701
|
Bacteriome genetic structures of urban deposits are indicative of their origin and impacted by chemical pollutants. Sci Rep 2017; 7:13219. [PMID: 29038457 PMCID: PMC5643393 DOI: 10.1038/s41598-017-13594-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/26/2017] [Indexed: 12/27/2022] Open
Abstract
Urban activities generate surface deposits over impervious surfaces that can represent ecological and health hazards. Bacteriome genetic structures of deposits washed off during rainfall events, over an urban industrial watershed, were inferred from 16 S rRNA gene (rrs) sequences generated by high throughput sequencing. Deposits were sampled over a 4 year-period from a detention basin (DB). Major shifts, matching key management practices, in the structure of these urban bacteriomes, were recorded. Correlation analyses of rrs similarities between samples and their respective concentrations in chemical pollutants, markers of human fecal contaminations (HF183) and antimicrobial resistances (integrons), were performed. Harsher environmental constraints building up in the older deposits led to an increase number of rrs reads from extremophiles such as Acidibacter and Haliangium. Deposits accumulating in the decantation pit of the DB showed an increase in rrs reads from warm blooded intestinal tract bacteria such as Bacteroides and Prevotella. This enrichment matched higher concentrations of Bacteroides HF183 genotypes normally restricted to humans. Bacteriomes of urban deposits appeared good indicators of human-driven environmental changes. Their composition was found representative of their origin. Soil particles and rain appeared to be major contributors of the inferred bacterial taxa recovered from recent deposits.
Collapse
|
702
|
Peng S, Feng Y, Wang Y, Guo X, Chu H, Lin X. Prevalence of antibiotic resistance genes in soils after continually applied with different manure for 30 years. JOURNAL OF HAZARDOUS MATERIALS 2017; 340:16-25. [PMID: 28711829 DOI: 10.1016/j.jhazmat.2017.06.059] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/16/2017] [Accepted: 06/24/2017] [Indexed: 05/08/2023]
Abstract
A 30year field experiment with a wheat-soybean cropping system were performed to compare the long-term anthropogenic influence on soil ARGs. Compared with chemical fertilization, the occurrence of 38 ARGs and the abundance of seven ARGs (tetL, tetB(P), tetO, tetW, sul1, ermB, and ermF) were significantly increased by long term exposure of pig manure. However, application of wheat straw and cow manure not substantially affected the abundance of ARGs except cow manure increased the abundance of tetM and tetW to a detectable level. Relative abundance of Firmicutes, Gammaproteobacteria and Bacteroidetes and ARGs observed in the soil were significantly correlated. Integrase gene I1 (intI1) is commonly linked to genes conferring resistance to antibiotics, it was significantly increased in pig manure treated soils and showed a high positive correlation with the abundance of ARGs which were significantly affected by pig manure. Concentrations of Cu, Zn and Pb were also increased in manure treated soil and positive correlated with the relative abundance of intI1 and most of the ARGs. These results indicated that long-term animal manure application to soils has polluted the soil, especially for pig manure, and it should be scrutinized as part of future stewardship programs.
Collapse
Affiliation(s)
- Shuang Peng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 Beijing East Road, Nanjing, 210008 Jiangsu Province, China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 Beijing East Road, Nanjing, 210008 Jiangsu Province, China
| | - Yiming Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 Beijing East Road, Nanjing, 210008 Jiangsu Province, China
| | - Xisheng Guo
- Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, South Nongke Road 40, Hefei 230031, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 Beijing East Road, Nanjing, 210008 Jiangsu Province, China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 Beijing East Road, Nanjing, 210008 Jiangsu Province, China.
| |
Collapse
|
703
|
Zhang J, Liu J, Wang Y, Yu D, Sui Q, Wang R, Chen M, Tong J, Wei Y. Profiles and drivers of antibiotic resistance genes distribution in one-stage and two-stage sludge anaerobic digestion based on microwave-H 2O 2 pretreatment. BIORESOURCE TECHNOLOGY 2017; 241:573-581. [PMID: 28601775 DOI: 10.1016/j.biortech.2017.05.157] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 06/07/2023]
Abstract
Three anaerobic digestion (AD) processes of waste activated sludge (WAS) were established including the control (mono-WAS), one-stage AD and two-stage AD along with microwave-H2O2 pre-treatment (MW-H2O2) to investigate the profiles and drivers of antibiotic resistance genes (ARGs) distribution concerning co-selection from heavy metals, intI1 and microbial community through qPCR and high-throughput sequencing method. Results showed that MW-H2O2 could reduce the absolute gene copies of all ARGs while increased the relative abundance of most ARGs. After subsequent AD, both total ARGs quantities and relative abundance were enriched while two-stage AD showed some advantages over ARGs abundance reduction. Besides, AD was more effective on the potential pathogens reduction than MW-H2O2. AD could reduce the role of intI1 on the spread of ARGs, while mantel test and procrustes analysis indicated that the variation of ARGs abundance was closely associated with the discrepancy of bacterial community.
