2.47 × 10-6). Backwashing can reduce the transferability of RP1 plasmid significantly in biofilms but introduces more transconjugants into the planktonic phase. Overall, the results of this study could enhance our understanding of the prevalence of ARGs in drinking water biofiltration treatment.
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Affiliation(s)
- Like Xu
- Department of Civil, Environmental & Geomatic Engineering, University College London, London, WC1E 6BT, UK
| | - Luiza C Campos
- Department of Civil, Environmental & Geomatic Engineering, University College London, London, WC1E 6BT, UK
| | - Melisa Canales
- Department of Civil, Environmental & Geomatic Engineering, University College London, London, WC1E 6BT, UK
| | - Lena Ciric
- Department of Civil, Environmental & Geomatic Engineering, University College London, London, WC1E 6BT, UK.
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158
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Zhao Y, Chen Z, Hou J, Mao D, Lin H, Xue Y, Luo Y. Monitoring antibiotic resistomes and bacterial microbiomes in the aerosols from fine, hazy, and dusty weather in Tianjin, China using a developed high-volume tandem liquid impinging sampler. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:139242. [PMID: 32438084 DOI: 10.1016/j.scitotenv.2020.139242] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Accurate quantification of the airborne antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) is critically important to assess their health risks. However, the currently widely used high-volume filter sampler (HVFS) often causes the desiccation of the sample, interfering with subsequent bacterial culture. To overcome this limitation, a high-volume tandem liquid impinging sampler (HVTLIS) was developed and optimized to investigate the airborne bacterial microbiomes and antibiotic resistomes under different weathers in Tianjin, China. Results revealed that HVTLIS can capture significantly more diverse culturable bacteria, ARB, and ARGs than HVFS. Compared with fine and hazy weathers, dusty weather had significantly more diverse and abundant airborne bacteria, ARGs, and human opportunistic pathogens with the resistance to last-resort antibiotics of carbapenems and polymyxin B, implicating a potential human health threat of dusty bioaerosols. Intriguingly, we represented the first report of Saccharibacteria predominance in the bioaerosol, demonstrating that the potential advantage of HVTLIS in collecting airborne microbes.
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Affiliation(s)
- Yanhui Zhao
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Zeyou Chen
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Jie Hou
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- Medical College, Nankai University, Tianjin 300071, China
| | - Huai Lin
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Yingang Xue
- Key Laboratory of Environmental Protection of Water Environment Biological Monitoring of Jiangsu Province, Changzhou Environmental Monitoring Center, Changzhou 213001, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China.
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159
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Kanger K, Guilford NGH, Lee H, Nesbø CL, Truu J, Edwards EA. Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard. FEMS Microbiol Ecol 2020; 96:5700280. [PMID: 31922542 DOI: 10.1093/femsec/fiaa006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/09/2020] [Indexed: 11/13/2022] Open
Abstract
Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.
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Affiliation(s)
- Kärt Kanger
- Faculty of Science and Technology, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Nigel G H Guilford
- BioZone Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - HyunWoo Lee
- BioZone Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Camilla L Nesbø
- BioZone Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada.,Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
| | - Jaak Truu
- Faculty of Science and Technology, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Elizabeth A Edwards
- BioZone Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
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160
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Cheng J, Tang X, Liu C. Occurrence and distribution of antibiotic resistance genes in various rural environmental media. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:29191-29203. [PMID: 32436087 DOI: 10.1007/s11356-020-09287-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance genes (ARGs) in rural environments have been poorly characterized in the literature. In this study, the diversity, abundance, and distribution of ARGs in surface waters, soils, and sediments of a typical hilly rural area in the Upper Yangtze River watershed were investigated using the high-throughput quantitative polymerase chain reaction, and their relationships with chemical properties of the samples were analyzed. No significant differences in the diversity and abundance of ARGs were observed among the three medium types while the ARG distribution pattern in the sediments was obviously different from that of the surface waters. According to the co-occurrence pattern of ARGs subtypes obtained by network analysis, blaOXA10-02, blaPSE, lnuB-02, and qacEΔ1-01 can be used to estimate the relative abundance of total ARGs for the study area. It appeared that the prevalence of ARGs in the sediments was promoted by the horizontal gene transfer (HGT) and vertical gene transfer together, while their spread in the surface waters and soils were facilitated by the supply of biogenic elements and HGT, respectively. Mobile genetic elements (MGEs) were abundant and detected in all samples, and their abundance was significantly and positively correlated with that of ARGs, implying that the potential horizontal transfer of ARGs to other bacteria and pathogens in rural environments should not be overlooked.
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Affiliation(s)
- Jianhua Cheng
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiangyu Tang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Chen Liu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
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161
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Yang Y, Wan K, Yang Z, Li D, Li G, Zhang S, Wang L, Yu X. Inactivation of antibiotic resistant Escherichia coli and degradation of its resistance genes by glow discharge plasma in an aqueous solution. CHEMOSPHERE 2020; 252:126476. [PMID: 32229364 DOI: 10.1016/j.chemosphere.2020.126476] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 06/10/2023]
Abstract
Emerging contaminants such as antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are becoming a global environmental problem. In this study, the glow discharge plasma (GDP) was applied for degrading antibiotic resistant Escherichia coli (E. coli) with resistance genes (tetA, tetR, aphA) and transposase gene (tnpA) in 0.9% sterile saline. The results showed that GDP was able to inactivate the antibiotic resistant E. coli and remove the ARGs and reduce the risk of gene transfer. The levels of E. coli determined by 16S rRNA decreased by approximately 4.7 logs with 15 min of discharge treatment. Propidium monoazide - quantitative polymerase chain reaction (PMA-qPCR) tests demonstrated that the cellular structure of 4.8 more logs E. coli was destroyed in 15 min. The reduction of tetA, tetR, aphA, tnpA genes was increased to 5.8, 5.4, 5.3 and 5.5 logs with 30 min discharge treatment, respectively. The removal of ARGs from high salinity wastewater was also investigated. The total abundance of ARGs was reduced by 3.9 logs in 30 min. Scavenging tests indicated that hydroxyl radicals (·OH) was the most probable agents for bacteria inactivation and ARGs degradation. In addition, the active chlorine (Cl· and Cl2) which formed during the discharge may also contribute to the inactivation and degradation.
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Affiliation(s)
- Ye Yang
- College of Environmental Science & Engineering, Xiamen University of Technology, Xiamen, 361024, P. R. China; College of Geography & Environmental Sciences, Northwest Normal University, Lanzhou, 730070, P. R. China
| | - Kun Wan
- Key Lab of Urban Environment & Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, P. R. China; College of the Environment & Ecology, Xiamen University, Xiamen, 361005, P. R. China
| | - Zhipeng Yang
- College of Environmental Science & Engineering, Xiamen University of Technology, Xiamen, 361024, P. R. China
| | - Dailin Li
- College of Environmental Science & Engineering, Xiamen University of Technology, Xiamen, 361024, P. R. China
| | - Guoxin Li
- College of Environmental Science & Engineering, Xiamen University of Technology, Xiamen, 361024, P. R. China
| | - Songlin Zhang
- College of Geography & Environmental Sciences, Northwest Normal University, Lanzhou, 730070, P. R. China
| | - Lei Wang
- College of Environmental Science & Engineering, Xiamen University of Technology, Xiamen, 361024, P. R. China.
| | - Xin Yu
- Key Lab of Urban Environment & Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, P. R. China; College of the Environment & Ecology, Xiamen University, Xiamen, 361005, P. R. China.
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162
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Association of sputum microbiome with clinical outcome of initial antibiotic treatment in hospitalized patients with acute exacerbations of COPD. Pharmacol Res 2020; 160:105095. [PMID: 32730904 DOI: 10.1016/j.phrs.2020.105095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/17/2020] [Accepted: 07/19/2020] [Indexed: 12/14/2022]
Abstract
Identification of risk factors for antibiotic treatment failure is urgently needed in acute exacerbations of chronic obstructive pulmonary disease (AECOPD). Here we investigated the relationship between sputum microbiome and clinical outcome of choice of initial antibiotics during hospitalization of AECOPD patients. Sputum samples of 41 AECOPD patients and 26 healthy controls were collected from Guangzhou Medical University, China. Samples were processed for 16S rRNA gene-based microbiome profiling. Thirty patients recovered with initial antibiotic treatment (antibiotic success or AS), while 11 patients showed poor outcome (antibiotic failure or AF). Substantial differences in microbiome were observed in AF versus AS patients and healthy controls. There was significantly decreased alpha diversity and increased relative abundances of Pseudomonas, Achromobacter, Stenotrophomonas and Ralstonia in AF patients. Conversely, Prevotella, Peptostreptococcus, Leptotrichia and Selenomonas were depleted. The prevalence of Selenomonas was markedly reduced in AF versus AS patients (9.1 % versus 60.0 %, P = 0.004). The AF patients with similar microbiome profiles in general responded well to the same new antibiotics in the adjusted therapy, indicating sputum microbiome may help guide the adjustment of antibiotics. Random forest analysis identified five microbiome operational taxonomic units together with C-reactive protein, procalcitonin and blood neutrophil count showing best predictability for antibiotic treatment outcome (area under curve 0.885). Functional inference revealed an enrichment of microbial genes in xenobiotic metabolism and antimicrobial resistance in AF patients, whereas genes in DNA repair and amino acid metabolism were depleted. Sputum microbiome may determine the clinical outcome of initial antibiotic treatment and be considered in the risk management of antibiotics in AECOPD.
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163
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Lau CHF, Tien YC, Stedtfeld RD, Topp E. Impacts of multi-year field exposure of agricultural soil to macrolide antibiotics on the abundance of antibiotic resistance genes and selected mobile genetic elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138520. [PMID: 32330714 DOI: 10.1016/j.scitotenv.2020.138520] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 06/11/2023]
Abstract
Exposure of environmental bacteria to antibiotics may be increasing the global resistome. Antibiotic residues are entrained into agricultural soil through the application of animal and human wastes, and irrigation with reclaimed water. The impact of a mixture of three macrolide antibiotics on the abundance of selected genes associated with antibiotic resistance and genetic mobility were determined in a long-term field experiment undertaken in London, Canada. Replicated plots received annual applications of a mixture of erythromycin, clarithromycin and azithromycin every spring since 2010. Each antibiotic was added directly to the soil at a concentration of either 0.1 or 10 mg kg soil-1 and all plots were cropped to soybeans. By means of qPCR, no gene targets were enriched in soil exposed to the 0.1 mg kg soil-1 dose compared to untreated control. In contrast, the relative abundance of several gene targets including int1, sul2 and mphE increased significantly with the annual exposure to the 10 mg kg soil-1 dose. By means of high-throughput qPCR, numerous gene targets associated with resistance to aminoglycosides, sulfonamides, trimethoprim, streptomycin, quaternary ammonium chemicals as well as mobile genetic elements (tnpA, IS26 and IS6100) were detected in soil exposed to 10 mg kg soil-1, but not the lower dose. Overall, exposure of soil to macrolide antibiotics increased the relative abundance of numerous gene targets associated with resistance to macrolides and other antibiotics, and mobile genetic elements. This occurred at an exposure dose that is unrealistically high, but did not occur at the lower more realistic exposure dose.
