151
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Ma L, Li B, Zhang T. New insights into antibiotic resistome in drinking water and management perspectives: A metagenomic based study of small-sized microbes. WATER RESEARCH 2019; 152:191-201. [PMID: 30669041 DOI: 10.1016/j.watres.2018.12.069] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 12/18/2018] [Accepted: 12/22/2018] [Indexed: 05/21/2023]
Abstract
The proliferation of antibiotic resistance genes (ARGs) in drinking water and their potential horizontal transfer to pathogenic microbes may cause failure of antibiotics. However, antimicrobial resistome monitoring in drinking water is not currently routine. The bacterial hosts of ARGs, especially small-sized microbes in drinking water, may not be effectively removed by membrane filtration disinfection and thus pose threats to human health. In the present study, using metagenomic based approach, we investigated antibiotic resistome of small-sized microbes (0.2-0.45 μm) in 20 household drinking water samples from 12 cities in Mainland China, Hong Kong and Singapore. A total of 265 ARG subtypes belonging to 17 ARG types were detected at abundances ranging from 4.0 × 10-2 to 1.0 × 100 copies/cell. Multidrug, bacitracin and aminoglycoside resistance genes are dominant, and 43 ARG subtypes were specifically carried by small-size microbes. Metagenomic assembly strategy revealed fragments of three opportunistic pathogen, i.e. Pseudomonas alcaligenes, Pseudomonas aeruginosa and Mycobacterium gordonae, carried mexW, aph(3')-I and aac(2')-I, respectively. Drinking water samples were classified into three groups based on the presence of ARG, pathogen and ARG-carrying pathogen. These new insights into the antibiotic resistome of small microbes in drinking water over a broad scale indicate the need for more comprehensive ARGs monitoring and surveillance of drinking water supplies. These findings, together with the perspectives and strategies proposed in this study, could support initiatives to improve drinking water safety.
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Affiliation(s)
- Liping Ma
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China; Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China; School of Public Health, The University of Hong Kong, Hong Kong, China; International Center for Antibiotic Resistance in the Environment, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China.
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152
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Asante J, Osei Sekyere J. Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: advances and applications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:62-86. [PMID: 30637962 DOI: 10.1111/1758-2229.12735] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
Our inability to cultivate most microorganisms, specifically bacteria, in the laboratory has for many years restricted our view and understanding of the bacterial meta-resistome in all living and nonliving environments. As a result, reservoirs, sources and distribution of antibiotic resistance genes (ARGS) and antibiotic-producers, as well as the effects of human activity and antibiotics on the selection and dissemination of ARGs were not well comprehended. With the advances made in the fields of metagenomics and metatranscriptomics, many of the hitherto little-understood concepts are becoming clearer. Further, the discovery of antibiotics such as lugdinin and lactocillin from the human microbiota, buttressed the importance of these new fields. Metagenomics and metatranscriptomics are becoming important clinical diagnostic tools for screening and detecting pathogens and ARGs, assessing the effects of antibiotics, other xenobiotics and human activity on the environment, characterizing the microbiome and the environmental resistome with lesser turnaround time and decreasing cost, as well as discovering antibiotic-producers. However, challenges with accurate binning, skewed ARGs databases, detection of less abundant and allelic variants of ARGs and efficient mobilome characterization remain. Ongoing efforts in long-read, phased- and single-cell sequencing, strain-resolved binning, chromosomal-conformation capture, DNA-methylation binning and deep-learning bioinformatic approaches offer promising prospects in reconstructing complete strain-level genomes and mobilomes from metagenomes.
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Affiliation(s)
- Jonathan Asante
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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153
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Zheng G, Lu Y, Wang D, Zhou L. Importance of sludge conditioning in attenuating antibiotic resistance: Removal of antibiotic resistance genes by bioleaching and chemical conditioning with Fe[III]/CaO. WATER RESEARCH 2019; 152:61-73. [PMID: 30660902 DOI: 10.1016/j.watres.2018.12.053] [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: 09/13/2018] [Revised: 12/14/2018] [Accepted: 12/23/2018] [Indexed: 06/09/2023]
Abstract
Conditioning can drastically improve the dewaterability of sewage sludge and thus it is widely practiced in most wastewater treatment plants (WWTPs). In WWTPs, various antibiotic resistance genes (ARGs) present in sewage are concentrated in the sewage sludge, but the effect of sludge conditioning on ARGs in sewage sludge remains unclear. Here, we evaluated and compared the effectiveness of four sludge conditioning methods (namely chemical conditioning with polyacrylamide (PAM), chemical conditioning with Fe[III]/CaO, bioleaching conditioning, and chemical acidification conditioning) and an aerobic incubation control in removing 46 target ARGs and intI1 from a municipal sewage sludge. The damage of sludge microbial cells and the change in the sludge bacterial community during the various sludge conditioning treatments were also characterized. The results suggested that the chemical conditioning with PAM and aerobic incubation treatment did not remove ARGs and intI1 from the sewage sludge. The chemical acidification reduced the absolute abundances of most ARGs and intI1, but increased their relative abundances. However, the chemical conditioning with Fe[III]/CaO and bioleaching conditioning reduced both the absolute and relative abundances of most ARGs and removed a majority of extracellular ARGs in the sludge. During sludge conditioning treatments, the sludge microbial cells were severely damaged to decrease the total bacterial biomass in sludge, and accordingly the bacterial hosts carrying ARGs and intI were effectively damaged to reduce the absolute abundances of most ARGs and intI1. In addition, the sludge bacterial community in conditioned sludge determined the relative abundances of residual ARGs. Our findings suggest that sludge conditioning can be an important sludge treatment process in attenuating antibiotic resistance in sewage sludge, and bioleaching and chemical conditioning with Fe[III]/CaO can be employed as effective conditioning ways to reduce ARGs in sewage sludge, potentially limiting their release to the environment.
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Affiliation(s)
- Guanyu Zheng
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi Lu
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dianzhan Wang
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lixiang Zhou
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
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154
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Li B, Qiu Y, Li J, Liang P, Huang X. Removal of antibiotic resistance genes in four full-scale membrane bioreactors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:112-119. [PMID: 30408659 DOI: 10.1016/j.scitotenv.2018.10.305] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/21/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Antibiotic resistance genes (ARGs) discharged through wastewater treatment plants (WWTPs) has aroused growing public concern for its risk to human health and ecological safety. Membrane bioreactor (MBR) has been recognized as an effective approach to remove ARGs in full-scale WWTPs, but its advantage over traditional processes was not clearly quantified. To address this, we investigated four full-scale WWTPs containing parallel MBR and traditional processes (oxidation ditch or sequencing batch reactor) to compare the reduction of eight types of ARGs (blaTEM, ermB, tetW, tetO, sul1, sul2, addD, and qnrS) and int1. In general, MBRs reduced the ARGs (1.1-7.3 log removal) better than parallel processes (0.4-4.2 log removal). Notably, the dominant ARGs in the influent, such as ermB, sul1 and int1 (106.39-107.79 copies/mL), were more effectively reduced by MBRs (1.5-7.3 log removal) than traditional processes (0.8-3.4 log removal). Meanwhile, the distribution of those ARGs in activated sludge was not significantly different between aforementioned processes (p > 0.05). The separation coefficient (Ksw) was proposed to represent the contribution of solid separation on ARG removal, subsequent analysis revealed surprisingly strong correlation between Ksw values of dominant ARGs (ermB, sul1 and int1) and their log removal by MBR (R = 0.79-0.96, p < 0.05), while such correlation was much weaker in traditional process (R = 0.33-0.37), indicating solid separation was the major pathway for removal of dominant ARGs and int1. According to the canonical correlation analysis between process operation and ARG removal in MBR, sludge retention time (SRT) seemed to be the major factor affecting removal of dominant ARGs and int1. This comparative study can be helpful for further understanding and operating MBR process to reduce the ARGs in effluent.
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Affiliation(s)
- Bing Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Yong Qiu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Ji Li
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi City, Jiangsu Province 214122, China
| | - Peng Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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155
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Chen H, Bai X, Jing L, Chen R, Teng Y. Characterization of antibiotic resistance genes in the sediments of an urban river revealed by comparative metagenomics analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:1513-1521. [PMID: 30759585 DOI: 10.1016/j.scitotenv.2018.11.052] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 11/04/2018] [Accepted: 11/04/2018] [Indexed: 06/09/2023]
Abstract
The over-use of antibiotics causes growing concerns about human health risks induced by increasing rates of antimicrobial resistance. Riverine systems are considered generally as a natural reservoir of antibiotic resistance genes (ARGs). In this study, several methods including high-throughput sequencing-based metagenomics approach, statistical analysis and network analysis were applied jointly to characterize the wide-spectrum profile of ARGs in the sediments of an urban river in Beijing. Furthermore, contribution of human activities for the presence of ARGs was identified through comparative studies on the metagenomic profiling of ARGs between the river sediments and pristine niches (remote Antarctic soils and deep sea sediments). In total, 442 ARG subtypes belonging to 22 ARG types were detected in the human-impacted river sediments with an abundance range of 1.1 × 10-1-8.1 × 10-1 copy of ARG per copy of 16S-rRNA gene. The most abundant and diverse ARGs were commonly associated with antibiotics that have been extensively used in that area, likely indicating the spread of ARGs in river environments because of the selective pressure resulting from antibiotic use. As a whole, anthropogenic activities were the dominant contributor of major ARG types, for example, occupying 100% for sulfonamide-ARGs, 97% for beta-lactam-ARGs, 94% for aminoglycoside-ARGs and 64% for tetracycline-ARGs. This study provides insights into the role of human activities in accelerating the dissemination and proliferation of ARGs in urban river environment and draws attention to controlling the use and discharge of antibiotics for protection of public health.
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Affiliation(s)
- Haiyang Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China.
| | - Xiaomei Bai
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Lijun Jing
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Ruihui Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China
| | - Yanguo Teng
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing 100875, China.
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156
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Pedrazzani R, Bertanza G, Brnardić I, Cetecioglu Z, Dries J, Dvarionienė J, García-Fernández AJ, Langenhoff A, Libralato G, Lofrano G, Škrbić B, Martínez-López E, Meriç S, Pavlović DM, Papa M, Schröder P, Tsagarakis KP, Vogelsang C. Opinion paper about organic trace pollutants in wastewater: Toxicity assessment in a European perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:3202-3221. [PMID: 30463169 DOI: 10.1016/j.scitotenv.2018.10.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Roberta Pedrazzani
- Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38 and University Research Center "Integrated Models for Prevention and Protection in Environmental and Occupational Health", University of Brescia, 25123 Brescia, Italy.
| | - Giorgio Bertanza
- Department of Civil, Environmental, Architectural Engineering and Mathematics, University of Brescia, Via Branze, 43 and University Research Center "Integrated Models for Prevention and Protection in Environmental and Occupational Health", University of Brescia, 25123, Italy.
| | - Ivan Brnardić
- Faculty of Metallurgy, University of Zagreb, Aleja narodnih heroja 3, 44103 Sisak, Croatia.
| | - Zeynep Cetecioglu
- Department of Chemical Engineering and Technology, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden.
| | - Jan Dries
- Faculty of Applied Engineering, University of Antwerp, Salesianenlaan 90, 2660 Antwerp, Belgium.
| | - Jolanta Dvarionienė
- Kaunas University of Technology, Institute of Environmental Engineering, Gedimino str. 50, 44239 Kaunas, Lithuania.
| | - Antonio J García-Fernández
- Department of Toxicology, Faculty of Veterinary Medicine, University of Murcia, 30100, Campus of Espinardo, Spain.
| | - Alette Langenhoff
- Department of Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708, WG, Wageningen, the Netherlands.
| | - Giovanni Libralato
- Department of Biology, University of Naples Federico II, Via Cinthia ed. 7, 80126 Naples, Italy.
| | - Giusy Lofrano
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Via Giovanni Paolo II, 132-84084 Fisciano, Italy.
| | - Biljana Škrbić
- Faculty of Technology, University of Novi Sad, Bulevar cara Lazara 1, 21000 Novi Sad, Serbia.
| | - Emma Martínez-López
- Department of Toxicology, Faculty of Veterinary Medicine, University of Murcia, 30100, Campus of Espinardo, Spain.
| | - Süreyya Meriç
- Çorlu Engineering Faculty, Environmental Engineering Department, Namik Kemal University, Çorlu, 59860, Tekirdağ, Turkey.
| | - Dragana Mutavdžić Pavlović
- Department of Analytical Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000 Zagreb, Croatia.
| | - Matteo Papa
- Department of Civil, Environmental, Architectural Engineering and Mathematics, University of Brescia, Via Branze, 43 and University Research Center "Integrated Models for Prevention and Protection in Environmental and Occupational Health", University of Brescia, 25123, Italy.
| | - Peter Schröder
- Helmholtz-Center for Environmental Health GmbH, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.
| | - Konstantinos P Tsagarakis
- Department of Environmental Engineering, Democritus University of Thrace, Vas. Sofias 12, 67100 Xanthi, Greece.
| | - Christian Vogelsang
- Norwegian Institute for Water Research, Gaustadalleen 21, 0349 Oslo, Norway.