Collapse
Affiliation(s)
- Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jibao Liu
- School of Environmental and Chemical Engineering, Tianjin Polytechnic University, Tianjin 300387, China
| | - Yawei Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dawei Yu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianwen Sui
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meixue Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juan Tong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuansong Wei
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
704
|
Chainier D, Barraud O, Masson G, Couve-Deacon E, François B, Couquet CY, Ploy MC. Integron Digestive Carriage in Human and Cattle: A "One Health" Cultivation-Independent Approach. Front Microbiol 2017; 8:1891. [PMID: 29021787 PMCID: PMC5624303 DOI: 10.3389/fmicb.2017.01891] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/15/2017] [Indexed: 01/14/2023] Open
Abstract
Objectives: Dissemination of antimicrobial resistance (AMR) is a global issue that requires the adoption of a "One-Health" approach promoting integration of human and animal health. Besides culture-dependent techniques frequently used for AMR surveillance, cultivation-independent methods can give additional insights into the diversity and reservoir of AMR genetic determinants. Integrons are molecular markers that can provide overall and reliable estimation of AMR dissemination. In this study, considering the "One-Health" approach, we have analyzed the integron digestive carriage from stools of humans and cattle living in a same area and exposed to different antibiotic selection pressures. Methods: Three collections of human [general population (GP) and intensive care unit patients (ICUs)] and bovine (BOV) stool samples were analyzed. The three main classes of integrons were detected using a multiplex qPCR both from total DNA extracted from stools, and from Gram-negative bacteria obtained by culture after an enrichment step. Results: With the cultivation-independent approach, integron carriage was 43.8, 52.7, and 65.6% for GP, ICU, and BOV respectively, percentages being at least twofold higher to those obtained with the cultivation-dependent approach. Class 1 integrons were the most prevalent; class 2 integrons seemed more associated to cattle than to humans; no class 3 integron was detected. The integron carriage was not significantly different between GP and ICU populations according to the antibiotic consumption, whatever the approach. Conclusion: The cultivation-independent approach constitutes a complementary exploratory method to investigate the integron digestive carriage of humans and bovines, notably within subjects under antibiotic treatment. The high frequency of carriage of integrons in the gut is of clinical significance, integrons being able to easily acquire and exchange resistant genes under antibiotic selective pressure and so leading to the dissemination of resistant bacteria.
Collapse
Affiliation(s)
| | - Olivier Barraud
- INSERM, CHU Limoges, UMR 1092, Université Limoges, Limoges, France
| | - Geoffrey Masson
- INSERM, CHU Limoges, UMR 1092, Université Limoges, Limoges, France
| | | | - Bruno François
- INSERM, CHU Limoges, UMR 1092, Université Limoges, Limoges, France.,INSERM, CIC1435, CHU Limoges, Limoges, France
| | - Claude-Yves Couquet
- Laboratoire Départemental d'Analyses et de Recherches de la Haute-Vienne, Limoges, France
| | | |
Collapse
|
705
|
Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. INFECTION GENETICS AND EVOLUTION 2017; 63:295-306. [PMID: 28951202 DOI: 10.1016/j.meegid.2017.09.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-the-art analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.
Collapse
Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain; Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Catarina Branco
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Nadine Castelhano
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago, Chile.
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, Washington, DC, United States; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal.
| |
Collapse
|
706
|
Wang M, Sun Y, Liu P, Sun J, Zhou Q, Xiong W, Zeng Z. Fate of antimicrobial resistance genes in response to application of poultry and swine manure in simulated manure-soil microcosms and manure-pond microcosms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:20949-20958. [PMID: 28721626 DOI: 10.1007/s11356-017-9623-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/23/2017] [Indexed: 06/07/2023]
Abstract
This study aimed to determine the occurrence, abundance, and fate of nine important antimicrobial resistance genes (ARGs) (sul1, sul2, tetB, tetM, ermB, ermF, fexA, cfr, and Intl1) in the simulated soil and pond microcosms following poultry and swine manure application. Absolute quantitative PCR method was used to determine the gene copies. The results were modeled as a logarithmic regression (N = mlnt + b) to explore the fate of target genes. Genes sul1, Intl1, sul2, and tetM had the highest abundance following the application of the two manure types. The logarithmic regression model fitted the results well (R 2 values up to 0.99). The reduction rate of all genes (except for the genes fexA and cfr) in manure-pond microcosms was faster than those in manure-soil microcosms. Importantly, sul1, intl1, sul2, and tetM had the lowest reduction rates in all the samples and the low reduction rates of tetM was the first time to be reported. These results indicated that ARG management should focus on using technologies for the ARG elimination before the manure applications rather than waiting for subsequent attenuation in soil or water, particularly the ARGs (such as sul1, intl1, sul2, and tetM investigated in this study) that had high abundance and low reduction rate in the soil and water after application of manure.
Collapse
Affiliation(s)
- Mianzhi Wang
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Peng Liu
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Jing Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Qin Zhou
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Wenguang Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Zhenling Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China.
| |
Collapse
|
707
|
Lupan I, Carpa R, Oltean A, Kelemen BS, Popescu O. Release of Antibiotic Resistant Bacteria by a Waste Treatment Plant from Romania. Microbes Environ 2017; 32:219-225. [PMID: 28781345 PMCID: PMC5606691 DOI: 10.1264/jsme2.me17016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The occurrence and spread of bacterial antibiotic resistance are subjects of great interest, and the role of wastewater treatment plants has been attracting particular interest. These stations are a reservoir of bacteria, have a large range of organic and inorganic substances, and the amount of bacteria released into the environment is very high. The main purpose of the present study was to assess the removal degree of bacteria with resistance to antibiotics and identify the contribution of a wastewater treatment plant to the microbiota of Someşul Mic river water in Cluj county. The resistance to sulfamethoxazole and tetracycline and some of their representative resistance genes: sul1, tet(O), and tet(W) were assessed in this study. The results obtained showed that bacteria resistant to sulphonamides were more abundant than those resistant to tetracycline. The concentration of bacteria with antibiotic resistance changed after the treatment, namely, bacteria resistant to sulfamethoxazole. The removal of all bacteria and antibiotic-resistant bacteria was 98–99% and the degree of removal of bacteria resistant to tetracycline was higher than the bacteria resistant to sulfamethoxazole compared to total bacteria. The wastewater treatment plant not only contributed to elevating ARG concentrations, it also enhanced the possibility of horizontal gene transfer (HGT) by increasing the abundance of the intI1 gene. Even though the treatment process reduced the concentration of bacteria by two orders of magnitude, the wastewater treatment plant in Cluj-Napoca contributed to an increase in antibiotic-resistant bacteria concentrations up to 10 km downstream of its discharge in Someşul Mic river.