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Affiliation(s)
- Calvin Ho-Fung Lau
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Yuan-Ching Tien
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada; Department of Biology, University of Western Ontario, London, ON, Canada.
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164
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Grembi JA, Mayer-Blackwell K, Luby SP, Spormann AM. High-Throughput Multiparallel Enteropathogen Detection via Nano-Liter qPCR. Front Cell Infect Microbiol 2020; 10:351. [PMID: 32766166 PMCID: PMC7381150 DOI: 10.3389/fcimb.2020.00351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/08/2020] [Indexed: 11/13/2022] Open
Abstract
Quantitative molecular diagnostic methods can effectively detect pathogen-specific nucleic acid sequences, but costs associated with multi-pathogen panels hinder their widespread use in research trials. Nano-liter qPCR (nL-qPCR) is a miniaturized tool for quantification of multiple targets in large numbers of samples based on assay parallelization on a single chip, with potentially significant cost-savings due to rapid throughput and reduced reagent volumes. We evaluated a suite of novel and published assays to detect 17 enteric pathogens using a commercially available nL-qPCR technology. Amplification efficiencies ranged from 88 to 98% (mean 91%) and were reproducible across four operators at two separate facilities. When applied to fecal material, assays were sensitive and selective (99.8% of DNA amplified were genes from the target organism). Due to nanofluidic volumes, detection limits were 1-2 orders of magnitude less sensitive for nL-qPCR than an enteric TaqMan Array Card (TAC). However, higher detection limits do not hinder detection of diarrhea-causing pathogen concentrations. Compared to TAC, nL-qPCR displayed 99% (95% CI 0.98, 0.99) negative percent agreement and 62% (95% CI 0.59, 0.65) overall positive percent agreement for presence of pathogens across diarrheal and non-diarrheal fecal samples. Positive percent agreement was 89% among samples with concentrations above the nL-qPCR detection limits. nL-qPCR assays showed an underestimation bias of 0.34 log10 copies/gram of stool [IQR -0.40, -0.28] compared with TAC. With 12 times higher throughput for a sixth of the per-sample cost of the enteric TAC, the nL-qPCR chip is a viable alternative for enteropathogen quantification for studies where other technologies are cost-prohibitive.
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Affiliation(s)
- Jessica A Grembi
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States
| | - Koshlan Mayer-Blackwell
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States
| | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, United States
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States.,Department of Chemical Engineering, Stanford University, Stanford, CA, United States
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165
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Wang L, Wang J, Wang J, Zhu L, Conkle JL, Yang R. Soil types influence the characteristic of antibiotic resistance genes in greenhouse soil with long-term manure application. JOURNAL OF HAZARDOUS MATERIALS 2020; 392:122334. [PMID: 32092657 DOI: 10.1016/j.jhazmat.2020.122334] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 02/10/2020] [Accepted: 02/15/2020] [Indexed: 06/10/2023]
Abstract
Composted livestock and poultry manure, which may contain antibiotic resistance genes (ARGs), is widely used as natural fertilizer in China. But the influence of soil types on ARGs is not well characterized, particularly at greenhouse sites with long-term manure application. We investigated the distribution of ARGs in the cinnamon, fluvo-aquic and saline-alkali soils in greenhouse of Yellow River Delta region, China. A total of 193 ARGs subtypes were detected, with multidrug and aminoglycoside resistance genes as the most universal ARGs subtypes. Soil types influenced the ARGs distribution, where higher levels of diversity and relative abundance of ARGs in the fluvo-aquic and saline-alkali soils compared with those in the cinnamon soils. Among abiotic factors, sand, pH and Zn contributed more to the pattern of ARGs in the cinnamon soils, whereas sand and Cd, clay and Pb contributed the most in the fluvo-aquic and saline-alkali soils respectively. Furthermore, positive correlations between the relative abundances of ARGs and mobile genetic elements (MGEs) in the fluvo-aquic soils, suggesting higher dissemination potential of ARGs in this type of soil. Overall, MGEs played a positive primary role in the ARGs distribution in greenhouse soil than heavy metal co-selection and soil physicochemical properties.
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Affiliation(s)
- Lanjun Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Jinhua Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Jun Wang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Lusheng Zhu
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
| | - Jeremy L Conkle
- Department of Physical & Environmental Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, 78412, United States.
| | - Rui Yang
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, Taian, 271018, China.
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166
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Liu X, Wang H, Zhao H. Propagation of antibiotic resistance genes in an industrial recirculating aquaculture system located at northern China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 261:114155. [PMID: 32066059 DOI: 10.1016/j.envpol.2020.114155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/02/2020] [Accepted: 02/08/2020] [Indexed: 06/10/2023]
Abstract
The increasing prevalence and spread of antibiotic resistance genes (ARGs) in intensive aquaculture environments are of great concern to food safety and public health. However, the level of ARGs and their potential propagation factors in an industrial recirculating aquaculture system (RAS) have not previously been comprehensive explored. In this study, the levels of 14 different ARG markers and 2 kinds of mobile genetic elements (MGEs) were investigated in a RAS (including water, fish, feces, pellet feed meal, and biofilm samples) located northern China. qnrA, qnrB, qnrS, qepA, aac(6')-Ib, and floR were dominant ARGs, which average concentration levels were presented at 4.51-7.74 copies/L and 5.36-13.07 copies/g, respectively, suggesting that ARGs were prevalent in RAS with no recorded history of antibiotic use. Elevated level of ARGs was found in water of RAS even after the final UV treatment compared with its influent. In RAS, Proteobacteria, Verrucomicrobia, Bacteroidetes, and Planctomycetes were the predominant phyla. Notably, elevated levels of potential opportunistic pathogens were observed along with abundant ARGs suggesting an increasing risk of capturing ARGs and MGEs for human pathogens. This study has revealed for the first time that reared fish, their feces, pellet feed meal as the introduction sources and the selection roles of treatment units co-driven the ARG profile, and the co-selection of water environmental factors and their consequently induced bacterial community shifts formed by their influence are the determining drivers for the ARG propagation in RAS.
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Affiliation(s)
- Xuan Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Hua Wang
- School of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Huimin Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
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167
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Wu W, Liao R, Hu Y, Wang H, Liu H, Yin S. Quantitative assessment of groundwater pollution risk in reclaimed water irrigation areas of northern China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 261:114173. [PMID: 32078883 DOI: 10.1016/j.envpol.2020.114173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/26/2020] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
The application of reclaimed water for agricultural irrigation can effectively reduce the use of freshwater resources including groundwater, addressing the increasingly severe challenge of water shortage. However, reclaimed water irrigation will cause potential pollution risks to groundwater, which needs to be further studied to ensure the safety of reclaimed water irrigation. An integrated quantitative assessment system including the modified DRASTIC model was developed to evaluate the pollution risks caused by reclaimed water irrigation and scientific strategies were offered for the development of reclaimed water irrigation in water shortage areas to avoid groundwater pollution. The groundwater intrinsic vulnerability index, the hazards of the characteristic pollutants, and the groundwater values were quantified to obtain the pollution risks distribution map. In the Beijing plain of north China, the low groundwater pollution risk areas were located in the midstream of Chaobai river baisin, Beiyun river basin, and Yongding river basin, accounting for 48.3% of the total study area. These areas in low pollution risk can be considered as safety areas for reclaimed water irrigation. The moderate groundwater pollution risk areas accounting for 46.9% of the total study area were suggested to apply water-saving irrigation measures for preventing groundwater pollution. The reclaimed water irrigation should be prohibited in the high groundwater pollution risk areas, which accounted for 4.8% of the total study area. This study highlights the reasonable strategy for the development of reclaimed water irrigation in water shortage areas and lay a foundation for finding alternative water sources for agricultural irrigation.
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Affiliation(s)
- Wenyong Wu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, 100048, China
| | - Renkuan Liao
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, 100048, China; Department of Biological & Environmental Engineering, Cornell University, Ithaca, NY, 14853, United States.
| | - Yaqi Hu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, 100048, China
| | - Hao Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, 100048, China
| | - Honglu Liu
- Engineering Technique Research Center for the Exploration and Utilization of Non-Conventional Water Resources and Water Use Efficiency, Beijing, 100048, China
| | - Shiyang Yin
- Engineering Technique Research Center for the Exploration and Utilization of Non-Conventional Water Resources and Water Use Efficiency, Beijing, 100048, China
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168
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Fu W, Wang C, Zhu P, Xu W, Li X, Zhu S. A universal analytical approach for screening and monitoring of authorized and unauthorized GMOs. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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169
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Loayza F, Graham JP, Trueba G. Factors Obscuring the Role of E. coli from Domestic Animals in the Global Antimicrobial Resistance Crisis: An Evidence-Based Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E3061. [PMID: 32354184 PMCID: PMC7246672 DOI: 10.3390/ijerph17093061] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 01/01/2023]
Abstract
Recent studies have found limited associations between antimicrobial resistance (AMR) in domestic animals (and animal products), and AMR in human clinical settings. These studies have primarily used Escherichia coli, a critically important bacterial species associated with significant human morbidity and mortality. E. coli is found in domestic animals and the environment, and it can be easily transmitted between these compartments. Additionally, the World Health Organization has highlighted E. coli as a "highly relevant and representative indicator of the magnitude and the leading edge of the global antimicrobial resistance (AMR) problem". In this paper, we discuss the weaknesses of current research that aims to link E. coli from domestic animals to the current AMR crisis in humans. Fundamental gaps remain in our understanding the complexities of E. coli population genetics and the magnitude of phenomena such as horizontal gene transfer (HGT) or DNA rearrangements (transposition and recombination). The dynamic and intricate interplay between bacterial clones, plasmids, transposons, and genes likely blur the evidence of AMR transmission from E. coli in domestic animals to human microbiota and vice versa. We describe key factors that are frequently neglected when carrying out studies of AMR sources and transmission dynamics.