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157
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Li AD, Metch JW, Wang Y, Garner E, Zhang AN, Riquelme MV, Vikesland PJ, Pruden A, Zhang T. Effects of sample preservation and DNA extraction on enumeration of antibiotic resistance genes in wastewater. FEMS Microbiol Ecol 2019; 94:4781310. [PMID: 29300934 DOI: 10.1093/femsec/fix189] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/27/2017] [Indexed: 11/15/2022] Open
Abstract
With the growing application of high-throughput sequencing-based metagenomics for profiling antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), comparison of sample pretreatment and DNA extraction methods are needed to move toward standardized comparisons among laboratories. Three widely employed DNA extraction methods (FastDNA® Spin Kit for Soil, PowerSoil® DNA Isolation Kit and ZR Fecal DNA MiniPrep), with and without preservation in 50% ethanol and freezing, were applied to the influent, activated sludge and effluent of two WWTPs, in Hong Kong and in the USA. Annotated sequences obtained from the DNA extracted using the three kits shared similar taxonomy and ARG profiles. Overall, it was found that the DNA yield and purity, and diversity of ARGs captured were all highest when applying the FastDNA SPIN Kit for Soil for all three WWTP sample types investigated here (influent, activated sludge, effluent). Quantitative polymerase chain reaction of 16S rRNA genes confirmed the same trend as DNA extraction yields and similar recovery of a representative Gram-negative bacterium (Escherichia coli). Moreover, sample fixation in ethanol, deep-freezing and overseas shipment had no discernable effect on ARG profiles, as compared to fresh samples. This approach serves to inform future efforts toward global comparisons of ARG distributions in WWTPs.
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Affiliation(s)
- An-Dong Li
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Jacob W Metch
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Yulin Wang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Emily Garner
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - An Ni Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Maria V Riquelme
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong
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158
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Chen H, Chen R, Jing L, Bai X, Teng Y. A metagenomic analysis framework for characterization of antibiotic resistomes in river environment: Application to an urban river in Beijing. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 245:398-407. [PMID: 30453138 DOI: 10.1016/j.envpol.2018.11.024] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 11/08/2018] [Accepted: 11/08/2018] [Indexed: 05/21/2023]
Abstract
River is considered generally as a natural reservoir of antibiotic resistance genes (ARGs) in environments. For the prevention and control of ARG risks, it is critical to comprehensively characterize the antibiotic resistomes and their associations in riverine systems. In this study, we proposed a metagenomic framework for identifying antibiotic resistomes in river sediments from multiple categories, including ARG potential, ARG hosts, pathogenicity potential, co-selection potential and gene transfer potential, and applied it to understand the presence, hosts, and co-occurrence of ARGs in the sediments of an urban river in Beijing. Results showed that a total of 203 ARG subtypes belonging to 21 ARG types were detected in the river sediments with an abundance range of 107.7-1004.1×/Gb, dominated by multidrug, macrolide-lincosamide-streptogramin, bacitracin, quinolone and sulfonamide resistance genes. Host-tracking analysis identified Dechloromonas, Pseudoxanthomonas, Arenimonas, Lysobacter and Pseudomonas as the major hosts of ARGs. A number of ARG-carrying contigs (ACCs) were annotated as fragments of pathogenic bacteria and carried multiple multidrug-ARGs. In addition, various biocide/metal resistance genes (B/MRGs) and mobile genetic elements (MGEs), including prophages, plasmids, integrons and transposons, were detected in the river sediments. More importantly, the co-occurrence analysis via ACCs showed a strong association of ARGs with B/MRGs and MGEs, indicating high potential of co-selection and active horizontal transmission for ARGs in the river environment, likely driven by the frequent impact of anthropogenic activities in that area.
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Affiliation(s)
- Haiyang Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Ruihui Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Lijun Jing
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Xiaomei Bai
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China
| | - Yanguo Teng
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, No 19, Xinjiekouwai Street, Beijing, 100875, China.
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159
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Leng L, Nobu MK, Narihiro T, Yang P, Amy Tan GY, Lee PH. Shaping microbial consortia in coupling glycerol fermentation and carboxylate chain elongation for Co-production of 1,3-propanediol and caproate: Pathways and mechanisms. WATER RESEARCH 2019; 148:281-291. [PMID: 30390509 DOI: 10.1016/j.watres.2018.10.063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 10/21/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Glycerol is presently being generated in surplus with the rapid growth of the biodiesel industry and seeks ways to be upcycled, rather than to be treated with costs. Glycerol for the co-production of 1,3-propanediol (1,3-PDO) and caproate has a great prospect. Yet, its technical difficulty lies in the enhancement of caproate productivity, which requires the presence of ethanol as a co-substrate and necessitates the co-existence of functional microbes for glycerol fermentation and chain elongation. This study successfully achieved 6.38 mM C 1,3-PDO d-1 and 2.95 mM C caproate d-1 in a 2-L mixed-cultured semi-continuous fermenter with a glycerol-ethanol-acetate stoichiometric ratio of 4:3:1. Such conversions were mainly facilitated by a microbial community of Eubacterium limosum, Clostridium kluyveri and Massilibacterium senegalense. With such a synergistic microbiome, the co-production of 1,3-PDO and caproate was achieved from glycerol without ethanol addition. Based on metagenomics, E. limosum is capable of converting glycerol to 1,3-PDO, ethanol and H2, and also redirecting the electron potential of H2 into acetate via the Wood-Ljungdahl pathway, which is then used for chain elongation. C. kluyveri worked synergistically with E. limosum by consuming ethanol and acetate for caproate production. M. senegalense encodes for ethanol oxidation to acetate and butyrate, facilitating the generation of these intermediates for C. kluyveri elongation to caproate. During the transition between fermentation and elongation, an unexpected observation of poly-β-hydroxybutyrate (PHB) formation and reutilization by M. senegalense may be associated with butyrate formation for further caproate generation. The knowledge gleaned from the substrate constitute, microbial consortium and their synergetic metabolism demonstrates a resource upgrade potential for crude glycerol or glycerol-containing wastewater generated from the biodiesel industry.
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Affiliation(s)
- Ling Leng
- Department of Civil and Environmental Engineering, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, PR China.
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan.
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan.
| | - Peixian Yang
- Department of Civil and Environmental Engineering, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, PR China.
| | - Giin-Yu Amy Tan
- Department of Civil and Environmental Engineering, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, PR China.
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, PR China.
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160
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Petrovich ML, Rosenthal AF, Griffin JS, Wells GF. Spatially resolved abundances of antibiotic resistance genes and intI1 in wastewater treatment biofilms. Biotechnol Bioeng 2018; 116:543-554. [PMID: 30512194 DOI: 10.1002/bit.26887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/15/2018] [Accepted: 11/29/2018] [Indexed: 12/12/2022]
Abstract
Attached growth bioprocesses that use biofilms to remove organic matter or nutrients from wastewater are known to harbor antibiotic resistance genes (ARGs). Biofilms in these processes are spatially heterogeneous, but little is known about depth stratification of ARGs in complex, mixed culture biofilms. To address this knowledge gap, we used an experimental approach combining cryosectioning and quantitative polymerase chain reaction to quantify the spatial distribution of three ARGs (sul1, ermB, and qnrS) and the class 1 integron-integrase gene intI1 in biofilms from a lab-scale rotating annular reactor fed with synthetic wastewater. We also used high throughput 16S ribosomal RNA (rRNA) gene sequencing to characterize community structure with depth in biofilms. The ARG sul1 and the integron-integrase gene intI1 were found in higher abundances in upper layers of biofilm near the fluid-biofilm interface than in lower layers and exhibited significant correlations between the distance from substratum and gene abundances. The genes ermB and qnrS were present in comparatively low relative abundances. Microbial community structure varied significantly by date of sampling and distance from the substratum. These findings highlight the genetic and taxonomic heterogeneity with distance from substratum in wastewater treatment biofilms and show that sul1 and intI1 are particularly abundant near fluid-biofilm interfaces where cells are most likely to detach and flow into downstream portions of treatment systems and can ultimately be released into the environment through effluent.
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Affiliation(s)
- Morgan L Petrovich
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois
| | - Alex F Rosenthal
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois
| | - James S Griffin
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois
| | - George F Wells
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois
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161
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Wang F, Xu M, Stedtfeld RD, Sheng H, Fan J, Liu M, Chai B, Soares de Carvalho T, Li H, Li Z, Hashsham SA, Tiedje JM. Long-Term Effect of Different Fertilization and Cropping Systems on the Soil Antibiotic Resistome. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13037-13046. [PMID: 30375866 DOI: 10.1021/acs.est.8b04330] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Different fertilization and cropping systems may influence short- and long-term residues of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in soil. Soils from dryland (peanut) and paddy (rice) fields, which originated from the same nonagricultural land (forested), were treated with either chemical fertilizer, composted manure, or no fertilizer for 26 years before sampling, which occurred one year after the last applications. ARGs and MGEs were investigated using highly parallel qPCR and high-throughput sequencing. Six of the 11 antibiotics measured by LC-MS/MS were detected in the manure applied soil, but not in the nonmanured soils, indicating their source was from previous manure applications. Compared to the unfertilized control, manure application did not show a large accumulation of ARGs in either cropping system but there were some minor effects of soil management on indigenous ARGs. Paddy soil showed higher accumulation of these ARGs, which corresponded to higher microbial biomass than the dryland soil. Chemical fertilizer increased relative abundance of these ARGs in dryland soil but decreased their relative abundance in paddy soil. These results show how long-term common soil management practices affect the abundance and type of ARGs and MGEs in two very different soil environments, one aerobic and the other primarily anaerobic.