Collapse
Affiliation(s)
- Iulia Lupan
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University
| | - Rahela Carpa
- Babeş Bolyai University, Faculty of Biology and Geology, Department of Molecular Biology and Biotechnology
| | - Andreea Oltean
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University
| | - Beatrice Simona Kelemen
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University
| | - Octavian Popescu
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University
| |
Collapse
|
708
|
Gillings MR. Class 1 integrons as invasive species. Curr Opin Microbiol 2017; 38:10-15. [DOI: 10.1016/j.mib.2017.03.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/02/2017] [Accepted: 03/07/2017] [Indexed: 02/05/2023]
|
709
|
Stedtfeld RD, Stedtfeld TM, Waseem H, Fitschen-Brown M, Guo X, Chai B, Williams MR, Shook T, Logan A, Graham A, Chae JC, Sul WJ, VanHouten J, Cole JR, Zylstra GJ, Tiedje JM, Upham BL, Hashsham SA. Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 198:213-220. [PMID: 28460328 PMCID: PMC5513725 DOI: 10.1016/j.jenvman.2017.04.079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/20/2017] [Accepted: 04/24/2017] [Indexed: 05/05/2023]
Abstract
Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP). In this study, LAMP assays were designed and tested for estimating relative abundance of the intI1 gene, which included design of a universal bacteria 16S rRNA gene assay. Following validation of sensitivity and specificity with known bacterial strains, the assays were tested using DNA extracted from river and lake samples. Results showed a significant Pearson correlation (R2 = 0.8) between the intI1 gene LAMP assay and ARG relative abundance (measured via qPCR). To demonstrate the ruggedness of the LAMP assays, experiments were also run in the hands of relatively "untrained" personnel by volunteer undergraduate students at a local community college using a hand-held real-time DNA analysis device - Gene-Z. Overall, results support use of the intI1 gene as an indicator of ARGs and the LAMP assays exhibit the opportunity for volunteers to monitor environmental samples for anthropogenic pollution outside of a specialized laboratory.
Collapse
Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | - Hassen Waseem
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | | | - Xueping Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Maggie R Williams
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA
| | - Trevor Shook
- Science Division, Delta College, University Center, MI, 48710, USA
| | - Amanda Logan
- Science Division, Delta College, University Center, MI, 48710, USA
| | - Ally Graham
- Science Division, Delta College, University Center, MI, 48710, USA
| | - Jong-Chan Chae
- Division of Biotechnology, Chonbuk National University, Iksan, 54596, Republic of Korea
| | - Woo-Jun Sul
- Department of Systems Biotechnology, Chung Ang University, Anseong, 17546, Republic of Korea
| | - Jacob VanHouten
- Science Division, Delta College, University Center, MI, 48710, USA
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Gerben J Zylstra
- Department of Biochemistry & Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Brad L Upham
- Pediatrics and Human Development, Michigan State University, East Lansing, MI, 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, East Lansing, MI, 48824, USA; Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA.
| |
Collapse
|
710
|
Yang Y, Xu C, Cao X, Lin H, Wang J. Antibiotic resistance genes in surface water of eutrophic urban lakes are related to heavy metals, antibiotics, lake morphology and anthropic impact. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:831-840. [PMID: 28516210 DOI: 10.1007/s10646-017-1814-3] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/02/2017] [Indexed: 05/19/2023]
Abstract
Urban lakes are impacted by heavy human activities and represent potential reservoirs for antibiotic resistance genes. In this study, six urban lakes in Wuhan, central China were selected to analyze the distribution of sulfonamide resistance (sul) genes, tetracycline resistance (tet) genes and quinolone resistance (qnr) genes and their relationship with heavy metals, antibiotics, lake morphology and anthropic impact. sul1 and sul2 were detected in all six lakes and dominated the types of antibiotic resistance genes, which accounted for 86.28-97.79% of the total antibiotic resistance gene abundance. For eight tested tet genes, antibiotic efflux pumps (tetA, tetB, tetC, and tetG) genes were all observed in six lakes and had higher relative abundance than ribosomal protection protein genes (tetM and tetQ). For 4 plasmid mediated quinolone resistance genes, only qnrD is found in all six lakes. The class I integron (intI1) is also found to be a very important media for antibiotic resistance gene propagation in urban lakes. The results of redundancy analysis and variation partitioning analysis showed that antibiotic and co-selection with heavy metals were the major factors driving the propagation of antibiotic resistance genes in six urban lakes. The heavily eutrophic Nanhu Lake and Shahu Lake which located in a high density building area with heavy human activities had the higher relative abundance of total antibiotic resistance genes. Our study could provide a useful reference for antibiotic resistance gene abundance in urban lakes with high anthropic impact.
Collapse
Affiliation(s)
- Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Chen Xu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinhua Cao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Lin
- Institute of Environmental Resources and Soil Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jun Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
| |
Collapse
|
711
|
Yang Y, Liu W, Xu C, Wei B, Wang J. Antibiotic resistance genes in lakes from middle and lower reaches of the Yangtze River, China: Effect of land use and sediment characteristics. CHEMOSPHERE 2017; 178:19-25. [PMID: 28314124 DOI: 10.1016/j.chemosphere.2017.03.041] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/16/2017] [Accepted: 03/10/2017] [Indexed: 06/06/2023]
Abstract
Freshwater lakes provided an ideal media for the accumulation and propagation of antibiotic resistance genes (ARGs), because they were susceptible to anthropogenic impacts. Land reclamation and urbanization exerted severe anthropogenic impacts on lakes from middle and lower reaches of the Yangtze River, China over the past decades. In this study, 15 lakes in the region were selected to understand the level and variability of ARGs. Proportion of different land use types was applied to display the land reclamation and urbanization around each lake. For sulfonamide resistance (sul) genes, sul1 had the highest relative abundance in sediments, with maximum 2.11 × 10-1 copies/16SrRNA copy in Gehu Lake. For tetracycline resistance (tet) genes, tetG had the highest average value of relative abundance (4.74 × 10-3 copies/16SrRNA copy), followed by tetB, tetA, tetQ and tetM. Class I integron (intI1) played an important role in acquisition and dissemination of sul1 and tetG. Sediment characteristics (moisture, density, total nitrogen, total carbon, ammonium, and nitrate) were found to have no significant effect on ARG distribution. Taihu Lake and Yangcheng Lake which exhibited high sul and tet genes had the high proportion of built-up land use.