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Affiliation(s)
- Fernanda Loayza
- Microbiology Institute, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Diego de Robles y Pampite, Cumbayá-Quito P.O. BOX 170901, Ecuador
| | - Jay P. Graham
- Berkeley School of Public Health, University of California, 2121 Berkeley Way, Room 5302, Berkeley, CA 94720-7360, USA
| | - Gabriel Trueba
- Microbiology Institute, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Diego de Robles y Pampite, Cumbayá-Quito P.O. BOX 170901, Ecuador
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170
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Yu K, Li P, Chen Y, Zhang B, Huang Y, Huang FY, He Y. Antibiotic resistome associated with microbial communities in an integrated wastewater reclamation system. WATER RESEARCH 2020; 173:115541. [PMID: 32036288 DOI: 10.1016/j.watres.2020.115541] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/19/2020] [Accepted: 01/22/2020] [Indexed: 05/08/2023]
Abstract
Antibiotic resistome is a raising concern around the world, especially considering treated wastewater for reclamation. A wastewater reclamation system (WWRS), composed by a treatment system (TS) and a reclaimed system (RS) with supplementation from the treated effluent and considered as an integrated system of treatment and reclamation, was selected in this study. High-throughput qPCR (HT-qPCR) was applied to profile 283 antibiotic resistance genes (ARGs) and 12 mobile genetic elements (MGEs) in the WWRS. A total of 251 ARG and 12 MGE subtypes were detected in the WWRS. The TS exhibited good performance for the removal of ARGs with the number, relative and absolute abundances of ARGs largely decreased (99.07% removal efficiency) in the final effluent, which might be ascribed to biosolid sedimentation. Enhancement of biosolids removal contributed the lessening of ARGs. In the RS, high quality effluent significantly reduced the number and abundance of ARGs along the flow to downstream. MGEs were less reduced in the treated effluent than that of the influent (R2 = -0.16, p > 0.05), and exhibited close connections with ARGs. Arcobacter, Cloacibacterium, Cyanobacteria, Acinetobacter, Flavobacterium and Dechloromonas were the relatively abundant genera in the WWRS, and exhibited significantly correlations with ARGs. Microbial communities and MGEs contributed 65.64% to the changes of ARGs. These two factors may be the main drivers of ARG proliferation in the WWRS. Thus, attention should be paid to MGEs and those abundant genera when considering treated wastewater for reclamation.
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Affiliation(s)
- Kaifeng Yu
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Peng Li
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yihan Chen
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 246011, China
| | - Bo Zhang
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yuansheng Huang
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Fu-Yi Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Yiliang He
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China; Shanghai Institute of Pollution Control and Ecological Security, 800 Dongchuan Road, Shanghai, 200240, China.
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171
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Khan H, Miao X, Liu M, Ahmad S, Bai X. Behavior of last resort antibiotic resistance genes (mcr-1 and bla NDM-1) in a drinking water supply system and their possible acquisition by the mouse gut flora. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 259:113818. [PMID: 31896482 DOI: 10.1016/j.envpol.2019.113818] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/05/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
Mcr-1 and blaNDM-1 antibiotic resistance genes (ARGs) confer resistance to colistins and carbapenems, which are often antibiotics used as a last resort in tertiary care hospitals. Dissemination of these two ARGs in drinking water supply systems and their effect on healthy gut bacteria are poorly studied. In this study, the dissemination of mcr-1 and blaNDM-1 in a drinking water supply system, and their effect on the antibiotic resistance of mouse gut bacteria are explored. Metagenome analysis revealed that source water (Taipu river and Jinze reservoir) was polluted with ARGs. Mcr-1 and blaNDM-1 can be disseminated through the water distribution system. Even advanced water treatments (ozone and biological activated carbon (BAC)) could not effectively remove mcr-1 and blaNDM-1. Low concentrations of chloramine disinfectants in the water distribution system were not effective at limiting ARG abundance. Mobile genetic elements were also found to play a major role in the dissemination of ARGs via horizontal gene transfer (HGT) throughout the water supply system. Statistical analysis revealed that there was no effect of temperature on the abundance of mcr-1 and blaNDM-1 throughout the water supply system. A last resort ARG, mcr-1 can disseminate from drinking water to the healthy mouse gut. The presence of mcr-1 in a strain belonging to Enterococcus hirae, which is different from the strain belonging to the Bacillus cereus group isolated from drinking water, strongly supports the phenomena of HGT inside the gut. This research provides novel insights into the role of drinking water in disseminating ARGs to the gut and strongly suggests that drinking water may also play a major role apart from other factors known to be involved in the prevalence of last resort ARGs in the gut.
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Affiliation(s)
- Hira Khan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Xiaocao Miao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Mingkun Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Shakeel Ahmad
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Department of Biosciences, COMSATS University Islamabad, Pakistan
| | - Xiaohui Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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172
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Li DC, Gao JF, Zhang SJ, Gao YQ, Sun LX. Emergence and spread patterns of antibiotic resistance genes during two different aerobic granular sludge cultivation processes. ENVIRONMENT INTERNATIONAL 2020; 137:105540. [PMID: 32032776 DOI: 10.1016/j.envint.2020.105540] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/25/2020] [Accepted: 01/29/2020] [Indexed: 05/15/2023]
Abstract
The prevalence and accumulation of antibiotic resistance genes (ARGs) were frequently detected in biological wastewater treatment processes, which might cause potential health crisis to human. In present study, the fates of ARGs during two different aerobic granular sludge (AGS) cultivation processes were investigated. The results showed that traditional AGS (T-AGS) cultivation process and enhanced AGS (E-AGS) cultivation process had significant differences (P < 0.005) in ARGs shift patterns. E-AGS process had higher average relative abundance (0.280 ± 0.079) of ARGs than T-AGS process (0.130 ± 0.041), while the intensity of ARGs enrichment during E-AGS (1.52-5.29 fold) was lower than T-AGS (3.79-75.31 fold) process. TnpA and intI1 as two different types of mobile genetic elements (MGEs) carrying ARGs, were observed to contribute significantly to the horizontal gene transfer (HGT) during T-AGS (r = 0.902, P < 0.050) and E-AGS (r = 0.823, P < 0.001) processes, respectively. Higher HGT level took place and more possible potential hosts (25 hosts) harboring ARGs were detected during E-AGS process comparing with T-AGS process (17 hosts). Meanwhile, over large AGS might increase the propagation of several antibiotic deactivation ARGs, so it was not advised. Overall, whether during T-AGS or during E-AGS process which was applied in a pilot-scale sequencing batch reactor treating municipal wastewater, the accumulation and spread of ARGs were inevitable. It should be valued that some suitable pre-treatments of seed sludge should be executed, meanwhile, advanced treatment for removing of ARGs in AGS should be conducted to maintain the relative abundances of ARGs at relatively low level.
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Affiliation(s)
- Ding-Chang Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Jing-Feng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China.
| | - Shu-Jun Zhang
- Research and Development Center of Beijing Drainage Group Co. Ltd, Beijing 100124, China
| | - Yong-Qing Gao
- Research and Development Center of Beijing Drainage Group Co. Ltd, Beijing 100124, China
| | - Li-Xin Sun
- Research and Development Center of Beijing Drainage Group Co. Ltd, Beijing 100124, China
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173
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Wang B, Yan J, Li G, Zhang J, Zhang L, Li Z, Chen H. Risk of penicillin fermentation dreg: Increase of antibiotic resistance genes after soil discharge. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 259:113956. [PMID: 32023801 DOI: 10.1016/j.envpol.2020.113956] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/25/2019] [Accepted: 01/08/2020] [Indexed: 06/10/2023]
Abstract
Penicillin fermentation dreg (PFD) is a solid waste discharged by pharmaceutical enterprises in the fermentation production process. Due to the residual antibiotic of PFD, the risk of antibiotic resistance bacteria (ARB) generation should be considered in the disposal process. High-throughput quantitative PCR (HT-qPCR) and 16S rRNA gene sequencing were performed to investigate the effect of PFD on the dynamics of antibiotic resistance genes (ARGs) and bacterial community during a lab-scale soil experiment. After the application of PFD, the bacterial number and diversity showed an obvious decrease in the initial days. The abundances of Streptomyces and Bacillus, which are the most widespread predicted source phyla of ARGs, increased remarkably from 4.42% to 2.59%-22.97% and 21.35%. The increase of ARGs was observed during the PFD application and the ARGs carried by PFD itself contributed to the initiation of soil ARGs. The results of redundancy analysis (RDA) show that the shift in bacterial community induced by variation of penicillin content is the primary driver shaping ARGs compositions.
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Affiliation(s)
- Bing Wang
- College of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China
| | - Jianquan Yan
- College of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China
| | - Guomin Li
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150090, China
| | - Jian Zhang
- College of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China.
| | - Lanhe Zhang
- College of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China
| | - Zheng Li
- College of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China
| | - Houhe Chen
- School of Electrical Engineering, Northeast Electric Power University, Jilin, 132012, China
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174
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Lu XM, Lu PZ, Liu XP. Fate and abundance of antibiotic resistance genes on microplastics in facility vegetable soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 709:136276. [PMID: 31905565 DOI: 10.1016/j.scitotenv.2019.136276] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 05/06/2023]
Abstract
Microplastics (MPs) and antibiotic resistance genes (ARGs) coexist widely in farmland soils, but the fate and abundance of ARGs on MPs is rarely explored. In this study, high-throughput fluorescent quantitative polymerase chain reaction was used to determine ARGs on MPs in facility vegetable soil. The results indicated that when the particle size of the MPs was larger, the weathering was more serious, or the MPs came from soils with a long vegetable cultivation period, the levels of antibiotics and heavy metals on the MPs were higher. The distribution of the detected ARGs types on distinct MPs showed changes. Compared with weakly weathered MPs, the detected beta lactamase and aminoglycoside resistance genes on strongly weathered MPs were decreased by 2.6% and 1.7%, while the detected sul-ARGs and Macrolide-Lincosamide-Streptogramin B (MLSB) resistance genes were increased by 1.5% and 2.8%. Compared with smaller MPs, the detected MLSB and vancomycin resistance genes on larger MPs were decreased by 2.0% and 1.4%, while the detected fluoroquinolone, quinolone, florfenicol, chloramphenicol, and amphenicol (FCA) resistance genes and sul-ARGs were increased by 1.2% and 1.0%. Compared with MPs in soil after three years of vegetable cultivation, the detected FCA resistance genes and sul-ARGs on MPs in soil after ten years of vegetable cultivation were decreased by 1.3% and 1.6%, while the detected beta lactamase and aminoglycoside resistance genes were increased by 1.0% and 1.7%. This study suggests that MPs with larger size, stronger weathering or from soil after long-term vegetable cultivation adsorb more antibiotics and heavy metals and cause more mobile genetic elements, which can contribute to antibiotic resistance on the MPs.
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Affiliation(s)
- Xiao-Ming Lu
- Fujian Provincial Indoor Environmental Engineering Technology Research Center, Fujian University of Technology, Fuzhou 350118, China.
| | - Peng-Zhen Lu
- Faculty of Civil Engineering and Architecture, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xue-Ping Liu
- Fujian Provincial Indoor Environmental Engineering Technology Research Center, Fujian University of Technology, Fuzhou 350118, China
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175
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Liu Y, Dyall-Smith M, Marenda M, Hu HW, Browning G, Billman-Jacobe H. Antibiotic Resistance Genes in Antibiotic-Free Chicken Farms. Antibiotics (Basel) 2020; 9:antibiotics9030120. [PMID: 32183177 PMCID: PMC7148458 DOI: 10.3390/antibiotics9030120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 12/22/2022] Open
Abstract
Rising concern about the use of antibiotics in food production has resulted in many studies on the occurrence of antibiotic resistance genes (ARGs) in animal-associated bacterial communities. There are few baseline data on the abundance of ARGs on farms where chickens are intensively raised with little or no use of antibiotics. This study used a high-throughput quantitative PCR array to survey two antibiotic-free chicken farms for the occurrence of ARGs and mobile genetic elements known to enhance the spread of ARGs. No antibiotics had been used on the study farms for five years prior to this study. The results provide a baseline for the occurrence of resistance genes in the chicken production system without direct selective pressure.