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Affiliation(s)
- Fang Wang
- 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
| | - 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
| | | | - Hongjie Sheng
- 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
| | - Jianbo Fan
- Key Laboratory of Soil Environment and Pollution Remediation , Institute of Soil Science, Chinese Academy of Sciences , Nanjing 210008 , China
| | - Ming Liu
- Key Laboratory of Soil Environment and Pollution Remediation , Institute of Soil Science, Chinese Academy of Sciences , Nanjing 210008 , China
| | | | | | | | - Zhongpei Li
- Key Laboratory of Soil Environment and Pollution Remediation , Institute of Soil Science, Chinese Academy of Sciences , Nanjing 210008 , China
| | | | - James M Tiedje
- Key Laboratory of Soil Environment and Pollution Remediation , Institute of Soil Science, Chinese Academy of Sciences , Nanjing 210008 , China
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162
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Qiu Y, Zhang J, Li B, Wen X, Liang P, Huang X. A novel microfluidic system enables visualization and analysis of antibiotic resistance gene transfer to activated sludge bacteria in biofilm. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:582-590. [PMID: 29909325 DOI: 10.1016/j.scitotenv.2018.06.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 05/25/2023]
Abstract
Antibiotic resistance genes (ARGs) in environment have become a growing public concern, due to their potential to be obtained by pathogens and their duplication along cell division. Horizontal gene transfer (HGT) was reported to be responsible for ARGs dissemination in microbes, but the HGT feature in environmental biofilm was still unclear due to insufficient assay tools. To address this challenge, we applied a novel microfluidic system to cultivate thin biofilm by continuous supply of nutrients and close contact between cells. Resembling the living state of biofilm in open environment, this chip visualized the transfer of ARG-encoded plasmids RP4 and pKJK5 to the receptors, e.g., activated sludge bacteria. The average plasmid transfer frequency per receptor (T/R) from RP4-hosted Pseudomonas putida KT2440 to activated sludge bacteria was quantified to be 2.5 × 10-3 via flow cytometry, and T/R for pKJK5-hosted Escherichia coli MG1655 was 8.9 × 10-3, while the corresponding average frequencies per donor (T/D) were diverse for the two host strains as 4.3 × 10-3 and 1.4 × 10-1 respectively. The difference between T/R and T/D was explained by the plasmid transfer kinetics, implying specific purposes of the two calculations. Finally, we collected the transconjugants by fluorescent activated cell sorting and further sequenced their 16S rDNA. Bacteria from phyla Proteobacteria and Firmicutes were found more susceptible to be transconjugants than those from Bacteroidetes. Our work demonstrated that microfluidic system was advantageous in biofilm HGT study, which can provide more insights into environmental ARG control.
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Affiliation(s)
- Yong Qiu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jing Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Bing Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Xianghua Wen
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Peng Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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163
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Rowe WPM, Winn MD. Indexed variation graphs for efficient and accurate resistome profiling. Bioinformatics 2018; 34:3601-3608. [PMID: 29762644 PMCID: PMC6198860 DOI: 10.1093/bioinformatics/bty387] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/30/2018] [Accepted: 05/10/2018] [Indexed: 01/05/2023] Open
Abstract
Motivation Antimicrobial resistance (AMR) remains a major threat to global health. Profiling the collective AMR genes within a metagenome (the 'resistome') facilitates greater understanding of AMR gene diversity and dynamics. In turn, this can allow for gene surveillance, individualized treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools. Results Our method combines a variation graph representation of gene sets with a locality-sensitive hashing Forest indexing scheme to allow for fast classification of metagenomic sequence reads using similarity-search queries. Subsequent hierarchical local alignment of classified reads against graph traversals enables accurate reconstruction of full-length gene sequences using a scoring scheme. We provide our implementation, graphing Resistance Out Of meTagenomes (GROOT), and show it to be both faster and more accurate than a current reference-dependent tool for resistome profiling. GROOT runs on a laptop and can process a typical 2 gigabyte metagenome in 2 min using a single CPU. Our method is not restricted to resistome profiling and has the potential to improve current metagenomic workflows. Availability and implementation GROOT is written in Go and is available at https://github.com/will-rowe/groot (MIT license). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Will P M Rowe
- Institute of Integrative Biology, The University of Liverpool, Liverpool, UK
- Scientific Computing Department, The Hartree Centre, STFC Daresbury Laboratory, Warrington, UK
| | - Martyn D Winn
- Scientific Computing Department, The Hartree Centre, STFC Daresbury Laboratory, Warrington, UK
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164
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Lim MY, Cho Y, Rho M. Diverse Distribution of Resistomes in the Human and Environmental Microbiomes. Curr Genomics 2018; 19:701-711. [PMID: 30532649 PMCID: PMC6225452 DOI: 10.2174/1389202919666180911130845] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 04/14/2018] [Accepted: 09/03/2018] [Indexed: 11/22/2022] Open
Abstract
The routine therapeutic use of antibiotics has caused resistance genes to be disseminated across microbial populations. In particular, bacterial strains having antibiotic resistance genes are frequently observed in the human microbiome. Moreover, multidrug-resistant pathogens are now widely spread, threatening public health. Such genes are transferred and spread among bacteria even in different environments. Advances in high throughput sequencing technology and computational algorithms have accelerated investigation into antibiotic resistance genes of bacteria. Such studies have revealed that the antibiotic resistance genes are located close to the mobility-associated genes, which promotes their dissemination. An increasing level of information on genomic sequences of resistome should expedite research on drug-resistance in our body and environment, thereby contributing to the development of public health policy. In this review, the high prevalence of antibiotic resistance genes and their exchange in the human and environmental microbiome is discussed with respect to the genomic contents. The relationships among diverse resistomes, related bacterial species, and the antibiotics are reviewed. In addition, recent advances in bioinformatics approaches to investigate such relationships are discussed.
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Affiliation(s)
- Mi Young Lim
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
| | - Youna Cho
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
| | - Mina Rho
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
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165
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Li J, Cao J, Zhu YG, Chen QL, Shen F, Wu Y, Xu S, Fan H, Da G, Huang RJ, Wang J, de Jesus AL, Morawska L, Chan CK, Peccia J, Yao M. Global Survey of Antibiotic Resistance Genes in Air. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:10975-10984. [PMID: 30043612 DOI: 10.1021/acs.est.8b02204] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Despite its emerging significant public health concern, the presence of antibiotic resistance genes (ARGs) in urban air has not received significant attention. Here, we profiled relative abundances (as a fraction, normalized by 16S rRNA gene) of 30 ARG subtypes resistant to seven common classes of antibiotics, which are quinolones, β-lactams, macrolides, tetracyclines, sulfonamides, aminoglycosides, and vancomycins, in ambient total particulate matter (PM) using a novel protocol across 19 world cities. In addition, their longitudinal changes in PM2.5 samples in Xi'an, China as an example were also studied. Geographically, the ARGs were detected to vary by nearly 100-fold in their abundances, for example, from 0.07 (Bandung, Indonesia) to 5.6 (San Francisco, USA). The β-lactam resistance gene blaTEM was found to be most abundant, seconded by quinolone resistance gene qepA; and their corresponding relative abundances have increased by 178% and 26%, respectively, from 2004 to 2014 in Xi'an. Independent of cities, gene network analysis indicates that airborne ARGs were differentially contributed by bacterial taxa. Results here reveal that urban air is being polluted by ARGs, and different cities are challenged with varying health risks associated with airborne ARG exposure. This work highlights the threat of urban airborne transmission of ARGs and the need of redefining our current air quality standards in terms with public health.
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Affiliation(s)
- Jing Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering , Peking University , Beijing 100871 , China
| | - Junji Cao
- Key Lab of Aerosol Chemistry & Physics, Institute of Earth Environment , Chinese Academy of Sciences , Xi'an 710049 , China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , China
| | - Fangxia Shen
- School of Space and Environment , Beihang University , Beijing 100191 , China
| | - Yan Wu
- School of Environmental Science and Engineering , Shandong University , Jinan 250100 , China
| | - Siyu Xu
- Department of Environmental Health Sciences, Graduate School of Public Health , Seoul National University , Seoul 08826 , South Korea
| | - Hanqing Fan
- Department of Earth and Environmental Engineering , Columbia University , New York , New York 10027 , United States
| | - Guillaume Da
- CERTES, Université Paris-Est Créteil , Centre d'études et de Recherche en Thermique, Environnement et Systèmes (CERTES) , Créteil 94000 , France
| | - Ru-Jin Huang
- Key Lab of Aerosol Chemistry & Physics, Institute of Earth Environment , Chinese Academy of Sciences , Xi'an 710049 , China
| | - Jing Wang
- Institute of Environmental Engineering , ETH Zurich , Zurich 8093 , Switzerland
- Advanced Analytical Technologies , Empa , Dübendorf 8600 , Switzerland
| | - Alma Lorelei de Jesus
- International Laboratory for Air Quality and Health , Queensland University of Technology , GPO Box 2434, Brisbane , Queensland 4001 , Australia
| | - Lidia Morawska
- International Laboratory for Air Quality and Health , Queensland University of Technology , GPO Box 2434, Brisbane , Queensland 4001 , Australia
| | - Chak K Chan
- School of Energy and Environment , City University of Hong Kong , Tat Chee Avenue , Kowloon , Hong Kong China
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering , Yale University , New Haven , Connecticut 06520 , United States
| | - Maosheng Yao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering , Peking University , Beijing 100871 , China
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166
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Li B, Qiu Y, Zhang J, Huang X, Shi H, Yin H. Real-Time Study of Rapid Spread of Antibiotic Resistance Plasmid in Biofilm Using Microfluidics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:11132-11141. [PMID: 30179497 DOI: 10.1021/acs.est.8b03281] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Gene transfer in biofilms is known to play an important role in antibiotic resistance dissemination. However, the process remains poorly understood. In this study, microfluidics with time-lapse imaging was used for real-time monitoring of plasmid-mediated horizontal gene transfer (HGT) in biofilms. Pseudomonas putida KT2440 harboring an antibiotic resistance plasmid RP4 was chosen as the donor while Escherichia coli and activated sludge bacteria were used as the recipient cells. Dynamic features of the transfer process, including the transfer rate, cell growth rate and kinetic changes of the transfer frequency, were determined. It was found that the routes for gene transfer strongly depend on the structure and composition of a biofilm. While intraspecies HGT is essential to initiate a transfer event, the secondary retransfer from transconjugants to the same species is more efficient and can cause cascading gene spread in single-strain biofilms. For the activated sludge biofilm, only small and scattered colonies formed and vertical gene transfer appears to be the dominant route after initial intraspecies transfer. Furthermore, more than 46% of genera in the activated sludge were permissive to plasmid RP4, many of which are associated with human pathogens. These phenomena imply early prevention and interruptions to biofilm structure could provide an effect way to inhibit rapid antibiotic resistance gene spread and reduce the likelihood of catastrophic events associated with antibiotic resistance.
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Affiliation(s)
- Bing Li
- School of Energy and Environmental Engineering , University of Science and Technology Beijing , Beijing , 100083 , China
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment , Tsinghua University , Beijing 100084 , P. R. China
- Division of Biomedical Engineering, School of Engineering, University of Glasgow , Glasgow , G12 8LT , U.K
| | - Yong Qiu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment , Tsinghua University , Beijing 100084 , P. R. China
| | - Jing Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment , Tsinghua University , Beijing 100084 , P. R. China
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment , Tsinghua University , Beijing 100084 , P. R. China
| | - Hanchang Shi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment , Tsinghua University , Beijing 100084 , P. R. China
| | - Huabing Yin
- Division of Biomedical Engineering, School of Engineering, University of Glasgow , Glasgow , G12 8LT , U.K
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167
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Nõlvak H, Truu M, Oopkaup K, Kanger K, Krustok I, Nehrenheim E, Truu J. Reduction of antibiotic resistome and integron-integrase genes in laboratory-scale photobioreactors treating municipal wastewater. WATER RESEARCH 2018; 142:363-372. [PMID: 29908464 DOI: 10.1016/j.watres.2018.06.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/25/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Wastewater treatment systems receiving municipal wastewater are major dissemination nodes of antibiotic resistance genes (ARGs) between anthropogenic and natural environments. This study examined the fate of antibiotic resistome and class 1-3 integron-integrase genes in photobioreactors that were treating municipal wastewater diluted (70/30) with lake or tap water for the algal biomass production. A combined approach of metagenomic and quantitative (qPCR) analysis was undertaken. Municipal wastewater treatment in the photobioreactors led to reduced antibiotic resistome proportion, number of ARG subtypes, and abundances of individual ARGs in the bacterial community. The ARGs and intI1 gene abundances and relative abundances in the discharges of the photobioreactors were either comparable or lower than the respective values in the effluents of conventional wastewater treatment plants. The reduction of the resistome proved to be strongly related to the changes in the bacterial community composition during the wastewater treatment process as it was responding to rising pH levels caused by intense algal growth. Several bacterial genera (e.g., Azoarcus, Dechloromonas, and Sulfuritalea) were recognized as potential hosts of multiple antibiotic resistance types. Although the lake water contributed a diverse and abundant resistome and intI genes profile to the treatment system, it proved to be considerably more beneficial for wastewater dilution than the tap water. The diversity (number of detected resistance types and subtypes) and proportion of the antibiotic resistome, the amount of plasmid borne integron-integrase gene reads, and the abundances and relative abundances of the majority of quantified ARGs (aadA, sul1, tetQ, tetW, qnrS, ermB, blaOXA2-type) and intI1 gene as well as the amount of multi-resistance determinants were significantly lower in the discharges of photobioreactors where lake water was used to dilute wastewater.