Collapse
Affiliation(s)
- Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Chen Xu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Buqing Wei
- Wuhan Land Trade Center, Wuhan, 430014, China
| | - Jun Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
| |
Collapse
|
712
|
Harvey PJ, Taylor MP, Handley HK, Foster S, Gillings MR, Asher AJ. Chemical, biological, and DNA markers for tracing slaughterhouse effluent. ENVIRONMENTAL RESEARCH 2017; 156:534-541. [PMID: 28432993 DOI: 10.1016/j.envres.2017.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 06/07/2023]
Abstract
Agricultural practices, if not managed correctly, can have a negative impact on receiving environments via waste disposal and discharge. In this study, a chicken slaughter facility on the rural outskirts of Sydney, Australia, has been identified as a possible source of persistent effluent discharge into a peri-urban catchment. Questions surrounding the facility's environmental management practices go back more than four decades. Despite there having never been a definitive determination of the facility's impact on local stream water quality, the New South Wales Environment Protection Authority (NSW EPA) has implemented numerous pollution reduction requirements to manage noise and water pollution at the slaughter facility. However, assessment of compliance remains complicated by potential additional sources of pollution in the catchment. To unravel this long-standing conundrum related to water pollution we apply a forensic, multiple lines of evidence approach to delineate the origin of the likely pollution source(s). Water samples collected between 2014 and 2016 from irrigation pipes and a watercourse exiting the slaughter facility had elevated concentrations of ammonia (max: 63,000µg/L), nitrogen (max: 67,000µg/L) and phosphorus (max: 39,000µg/L), which were significantly higher than samples from adjacent streams that did not receive direct runoff from the facility. Arsenic, sometimes utilised in growth promoting compounds, was detected in water discharging from the facility up to ~4 times (max 3.84µg/L) local background values (<0.5µg/L), with inorganic As(∑V+III) being the dominant species. The spatial association of elevated water pollution to the facility could not unequivocally distinguish a source and consequently DNA analysis of a suspected pollution discharge event was undertaken. Analysis of catchment runoff from several local streams showed that only water sampled at the downstream boundary of the facility tested positive for chicken DNA, with traces of duck DNA being absent, which was a potential confounder given that wild ducks are present in the area. Further, PCR analysis showed that only the discharge water emanating from the slaughter facility tested positive for a generalized marker of anthropogenic pollution, the clinical class 1 integron-integrase gene. The environmental data collected over a three-year period demonstrates that the slaughter facility is indisputably the primary source of water-borne pollution in the catchment. Moreover, application of DNA and PCR for confirming pollution sources demonstrates its potential for application by regulators in fingerprinting pollution sources.
Collapse
Affiliation(s)
- P J Harvey
- Department of Earth and Planetary Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia.
| | - M P Taylor
- Department of Environmental Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia.
| | - H K Handley
- Department of Earth and Planetary Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - S Foster
- Ecochemistry Laboratory, Institute for Applied Ecology, University of Canberra, Bruce, ACT 2601, Australia
| | - M R Gillings
- Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia
| | - A J Asher
- Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia
| |
Collapse
|
713
|
Abstract
Antibiotic resistance is a global public health issue of growing proportions. All antibiotics are susceptible to resistance. The evidence is now clear that the environment is the single largest source and reservoir of resistance. Soil, aquatic, atmospheric, animal-associated, and built ecosystems are home to microbes that harbor antibiotic resistance elements and the means to mobilize them. The diversity and abundance of resistance in the environment is consistent with the ancient origins of antibiotics and a variety of studies support a long natural history of associated resistance. The implications are clear: Understanding the evolution of resistance in the environment, its diversity, and mechanisms is essential to the management of our existing and future antibiotic resources.
Collapse
Affiliation(s)
- Matthew D Surette
- M.G. DeGroote Institute for Infectious Disease Research and.,Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8N 4K1;
| | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research and.,Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8N 4K1;
| |
Collapse
|
714
|
Gat D, Mazar Y, Cytryn E, Rudich Y. Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:6709-6718. [PMID: 28422476 DOI: 10.1021/acs.est.7b00362] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Microorganisms carried by dust storms are transported through the atmosphere and may affect human health and the functionality of microbial communities in various environments. Characterizing the dust-borne microbiome in dust storms of different origins or that followed different trajectories provides valuable data to improve our understanding of global health and environmental impacts. We present a comparative study on the diversity of dust-borne bacterial communities in dust storms from three distinct origins (North Africa, Syria and Saudi Arabia) and compare them with local bacterial communities sampled on clear days, all collected at a single location: Rehovot, Israel. Storms from different dust origins exhibited distinct bacterial communities, with signature bacterial taxa. Dust storms were characterized by a lower abundance of selected antibiotic resistance genes (ARGs) compared with ambient dust, asserting that the origin of these genes is local and possibly anthropogenic. With the progression of the storm, the storm-borne bacterial community showed increasing resemblance to ambient dust, suggesting mixing with local dust. These results show, for the first time, that dust storms from different sources display distinct bacterial communities, suggesting possible diverse effects on the environment and public health.