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Affiliation(s)
- Yuhong Liu
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
- National Centre for Antimicrobial Stewardship, The Peter Doherty Institute, Elizabeth St Melbourne, VIC 3000, Australia
| | - Michael Dyall-Smith
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
| | - Marc Marenda
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Glenn Browning
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
- National Centre for Antimicrobial Stewardship, The Peter Doherty Institute, Elizabeth St Melbourne, VIC 3000, Australia
| | - Helen Billman-Jacobe
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
- National Centre for Antimicrobial Stewardship, The Peter Doherty Institute, Elizabeth St Melbourne, VIC 3000, Australia
- Correspondence:
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176
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Li P, Wu Y, He Y, Zhang B, Huang Y, Yuan Q, Chen Y. Occurrence and fate of antibiotic residues and antibiotic resistance genes in a reservoir with ecological purification facilities for drinking water sources. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 707:135276. [PMID: 31864005 DOI: 10.1016/j.scitotenv.2019.135276] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/16/2019] [Accepted: 10/28/2019] [Indexed: 05/24/2023]
Abstract
Antibiotics and antibiotic resistance genes (ARGs) are emerging contaminants in surface waters, especially drinking water sources, where they can pose a risk to human health and aquatic ecology. The ecological purification facilities constructed in the drinking water reservoirs are intended to safeguard water quality. However, their ability to remove antibiotics and ARGs from the water and the presence of ARGs in such river-reservoir systems have not been comprehensively characterized yet. The occurrence, distribution and spatiotemporal variations in antibiotics, ARGs, and mobile genetic elements (MGEs) were investigated in a representative river-reservoir system in Shanghai, China. A total of 283 ARGs and 12 MGEs were detected in the water using high- throughput quantitative PCR analysis. Antibiotic residues and the absolute abundance of total ARGs and MGEs in reservoir inflow were significantly reduced when water from the river passed through the ecological purification processes in the reservoir. Antibiotics in this river-reservoir system posed only limited risks to the aquatic ecosystem and human health. No significant correlation was observed between the distribution pattern of ARGs and spatiotemporal factors. The dominant ARGs were strongly and significantly correlated with integrons. Through redundancy analysis and variation partitioning analysis, we determined that MGEs were the major driver shifting the distribution of ARGs, and the effects of environmental factors and antibiotic residues were reflected in the joint effects with MGEs. The small ecological reservoir was verified as an effective engineering to mitigate ecological risk in the drinking water source.
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Affiliation(s)
- Peng Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yunfei Wu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Shanghai Institute of Pollution Control and Ecological Security, 800 Dongchuan Road, Shanghai 200240, China.
| | - Bo Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yuansheng Huang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qiyi Yuan
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yihan Chen
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
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177
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Chen QL, Hu HW, Zhu D, Ding J, Yan ZZ, He JZ, Zhu YG. Host identity determines plant associated resistomes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113709. [PMID: 31838394 DOI: 10.1016/j.envpol.2019.113709] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/12/2019] [Accepted: 11/30/2019] [Indexed: 05/20/2023]
Abstract
Plant microbiome, as the second genome of plant, and the interface between human and environmental microbiome, represents a potential pathway of human exposure to environmental pathogens and resistomes. However, the impact of host identity on the profile of resistomes in plant phyllosphere is unclear and this knowledge is vital for establishing a framework to evaluate the dissemination of antibiotic resistance via the plant microbiome. Here, we explored the phyllosphere microbiome and resistomes in 12 selected plant species. By using High-throughput quantitative PCR, we identified a total of 172 unique resistance genes in plant phyllosphere microbiome, which was significantly divergent from the profile of resistomes in associated soils (Adonis, P < 0.01). Host identity had a significant effect on the plant resistome, which was mainly attributed to the dissimilarity of phyllosphere bacterial phylogeny across different plants. We identified a core set of plant resistomes shared in more than 80% of samples, which accounted for more than 64% of total resistance genes. These plant core resistomes conferred resistance to antibiotics that are commonly administered to humans and animals. Our findings extend our knowledge regarding the resistomes in plant phyllosphere microbiome and highlight the role of host identity in shaping the plant associated antibiotic resistance genes.
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Affiliation(s)
- Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jing Ding
- School of Environmental and Material Engineering, Yantai University, 30 Qingquan Road, Yantai, 264005, China
| | - Zhen-Zhen Yan
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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178
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Yao L, Li Y, Li Z, Shen D, Feng H, Zhou H, Wang M. Prevalence of fluoroquinolone, macrolide and sulfonamide-related resistance genes in landfills from East China, mainly driven by MGEs. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 190:110131. [PMID: 31901538 DOI: 10.1016/j.ecoenv.2019.110131] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
Landfills are one of the most important reservoirs of antibiotic resistance genes (ARGs), and ARG pollution in landfills has been well investigated. However, the various factors contributing to the widespread prevalence of ARGs in landfills have rarely been explored. Here, we quantified three classes of antibiotics, six kinds of heavy metals, eight types of ARGs, and five varieties of mobile genetic elements (MGEs) in refuse samples from 10 landfills in Zhejiang Province, China. Compared with sulfonamides and macrolides, fluoroquinolones were present at much higher concentrations in all refuse samples, reaching a concentration of 1406.85 μg/kg in the Jiaxing region. The relative abundances of qnrD, qnrS, mexF, ermA, ermB, mefA, sul1, and sul2 in most landfills were >10-4 copies per 16S rRNA, suggesting the presence of highly contaminated ARGs. No significant correlations between most target antibiotics and their corresponding ARGs were found. Variation partitioning analysis indicated that MGEs could be the determining factor in the spread of ARGs in landfills. This research not only reveals high levels of ARGs and the ubiquitous presence of antibiotics in refuse, but also provides guidance for controlling the spread of ARGs in landfills.
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Affiliation(s)
- Lihua Yao
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Yue Li
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Zhangqiang Li
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Dongsheng Shen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Huajun Feng
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Huihua Zhou
- Zhejiang Province Industrial EP Design & Research Institute Co. L.td, Hangzhou, 310012, China
| | - Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China.
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179
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Paulus GK, Hornstra LM, Medema G. International tempo-spatial study of antibiotic resistance genes across the Rhine river using newly developed multiplex qPCR assays. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135733. [PMID: 31818563 DOI: 10.1016/j.scitotenv.2019.135733] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/09/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
The aim of this study was to capture and explain changes in antibiotic resistance gene (ARG) presence and concentration internationally across the Rhine river. Intl1 concentrations and national antibiotic usage were investigated as proxies to predict anthropogenic ARG pollution. Newly-developed multiplex qPCR assays were employed to investigate ARG profiles across 8 locations (L1-L8) in three countries (Switzerland, Germany, the Netherlands) and to detect potential regional causes for variation. Two of these locations were further monitored, over the duration of one month. A total of 13 ARGs, Intl1 and 16S rRNA were quantified. ARG presence and concentrations initially increased from L1(Diepoldsau) to L3(Darmstadt). A continuous increase could not be observed at subsequent locations, with the large river volume likely being a major contributing factor for stability. ARG presence and concentrations fluctuated widely across different locations. L2(Basel) and L3 were the two most polluted locations, coinciding with these locations being well-developed pharmaceutical production locations. We draw attention to the characteristic, clearly distinct ARG profiles, with gene presence being consistent and gene concentrations varying significantly less over time than across different locations. Five genes were Rhine-typical (ermB, ermF, Intl1, sul1 and tetM). Intl1 and sul1 were the genes with highest and second-highest concentration, respectively. Aph(III)a and blaOXA were permanently introduced downstream of L1, indicating no source of these genes prior to L1. We highlight that correlations between Intl1 and ARG concentrations (R2 = 0.72) were driven by correlations to sul1 and disappeared when excluding sul1 from the analysis (R2 = 0.05). Intl1 therefore seems to be a good proxy for sul1 concentrations but not necessarily for overall (anthropogenic) ARG pollution. Aminoglycoside usage per country correlated with concentrations of aph(III)a and several unrelated antibiotic resistance genes (blaOXA,ermB, ermF and tetM). This correlation can be explained by co-resistance caused by mobile genetic elements (MGEs), such as Tn1545.
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Affiliation(s)
- Gabriela K Paulus
- KWR Watercycle Research Institute, Groningenhaven 7, 3433PE Nieuwegein, the Netherlands; Delft University of Technology, Faculty of Civil Engineering & Geosciences, Department of Water Management, Stevinweg 1, 2628CN Delft, The Netherlands.
| | - Luc M Hornstra
- KWR Watercycle Research Institute, Groningenhaven 7, 3433PE Nieuwegein, the Netherlands
| | - Gertjan Medema
- KWR Watercycle Research Institute, Groningenhaven 7, 3433PE Nieuwegein, the Netherlands; Delft University of Technology, Faculty of Civil Engineering & Geosciences, Department of Water Management, Stevinweg 1, 2628CN Delft, The Netherlands
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180
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Chopyk J, Nasko DJ, Allard S, Callahan MT, Bui A, Ferelli AMC, Chattopadhyay S, Mongodin EF, Pop M, Micallef SA, Sapkota AR. Metagenomic analysis of bacterial and viral assemblages from a freshwater creek and irrigated field reveals temporal and spatial dynamics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135395. [PMID: 31846873 DOI: 10.1016/j.scitotenv.2019.135395] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
Lotic surface water sites (e.g. creeks) are important resources for localized agricultural irrigation. However, there is concern that microbial contaminants within untreated surface water may be transferred onto irrigated soil and crops. To evaluate this issue, water samples were collected between January 2017 and August 2018 from a freshwater creek used to irrigate kale and radish plants on a small farm in the Mid-Atlantic, United States. In addition, on one sampling date, a field survey was conducted in which additional water (creek source and point-of-use) and soil samples were collected to assess the viral and bacterial communities pre- and post- irrigation. All samples were processed for DNA extracts and shotgun sequenced on the Illumina HiSeq platform. The resulting metagenomic libraries were assembled de novo and taxonomic and functional features were assigned at the contig and peptide level. From these data, we observed that Betaproteobacteria (e.g. Variovorax) dominated the water, both at the source and point-of-use, and Alphaproteobacteria (e.g. Streptomyces) dominated both pre- and post-irrigated soil. Additionally, in the creek source water there were variations in the abundance of the dominant bacterial genera and functional annotations associated with seasonal characteristics (e.g. water temperature). Antibiotic resistance genes and virulence factors were also identified in the creek water and soil, with the majority specific to their respective habitat. Moreover, an analysis of clustered regularly interspaced short palindromic repeat (CRISPR) arrays showed the persistence of certain spacers through time in the creek water, as well as specific interactions between creek bacteriophages and their hosts. Overall, these findings provide a more holistic picture of bacterial and viral composition, dynamics, and interactions within a freshwater creek that can be utilized to further our knowledge on its suitability and safety for irrigation.