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Affiliation(s)
- Hiie Nõlvak
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia.
| | - Marika Truu
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Kristjan Oopkaup
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Kärt Kanger
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Ivo Krustok
- School of Business, Society and Engineering, Mälardalen University, P.O. Box 883, SE-271 23 Västerås, Sweden
| | - Emma Nehrenheim
- School of Business, Society and Engineering, Mälardalen University, P.O. Box 883, SE-271 23 Västerås, Sweden
| | - Jaak Truu
- Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
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168
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Jiang H, Zhou R, Zhang M, Cheng Z, Li J, Zhang G, Chen B, Zou S, Yang Y. Exploring the differences of antibiotic resistance genes profiles between river surface water and sediments using metagenomic approach. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 161:64-69. [PMID: 29859409 DOI: 10.1016/j.ecoenv.2018.05.044] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/17/2018] [Accepted: 05/19/2018] [Indexed: 06/08/2023]
Abstract
To better understand the potential genic communication and dissemination of antibiotic resistance genes (ARGs) in different environmental matrices, the differences of ARG profiles between river surface water and sediments were explored. Metagenomic analysis was applied to investigate the comprehensive ARG profiles in water and sediment samples collected from the highly human-impacted catchment of the Beijiang River and its river source. A total of 135 ARG subtypes belonging to 18 ARG types were identified. Generally, ARGs in surface water were more diverse and abundant than those in sediments. ARG profiles in the surface water and sediment samples were distinct from each other, but some ARGs were shared by the surface water and sediments. Results revealed that multidrug and bacitracin resistance genes were the predominant ARGs types in both surface water (0.30, 0.17 copies/cell) and sediments (0.19, 0.15 copies/cell). 73 ARG subtypes were shared by the water and sediment samples and had taken over 90% of the total detected ARG abundance. Most of the shared ARGs are resistant to the clinically relevant antibiotics. Furthermore, significant correlations between the ARGs and 21 shared genera or mobile genetic elements (MGEs) (plasmids and integrons) were found in surface water and sediments, suggesting the important role of genera or MGEs in shaping ARGs profiles, propagation and distribution. These findings provide deeper insight into mitigating the propagation of ARGs and the associated risks to public health.
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Affiliation(s)
- Haoyu Jiang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 510006, China; State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Renjun Zhou
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Mengdi Zhang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhineng Cheng
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Li
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baowei Chen
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Shichun Zou
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ying Yang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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169
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Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes. ISME JOURNAL 2018; 13:346-360. [PMID: 30250051 DOI: 10.1038/s41396-018-0277-8] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/19/2018] [Accepted: 08/26/2018] [Indexed: 01/22/2023]
Abstract
Wastewater treatment plants (WWTPs) are implicated as hotspots for the dissemination of antibacterial resistance into the environment. However, the in situ processes governing removal, persistence, and evolution of resistance genes during wastewater treatment remain poorly understood. Here, we used quantitative metagenomic and metatranscriptomic approaches to achieve a broad-spectrum view of the flow and expression of genes related to antibacterial resistance to over 20 classes of antibiotics, 65 biocides, and 22 metals. All compartments of 12 WWTPs share persistent resistance genes with detectable transcriptional activities that were comparatively higher in the secondary effluent, where mobility genes also show higher relative abundance and expression ratios. The richness and abundance of resistance genes vary greatly across metagenomes from different treatment compartments, and their relative and absolute abundances correlate with bacterial community composition and biomass concentration. No strong drivers of resistome composition could be identified among the chemical stressors analyzed, although the sub-inhibitory concentration (hundreds of ng/L) of macrolide antibiotics in wastewater correlates with macrolide and vancomycin resistance genes. Contig-based analysis shows considerable co-localization between resistance and mobility genes and implies a history of substantial horizontal resistance transfer involving human bacterial pathogens. Based on these findings, we propose future inclusion of mobility incidence (M%) and host pathogenicity of antibiotic resistance genes in their quantitative health risk ranking models with an ultimate goal to assess the biological significance of wastewater resistomes with regard to disease control in humans or domestic livestock.
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170
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Jong MC, Su JQ, Bunce JT, Harwood CR, Snape JR, Zhu YG, Graham DW. Co-optimization of sponge-core bioreactors for removing total nitrogen and antibiotic resistance genes from domestic wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 634:1417-1423. [PMID: 29710641 DOI: 10.1016/j.scitotenv.2018.04.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/04/2018] [Accepted: 04/04/2018] [Indexed: 06/08/2023]
Abstract
Inadequate sanitation can lead to the spread of infectious diseases and antimicrobial resistance (AMR) via contaminated water. Unfortunately, wastewater treatment is not universal in many developing and emerging countries, especially in rural and peri-urban locations that are remote from central sewers. As such, small-scale, more sustainable treatment options are needed, such as aerobic-Denitrifying Downflow Hanging Sponge (DDHS) bioreactors. In this study, DDHS reactors were assessed for such applications, and achieved over 79% and 84% removal of Chemical Oxygen Demand and Ammonium, respectively, and up to 71% removal of Total Nitrogen (TN) from domestic wastes. Elevated TN removals were achieved via bypassing a fraction of raw wastewater around the top layer of the DDHS system to promote denitrification. However, it was not known how this bypass impacts AMR gene (ARG) and mobile genetic element (MGE) levels in treated effluents. High-throughput qPCR was used to quantify ARG and MGE levels in DDHS bioreactors as a function of percent bypass (0, 10, 20 and 30% by volume). All systems obtained over 90% ARG reduction, although effluent ARG and TN levels differed among bypass regimes, with co-optimal reductions occurring at ~20% bypass. ARG removal paralleled bacterial removal rate, although effluent bacteria tended to have greater genetic plasticity based on higher apparent MGE levels per cell. Overall, TN removal increased and ARG removal decreased with increasing bypass, therefore co-optimization is needed in each DDHS application to achieve locally targeted TN and AMR effluent levels.
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Affiliation(s)
- Mui-Choo Jong
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Science, Xiamen, China
| | - Joshua T Bunce
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - Colin R Harwood
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Jason R Snape
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK; AstraZeneca UK Limited, Global Environment, Alderley Park, UK; School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK
| | - 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 100085, China
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK.
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171
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Wei Z, Feng K, Li S, Zhang Y, Chen H, Yin H, Xu M, Deng Y. Exploring abundance, diversity and variation of a widespread antibiotic resistance gene in wastewater treatment plants. ENVIRONMENT INTERNATIONAL 2018; 117:186-195. [PMID: 29753149 DOI: 10.1016/j.envint.2018.05.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/24/2018] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
An updated sul1 gene sequence database was constructed and new degenerate primers were designed to better investigate the abundance, diversity, and variation of a ubiquitous antibiotic resistance gene, sul1, with PCR-based methods in activated sludge from wastewater treatment plants (WWTPs). The newly designed degenerate primers showed high specificity and higher coverage in both in-silico evaluations and activated sludge samples compared to previous sul1 primers. Using the new primers, the abundance and diversity of sul1 gene, together with 16S rRNA gene, in activated sludge from five WWTPs in summer and winter were determined by quantitative PCR and MiSeq sequencing. The sul1 gene was found to be prevalent and displayed a comparable abundance (0.081 copies per bacterial cell in average) to the total bacteria across all samples. However, compared to the significant seasonal and geographical divergences in the quantity and diversity of bacterial communities in WWTPs, there were no significant seasonal or geographical variations of representative clusters of sul1 gene in most cases. Additionally, the representative sul1 clusters showed fairly close phylogeny and there was no obvious correlation between sul1 gene and the dominant bacterial genera, as well as the int1 gene, suggesting that bacterial hosts of sul1 gene is not stable, the sul1 gene may be carried by mobile genetic elements, sometimes integrated with class 1 integrons and sometimes not. Thus mobile genetic elements likely play a greater role than specific microbial taxa in determining the composition of sul1 gene in WWTPs.
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Affiliation(s)
- Ziyan Wei
- Key Laboratory of Environmental Biotechnology of CAS, 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
| | - Kai Feng
- Key Laboratory of Environmental Biotechnology of CAS, 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
| | - Shuzhen Li
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, 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
| | - Hongrui Chen
- State Key Laboratory of Environmental Aquatic Chemistry, 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
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology of CAS, 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.
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172
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An XL, Su JQ, Li B, Ouyang WY, Zhao Y, Chen QL, Cui L, Chen H, Gillings MR, Zhang T, Zhu YG. Tracking antibiotic resistome during wastewater treatment using high throughput quantitative PCR. ENVIRONMENT INTERNATIONAL 2018; 117:146-153. [PMID: 29751164 DOI: 10.1016/j.envint.2018.05.011] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/18/2018] [Accepted: 05/05/2018] [Indexed: 05/25/2023]
Abstract
Wastewater treatment plants (WWTPs) contain diverse antibiotic resistance genes (ARGs), and thus are considered as a major pathway for the dissemination of these genes into the environments. However, comprehensive evaluations of ARGs dynamic during wastewater treatment process lack extensive investigations on a broad spectrum of ARGs. Here, we investigated the dynamics of ARGs and bacterial community structures in 114 samples from eleven Chinese WWTPs using high-throughput quantitative PCR and 16S rRNA-based Illumina sequencing analysis. Significant shift of ARGs profiles was observed and wastewater treatment process could significantly reduce the abundance and diversity of ARGs, with the removal of ARGs concentration by 1-2 orders of magnitude. Whereas, a considerable number of ARGs were detected and enriched in effluents compared with influents. In particular, seven ARGs mainly conferring resistance to beta-lactams and aminoglycosides and three mobile genetic elements persisted in all WWTPs samples after wastewater treatment. ARGs profiles varied with wastewater treatment processes, seasons and regions. This study tracked the footprint of ARGs during wastewater treatment process, which would support the assessment on the spread of ARGs from WWTPs and provide data for identifying management options to improve ARG mitigation in WWTPs.
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Affiliation(s)
- Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Bing Li
- Division of Energy & Environment, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Wei-Ying Ouyang
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Yi Zhao
- Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong.
| | - Yong-Guan Zhu
- Key Lab 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 Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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173
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Zhang QQ, Tian GM, Jin RC. The occurrence, maintenance, and proliferation of antibiotic resistance genes (ARGs) in the environment: influencing factors, mechanisms, and elimination strategies. Appl Microbiol Biotechnol 2018; 102:8261-8274. [PMID: 30056512 DOI: 10.1007/s00253-018-9235-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 01/10/2023]
Abstract
Here, we review the possible reasons responsible for the occurrence, maintenance and proliferation of antibiotic resistance genes (ARGs) in the environment, as well as the corresponding mechanisms of their development, diffusion and transfer. Additionally, elimination strategies are also discussed. The factors that influence the development of ARGs are selection pressure, including that from antibiotics, metal and multiple other factors, co-resistance and cross-resistance, microbial consortium structure, nutrients in the environment and oxidative stress responses. Process parameters, transport pathways, and elimination strategies to reduce the health risk caused by ARGs are also reviewed in detail. Moreover, knowledge gaps and future opportunities of ARGs are addressed.