Collapse
Affiliation(s)
- Daniella Gat
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Yinon Mazar
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agriculture Research Organization , Rishon Lezion 7528809, Israel
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| |
Collapse
|
715
|
Ghaly TM, Chow L, Asher AJ, Waldron LS, Gillings MR. Evolution of class 1 integrons: Mobilization and dispersal via food-borne bacteria. PLoS One 2017; 12:e0179169. [PMID: 28586403 PMCID: PMC5460862 DOI: 10.1371/journal.pone.0179169] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 05/24/2017] [Indexed: 11/18/2022] Open
Abstract
Class 1 integrons have played a major role in the global dissemination of antibiotic resistance. Reconstructing the history of class 1 integrons might help us control further spread of antibiotic resistance by understanding how human activities influence microbial evolution. Here we describe a class 1 integron that represents an intermediate stage in the evolutionary history of clinical integrons. It was embedded in a series of nested transposons, carried on an IncP plasmid resident in Enterobacter, isolated from the surface of baby spinach leaves. Based on the structure of this integron, we present a modified hypothesis for integron assembly, where the ancestral clinical class 1 integron was captured from a betaproteobacterial chromosome to form a Tn402-like transposon. This transposon then inserted into a plasmid-borne Tn21-like ancestor while in an environmental setting, possibly a bacterium resident in the phyllosphere. We suggest that the qacE gene cassette, conferring resistance to biocides, together with the mercury resistance operon carried by Tn21, provided a selective advantage when this bacterium made its way into the human commensal flora via food. The integron characterized here was located in Tn6007, which along with Tn6008, forms part of the larger Tn6006 transposon, itself inserted into another transposable element to form the Tn21-like transposon, Tn6005. This element has previously been described from the human microbiota, but with a promoter mutation that upregulates integron cassette expression. This element we describe here is from an environmental bacterium, and supports the hypothesis that the ancestral class 1 integron migrated into anthropogenic settings via foodstuffs. Selection pressures brought about by early antimicrobial agents, including mercury, arsenic and disinfectants, promoted its initial fixation, the acquisition of promoter mutations, and subsequent dissemination into various species and pathogens.
Collapse
Affiliation(s)
- Timothy M. Ghaly
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
- * E-mail:
| | - Louise Chow
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Amy J. Asher
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Liette S. Waldron
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Michael R. Gillings
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| |
Collapse
|
716
|
Muurinen J, Stedtfeld R, Karkman A, Pärnänen K, Tiedje J, Virta M. Influence of Manure Application on the Environmental Resistome under Finnish Agricultural Practice with Restricted Antibiotic Use. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:5989-5999. [PMID: 28453251 DOI: 10.1021/acs.est.7b00551] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The co-occurrence of antibiotic-resistance genes (ARGs) and mobile genetic elements (MGEs) in farm environments can potentially foster the development of antibiotic-resistant pathogens. We studied the resistome of Finnish dairy and swine farms where use of antibiotics is limited to treating bacterial infections and manure is only applied from April to September. The resistome of manure, soil, and tile drainage water from the ditch was investigated from the beginning of the growing season until forage harvest. The relative ARG and MGE abundance was measured using a qPCR array with 363 primer pairs. Manure samples had the highest abundance of ARGs and MGEs, which increased during storage. Immediately following land application, the ARGs abundant in manure were detected in soil, but their abundance decreased over time with many becoming undetectable. This suggests that increases in ARG abundances after fertilizing are temporary and occur annually under agricultural practices that restrict antibiotic use. A few of the ARGs were detected in the ditch water, but most of them were undetected in the manure. Our results document the dissipation and dissemination off farm of ARGs under Finnish limited antibiotic use and suggest that such practices could help reduce the load of antibiotic-resistance genes in the environment.
Collapse
Affiliation(s)
- Johanna Muurinen
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki , Viikinkaari 9, Helsinki 00014, Finland
| | - Robert Stedtfeld
- Center for Microbial Ecology, Department of Civil and Environmental Engineering, Michigan State University , East Lansing, Michigan 48824-1325, United States
| | - Antti Karkman
- Department of Biosciences, University of Helsinki , Viikinkaari 1, Helsinki 00014, Finland
| | - Katariina Pärnänen
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki , Viikinkaari 9, Helsinki 00014, Finland
| | - James Tiedje
- Center for Microbial Ecology, Department of Civil and Environmental Engineering, Michigan State University , East Lansing, Michigan 48824-1325, United States
| | - Marko Virta
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki , Viikinkaari 9, Helsinki 00014, Finland
| |
Collapse
|
717
|
Szekeres E, Baricz A, Chiriac CM, Farkas A, Opris O, Soran ML, Andrei AS, Rudi K, Balcázar JL, Dragos N, Coman C. Abundance of antibiotics, antibiotic resistance genes and bacterial community composition in wastewater effluents from different Romanian hospitals. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 225:304-315. [PMID: 28347610 DOI: 10.1016/j.envpol.2017.01.054] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 05/21/2023]
Abstract
Antimicrobial resistance represents a growing and significant public health threat, which requires a global response to develop effective strategies and mitigate the emergence and spread of this phenomenon in clinical and environmental settings. We investigated, therefore, the occurrence and abundance of several antibiotics and antibiotic resistance genes (ARGs), as well as bacterial community composition in wastewater effluents from different hospitals located in the Cluj County, Romania. Antibiotic concentrations ranged between 3.67 and 53.05 μg L-1, and the most abundant antibiotic classes were β-lactams, glycopeptides, and trimethoprim. Among the ARGs detected, 14 genes confer resistance to β-lactams, aminoglycosides, chloramphenicol, macrolide-lincosamide-streptogramin B (MLSB) antibiotics, sulfonamides, and tetracyclines. Genes encoding quaternary ammonium resistance and a transposon-related element were also detected. The sulI and qacEΔ1 genes, which confer resistance to sulfonamides and quaternary ammonium, had the highest relative abundance with values ranging from 5.33 × 10-2 to 1.94 × 10-1 and 1.94 × 10-2 to 4.89 × 10-2 copies/16 rRNA gene copies, respectively. The dominant phyla detected in the hospital wastewater samples were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Among selected hospitals, one of them applied an activated sludge and chlorine disinfection process before releasing the effluent to the municipal collector. This conventional wastewater treatment showed moderate removal efficiency of the studied pollutants, with a 55-81% decrease in antibiotic concentrations, 1-3 order of magnitude lower relative abundance of ARGs, but with a slight increase of some potentially pathogenic bacteria. Given this, hospital wastewaters (raw or treated) may contribute to the spread of these emerging pollutants in the receiving environments. To the best of our knowledge, this study quantified for the first time the abundance of antibiotics and ARGs in wastewater effluents from different Romanian hospitals.