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Affiliation(s)
- Jessica Chopyk
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA
| | - Daniel J Nasko
- Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Sciences, University of Maryland, College Park, MD, USA; University of Maryland Institute for Advanced Computer Studies, College Park, MD, USA
| | - Sarah Allard
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA
| | | | - Anthony Bui
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA
| | | | - Suhana Chattopadhyay
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA
| | - Emmanuel F Mongodin
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Sciences, University of Maryland, College Park, MD, USA; University of Maryland Institute for Advanced Computer Studies, College Park, MD, USA
| | - Shirley A Micallef
- Department of Plant Science and Landscape Architecture, College Park, MD, USA; Center for Food Safety and Security Systems, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amy R Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA.
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181
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Duan Y, Chen Z, Tan L, Wang X, Xue Y, Wang S, Wang Q, Das R, Lin H, Hou J, Li L, Mao D, Luo Y. Gut resistomes, microbiota and antibiotic residues in Chinese patients undergoing antibiotic administration and healthy individuals. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135674. [PMID: 31785918 DOI: 10.1016/j.scitotenv.2019.135674] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 05/21/2023]
Abstract
Human gut microbiota is an important reservoir of antibiotic resistance genes (ARGs). Although dysbacteriosis after the antibiotic course has been previously observed in the patient guts, a comprehensive comparison of gut resistomes, microbiota and antibiotic residues in healthy individuals and patients undergoing antibiotic administration is little. Using high-throughput qPCR, 16S rRNA gene amplicon sequencing and UPLC-MS/MS, we systematically examined the antibiotic resistome, gut microbiota, and antibiotic residues in fecal samples from both Chinese healthy individuals and patients receiving antibiotic therapy. Compared with healthy individuals, patients' guts harbored lower diverse gut resistome and microbiota, but higher concentrations of antibiotics and ARGs. Antibiotic concentration in human guts was positively correlated with ARG total abundance, but was negatively related to the diversity of both ARGs and bacterial communities, which demonstrated that antibiotic administration could shape the antibiotic resistomes and bacterial communities in the patient guts. Gene cfxA was evaluated as a potential biomarker to distinguish the patients receiving antibiotic therapy from the healthy individuals in China since its wide detection and significant enrichment in the guts of the patients. The detection of some veterinary antibiotics in human guts illustrated the potential transmission of antibiotic from the external environment to human via the food chain. The obtained results could help to better understand the influence of antibiotic therapy in shaping antibiotic reistomes and bacterial communities in Chinese individuals.
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Affiliation(s)
- Yujing Duan
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Zeyou Chen
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Lu Tan
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Xiaolong Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Yingang Xue
- Key Laboratory of Environmental Protection of Water Environment Biological Monitoring of Jiangsu Province, Changzhou Environmental Monitoring Center, Changzhou 213001, China
| | - Shaopeng Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Qing Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Ranjit Das
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Huai Lin
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Jie Hou
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Linyun Li
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin 300071, China.
| | - Yi Luo
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China.
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182
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Zhou Z, Yao H. Effects of Composting Different Types of Organic Fertilizer on the Microbial Community Structure and Antibiotic Resistance Genes. Microorganisms 2020; 8:microorganisms8020268. [PMID: 32079314 PMCID: PMC7074733 DOI: 10.3390/microorganisms8020268] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 12/25/2022] Open
Abstract
Organic fertilizer is a major carrier that stores and transmits antibiotic resistance genes (ARGs). In the environment, due to the application of organic fertilizers in agriculture, the increasing diversity and abundance of ARGs poses a potential threat to human health and environmental safety. In this paper, the microbial community structure and ARGs in different types of organic fertilizer treated with composting were examined. We found that the abundance and diversity of ARGs in earthworm cast organic fertilizer were the lowest and the highest in chicken manure organic fertilizer. Interestingly, the abundance and diversity of ARGs, especially beta-lactam resistance genes, sulfonamide resistance genes, and macrolide-lincosamide-streptogramin B (MLSB) resistance genes, in organic fertilizers were reduced significantly, while composting caused no significant change in mobile genetic elements (MGEs), where antibiotic deactivation and the use of efflux pumps were the two most dominant mechanisms. It was clear that removal of ARGs became more efficient with increasing reduction in the bacterial abundances and diversity of potential ARG hosts, and integron-mediated horizontal gene transfers (HGTs) played an important role in the proliferation of most ARG types. Therefore, the reduction in ARGs was mainly driven by changes in bacterial community composition caused by composting. Furthermore, rather than HGTs, the diversity and abundance of bacterial communities affected by compost physical and chemical properties were the main drivers shaping and altering the abundance and diversity of ARGs, which was indicated by a correlation analysis of these properties, antibiotic residues, microbial community structure, and ARGs. In general, high-temperature composting effectively removed antibiotic residues and ARGs from these organic fertilizers; however, it cannot prevent the proliferation of MGEs. The insights gained from these results may be of assistance in the safe and rational use of organic fertilizers by indicating the changes in microbial community structure and ARGs in different types of organic fertilizer treated with composting.
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Affiliation(s)
- Zeming Zhou
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, China;
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, China;
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315800, China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Correspondence:
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183
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Sacristán I, Esperón F, Acuña F, Aguilar E, García S, López MJ, Cevidanes A, Neves E, Cabello J, Hidalgo-Hermoso E, Poulin E, Millán J, Napolitano C. Antibiotic resistance genes as landscape anthropization indicators: Using a wild felid as sentinel in Chile. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:134900. [PMID: 31757538 DOI: 10.1016/j.scitotenv.2019.134900] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/24/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
Antimicrobial resistance is a global emerging public health issue whose presence and impact in wildlife are widely unknown. Antimicrobial resistance genes (ARGs) are considered environmental contaminants, suitable to evaluate the degree of anthropic impact on wildlife and the environment. We used a wild felid, the guigna (Leopardus guigna), as a sentinel for the presence of ARGs in anthropized and pristine areas across their entire distribution range in Chile. We evaluated fecal samples from 51 wild guignas, collected between 2009 and 2018. Real-time PCR essays were employed to detect and quantify 22 selected ARGs in their fecal microbiome. All animals (100%) were positive for at least one ARG. The most prevalent ARG families were those that confer resistance to tetracycline (88.2%) and beta-lactamase (68.9%), with tet(Q) (60.8%), tet(W) (60.8%), and blaTEM (66.7%) as the most prevalent ARGs. Multi-resistance profiles were observed in 43% of the guignas. Statistically significant differences were found between anthropized and pristine areas for tet(Q) (p = 0.014), tet(W) (p = 0.0037), tetracycline family (p = 0.027), multi-resistance profile prevalence (p = 0.043) and tet(W) quantification (p = 0.004). Two animals from anthropized landscapes were positive for mecA, a gene associated with Staphylococcus aureus and other staphylococci resistant to methicillin, while three animals from anthropized areas were positive for blaCTX-M, that encodes class A extended-spectrum beta-lactamase. Both genes have been identified in bacteria causing relevant nosocomial infections worldwide. This is the first study on ARGs in wild felids from Chile and the first detection of mecA in South American wild felids. We observed an association between the degree of landscape anthropization and ARG prevalence, confirming that ARGs are important indicators of wildlife exposure to human activity/presence, with a widespread distribution.
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Affiliation(s)
- Irene Sacristán
- PhD Program in Conservation Medicine, Facultad de Ciencias de la Vida, Universidad Andres Bello, República 252, Santiago, Chile.
| | - Fernando Esperón
- Grupo de Epidemiología y Sanidad Ambiental, Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - Francisca Acuña
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avda. Santa Rosa 11735, La Pintana, Santiago, Chile
| | - Emilio Aguilar
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avda. Santa Rosa 11735, La Pintana, Santiago, Chile
| | - Sebastián García
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avda. Santa Rosa 11735, La Pintana, Santiago, Chile
| | - María José López
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avda. Santa Rosa 11735, La Pintana, Santiago, Chile
| | - Aitor Cevidanes
- PhD Program in Conservation Medicine, Facultad de Ciencias de la Vida, Universidad Andres Bello, República 252, Santiago, Chile
| | - Elena Neves
- Grupo de Epidemiología y Sanidad Ambiental, Centro de Investigación en Sanidad Animal (INIA-CISA), Madrid, Spain
| | - Javier Cabello
- Facultad de Medicina Veterinaria, Universidad San Sebastián, sede de la Patagonia, Puerto Montt, Chile; Centro de Conservación de la Biodiversidad Chiloé Silvestre, Ancud, Chile
| | - Ezequiel Hidalgo-Hermoso
- Departamento de Conservación e Investigación, Parque Zoológico Buin Zoo, Panamericana Sur Km 32, Buin, Chile
| | - Elie Poulin
- Instituto de Ecología y Biodiversidad (IEB), Santiago, Chile; Laboratorio de Ecología Molecular, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Javier Millán
- Facultad de Ciencias de la Vida, Universidad Andres Bello, República 252, Santiago, Chile
| | - Constanza Napolitano
- Instituto de Ecología y Biodiversidad (IEB), Santiago, Chile; Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile.
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184
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Uddin M, Chen J, Qiao X, Tian R, Zhu M. Insight into dynamics and bioavailability of antibiotics in paddy soils by in situ soil moisture sampler. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 703:135562. [PMID: 31767303 DOI: 10.1016/j.scitotenv.2019.135562] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Plant-soil systems have complex regulatory mechanisms for xenobiotics uptake by plant, and these chemicals in soil pore water (SPW) are regarded as the bioavailable fraction. To date, little is known about the role of SPW in regard to the bioavailability of antibiotics for plant. In this study, in situ soil moisture sampler (SMS) was adopted to collect SPW from four paddy soils without disrupting the rhizosphere zone to evaluate antibiotic uptake in rice. The results show that SMS is applicable for antibiotics that have small molecular sizes and Log Kow values, e.g., sulfadiazine (SDZ), sulfamethoxazole (SMZ), trimethoprim (TRM), and florfenicol (FLR). However, SMS performance was not feasible for large size and medium hydrophobic clarithromycin (CLR). Antibiotics in SPW demonstrated differences among chemicals and soils. Relatively higher levels of SDZ, SMZ, and FLR were observed in SPW than TRM, and neutral Panjin soil had the highest levels of antibiotics in SPW among four soils. The levels of antibiotics in SPW were negatively correlated with their soil partition parameter, Kd. Rapid decreases of SMZ, FLR, and SDZ in the SPW were consistent with their low residues in the final soils. All antibiotics were detectable in rice roots, followed by low detection levels in a few shoot samples, while no antibiotics were detectable in the grains of four soils. Relatively higher levels of SDZ, SMZ and FLR were observed in the roots of Panjin soil, consistent with their levels in SPW and Kd values. Furthermore, CLR and TRM were observed to have higher levels in roots, which was regarded as a consequence of their relatively longer persistence. Our study indicates that SMS is an applicable technique for in situ sampling of SPW, and level of antibiotics in SPW can work as a useful indicator to explore their bioavailability to plants.