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Affiliation(s)
- Qian-Qian Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China.,Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Guang-Ming Tian
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| | - Ren-Cun Jin
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China.
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174
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Tian Z, Zhang Y, Yang M. Chronic impacts of oxytetracycline on mesophilic anaerobic digestion of excess sludge: Inhibition of hydrolytic acidification and enrichment of antibiotic resistome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 238:1017-1026. [PMID: 29449116 DOI: 10.1016/j.envpol.2018.02.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 06/08/2023]
Abstract
We evaluated the chronic impact of oxytetracycline (OTC) on performance and antibiotic resistance development during the mesophilic anaerobic digestion (AD) of antibiotic-containing biomass. Mesophilic AD was conducted in a completely stirred tank reactor by constantly feeding municipal excess sludge spiked with increasing concentrations of OTC (0-1000 mg L-1) under a solid retention time of 20 days over a period of 265 days. Results showed that methane generation of mesophilic AD was inhibited when the OTC concentration in digested sludge was increased to around 18,000 mg kg-1 (OTC dose, 1000 mg L-1), due to the inhibition of fermenting and acidogenic bacteria. Metagenomic sequencing and high-throughput quantitative PCR analysis demonstrated that tetracycline resistance genes were the most dominant type (38.47-43.76%) in the resistome, with tetG, tetX, tetM, tetR, tetQ, tetO, and tetL as the dominant resistant subtypes throughout the whole experimental period. The relative abundance of these tet genes increased from 2.10 × 10-1 before spiking OTC (OTC concentration in digested sludge, 8.97 mg kg-1) to 2.83 × 10-1 (p < 0.05) after spiking OTC at a dose of 40 mg L-1 (OTC concentration in digested sludge, 528.52 mg kg-1). Furthermore, mobile genetic elements, including integrons, transposons, and plasmids, were also enriched with the increase in OTC dose. Based on partial canonical correspondence analysis, the contributions of horizontal (mobile element alteration) and vertical (bacterial community shift) gene transfer to antibiotic resistome variation were 29.35% and 21.51%, respectively. Thus, considering the inhibition of hydrolytic acidification and enrichment of antibiotic resistome, mesophilic AD is not suggested to directly treat the biomass containing OTC concentration higher than 200 mg L-1.
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Affiliation(s)
- Zhe Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
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175
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Bengtsson-Palme J, Larsson DGJ, Kristiansson E. Using metagenomics to investigate human and environmental resistomes. J Antimicrob Chemother 2018; 72:2690-2703. [PMID: 28673041 DOI: 10.1093/jac/dkx199] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance is a global health concern declared by the WHO as one of the largest threats to modern healthcare. In recent years, metagenomic DNA sequencing has started to be applied as a tool to study antibiotic resistance in different environments, including the human microbiota. However, a multitude of methods exist for metagenomic data analysis, and not all methods are suitable for the investigation of resistance genes, particularly if the desired outcome is an assessment of risks to human health. In this review, we outline the current state of methods for sequence handling, mapping to databases of resistance genes, statistical analysis and metagenomic assembly. In addition, we provide an overview of important considerations related to the analysis of resistance genes, and recommend some of the currently used tools and methods that are best equipped to inform research and clinical practice related to antibiotic resistance.
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Affiliation(s)
- Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-41346, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-41346, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden
| | - Erik Kristiansson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Box 440, SE-40530, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
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176
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Garner E, Chen C, Xia K, Bowers J, Engelthaler DM, McLain J, Edwards MA, Pruden A. Metagenomic Characterization of Antibiotic Resistance Genes in Full-Scale Reclaimed Water Distribution Systems and Corresponding Potable Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6113-6125. [PMID: 29741366 DOI: 10.1021/acs.est.7b05419] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Water reclamation provides a valuable resource for meeting nonpotable water demands. However, little is known about the potential for wastewater reuse to disseminate antibiotic resistance genes (ARGs). Here, samples were collected seasonally in 2014-2015 from four U.S. utilities' reclaimed and potable water distribution systems before treatment, after treatment, and at five points of use (POU). Shotgun metagenomic sequencing was used to profile the resistome (i.e., full contingent of ARGs) of a subset ( n = 38) of samples. Four ARGs ( qnrA, blaTEM, vanA, sul1) were quantified by quantitative polymerase chain reaction. Bacterial community composition (via 16S rRNA gene amplicon sequencing), horizontal gene transfer (via quantification of intI1 integrase and plasmid genes), and selection pressure (via detection of metals and antibiotics) were investigated as potential factors governing the presence of ARGs. Certain ARGs were elevated in all ( sul1; p ≤ 0.0011) or some ( blaTEM, qnrA; p ≤ 0.0145) reclaimed POU samples compared to corresponding potable samples. Bacterial community composition was weakly correlated with ARGs (Adonis, R2 = 0.1424-0.1734) and associations were noted between 193 ARGs and plasmid-associated genes. This study establishes that reclaimed water could convey greater abundances of certain ARGs than potable waters and provides observations regarding factors that likely control ARG occurrence in reclaimed water systems.
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Affiliation(s)
- Emily Garner
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Chaoqi Chen
- Department of Crop and Soil Environmental Sciences , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Kang Xia
- Department of Crop and Soil Environmental Sciences , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Jolene Bowers
- Translational Genomics Research Institute , Flagstaff , Arizona 86005 , United States
| | - David M Engelthaler
- Translational Genomics Research Institute , Flagstaff , Arizona 86005 , United States
| | - Jean McLain
- Water Resources Research Center , University of Arizona , Tucson , Arizona 85719 , United States
| | - Marc A Edwards
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
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177
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Jia Y, Khanal SK, Shu H, Zhang H, Chen GH, Lu H. Ciprofloxacin degradation in anaerobic sulfate-reducing bacteria (SRB) sludge system: Mechanism and pathways. WATER RESEARCH 2018; 136:64-74. [PMID: 29494897 DOI: 10.1016/j.watres.2018.02.057] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
Ciprofloxacin (CIP), a fluoroquinolone antibiotic, removal was examined for the first time, in an anaerobic sulfate-reducing bacteria (SRB) sludge system. About 28.0% of CIP was biodegraded by SRB sludge when the influent CIP concentration was 5000 μg/L. Some SRB genera with high tolerance to CIP (i.e. Desulfobacter), were enriched at CIP concentration of 5000 μg/L. The changes in antibiotic resistance genes (ARGs) of SRB sludge coupled with CIP biodegradation intermediates were used to understand the mechanism of CIP biodegradation for the first time. The percentage of efflux pump genes associated with ARGs increased, while the percentage of fluoroquinolone resistance genes that inhibit the DNA copy of bacteria decreased during prolonged exposure to CIP. It implies that some intracellular CIP was extruded into extracellular environment of microbial cells via efflux pump genes to reduce fluoroquinolone resistance genes accumulation caused by exposure to CIP. Additionally, the degradation products and the possible pathways of CIP biodegradation were also examined using the new method developed in this study. The results suggest that CIP was biodegraded intracellularly via desethylation reaction in piperazinyl ring and hydroxylation reaction catalyzed by cytochrome P450 enzymes. This study provides an insight into the mechanism and pathways of CIP biodegradation by SRB sludge, and opens-up a new opportunity for the treatment of CIP-containing wastewater using sulfur-mediated biological process.
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Affiliation(s)
- Yanyan Jia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, USA
| | - Haoyue Shu
- State Key Laboratory of Biocontrol and Guangdong School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huiqun Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.
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178
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Zhao R, Feng J, Yin X, Liu J, Fu W, Berendonk TU, Zhang T, Li X, Li B. Antibiotic resistome in landfill leachate from different cities of China deciphered by metagenomic analysis. WATER RESEARCH 2018; 134:126-139. [PMID: 29407646 DOI: 10.1016/j.watres.2018.01.063] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/20/2018] [Accepted: 01/25/2018] [Indexed: 05/08/2023]
Abstract
High throughput sequencing-based metagenomic analysis and network analysis were applied to investigate the broad-spectrum profiles of ARGs in landfill leachate from 12 cities in China. In total, 526 ARG subtypes belonging to 21 ARG types were detected with abundances ranging from 1.1 × 10-6 to 2.09 × 10-1 copy of ARG/copy of 16S rRNA gene. 68 ARG subtypes that accounted for 73.4%-93.4% of the total ARG abundances were shared by all leachate samples. The four most abundant ARGs, sul1, sul2, aadA and bacA can be served as ARG indicators to quantitatively predict the total abundances by linear functions (r2 = 0.577-0.819, P < 0.001). No distinct regional distribution pattern of the ARGs was observed among different cities in China, while the ARG compositions of the leachate were clearly distinct from those of other environmental sample types. Nearly 90% ARG subtypes in the anaerobic digestion sludge from sewage treatment plants (STPADS) were shared by the leachate and the abundances of leachate and STPADS ARGs generalists accounted for 84.5% and 87.7% of total abundances in these two types of anaerobic samples, respectively. Furthermore, Procrustes analysis suggested that microbial community composition might be the determining factor of ARG compositions in landfill leachate. ARGs within the same type or among the different types showed higher incidences of non-random co-occurrence and 17 genera might be potential hosts of multiple ARGs. This study highlighted that landfill leachate is an important reservoir of various ARGs and provided a useful reference for the surveillance and risk management of ARGs in landfill environments.
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Affiliation(s)
- Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; School of Environment, Tsinghua University, Beijing 100084, China
| | - Jie Feng
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Xiaole Yin
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Wenjie Fu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; School of Environment, Tsinghua University, Beijing 100084, China
| | | | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China.
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179
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Chen B, Lin L, Fang L, Yang Y, Chen E, Yuan K, Zou S, Wang X, Luan T. Complex pollution of antibiotic resistance genes due to beta-lactam and aminoglycoside use in aquaculture farming. WATER RESEARCH 2018; 134:200-208. [PMID: 29427962 DOI: 10.1016/j.watres.2018.02.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 01/14/2018] [Accepted: 02/01/2018] [Indexed: 05/26/2023]
Abstract
The prevalence of antibiotic resistance in the modern world has raised global concerns for public health. Establishing relationships between antibiotic use and antibiotic resistance genes (ARGs) is essential to understanding the dissemination and accumulation of ARGs in a human-impacted environment. In this study, ARG profiles in the sediments from a bullfrog farm, where penicillin and amoxicillin (beta-lactams) and gentamicin (aminoglycoside) were used for prophylactic purposes, were analyzed using metagenomic approaches. Analysis of both extracellular and intracellular DNA (eDNA and iDNA) demonstrated that use of the above-mentioned antibiotics led to complex pollution of ARGs not only related to beta-lactams and aminoglycoside but also to sulfonamides, tetracyclines, and macrolides. Most of the ARGs in the sediments from the bullfrog farm were likely carried by plasmids. A significant correlation was observed between the total abundance of ARG-related plasmids and that of plasmid-carrying ARGs. Approximately 85% of the plasmids likely present in the sediment from the bullfrog farm possessed at least 3 ARG subtypes, which conferred the resistance of bacterial hosts to different antibiotic categories. Our results suggest that antibiotics could lead to complex pollution of ARGs unrelated to those administered due to the concurrence of ARGs in the plasmids.