Collapse
Affiliation(s)
- Edina Szekeres
- NIRDBS, Institute of Biological Research, Cluj-Napoca, Romania; Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Andreea Baricz
- NIRDBS, Institute of Biological Research, Cluj-Napoca, Romania
| | - Cecilia Maria Chiriac
- NIRDBS, Institute of Biological Research, Cluj-Napoca, Romania; Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Anca Farkas
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Ocsana Opris
- National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
| | - Maria-Loredana Soran
- National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
| | - Adrian-Stefan Andrei
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Jose Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Nicolae Dragos
- NIRDBS, Institute of Biological Research, Cluj-Napoca, Romania; Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Cristian Coman
- NIRDBS, Institute of Biological Research, Cluj-Napoca, Romania.
| |
Collapse
|
718
|
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.
Collapse
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
| |
Collapse
|
719
|
Vila-Costa M, Gioia R, Aceña J, Pérez S, Casamayor EO, Dachs J. Degradation of sulfonamides as a microbial resistance mechanism. WATER RESEARCH 2017; 115:309-317. [PMID: 28288310 DOI: 10.1016/j.watres.2017.03.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/02/2017] [Accepted: 03/04/2017] [Indexed: 05/03/2023]
Abstract
Two of the main mechanisms of bacterial resistance to sulfonamides in aquatic systems, spread of antibiotic resistance genes (ARG) among the microbial community and in-situ bacterial sulfonamide degradation, were studied in mesocosms experiments using water and cobble biofilms from upstream (pristine waters) and downstream (polluted waters) from the Llobregat river, NE Iberian Peninsula. Mesocosms were prepared at two different concentrations (5000 ng/L and 1000 ng/L) of sulfonamides antibiotics (sulfamethazine and sulfamethoxazole). Concentrations of ARG, nutrients, sulfonamides and their degradation products were measured during the time course of the experiments. Sulfonamides were efficiently degraded by the biofilms during the first four weeks of the experiment. The abundance of ARG in biofilms sharply decreased after addition of high concentrations of sulfonamides, but this was not observed in the mesocosms treated with low concentrations of sulfonamides. Sulfonamide degradation was faster in polluted waters and at high concentrations of sulfonamide (and lower ARG abundances), suggesting that both degradation and ARG are two complementary resistance strategies employed by the microbial community. This study shows that microbial degradation of antibiotics is an efficient resistance mechanism coupled with the presence of ARG, and suggests that in situ degradation prevails at high concentrations of antibiotics whereas physiological adaptation by ARG spread would be more important under relatively lower concentrations of antibiotics.
Collapse
Affiliation(s)
- Maria Vila-Costa
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-24, Barcelona 08034, Catalunya, Spain; Integrative Freshwater Ecology Group, Centre for Advanced Studies of Blanes, CEAB-CSIC, Accés Cala St. Francesc 14, E-17300 Blanes, Spain.
| | - Rosalinda Gioia
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-24, Barcelona 08034, Catalunya, Spain.
| | - Jaume Aceña
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-24, Barcelona 08034, Catalunya, Spain
| | - Sandra Pérez
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-24, Barcelona 08034, Catalunya, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centre for Advanced Studies of Blanes, CEAB-CSIC, Accés Cala St. Francesc 14, E-17300 Blanes, Spain
| | - Jordi Dachs
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-24, Barcelona 08034, Catalunya, Spain
| |
Collapse
|
720
|
Devarajan N, Köhler T, Sivalingam P, van Delden C, Mulaji CK, Mpiana PT, Ibelings BW, Poté J. Antibiotic resistant Pseudomonas spp. in the aquatic environment: A prevalence study under tropical and temperate climate conditions. WATER RESEARCH 2017; 115:256-265. [PMID: 28284092 DOI: 10.1016/j.watres.2017.02.058] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 02/20/2017] [Accepted: 02/25/2017] [Indexed: 06/06/2023]
Abstract
Microbial populations which are resistant to antibiotics are an emerging environmental concern with potentially serious implications for public health. Thus, there is a growing concern in exploring the occurrence of antibiotic resistance in the environment with no limitations to the factors that contribute to their emergence. The aquatic environment is considered to be a hot-spot for the acquisition and spread of antibiotic resistance due to pollution with emerging contaminants derived from anthropogenic activities. In this study, we report on the isolation and characterization of 141 Pseudomonas spp. from aquatic sediments receiving partially (un)treated hospital and communal effluents from three distinct geographical locations: Democratic Republic of the Congo (DRC), India (IN), and Switzerland (CH). P. putida (42%) and P. aeruginosa (39%) were the dominant Pseudomonas species. The highest frequency of antibiotic resistance against eight anti-pseudomonas agents was found among IN isolates (35-60%), followed by DRC (18-50%) and CH (12-54%). CTX-M was the most frequent β-lactamase found in CH (47% of isolates), while VIM-1 was dominant in isolates from DRC (61%) and IN (29%). NDM-1 was found in 29% of the total IN isolates and surprisingly also in 6% of CH isolates. Chromosomally-encoded efflux mechanisms were overexpressed in P. aeruginosa isolates from all three geographic locations. In vitro conjugative transfers of antibiotic resistance plasmids occurred more frequently under tropical temperatures (30 and 37 °C) than under temperate conditions (10 °C). The presence of Extended Spectrum β-lactamases (ESBLs) and Metallo β-lactamases (MBLs) in the isolates from environmental samples has important implications for humans who depend on public water supply and sanitation facilities. To our knowledge, this is the first study to demonstrate a comparison between treated/untreated effluents from urban and hospital settings as a source of microbial resistance by evaluating the aquatic ecosystems sediments from tropical and temperate climate conditions. Taken together, our findings demonstrate a widespread occurrence of antibiotic resistance in aquatic ecosystems sediments receiving untreated/treated wastewater and how these contemporary sources of contamination, contribute to the spread of microbial resistance in the aquatic environment. This research presents also useful tools to evaluate sediment quality in the receiving river/reservoir systems which can be applied to similar environments.