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Affiliation(s)
- Misbah Uddin
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Xianliang Qiao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China.
| | - Run Tian
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
| | - Minghua Zhu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China
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185
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Wang F, Han W, Chen S, Dong W, Qiao M, Hu C, Liu B. Fifteen-Year Application of Manure and Chemical Fertilizers Differently Impacts Soil ARGs and Microbial Community Structure. Front Microbiol 2020; 11:62. [PMID: 32117108 PMCID: PMC7015874 DOI: 10.3389/fmicb.2020.00062] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/13/2020] [Indexed: 12/18/2022] Open
Abstract
Manure, which contains large amounts of antibiotics and antibiotic resistance genes (ARGs), is widely used in agricultural soils and may lead to the evolution and dispersal of ARGs in the soil environment. In the present study, soils that received manure or chemical fertilizers for 15 years were sampled on the North China Plain (NCP), which is one of the primary areas of intensive agriculture in China. High-throughput quantitative PCR and sequencing technologies were employed to assess the effects of long-term manure or chemical fertilizer application on the distribution of ARGs and microbial communities. A total of 114 unique ARGs were successfully amplified from all soil samples. Manure application markedly increased the relative abundance and detectable numbers of ARGs, with up to 0.23 copies/16S rRNA gene and 81 unique ARGs. The increased abundance of ARGs in manure-fertilized soil was mainly due to the manure increasing the abundance of indigenous soil ARGs. In contrast, chemical fertilizers only moderately affected the diversity of ARGs and had no significant effect on the relative abundance of the total ARGs. In addition, manure application increased the abundance of mobile genetic elements (MGEs), which were significantly and positively correlated with most types of ARGs, indicating that horizontal gene transfer via MGEs may play an important role in the spread of ARGs. Furthermore, the application of manure and chemical fertilizers significantly affected microbial community structure, and variation partitioning analysis showed that microbial community shifts represented the major driver shaping the antibiotic resistome. Taken together, our results provide insight into the long-term effects of manure and chemical fertilization on the dissemination of ARGs in intensive agricultural ecosystems.
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Affiliation(s)
- Fenghua Wang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Wanxue Han
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuaimin Chen
- Institute of Agricultural Resource and Environment, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Wenxu Dong
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Min Qiao
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Chunsheng Hu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Binbin Liu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
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186
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Lu XM, Lu PZ. Seasonal variations in antibiotic resistance genes in estuarine sediments and the driving mechanisms. JOURNAL OF HAZARDOUS MATERIALS 2020; 383:121164. [PMID: 31520936 DOI: 10.1016/j.jhazmat.2019.121164] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 08/19/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Estuary sediments are chemically contaminated by adjacent coastal industrial cities, but the impact of organic pollutants on antibiotic resistance genes (ARGs) in estuarine sediments is unknown. We comprehensively analyzed the complex interactions between chemical pollutants (heavy metals and organic pollutants), mobile genetic elements (MGEs), and ARGs in estuarine sediments during various seasons. The results indicate that under the effects of the chemically polluted river water, the number of different estuarine sediment ARGs increased by 76.9%-92.3% in summer and 5.9%-35.3% in winter, and the abundance of these ARGs increased by 29-5195 times in summer and 48-239 times in winter. The abundance of sediment ARGs in distinct estuaries showed different seasonal trends. Seasonal changes had a greater impact on the abundance of estuarine sediment ARGs than on their diversity. The diversity of estuarine sediment ARGs was positively correlated with the chemical pollution levels. Furthermore, chemical pollution was positively correlated with MGEs, and MGEs were correlated with ARG abundance. These results indicate that ARGs are enriched in bacteria via horizontal gene transfer triggered by chemical pollution, promoting multi-antibiotic resistance in estuarine sediment bacteria. These findings have implications for our understanding of the distribution and propagation of ARGs in chemically polluted estuarine sediments.
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Affiliation(s)
- Xiao-Ming Lu
- School of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou 350118, China.
| | - Peng-Zhen Lu
- Faculty of Civil Engineering and Architecture, Zhejiang University of Technology, Hangzhou 310014, China
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187
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Zhao Z, Zhang K, Wu N, Li W, Xu W, Zhang Y, Niu Z. Estuarine sediments are key hotspots of intracellular and extracellular antibiotic resistance genes: A high-throughput analysis in Haihe Estuary in China. ENVIRONMENT INTERNATIONAL 2020; 135:105385. [PMID: 31855802 DOI: 10.1016/j.envint.2019.105385] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 10/17/2019] [Accepted: 12/02/2019] [Indexed: 05/25/2023]
Abstract
Estuaries lie between terrestrial/freshwater and marine ecosystems, receive considerable pollutant input from land-based sources, and are considerably influenced by human activities. However, little attention has been paid to combined research on extracellular antibiotic resistance genes (eARGs) and intracellular ARGs (iARGs) in the estuarine environment. In this study, we profiled eARGs and iARGs in sediments from Haihe Estuary, China by adopting high-throughput quantitative PCR and investigated their relationship with mobile genetic elements (MGEs), the bacterial community and environmental factors. The results showed that the abundance of eARGs ranged from 9.06 × 106 to 1.32 × 108 copies/g and that of iARGs ranged from 3.31 × 107 to 2.93 × 108 copies/g, indicating that estuarine sediments were key hotspots of eARGs and iARGs. Additionally, multidrug resistance genes were both highly diverse and abundant in Haihe Estuary, especially in coastal samples. The high abundance of vancomycin and carbapenemase resistance genes may pose a potential health risk to human. Salinity altered the composition and structure of the bacterial community. Partial redundancy analysis showed that the bacterial community and MGEs appeared to be the major drivers of ARG variance in estuarine sediment. This study provides an overview of the distribution of eARG and iARG along the Haihe Estuary and draws attention to the need to control pollutants in estuary ecosystems.
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Affiliation(s)
- Ze Zhao
- School of Marine Science and Technology, Tianjin University, Tianjin 300072, China
| | - Kai Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China; Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, School of Geographic Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Nan Wu
- School of Marine Science and Technology, Tianjin University, Tianjin 300072, China
| | - Wenjie Li
- School of Marine Science and Technology, Tianjin University, Tianjin 300072, China
| | - Weian Xu
- School of Marine Science and Technology, Tianjin University, Tianjin 300072, China
| | - Ying Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Zhiguang Niu
- School of Marine Science and Technology, Tianjin University, Tianjin 300072, China; School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
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188
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Lee K, Kim DW, Lee DH, Kim YS, Bu JH, Cha JH, Thawng CN, Hwang EM, Seong HJ, Sul WJ, Wellington EMH, Quince C, Cha CJ. Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance. MICROBIOME 2020; 8:2. [PMID: 31910889 PMCID: PMC6947943 DOI: 10.1186/s40168-019-0774-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/09/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthropogenically impacted environments is just a result of contamination by resistant fecal microbes or is mediated by indigenous environmental organisms. Here, to determine exactly how anthropogenic influences shape the environmental resistome, we resolved the microbiome, resistome, and mobilome of the planktonic microbial communities along a single river, the Han, which spans a gradient of human activities. RESULTS The bloom of antibiotic resistance genes (ARGs) was evident in the downstream regions and distinct successional dynamics of the river resistome occurred across the spatial continuum. We identified a number of widespread ARG sequences shared between the river, human gut, and pathogenic bacteria. These human-related ARGs were largely associated with mobile genetic elements rather than particular gut taxa and mainly responsible for anthropogenically driven bloom of the downstream river resistome. Furthermore, both sequence- and phenotype-based analyses revealed environmental relatives of clinically important proteobacteria as major carriers of these ARGs. CONCLUSIONS Our results demonstrate a more nuanced view of the impact of anthropogenic activities on the river resistome: fecal contamination is present and allows the transmission of ARGs to the environmental resistome, but these mobile genes rather than resistant fecal bacteria proliferate in environmental relatives of their original hosts. Video abstract.
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Affiliation(s)
- Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dae-Wi Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Do-Hoon Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Ji-Hye Bu
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Ju-Hee Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Cung Nawl Thawng
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Eun-Mi Hwang
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | | | | | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea.
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189
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Bougnom BP, Thiele-Bruhn S, Ricci V, Zongo C, Piddock LJV. Raw wastewater irrigation for urban agriculture in three African cities increases the abundance of transferable antibiotic resistance genes in soil, including those encoding extended spectrum β-lactamases (ESBLs). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134201. [PMID: 31505362 DOI: 10.1016/j.scitotenv.2019.134201] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Abstract
A study was conducted to investigate the impact of raw wastewater use for irrigation on dissemination of bacterial resistance in urban agriculture in African cities. The pollution of agricultural fields by selected antibiotic residues was assessed. The structure and functions of the soil microbial communities, presence of antibiotic resistance genes of human clinical importance and Enterobacteriaceae plasmid replicons were analysed using high throughput metagenomic sequencing. In irrigated fields, the richness of Bacteroidetes and Firmicutes phyla increased by 65% and 15.7%, respectively; functions allocated to microbial communities' adaptation and development increased by 3%. Abundance of antibiotic resistance genes of medical interest was 27% greater in irrigated fields. Extended spectrum β-lactamase genes identified in irrigated fields included blaCARB-3, blaOXA-347, blaOXA-5 and blaRm3. The presence of ARGs encoding resistance to amphenicols, β-lactams, and tetracyclines were associated with the higher concentrations of ciprofloxacin, enrofloxacin and sulfamethoxazole in irrigated fields. Ten Enterobacteriaceae plasmid amplicon groups involved in the wide distribution of ARGs were identified in the fields. IncQ2, ColE, IncFIC, IncQ1, and IncFII were found in both farming systems; IncW and IncP1 in irrigated fields; and IncY, IncFIB and IncFIA in non-irrigated fields. In conclusion, raw wastewater irrigated soils in African cities could represent a vector for the spread of antibiotic resistance, thus threatening human and animal health. Consumers of products from these farms and farmers could be at risk of acquiring infections due to drug-resistant bacteria.
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Affiliation(s)
- B P Bougnom
- Institute of Microbiology and Infection, University of Birmingham, B15 2TT, UK; Department of Microbiology, Faculty of Science, University of Yaounde 1, P.O. Box 812, Yaounde, Cameroon
| | - S Thiele-Bruhn
- Department of Soil Science, University of Trier, D-54286 Trier, Germany
| | - V Ricci
- Institute of Microbiology and Infection, University of Birmingham, B15 2TT, UK
| | - C Zongo
- Department of Biochemistry and Microbiology, University Ouaga, I Pr Joseph KI-ZERBO, 03 BP 7021, Ouagadougou 03, Burkina Faso
| | - L J V Piddock
- Institute of Microbiology and Infection, University of Birmingham, B15 2TT, UK.