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Affiliation(s)
- Baowei Chen
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Lan Lin
- Zhujiang Hospital of Southern Medical University, Guangzhou 510282, China
| | - Ling Fang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ying Yang
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Enzhong Chen
- Zhujiang Hospital of Southern Medical University, Guangzhou 510282, China
| | - Ke Yuan
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Shichun Zou
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiaowei Wang
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Tiangang Luan
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China; School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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180
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Wang JH, Lu J, Zhang YX, Wu J, Luo Y, Liu H. Metagenomic analysis of antibiotic resistance genes in coastal industrial mariculture systems. BIORESOURCE TECHNOLOGY 2018; 253:235-243. [PMID: 29353751 DOI: 10.1016/j.biortech.2018.01.035] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/04/2018] [Accepted: 01/07/2018] [Indexed: 06/07/2023]
Abstract
The overuse of antibiotics has posed a propagation of antibiotic resistance genes (ARGs) in aquaculture systems. This study firstly explored the ARGs profiles of the typical mariculture farms including conventional and recirculating systems using metagenomics approach. Fifty ARGs subtypes belonging to 21 ARGs types were identified, showing the wide-spectrum profiles of ARGs in the coastal industrial mariculture systems. ARGs with multiple antibiotics resistance have emerged in the mariculure systems. The co-occurrence pattern between ARGs and microbial taxa showed that Proteobacteria and Bacteroidetes were potential dominant hosts of ARGs in the industrial mariculture systems. Typical nitrifying bacteria such as Nitrospinae in mariculture systems also carried with some resistance genes. Relative abundance of ARGs in fish ponds and wastewater treatment units was relatively high. The investigation showed that industrial mariculture systems were important ARGs reservoirs in coastal area, indicating the critical role of recirculating systems in the terms of ARGs pollution control.
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Affiliation(s)
- Jian-Hua Wang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, People's Republic of China
| | - Jian Lu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, People's Republic of China.
| | - Yu-Xuan Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, People's Republic of China
| | - Jun Wu
- Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, Qinghai 810008, People's Republic of China
| | - Yongming Luo
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, People's Republic of China
| | - Hao Liu
- Shandong Oriental Ocean Sci-tech Co. Ltd, Yantai, Shandong 264003, People's Republic of China
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181
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Espenberg M, Truu M, Mander Ü, Kasak K, Nõlvak H, Ligi T, Oopkaup K, Maddison M, Truu J. Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils. Sci Rep 2018; 8:4742. [PMID: 29549345 PMCID: PMC5856767 DOI: 10.1038/s41598-018-23032-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 03/06/2018] [Indexed: 01/02/2023] Open
Abstract
Tropical peatlands, which play a crucial role in the maintenance of different ecosystem services, are increasingly drained for agriculture, forestry, peat extraction and human settlement purposes. The present study investigated the differences between natural and drained sites of a tropical peatland in the community structure of soil bacteria and archaea and their potential to perform nitrogen transformation processes. The results indicate significant dissimilarities in the structure of soil bacterial and archaeal communities as well as nirK, nirS, nosZ, nifH and archaeal amoA gene-possessing microbial communities. The reduced denitrification and N2-fixing potential was detected in the drained tropical peatland soil. In undisturbed peatland soil, the N2O emission was primarily related to nirS-type denitrifiers and dissimilatory nitrate reduction to ammonium, while the conversion of N2O to N2 was controlled by microbes possessing nosZ clade I genes. The denitrifying microbial community of the drained site differed significantly from the natural site community. The main reducers of N2O were microbes harbouring nosZ clade II genes in the drained site. Additionally, the importance of DNRA process as one of the controlling mechanisms of N2O fluxes in the natural peatlands of the tropics revealed from the results of the study.
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Affiliation(s)
- Mikk Espenberg
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia.
| | - Marika Truu
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Ülo Mander
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Kuno Kasak
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Hiie Nõlvak
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Teele Ligi
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Kristjan Oopkaup
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Martin Maddison
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
| | - Jaak Truu
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise Street, 51014, Tartu, Estonia
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182
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Zhang S, Yang G, Hou S, Zhang T, Li Z, Liang F. Distribution of ARGs and MGEs among glacial soil, permafrost, and sediment using metagenomic analysis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 234:339-346. [PMID: 29195175 DOI: 10.1016/j.envpol.2017.11.031] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/03/2017] [Accepted: 11/08/2017] [Indexed: 06/07/2023]
Abstract
Antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) can be identified with metagenomic analyses comparing relatively pristine and human-impacted environments. We collected samples from 3 different environments: glacial soil little affected by anthropogenic activity, deep permafrost dated to 5821 BP (before human antibiotics), and sediment from the Pearl River. Sulfonamides, tetracyclines, and fluoroquinolones were common in the sediment samples. Sulfonamides and tetracycline were not found in permafrost; tetracycline was also not found in glacial soil. ARGs from the sediment were more abundant and diverse than those from glacial soil and permafrost. More types of resistance mechanisms were also present in the sediment. The diversity of MGEs was significantly correlated with the abundance and diversity of ARGs. The result will help future workers to better understand the distribution of ARGs among environments more or less impacted by anthropogenic activities.
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Affiliation(s)
- Shuhong Zhang
- College of Food and Science, Shangqiu Normal University, Shangqiu 476000, China.
| | - Guangli Yang
- College of Food and Science, Shangqiu Normal University, Shangqiu 476000, China
| | - Shugui Hou
- Department of Geographic and Oceanographic Sciences, Nanjing University, Nanjing 210023, China
| | - Tingjun Zhang
- Key Laboratory of Western China's Environmental Systems (DOE), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zhiguo Li
- College of Environment & Planning, Shangqiu Normal University, Shangqiu 476000, China
| | - Feng Liang
- Biorefinery Engineering Lab of Henan Province, Shangqiu 476000, China
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183
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Hu J, Zhao F, Zhang XX, Li K, Li C, Ye L, Li M. Metagenomic profiling of ARGs in airborne particulate matters during a severe smog event. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 615:1332-1340. [PMID: 29751438 DOI: 10.1016/j.scitotenv.2017.09.222] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/07/2017] [Accepted: 09/21/2017] [Indexed: 06/08/2023]
Abstract
Information is currently limited regarding the distribution of antibiotic resistance genes (ARGs) in smog and their correlations with airborne bacteria. This study characterized the diversity and abundance of ARGs in the particulate matters (PMs) of severe smog based on publicly available metagenomic data, and revealed the occurrence of 205 airborne ARG subtypes, including 31 dominant ones encoding resistance to 11 antibiotic types. Among the detectable ARGs, tetracycline, β-lactam and aminoglycoside resistance genes had the highest abundance, and smog and soil had similar composition characteristics of ARGs. During the smog event, the total abundance of airborne ARGs ranged from 4.90 to 38.07ppm in PM2.5 samples, and from 7.61 to 38.49ppm in PM10 samples, which were 1.6-7.7 times and 2.1-5.1 times of those in the non-smog day, respectively. The airborne ARGs showed complicated co-occurrence patterns, which were heavily influenced by the interaction of bacterial community, and physicochemical and meteorological factors. Lactobacillus and sulfonamide resistance gene sul1 were determined as keystones in the co-occurrence network of microbial taxa and airborne ARGs. The results may help to understand the distribution patterns of ARGs in smog for the potential health risk evaluation.
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Affiliation(s)
- Jialin Hu
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Fuzheng Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Kan Li
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Chaoran Li
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Mei Li
- State Key Laboratory of Pollution Control and Resource Reuse, Environmental Health Research Center, School of the Environment, Nanjing University, Nanjing 210023, China.
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184
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Xiong W, Wang Y, Sun Y, Ma L, Zeng Q, Jiang X, Li A, Zeng Z, Zhang T. Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes. MICROBIOME 2018; 6:34. [PMID: 29439741 PMCID: PMC5811963 DOI: 10.1186/s40168-018-0419-2] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 01/30/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels. RESULTS The effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes (tetA and tetW) and inhibited multidrug resistance genes (mdtA, mdtC, mdtK, ompR, and TolC). The therapeutic dose of chlortetracycline led to loss of Proteobacteria mainly due to the decrease of Escherichia/Shigella (from 72 to 58%). Inhibition of Escherichia by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host Bifidobacterium were enriched due to tetW harbored by Bifidobacterium under chlortetracycline treatment. Escherichia was always the major host for multidrug resistance genes, whereas the primary host was changed from Escherichia to Klebsiella for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline. CONCLUSIONS We provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms. Resistome variations in faecal microbiome of chickens exposed to chlortetracycline.
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Affiliation(s)
- Wenguang Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yulin Wang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Liping Ma
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Qinglin Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Andong Li
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhenling Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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185
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Zhang J, Mao F, Loh KC, Gin KYH, Dai Y, Tong YW. Evaluating the effects of activated carbon on methane generation and the fate of antibiotic resistant genes and class I integrons during anaerobic digestion of solid organic wastes. BIORESOURCE TECHNOLOGY 2018; 249:729-736. [PMID: 29096147 DOI: 10.1016/j.biortech.2017.10.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/21/2017] [Accepted: 10/23/2017] [Indexed: 06/07/2023]
Abstract
The effects of activated carbon (AC) on methane production and the fate of antibiotic resistance genes (ARGs) were evaluated through comparing the anaerobic digestion performance and transformation of ARGs among anaerobic mono-digestion of food waste, co-digestion of food waste and chicken manure, and co-digestion of food waste and waste activated sludge. Results showed that adding AC in anaerobic digesters improved methane yield by at least double through the enrichment of bacteria and archaea. Conventional digestion process showed ability in removing certain types of ARGs, such as tetA, tetX, sul1, sul2, cmlA, floR, and intl1. Supplementing AC in anaerobic digester enhanced the removal of most of the ARGs in mono-digestion of food waste. The effects tended to be minimal in co-digestion of co-substrates such as chicken manure and waste activated sludge, both of which contain a certain amount of antibiotics.
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Affiliation(s)
- Jingxin Zhang
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore
| | - Feijian Mao
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Kai-Chee Loh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576, Singapore
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore; Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Yanjun Dai
- Institute of Refrigeration and Cryogenics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yen Wah Tong
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576, Singapore.
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186
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Characteristics of ARG-carrying plasmidome in the cultivable microbial community from wastewater treatment system under high oxytetracycline concentration. Appl Microbiol Biotechnol 2018; 102:1847-1858. [DOI: 10.1007/s00253-018-8738-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 12/19/2017] [Accepted: 12/26/2017] [Indexed: 11/26/2022]
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187
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Liu P, Jia S, He X, Zhang X, Ye L. Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils. CHEMOSPHERE 2017; 188:455-464. [PMID: 28898777 DOI: 10.1016/j.chemosphere.2017.08.162] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 07/03/2017] [Accepted: 08/25/2017] [Indexed: 06/07/2023]
Abstract
Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash. The results showed that the application of fertilizers could significantly change the soil bacterial community and the abundance of Gaiella under phylum Actinobacteria was significantly reduced from 12.9% in unfertilized soil to 4.1%-7.4% in fertilized soil (P < 0.05). It was also found that the application of manure could cause a transient effect on soil resistome composition and the relative abundance of ARGs increased from 7.37 ppm to 32.10 ppm. The abundance of aminoglycoside, sulfonamide and tetracycline resistance genes greatly increased after manure fertilization and then gradually returned to normal levels with the decay of some intestinal bacteria carrying ARGs. In contrast, the application of chemical fertilizers and straw ash significantly changed the bacterial community structure but exerted little effect on soil resistome. Overall, the results of this study illustrated the different effects of different fertilizers on the soil resistome and revealed that the changes of soil resistome induced by manure application mainly resulted from alteration of bacteria community rather than the horizontal gene transfer.