Collapse
Affiliation(s)
- Naresh Devarajan
- University of Geneva, Faculty of Sciences, Section of Earth and Environmental Science, Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, Blvd Carl-Vogt 66, CH-1205 Geneva, Switzerland
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine, University of Geneva, 1, rue Michel Servet, CH-1211 Geneva 4, Switzerland; Transplant Infectious Diseases Unit, University Hospitals Geneva, 4, rue Gabrielle-Perret-Gentil, CH-1211 Geneva 14, Switzerland
| | - Periyasamy Sivalingam
- University of Geneva, Faculty of Sciences, Section of Earth and Environmental Science, Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, Blvd Carl-Vogt 66, CH-1205 Geneva, Switzerland
| | - Christian van Delden
- Department of Microbiology and Molecular Medicine, University of Geneva, 1, rue Michel Servet, CH-1211 Geneva 4, Switzerland; Transplant Infectious Diseases Unit, University Hospitals Geneva, 4, rue Gabrielle-Perret-Gentil, CH-1211 Geneva 14, Switzerland
| | - Crispin K Mulaji
- University of Kinshasa (UNIKIN), Faculty of Science, Department of Chemistry, B.P. 190, Kinshasa XI, Democratic Republic of the Congo
| | - Pius T Mpiana
- University of Kinshasa (UNIKIN), Faculty of Science, Department of Chemistry, B.P. 190, Kinshasa XI, Democratic Republic of the Congo
| | - Bastiaan W Ibelings
- University of Geneva, Faculty of Sciences, Section of Earth and Environmental Science, Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, Blvd Carl-Vogt 66, CH-1205 Geneva, Switzerland
| | - John Poté
- University of Geneva, Faculty of Sciences, Section of Earth and Environmental Science, Department F.-A. Forel for Environmental and Aquatic Sciences and Institute of Environmental Sciences, Blvd Carl-Vogt 66, CH-1205 Geneva, Switzerland; University of Kinshasa (UNIKIN), Faculty of Science, Department of Chemistry, B.P. 190, Kinshasa XI, Democratic Republic of the Congo.
| |
Collapse
|
721
|
Wieland N, Boss J, Lettmann S, Fritz B, Schwaiger K, Bauer J, Hölzel C. Susceptibility to disinfectants in antimicrobial-resistant and -susceptible isolates of Escherichia coli, Enterococcus faecalis and Enterococcus faecium from poultry-ESBL/AmpC-phenotype of E. coli is not associated with resistance to a quaternary ammonium. J Appl Microbiol 2017; 122:1508-1517. [DOI: 10.1111/jam.13440] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 02/17/2017] [Accepted: 03/01/2017] [Indexed: 11/28/2022]
Affiliation(s)
- N. Wieland
- Chair of Animal Hygiene; WZW; TUM; Freising Germany
| | - J. Boss
- Bavarian Health and Food Safety Authority (LGL); Oberschleißheim Germany
| | - S. Lettmann
- Department of Veterinary Sciences; Faculty of Veterinary Medicine; LMU; München Germany
| | - B. Fritz
- Department of Veterinary Sciences; Faculty of Veterinary Medicine; LMU; München Germany
| | - K. Schwaiger
- Department of Veterinary Sciences; Faculty of Veterinary Medicine; LMU; München Germany
| | - J. Bauer
- Chair of Animal Hygiene; WZW; TUM; Freising Germany
| | - C.S. Hölzel
- Department of Veterinary Sciences; Faculty of Veterinary Medicine; LMU; München Germany
| |
Collapse
|
722
|
Abstract
Antibiotic resistance is recognised as a major global threat to public health by the World Health Organization. Currently, several hundred thousand deaths yearly can be attributed to infections with antibiotic-resistant bacteria. The major driver for the development of antibiotic resistance is considered to be the use, misuse and overuse of antibiotics in humans and animals. Nonantibiotic compounds, such as antibacterial biocides and metals, may also contribute to the promotion of antibiotic resistance through co-selection. This may occur when resistance genes to both antibiotics and metals/biocides are co-located together in the same cell (co-resistance), or a single resistance mechanism (e.g. an efflux pump) confers resistance to both antibiotics and biocides/metals (cross-resistance), leading to co-selection of bacterial strains, or mobile genetic elements that they carry. Here, we review antimicrobial metal resistance in the context of the antibiotic resistance problem, discuss co-selection, and highlight critical knowledge gaps in our understanding.