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190
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Yue Y, Shen C, Ge Y. Biochar accelerates the removal of tetracyclines and their intermediates by altering soil properties. JOURNAL OF HAZARDOUS MATERIALS 2019; 380:120821. [PMID: 31326833 DOI: 10.1016/j.jhazmat.2019.120821] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 06/12/2019] [Accepted: 06/24/2019] [Indexed: 06/10/2023]
Abstract
Tetracyclines accumulation in soil environment potentially threatens agroecosystem safety. Interestingly, biochar could clean up organic pollutants, but to what extent biochar affects the removal of tetracyclines is unknown. To investigate it, five types of biochars derived from cow manure (CMB) and other four plant materials were respectively added into soils contaminated with a mixture of tetracycline, oxytetracycline, and chlortetracycline for 60-day incubation in the dark. Three parent tetracyclines and their corresponding intermediates (epitetracycline, anhydrotetracycline, epianhydrotetracycline, epioxytetracycline, epichlortetracycline, and demethylchlortetracycline) were respectively determined and named as TTCs, OTCs and CTCs. Obtained results showed biochar especially CMB could effectively remove the antibiotics (P < 0.05). Compared to control, the removal rate of TTCs, OTCs and CTCs respectively increased by up to 10.86%, 10.29% and 10.12% in CMB-added soil. The increased removal rate of the antibiotics after biochar addition was due to the increasing accessibilities for degrading microorganisms via the elevating electrical conductivity. Moreover, biochar addition might stimulate these microbial activities through the increase of C and N supplement. Our results indicate biochar accelerates the removal of tetracyclines and their intermediates by altering soil properties and thus increasing the antibiotics accessibilities, which provide insights into how biochar accelerates the removal for these antibiotics.
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Affiliation(s)
- Yan Yue
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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191
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Lu XM, Lu PZ. Distribution of antibiotic resistance genes in soil amended using Azolla imbricata and its driving mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 692:422-431. [PMID: 31351286 DOI: 10.1016/j.scitotenv.2019.07.285] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
The floating aquatic plant of Azolla imbricata has an outstanding purification capability for polluted river water, and it is also employed to improve soil fertility. However, the occurrence and distribution of antibiotic resistance genes (ARGs) in soil amended using A.imbricata remain unclear. In the soil amendment with A. imbricata, heavy metals, antibiotics, transposase genes, ARGs, and bacterial communities in the soil were determined in this study. The results indicated that the diversity of bacteria and ARGs increased, while the diversity of ARGs decreased under the amendment using an appropriate amount of A. imbricata. The Firmicutes, Chloroflexi, Actinobacteria, and Cyanobacteria were the main host bacteria of ARGs. The vertical gene transfer of ARGs was weak, and the horizontal gene transfer became the dominant transfer pathway of ARGs. The amendment with A. imbricata altered the distribution of heavy metals, antibiotics, transposase genes, ARGs, and dominant bacteria. The amendment using A. imbricata promoted the degradation of antibiotics, decreased the concentrations of available heavy metals, and eliminated the abundance of ARGs and transposase genes. Our findings suggested a comprehensive effect of multiple stresses on the fate of ARGs in soil amended with A. imbricata, providing an insight into the distribution and propagation of ARGs in soil amended using plant residues.
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Affiliation(s)
- Xiao-Ming Lu
- School of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou 350118, China.
| | - Peng-Zhen Lu
- Faculty of Civil Engineering and Architecture, Zhejiang University of Technology, Hangzhou 310014, China
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192
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Ramsheh MY, Haldar K, Bafadhel M, George L, Free RC, John C, Reeve NF, Ziegler-Heitbrock L, Gut I, Singh D, Mistry V, Tobin MD, Oggioni MR, Brightling C, Barer MR. Resistome analyses of sputum from COPD and healthy subjects reveals bacterial load-related prevalence of target genes. Thorax 2019; 75:8-16. [PMID: 31699806 DOI: 10.1136/thoraxjnl-2019-213485] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 09/04/2019] [Accepted: 09/09/2019] [Indexed: 11/04/2022]
Abstract
BACKGROUND Antibiotic resistance is a major global threat. We hypothesised that the chronic obstructive pulmonary disease (COPD) airway is a reservoir of antimicrobial resistance genes (ARGs) that associate with microbiome-specific COPD subgroups. OBJECTIVE To determine the resistance gene profiles in respiratory samples from COPD patients and healthy volunteers. METHODS Quantitative PCR targeting 279 specific ARGs was used to profile the resistomes in sputum from subjects with COPD at stable, exacerbation and recovery visits (n=55; COPD-BEAT study), healthy controls with (n=7) or without (n=22) exposure to antibiotics in the preceding 12 months (EXCEED study) and in bronchial brush samples from COPD (n=8) and healthy controls (n=7) (EvA study). RESULTS ARG mean (SEM) prevalence was greater in stable COPD samples (35.2 (1.6)) than in healthy controls (27.6 (1.7); p=0.004) and correlated with total bacterial abundance (r2=0.23; p<0.001). Prevalence of ARG positive signals in individuals was not related to COPD symptoms, lung function or their changes at exacerbation. In the COPD subgroups designated High γProteobacteria and High Firmicutes, ARG prevalence was not different at stable state but significantly declined from stable through exacerbation to recovery in the former (p=0.011) without changes in total bacterial abundance. The ARG patterns were similar in COPD versus health, COPD microbiome-subgroups and between sputum and bronchoscopic samples independent of antibiotic exposure in the last 12 months. CONCLUSIONS ARGs are highly prevalent in sputum, broadly in proportion to bacterial abundance in both healthy and COPD subjects. Thus, COPD appears to be an ARG reservoir due to high levels of bacterial colonisation.
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Affiliation(s)
| | - Koirobi Haldar
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Mona Bafadhel
- Respiratory Medicine Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leena George
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Robert C Free
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Catherine John
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Ivo Gut
- Centre for Genomic Regulation, Barcelona Institute for Science and Technology, 5CNAG-CRG Centre Nacional d'Anàlisi Genòmica, Barcelona, Spain
| | - Dave Singh
- Medicines Evaluation Unit, University Hospital of South Manchester, University of Manchester, Manchester, UK
| | - Vijay Mistry
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Marco R Oggioni
- Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Chris Brightling
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Michael R Barer
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
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193
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Xiang Q, Zhu D, Chen QL, O'Connor P, Yang XR, Qiao M, Zhu YG. Adsorbed Sulfamethoxazole Exacerbates the Effects of Polystyrene (∼2 μm) on Gut Microbiota and the Antibiotic Resistome of a Soil Collembolan. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:12823-12834. [PMID: 31593455 DOI: 10.1021/acs.est.9b04795] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Microplastics pollution in the environment is now receiving worldwide attention; however, the effects of copollution of antibiotics and microplastics on the gut microbiome of globally distributed and functionally important nontarget soil animals remain poorly understood. We studied a model collembolan (Folsomia candida) and found that the ingestion of microplastics (polystyrene, 2-2.9 μm) substantially altered the gut microbiome, antibiotic resistance gene (ARG) profile, and the isotopic fractionation in the soil collembolan tissue. Importantly, collembolans exposed to polystyrene microplastics loaded with sulfamethoxazole (MA) presented a distinctive gut microbiome, ARG profile, and isotopic fractionation compared to those exposed to polystyrene alone (MH). We observed that the abundance of ARGs and mobile genetic elements (MGEs) in the MA-treated collembolan guts was significantly higher than in the MH and the control treatments. There were also strong interactions between the gut microbiome and ARGs in the collembolan guts. We further found that bacterial β-diversity correlated significantly with the δ13C and δ15N values in collembolan body tissues. Together, our results indicate that changes in isotopic fractionation and ARG profiles in the collembolan were induced by the changes in gut microbiota and suggest that microplastics from diverse sources may have profound influences on soil fauna and soil food webs.
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Affiliation(s)
- Qian Xiang
- State Key Laboratory of Urban and Regional Ecology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , 100085 , China
- University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing , 100049 , China
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , 100085 , China
- University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing , 100049 , China
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , 1799 Jimei Road , Xiamen , 361021 , China
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , 1799 Jimei Road , Xiamen , 361021 , China
| | - Patrick O'Connor
- Centre for Global Food and Resources , University of Adelaide , Adelaide , 5005 , Australia
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , 1799 Jimei Road , Xiamen , 361021 , China
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , 100085 , China
- University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing , 100049 , China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing , 100085 , China
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , 1799 Jimei Road , Xiamen , 361021 , China
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194
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Deng S, Yan X, Zhu Q, Liao C. The utilization of reclaimed water: Possible risks arising from waterborne contaminants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:113020. [PMID: 31421574 DOI: 10.1016/j.envpol.2019.113020] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/11/2019] [Accepted: 08/04/2019] [Indexed: 05/04/2023]
Abstract
Increasing interest of seeking substitutable water resources accrues from shortage of freshwater. One of the options considered is reclaimed water (also designated as recycled water) that has been widely used in daily life. Although reclaimed water can serve as a feasible reliever of water pressure, attention about its technologies and potential risks is growing in the meantime. Most established wastewater treatment plants (WWTPs) predate many new contaminants, which means treatment processes cannot ensure to dislodge certain contaminants completely from origin water. Furthermore, a wide range of factors, such as seasons and influent variations, affect occurrence and concentration of reclaimed water-borne contaminants, making research about quality of reclaimed water especially significant. Many reclaimed water-borne contaminants, including biological and chemical contaminants, are toxic to human health, and complex wastewater matrix may aggravate water quality of concern. The widespread use of reclaimed water continues to be a concern on agriculture, ecological environment and human health. This study aims to: 1) provide a critical review about occurrence and profiles of diverse contaminants in the treated reclaimed water, 2) discuss the possibility to avoid the secondary pollution in reuse of reclaimed water, and 3) reveal the prospective consequences of using reclaimed water on agriculture, ecological environment and human health.
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Affiliation(s)
- Shenxi Deng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueting Yan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingqing Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyang Liao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Environment and Health, Jianghan University, Wuhan, Hubei 430056, China.
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195
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Wang H, Wang J, Li S, Li J, Jing C. Prevalence of antibiotic resistance genes in cell culture liquid waste and the virulence assess for isolated resistant strains. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:32040-32049. [PMID: 31493078 DOI: 10.1007/s11356-019-06299-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
Cell culture liquid waste containing antibiotic resistance genes (ARGs) and microbial community were still not received enough recognition, which pose potential risks to human health. Sixty-eight resistance genes and intl1 were detected in eight samples by Quantitative real-time PCR, while intl1 was only detected in hospital group. Meanwhile, the bacterial community was complex and diverse in each sample by 16S rRNA gene high-throughput sequencing, in addition, Morganella and Enterococcus presented a significant difference between two groups. Whole genome shotgun sequencing revealed that Morganella morganii had more resistance genes and virulence factors in hospital group, and three extended-spectrum beta-lactamase (ESBL) genotypes were found to be blaDHA-5, blaOXA-1, and blaTEM-1. This study provided a preliminary report on ARGs and resistant strains, which reminded people attention to the health risks of potential pathogens in this waste.