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Affiliation(s)
- Peng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Shuyu Jia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiwei He
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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188
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Ma L, Li B, Jiang XT, Wang YL, Xia Y, Li AD, Zhang T. Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey. MICROBIOME 2017; 5:154. [PMID: 29179769 PMCID: PMC5704573 DOI: 10.1186/s40168-017-0369-0] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 11/02/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Excesses of antibiotic resistance genes (ARGs), which are regarded as emerging environmental pollutants, have been observed in various environments. The incidence of ARGs in drinking water causes potential risks to human health and receives more attention from the public. However, ARGs harbored in drinking water remain largely unexplored. In this study, we aimed at establishing an antibiotic resistome catalogue in drinking water samples from a wide range of regions and to explore the potential hosts of ARGs. RESULTS A catalogue of antibiotic resistome in drinking water was established, and the host-tracking of ARGs was conducted through a large-scale survey using metagenomic approach. The drinking water samples were collected at the point of use in 25 cities in mainland China, Hong Kong, Macau, Taiwan, South Africa, Singapore and the USA. In total, 181 ARG subtypes belonging to 16 ARG types were detected with an abundance range of 2.8 × 10-2 to 4.2 × 10-1 copies of ARG per cell. The highest abundance was found in northern China (Henan Province). Bacitracin, multidrug, aminoglycoside, sulfonamide, and beta-lactam resistance genes were dominant in drinking water. Of the drinking water samples tested, 84% had a higher ARG abundance than typical environmental ecosystems of sediment and soil. Metagenomic assembly-based host-tracking analysis identified Acidovorax, Acinetobacter, Aeromonas, Methylobacterium, Methyloversatilis, Mycobacterium, Polaromonas, and Pseudomonas as the hosts of ARGs. Moreover, potential horizontal transfer of ARGs in drinking water systems was proposed by network and Procrustes analyses. CONCLUSIONS The antibiotic resistome catalogue compiled using a large-scale survey provides a useful reference for future studies on the global surveillance and risk management of ARGs in drinking water. .
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Affiliation(s)
- Liping Ma
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Bing Li
- Graduate School at Shenzhen, Tsinghua University, Shenzhen, China
| | - Xiao-Tao Jiang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu-Lin Wang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yu Xia
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - An-Dong Li
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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189
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Vikesland PJ, Pruden A, Alvarez PJJ, Aga D, Bürgmann H, Li XD, Manaia CM, Nambi I, Wigginton K, Zhang T, Zhu YG. Toward a Comprehensive Strategy to Mitigate Dissemination of Environmental Sources of Antibiotic Resistance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:13061-13069. [PMID: 28976743 DOI: 10.1021/acs.est.7b03623] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Antibiotic resistance is a pervasive global health threat. To combat the spread of resistance, it is necessary to consider all possible sources and understand the pathways and mechanisms by which resistance disseminates. Best management practices are urgently needed to provide barriers to the spread of resistance and maximize the lifespan of antibiotics as a precious resource. Herein we advise upon the need for coordinated national and international strategies, highlighting three essential components: (1) Monitoring, (2) Risk Assessment, and (3) Mitigation of antibiotic resistance. Central to all three components is What exactly to monitor, assess, and mitigate? We address this question within an environmental framework, drawing from fundamental microbial ecological processes driving the spread of resistance.
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Affiliation(s)
- Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech , Blacksburg, Virginia United States
- Virginia Tech Global Change Center and Virginia Tech Institute of Critical Technology and Applied Science, Virginia Tech , Blacksburg, Virginia United States
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech , Blacksburg, Virginia United States
- Virginia Tech Global Change Center and Virginia Tech Institute of Critical Technology and Applied Science, Virginia Tech , Blacksburg, Virginia United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University , Houston, Texas United States
| | - Diana Aga
- Department of Chemistry, University at Buffalo , Buffalo, New York United States
| | - Helmut Bürgmann
- Eawag: Swiss Federal Institute of Aquatic Science and Technology , 6047 Kastanienbaum, Switzerland
| | - Xiang-Dong Li
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University , Hong Kong
| | - Celia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia , Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - Indumathi Nambi
- Department of Civil Engineering, Indian Institute of Technology - Madras , Chennai, India
| | - Krista Wigginton
- Department of Civil and Environmental Engineering, The University of Michigan , Ann Arbor, Michigan United States
| | - Tong Zhang
- Department of Civil Engineering, Hong Kong University , Hong Kong
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, China
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190
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Yuan K, Chen B, Qing Q, Zou S, Wang X, Luan T. Polycyclic aromatic hydrocarbons (PAHs) enrich their degrading genera and genes in human-impacted aquatic environments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 230:936-944. [PMID: 28743092 DOI: 10.1016/j.envpol.2017.07.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/18/2017] [Accepted: 07/18/2017] [Indexed: 06/07/2023]
Abstract
Bacterial degradation is an important clearance pathway for organic contaminants from highly human-impacted environments. However, it is not fully understood how organic contaminants are selected for degradation by bacteria and genes in aquatic environments. In this study, PAH degrading bacterial genera and PAH-degradation-related genes (PAHDGs) in sediments collected from the Pearl River (PR), the Pearl River Estuary (PRE) and the South China Sea (SCS), among which there were distinct differences in anthropogenic impact, were analyzed using metagenomic approaches. The diversity and abundance of PAH degrading genera and PAHDGs in the PR were substantially higher than those in the PRE and the SCS and were significantly correlated with the total PAH concentration. PAHDGs involved with the three key processes of PAH degradation (ring cleavage, side chain and central aromatic processes) were significantly correlated with each other in the sediments. In particular, plasmid-related PAHDGs were abundant in the PR sediments, indicating plasmid-mediated horizontal transfer of these genes between bacteria or the overgrowth of the bacteria containing these plasmids under the stresses of PAHs. Our results suggest that PAH degrading bacteria and genes were rich in PAH-polluted aquatic environments, which could facilitate the removal of PAHs by bacteria.
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Affiliation(s)
- Ke Yuan
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Science, Sun Yat-Sen University, Guangzhou 510275, China; South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Baowei Chen
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Science, Sun Yat-Sen University, Guangzhou 510275, China; South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Qing Qing
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Science, Sun Yat-Sen University, Guangzhou 510275, China; South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Shichun Zou
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Science, Sun Yat-Sen University, Guangzhou 510275, China; South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiaowei Wang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Science, Sun Yat-Sen University, Guangzhou 510275, China; South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Tiangang Luan
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Science, Sun Yat-Sen University, Guangzhou 510275, China; South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-Sen University, Guangzhou 510275, China; School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
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191
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Xia Y, Li AD, Deng Y, Jiang XT, Li LG, Zhang T. MinION Nanopore Sequencing Enables Correlation between Resistome Phenotype and Genotype of Coliform Bacteria in Municipal Sewage. Front Microbiol 2017; 8:2105. [PMID: 29163399 PMCID: PMC5671560 DOI: 10.3389/fmicb.2017.02105] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/16/2017] [Indexed: 11/18/2022] Open
Abstract
Wastewater treatment plants (WWTPs) functioned as the intersection between the human society and nature environment, are receiving increasingly more attention on risk assessment of the acquisition of environmental antibiotic resistance genes (ARGs) by pathogenetic populations during treatment. However, because of the general lack of robust resistome profiling methods, genotype, and resistance phenotype is still poorly correlated in human pathogens of sewage samples. Here we applied MinION sequencing to quantify the resistance genes of multiple antibiotic resistant (MAR) coliform bacteria, a common indicator for human enteric pathogens in sewage samples. Our pipeline could deliver the results within 30 h from sample collection and the resistome quantification was consistent to that based on the Illumina platform. Additionally, the long nanopore reads not only enabled a simultaneous identification of the carrier populations of ARGs detected, but also facilitated the genome reconstruction of a representative MAR strain, from which we identified an instance of chromosomal integration of environmental resistance gene obtained by plasmid exchange with a porcine pathogen. This study demonstrated the utilization of MinION sequencing in quick monitoring and simultaneous phylogenetic tracking of environmental ARGs to address potential health risk associated with them.
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Affiliation(s)
- Yu Xia
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam, Hong Kong
| | - An-Dong Li
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yu Deng
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam, Hong Kong
| | - Xiao-Tao Jiang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam, Hong Kong
| | - Li-Guan Li
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam, Hong Kong
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam, Hong Kong
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192
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Cultivation-dependent and high-throughput sequencing approaches studying the co-occurrence of antibiotic resistance genes in municipal sewage system. Appl Microbiol Biotechnol 2017; 101:8197-8207. [DOI: 10.1007/s00253-017-8573-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/28/2017] [Accepted: 10/04/2017] [Indexed: 10/18/2022]
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193
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Karkman A, Do TT, Walsh F, Virta MPJ. Antibiotic-Resistance Genes in Waste Water. Trends Microbiol 2017; 26:220-228. [PMID: 29033338 DOI: 10.1016/j.tim.2017.09.005] [Citation(s) in RCA: 418] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/17/2017] [Accepted: 09/19/2017] [Indexed: 12/29/2022]
Abstract
Waste water and waste water treatment plants can act as reservoirs and environmental suppliers of antibiotic resistance. They have also been proposed to be hotspots for horizontal gene transfer, enabling the spread of antibiotic resistance genes between different bacterial species. Waste water contains antibiotics, disinfectants, and metals which can form a selection pressure for antibiotic resistance, even in low concentrations. Our knowledge of antibiotic resistance in waste water has increased tremendously in the past few years with advances in the molecular methods available. However, there are still some gaps in our knowledge on the subject, such as how active is horizontal gene transfer in waste water and what is the role of the waste water treatment plant in the environmental resistome? The purpose of this review is to briefly describe some of the main methods for studying antibiotic resistance in waste waters and the latest research and main knowledge gaps on the issue. In addition, some future research directions are proposed.
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Affiliation(s)
- Antti Karkman
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Thi Thuy Do
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Fiona Walsh
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Marko P J Virta
- Department of Environmental Sciences, University of Helsinki, Helsinki, Finland.
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194
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Abstract
Broad and increasing interest in sustainable wastewater treatment has led a paradigm shift towards more efficient means of treatment system operation. A key aspect of improving overall sustainability is the potential for direct wastewater effluent reuse. Anaerobic membrane bioreactors (AnMBRs) have been identified as an attractive option for producing high quality and nutrient-rich effluents during the treatment of municipal wastewaters. The introduction of direct effluent reuse does, however, raise several safety concerns related to its application. Among those concerns are the microbial threats associated with pathogenic bacteria as well as the emerging issues associated with antibiotic-resistant bacteria and the potential for proliferation of antibiotic resistance genes. Although there is substantial research evaluating these topics from the perspectives of anaerobic digestion and membrane bioreactors separately, little is known regarding how AnMBR systems can contribute to pathogen and antibiotic resistance removal and propagation in wastewater effluents. The aim of this review is to provide a current assessment of existing literature on anaerobic and membrane-based treatment systems as they relate to these microbial safety issues and utilize this assessment to identify areas of potential future research to evaluate the suitability of AnMBRs for direct effluent reuse.
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195
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Su JQ, An XL, Li B, Chen QL, Gillings MR, Chen H, Zhang T, Zhu YG. Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China. MICROBIOME 2017; 5:84. [PMID: 28724443 PMCID: PMC5517792 DOI: 10.1186/s40168-017-0298-y] [Citation(s) in RCA: 192] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/04/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Antibiotic-resistant pathogens are challenging treatment of infections worldwide. Urban sewage is potentially a major conduit for dissemination of antibiotic resistance genes into various environmental compartments. However, the diversity and abundance of such genes in wastewater are not well known. METHODS Here, seasonal and geographical distributions of antibiotic resistance genes and their host bacterial communities from Chinese urban sewage were characterized, using metagenomic analyses and 16S rRNA gene-based Illumina sequencing, respectively. RESULTS In total, 381 different resistance genes were detected, and these genes were extensively shared across China, with no geographical clustering. Seasonal variation in abundance of resistance genes was observed, with average concentrations of 3.27 × 1011 and 1.79 × 1012 copies/L in summer and winter, respectively. Bacterial communities did not exhibit geographical clusters, but did show a significant distance-decay relationship (P < 0.01). The core, shared resistome accounted for 57.7% of the total resistance genes, and was significantly associated with the core microbial community (P < 0.01). The core human gut microbiota was also strongly associated with the shared resistome, demonstrating the potential contribution of human gut microbiota to the dissemination of resistance elements via sewage disposal. CONCLUSIONS This study provides a baseline for investigating environmental dissemination of resistance elements and raises the possibility of using the abundance of resistance genes in sewage as a tool for antibiotic stewardship.
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Affiliation(s)
- Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, 361021, Xiamen, China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, 361021, Xiamen, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
| | - Bing Li
- Division of Energy & Environment, Graduate School at Shenzhen, Tsinghua University, 518055, Shenzhen, China
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, 361021, Xiamen, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
| | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, 361021, Xiamen, China.
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China.
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196
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Bioprospecting for β-lactam resistance genes using a metagenomics-guided strategy. Appl Microbiol Biotechnol 2017; 101:6253-6260. [PMID: 28584911 DOI: 10.1007/s00253-017-8343-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 10/19/2022]
Abstract
Emergence of new antibiotic resistance bacteria poses a serious threat to human health, which is largely attributed to the evolution and spread of antibiotic resistance genes (ARGs). In this work, a metagenomics-guided strategy consisting of metagenomic analysis and function validation was proposed for rapidly identifying novel ARGs from hot spots of ARG dissemination, such as wastewater treatment plants (WWTPs) and animal feces. We used an antibiotic resistance gene database to annotate 76 putative β-lactam resistance genes from the metagenomes of sludge and chicken feces. Among these 76 candidate genes, 25 target genes that shared 40~70% amino acid identity to known β-lactamases were cloned by PCR from the metagenomes. Their resistances to four β-lactam antibiotics were further demonstrated. Furthermore, the validated ARGs were used as the reference sequences to identify novel ARGs in eight environmental samples, suggesting the necessity of re-examining the profiles of ARGs in environmental samples using the validated novel ARG sequences. This metagenomics-guided pipeline does not rely on the activity of ARGs during the initial screening process and may specifically select novel ARG sequences for function validation, which make it suitable for the high-throughput screening of novel ARGs from environmental metagenomes.
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197
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Lau CHF, Li B, Zhang T, Tien YC, Scott A, Murray R, Sabourin L, Lapen DR, Duenk P, Topp E. Impact of pre-application treatment on municipal sludge composition, soil dynamics of antibiotic resistance genes, and abundance of antibiotic-resistance genes on vegetables at harvest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 587-588:214-222. [PMID: 28242221 DOI: 10.1016/j.scitotenv.2017.02.123] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/14/2017] [Accepted: 02/14/2017] [Indexed: 05/15/2023]
Abstract
In many jurisdictions sludge recovered from the sewage treatment process is a valued fertilizer for crop production. Pre-treatment of sewage sludge prior to land application offers the potential to abate enteric microorganisms that carry genes conferring resistance to antibiotics. Pre-treatment practices that accomplish this should have the desirable effect of reducing the risk of contamination of crops or adjacent water with antibiotic resistance genes carried in these materials. In the present study, we obtained municipal sludge that had been subjected to one of five treatments. There were, anaerobic-digestion or aerobic-digestion, in both instances with and without dewatering; and heat-treatment and pelletization. Each of the five types of biosolids was applied to an agricultural field at commercial rates, following which lettuce, carrots and radishes were planted. Based on qPCR, the estimated antibiotic gene loading rates were comparable with each of the five biosolids. However, the gene abundance in soil following application of the pelletized biosolids was anomalously lower than expected. Following application, the abundance of antibiotic resistance genes decreased in a generally coherent fashion, except sul1 which increased in abundance during the growing season in the soil fertilized with pelletized biosolids. Based on qPCR and high throughput sequencing evidence for transfer of antibiotic resistance genes from the biosolids to the vegetables at harvest was weak. Clostridia were more abundant in soils receiving any of the biosolids except the pelletized. Overall, the behavior of antibiotic resistance genes in soils receiving aerobically or anaerobically-digested biosolids was consistent and coherent with previous studies. However, dynamics of antibiotic resistance genes in soils receiving the heat treated pelletized biosolids were very different, and the underlying mechanisms merit investigation.
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Affiliation(s)
| | - Bing Li
- Graduate School at Shenzhen, Tsinghua University, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong
| | | | - Andrew Scott
- Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Roger Murray
- Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Lyne Sabourin
- Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - David R Lapen
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Peter Duenk
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Edward Topp
- Agriculture and Agri-Food Canada, London, Ontario, Canada; Department of Biology, University of Western Ontario, London, Ontario, Canada.
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198
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Ma L, Li AD, Yin XL, Zhang T. The Prevalence of Integrons as the Carrier of Antibiotic Resistance Genes in Natural and Man-Made Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:5721-5728. [PMID: 28426231 DOI: 10.1021/acs.est.6b05887] [Citation(s) in RCA: 198] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Class 1 integrase intI1 has been considered as a good proxy for anthropogenic pollution because of being linked to genes conferring resistance to antibiotics. The gene cassettes of class 1 integrons could carry diverse antibiotic resistance genes (ARGs) and conduct horizontal gene transfer among microorganisms. The present study applied high-throughput sequencing technique combined with an intI1 database and genome assembly to quantify the abundance of intI1 in 64 environmental samples from 8 ecosystems, and to investigate the diverse arrangements of ARG-carrying gene cassettes (ACGCs) carried by class 1 integrons. The abundance of detected intI1 ranged from 3.83 × 10-4 to 4.26 × 10° intI1/cell. High correlation (Pearson's r = 0.852) between intI1 and ARG abundance indicated that intI1 could be considered as an important indicator of ARGs in environments. Aminoglycoside resistance genes were most frequently observed on gene cassettes, carried by 57% assembled ACGCs, followed by trimethoprim and beta-lactam resistance genes. This study established the pipeline for broad monitoring of intI1 in various environmental samples and scanning the ARGs carried by integrons. These findings supplemented our knowledge on the distribution of class 1 integrons and ARGs carried on mobile genetic elements, benefiting future studies on horizontal gene transfer of ARGs.
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Affiliation(s)
- Liping Ma
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
| | - An-Dong Li
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
| | - Xiao-Le Yin
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong
- International Center for Antibiotic Resistance in the Environment, School of Environmental Science and Engineering, Southern University of Science and Technology , Shenzhen, China
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199
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Heshiki Y, Dissanayake T, Zheng T, Kang K, Yueqiong N, Xu Z, Sarkar C, Woo PCY, Chow BKC, Baker D, Yan A, Webster CJ, Panagiotou G, Li J. Toward a Metagenomic Understanding on the Bacterial Composition and Resistome in Hong Kong Banknotes. Front Microbiol 2017; 8:632. [PMID: 28450856 PMCID: PMC5389987 DOI: 10.3389/fmicb.2017.00632] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/28/2017] [Indexed: 11/23/2022] Open
Abstract
Currency is possibly one of the main media transmitting pathogens and drug resistance due to its wide circulation in daily life. In this study, we made a comprehensive characterization of the bacterial community present on banknotes collected from different geographical regions of Hong Kong (HK) by performing in vitro characterization of the bacterial presence and resistome profile, as well as metagenomic analysis including microbial diversity, the prevalence of potential pathogens, the dissemination potential of antibiotic-resistance genes (ARGs), among others. When comparing the bacterial community of HK banknotes with other HK environmental samples, including water and marine sediment, we revealed that HK banknotes cover nearly 50% of total genera found in all the environmental samples, implying that banknotes harbor diverse bacteria originated from a variety of environments. Furthermore, the banknotes have higher abundance of potential pathogenic species (~5 times more) and ARGs (~5 times more) with higher dissemination potential (~48 times more) compared with other environmental samples. These findings unveiled the capabilities of this common medium of exchange to accommodate various bacteria, and transmit pathogens and antibiotic resistance. Furthermore, the observed independence of microbiome profile from the city's topological indices led us to formulate a hypothesis that due to their high circulation banknotes may harbor a homogenized microbiome.
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Affiliation(s)
- Yoshitaro Heshiki
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China
| | - Thrimendra Dissanayake
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China
| | - Tingting Zheng
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China
| | - Kang Kang
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China
| | - Ni Yueqiong
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China
| | - Zeling Xu
- School of Biological Sciences, Faculty of Science, University of Hong KongHong Kong, China
| | - Chinmoy Sarkar
- Healthy High Density Cities Lab, HKUrbanLab, University of Hong KongHong Kong, China
| | - Patrick C Y Woo
- Department of Microbiology, University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, University of Hong KongHong Kong, Hong Kong.,Research Centre of Infection and Immunology, University of Hong KongHong Kong, Hong Kong.,The Carol Yu Centre for Infection, University of Hong KongHong Kong.,Guangzhou Center for Disease Control and PreventionGuangzhou, China
| | - Billy K C Chow
- School of Biological Sciences, Faculty of Science, University of Hong KongHong Kong, China
| | - David Baker
- School of Biological Sciences, Faculty of Science, University of Hong KongHong Kong, China
| | - Aixin Yan
- School of Biological Sciences, Faculty of Science, University of Hong KongHong Kong, China
| | - Christopher J Webster
- Healthy High Density Cities Lab, HKUrbanLab, University of Hong KongHong Kong, China
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China.,Department of Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll InstituteJena, Germany
| | - Jun Li
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China
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200
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Luo G, Li B, Li LG, Zhang T, Angelidaki I. Antibiotic Resistance Genes and Correlations with Microbial Community and Metal Resistance Genes in Full-Scale Biogas Reactors As Revealed by Metagenomic Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:4069-4080. [PMID: 28272884 DOI: 10.1021/acs.est.6b05100] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Digested residues from biogas plants are often used as biofertilizers for agricultural crops cultivation. The antibiotic resistance genes (ARGs) in digested residues pose a high risk to public health due to their potential spread to the disease-causing microorganisms and thus reduce the susceptibility of disease-causing microorganisms to antibiotics in medical treatment. A high-throughput sequencing (HTS)-based metagenomic approach was used in the present study to investigate the variations of ARGs in full-scale biogas reactors and the correlations of ARGs with microbial communities and metal resistance genes (MRGs). The total abundance of ARGs in all the samples varied from 7 × 10-3 to 1.08 × 10-1 copy of ARG/copy of 16S-rRNA gene, and the samples obtained from thermophilic biogas reactors had a lower total abundance of ARGs, indicating the superiority of thermophilic anaerobic digestion for ARGs removal. ARGs in all the samples were composed of 175 ARG subtypes; however, only 7 ARG subtypes were shared by all the samples. Principal component analysis and canonical correspondence analysis clustered the samples into three groups (samples from manure-based mesophilic reactors, manure-based thermophilic reactors, and sludge-based mesophilic reactors), and substrate, temperature, and hydraulic retention time (HRT) as well as volatile fatty acids (VFAs) were identified as crucial environmental variables affecting the ARGs compositions. Procrustes analysis revealed microbial community composition was the determinant of ARGs composition in biogas reactors, and there was also a significant correlation between ARGs composition and MRGs composition. Network analysis further revealed the co-occurrence of ARGs with specific microorganisms and MRGs.
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Affiliation(s)
- Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University , 200433, Shanghai, China
| | - Bing Li
- Key Laboratory of Microorganism Application and Risk Control of Shenzhen, Graduate School at Shenzhen, Tsinghua University , Shenzhen, Guangdong 518055, China
| | - Li-Guan Li
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong SAR, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong , Hong Kong SAR, China
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark , DK-2800, Kongens Lyngby, Denmark
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