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Affiliation(s)
- Haichao Wang
- School of Civil Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Beijing Jiaotong University, Beijing, China
| | - Jin Wang
- School of Civil Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Beijing Jiaotong University, Beijing, China.
| | - Shuming Li
- School of Civil Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, Beijing Jiaotong University, Beijing, China
| | - Jinzhao Li
- China Shenhua Overseas Development & Investment Co., Limited, Beijing, China
| | - Chuanyong Jing
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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196
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Yan ZZ, Chen QL, Zhang YJ, He JZ, Hu HW. Antibiotic resistance in urban green spaces mirrors the pattern of industrial distribution. ENVIRONMENT INTERNATIONAL 2019; 132:105106. [PMID: 31473416 DOI: 10.1016/j.envint.2019.105106] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/05/2019] [Accepted: 08/16/2019] [Indexed: 06/10/2023]
Abstract
Urban green spaces are closely related to the activities and health of urban residents. Turf grass and soil are two major interfaces between the environmental and human microbiome, which represent potential pathways for the spread of antibiotic resistance genes (ARGs) from environmental to human microbiome through skin-surface contact. However, the information regarding the prevalence of ARGs in urban green spaces and drivers in shaping their distribution patterns remain unclear. Here, we profiled a wide spectrum of ARGs in grass phyllosphere and soils from 40 urban parks across Greater Melbourne, Australia, using high throughput quantitative PCR. A total of 217 and 218 unique ARGs and MGEs were detected in grass phyllosphere and soils, respectively, conferring resistance to almost all major classes of antibiotics commonly used in human and animals. The plant microbiome contained a core resistome, which occupied >84% of the total abundance of ARGs. In contrast, no core resistome was identified in the soil microbiome. The difference between plant and soil resistome composition was attributed to the difference in bacterial community structure and intensity of environmental and anthropogenic influence. Most importantly, the abundance of ARGs in urban green spaces was significantly positively related to industrial factors including total number of business, number of manufacturing, and number of electricity, gas, water and waste services in the region. Structural equation models further revealed that industrial distribution was a major factor shaping the ARG profiles in urban green spaces after accounting for multiple drivers. These findings have important implications for mitigation of the potential risks posed by ARGs to urban residents.
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Affiliation(s)
- Zhen-Zhen Yan
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC 3010, Australia
| | - Qing-Lin Chen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC 3010, Australia.
| | - Yu-Jing Zhang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC 3010, Australia
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC 3010, Australia
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC 3010, Australia.
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197
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Xu M, Stedtfeld RD, Wang F, Hashsham SA, Song Y, Chuang Y, Fan J, Li H, Jiang X, Tiedje JM. Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 689:1172-1180. [PMID: 31466157 DOI: 10.1016/j.scitotenv.2019.06.376] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/21/2019] [Accepted: 06/23/2019] [Indexed: 06/10/2023]
Abstract
Different long-term fertilization regimes may change indigenous microorganism diversity in the arable soil and thus might influence the persistence and transmission of manure-born antibiotic resistance genes (ARGs). Different manure origins and composting techniques might affect the fate of introduced ARGs in farmland. A four-month microcosm experiment was performed using two soils, which originated from the same field and applied with the same chemical fertilizer or swine manure for 26 years, to investigate the dynamics of ARGs in soil amended with manure or compost from the farm and an agro-technology company. High throughput qPCR and sequencing were applied to quantify ARGs using 144 primer sets and microorganism in soil. Fertilization history had little effect on dynamics of manure-borne ARGs in soil regardless of manure origin or composting. Very different half-lives of ARGs and mobile genetic elements from farm manure and commercial manure were observed in both soils. Composting decreased abundance of most ARGs in manure, but increased the persistence of manure-introduced ARGs in soil irrespective of fertilization history, especially for those from farm manure. These findings help understanding the fate of ARGs in manured soil and may inform techniques to mitigate ARGs transmission.
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Affiliation(s)
- Min Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
| | - Yang Song
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yahui Chuang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
| | - Jianbo Fan
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hui Li
- Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
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198
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Pu C, Yu Y, Diao J, Gong X, Li J, Sun Y. Exploring the persistence and spreading of antibiotic resistance from manure to biocompost, soils and vegetables. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 688:262-269. [PMID: 31229823 DOI: 10.1016/j.scitotenv.2019.06.081] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
The main avenue in which antibiotic resistance enters soils is through the application of livestock manure. However, whether antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) persist and spread to vegetables with the application of manure and manure products is still unclear. This study assessed seven kinds of cultured ARB, 221 ARGs subtypes and three transposon genes in the vegetable production chain (from manure to biocompost, soils and vegetables). Results showed that at least 80% of ARB, ARGs and transposon genes were removed after aerobic composting. However, aerobic composting did not reduce the diversity of ARGs in pig and chicken manure. A total of 19 ARGs subtypes still persisted during aerobic composting. Compared to the temperature-thermophilic stage, the number of bacteria resistant to erythromycin, the relative abundance of ARGs and IS613 increased 1.7-4.9 times at the temperature-decreasing stage. Direct application of biocompost introduced 11 ARGs subtypes to pakchoi, but these ARGs did not present in biocompost-amended soil. A transposon gene tnpA was also detected in the biocompost-amended soil, but surprisingly was found in the control vegetable. This demonstrated that the transposon gene is intrinsic in pakchoi. Bacterial community analysis and network analysis revealed that a specific genus Terrisporobacter carrying tetO, tetW ermB and tnpA persisted in the vegetable production chain, which may generate a potential risk in the following production. Our study illuminates the persistence and spreading of antibiotic resistance in the vegetable production chain which could help manage the ecological risks arising from antibiotic resistance in manure sources.
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Affiliation(s)
- Chengjun Pu
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Yao Yu
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Jianxiong Diao
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Xiaoyan Gong
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Ji Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China
| | - Ying Sun
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Science, China Agricultural University, Beijing 100193, China.
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199
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Quintela-Baluja M, Abouelnaga M, Romalde J, Su JQ, Yu Y, Gomez-Lopez M, Smets B, Zhu YG, Graham DW. Spatial ecology of a wastewater network defines the antibiotic resistance genes in downstream receiving waters. WATER RESEARCH 2019; 162:347-357. [PMID: 31295654 PMCID: PMC6650630 DOI: 10.1016/j.watres.2019.06.075] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/03/2019] [Accepted: 06/30/2019] [Indexed: 05/19/2023]
Abstract
Wastewater treatment plants (WWTPs) are an effective barrier in the protection of human and environment health around the world, although WWTPs also are suggested to be selectors and-or reservoirs of antibiotic resistance genes (ARGs) before entering the environment. The dogma about WWTPs as "ARG selectors" presumes that biotreatment compartments (e.g., activated sludge; AS) are single densely populated ecosystems with elevated horizontal gene transfer. However, recent work has suggested WWTP biotreatment compartments may be different than previously believed relative to antibiotic resistance (AR) fate, and other process factors, such as bacterial separation and specific waste sources, may be key to ARGs released to the environment. Here we combined 16S rRNA metagenomic sequencing and high-throughput qPCR to characterise microbial communities and ARGs across a wastewater network in Spain that includes both community (i.e., non-clinical urban) and hospital sources. Contrary to expectations, ARGs found in downstream receiving waters were not dominated by AS biosolids (RAS), but more resembled raw wastewater sources. In fact, ARGs and microbial communities in liquid-phase WWTP effluents and RAS were significantly different (Bray-Curtis dissimilarity index = 0.66 ± 0.11), with a consequential fraction of influent ARGs and organisms passing directly through the WWTP with limited association with RAS. Instead, ARGs and organisms in the RAS may be more defined by biosolids separation and biophysical traits, such as flocculation, rather than ARG carriage. This explains why RAS has significantly lower ARG richness (47 ± 4 ARGs) than liquid-phase effluents (104 ± 5 ARGs), and downstream water column (135 ± 4 ARGs) and river sediments (120 ± 5 ARGs) (Tukey's test, p < 0.001). These data suggest RAS and liquid-phase WWTP effluents may reflect two parallel ecosystems with potentially limited ARG exchange. As such, ARG mitigation in WWTPs should more focus on removing bacterial hosts from the liquid phase, AR source reduction, and possibly disinfection to reduce ARG releases to the environment.
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Affiliation(s)
| | - M Abouelnaga
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
| | - Jesus Romalde
- Departamento de Microbiología y Parasitología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Science, Xiamen, China
| | - Yongjie Yu
- School of Engineering, Newcastle University, Newcastle upon, Tyne, UK
| | | | - Barth Smets
- Department of Environmental Engineering, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Science, Xiamen, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon, Tyne, UK.
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200
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Chen Y, Li P, Huang Y, Yu K, Chen H, Cui K, Huang Q, Zhang J, Yew-Hoong Gin K, He Y. Environmental media exert a bottleneck in driving the dynamics of antibiotic resistance genes in modern aquatic environment. WATER RESEARCH 2019; 162:127-138. [PMID: 31260828 DOI: 10.1016/j.watres.2019.06.047] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 05/26/2023]
Abstract
With the rapid construction of dams worldwide, reservoir system has become a representation of modern aquatic environment. However, the profiles of antibiotic resistance genes (ARGs) and associated factor influencing their dynamics in modern aquatic environment (e.g., water phase, sediment phase, and soil phase) are largely unknown. Here, we comprehensively characterized the diversity, abundance, distribution of ARGs in a large drinking water reservoir using high-throughput quantitative PCR, as well as ranked the factors (e.g., mobile genetic elements (MGEs), bacteria community, bacterial biomass, antibiotics, and basic properties) influencing the profiles of ARGs on the basis of structural equation models (SEMs). Water phase was prone to harbor more diverse ARGs as compared to sediment phase and soil phase, and soil phase in drawdown area was a potential reservoir and hotspot for ARGs. Environmental media partially affected the ARG diversity in modern aquatic environment, while it observably influenced the distributions of ARGs and MGEs and their co-occurrence patterns. The pathways for the proliferation and spread of ARGs in water phase were both the horizontal gene transfer (HGT) and vertical gene transfer (VGT), while the dominant pathways in sediment phase and soil phase were the HGT and VGT, respectively. The SEMs demonstrated that MGEs contributed the most to drive the ARG dynamics in both water phase and sediment phase, while the most dominant factor for this in soil phase was bacterial community. Overall, environmental media exerted a bottleneck in driving the dynamics of ARGs in modern aquatic environment probably via diversifying the MGEs, bacterial community, bacterial biomass, antibiotics and basic properties.
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Affiliation(s)
- Yihan Chen
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China.
| | - Peng Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuansheng Huang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kaifeng Yu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongjie Chen
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, #02-01, Singapore, 117411, Singapore; Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, E1A 07-03, Singapore, 117576, Singapore
| | - Kangping Cui
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Qianli Huang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, #02-01, Singapore, 117411, Singapore; Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, E1A 07-03, Singapore, 117576, Singapore
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; Shanghai Institute of Pollution Control and Ecological Security, 800 Dongchuan Road, Shanghai, 200240, China.
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