Collapse
|
723
|
Gao P, Gu C, Wei X, Li X, Chen H, Jia H, Liu Z, Xue G, Ma C. The role of zero valent iron on the fate of tetracycline resistance genes and class 1 integrons during thermophilic anaerobic co-digestion of waste sludge and kitchen waste. WATER RESEARCH 2017; 111:92-99. [PMID: 28061387 DOI: 10.1016/j.watres.2016.12.047] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/18/2016] [Accepted: 12/27/2016] [Indexed: 06/06/2023]
Abstract
Activated sludge has been identified as a potential significant source of antibiotic resistance genes (ARGs) to the environment. Anaerobic digestion is extensively used for sludge stabilization and resource recovery, and represents a crucial process for controlling the dissemination of ARGs prior to land application of digested sludge. The objective of this study is to investigate the effect of zero valent iron (Fe0) on the attenuation of seven representative tetracycline resistance genes (tet, tet(A), tet(C), tet(G), tet(M), tet(O), tet(W), and tet(X)), and the integrase gene intI1 during thermophilic anaerobic co-digestion of waste sludge and kitchen waste. Significant decrease (P < 0.05) in the quantities of tet (except tet(W)) and intI1 genes was observed at Fe0 dosage of 5 g/L, whereas no significant differences (P > 0.05) were found for all gene targets between digesters with Fe0 dosages of 5 and 60 g/L. A first-order kinetic model favorably described the trends in concentrations of tet and intI1 gene targets during thermophilic anaerobic digestion with or without Fe0. Notably, tet genes encoding different resistance mechanisms behaved distinctly in anaerobic digesters, although addition of Fe0 could enhance their reduction. The overall results of this research suggest that thermophilic anaerobic digestion with Fe0 can be a potential alternative technology for the attenuation of tet and intI1 genes in waste sludge.
Collapse
Affiliation(s)
- Pin Gao
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai 201620, China.
| | - Chaochao Gu
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai 201620, China
| | - Xin Wei
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai 201620, China
| | - Xiang Li
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai 201620, China
| | - Hong Chen
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai 201620, China
| | - Hanzhong Jia
- Laboratory of Environmental Sciences and Technology, Xinjiang Technical Institute of Physics & Chemistry, Key Laboratory of Functional Materials and Devices for Special Environments, Chinese Academy of Sciences, Urumqi 830011, China
| | - Zhenhong Liu
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai 201620, China
| | - Gang Xue
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai 201620, China
| | - Chunyan Ma
- College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, Donghua University, Shanghai 201620, China.
| |
Collapse
|
724
|
Yin Y, Gu J, Wang X, Song W, Zhang K, Sun W, Zhang X, Zhang Y, Li H. Effects of Copper Addition on Copper Resistance, Antibiotic Resistance Genes, and intl1 during Swine Manure Composting. Front Microbiol 2017; 8:344. [PMID: 28316595 PMCID: PMC5335643 DOI: 10.3389/fmicb.2017.00344] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 02/20/2017] [Indexed: 12/01/2022] Open
Abstract
Copper is one of the most abundant heavy metals present in swine manure. In this study, a laboratory-scale aerobic composting system was amended with Cu at three levels (0, 200, and 2000 mg kg-1, i.e., control, Cu200, and Cu2000 treatments, respectively) to determine its effect on the fate of copper resistance genes [copper resistance genes (CRGs): pcoA, cusA, copA, and tcrB], antibiotic resistance genes [antibiotic resistance genes (ARGs): erm(A) and erm(B)], and intl1. The results showed that the absolute abundances of pcoA, tcrB, erm(A), erm(B), and intl1 were reduced, whereas those of copA and cusA increased after swine manure composting. Redundancy analysis showed that temperature significantly affected the variations in CRGs, ARGs, and intl1. The decreases in CRGs, ARGs, and intI1 were positively correlated with the exchangeable Cu levels. The bacterial community could be grouped according to the composting time under different treatments, where the high concentration of copper had a more persistent effect on the bacterial community. Network analysis determined that the co-occurrence of CRGs, ARGs, and intI1, and the bacterial community were the main contributors to the changes in CRGs, ARG, and intl1. Thus, temperature, copper, and changes in the bacterial community composition had important effects on the variations in CRGs, ARGs, and intl1 during manure composting in the presence of added copper.
Collapse
Affiliation(s)
- Yanan Yin
- College of Resources and Environmental Sciences, Northwest A&F University Yangling, China
| | - Jie Gu
- College of Resources and Environmental Sciences, Northwest A&F University Yangling, China
| | - Xiaojuan Wang
- College of Resources and Environmental Sciences, Northwest A&F University Yangling, China
| | - Wen Song
- College of Science, Northwest A&F University Yangling, China
| | - Kaiyu Zhang
- College of Resources and Environmental Sciences, Northwest A&F University Yangling, China
| | - Wei Sun
- College of Resources and Environmental Sciences, Northwest A&F University Yangling, China
| | - Xin Zhang
- College of Science, Northwest A&F University Yangling, China
| | - Yajun Zhang
- College of Resources and Environmental Sciences, Northwest A&F University Yangling, China
| | - Haichao Li
- College of Resources and Environmental Sciences, Northwest A&F University Yangling, China
| |
Collapse
|
725
|
Aubertheau E, Stalder T, Mondamert L, Ploy MC, Dagot C, Labanowski J. Impact of wastewater treatment plant discharge on the contamination of river biofilms by pharmaceuticals and antibiotic resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 579:1387-1398. [PMID: 27913024 DOI: 10.1016/j.scitotenv.2016.11.136] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/18/2016] [Accepted: 11/19/2016] [Indexed: 06/06/2023]
Abstract
Wastewater treatment plants (WWTPs) are one of the main sources of pharmaceutical residue in surface water. Epilithic biofilms were collected downstream from 12 WWTPs of various types and capacities to study the impacts of their discharge through the changes in biofilm composition (compared to a corresponding upstream biofilm) in terms of pharmaceutical concentrations and bacterial community modifications (microbial diversity and resistance integrons). The biofilm is a promising indicator to evaluate the impacts of WWTPs on the surrounding aquatic environment. Indeed, the use of biofilms reveals contamination hot spots. All of the downstream biofilms present significant concentrations (up to 965ng/g) of five to 11 pharmaceuticals (among the 12 analysed). Moreover, the exposition to the discharge point increases the presence of resistance integrons (three to 31 fold for Class 1) and modifies the diversity of the bacterial communities (for example cyanobacteria). The present study confirms that the discharge from WWTPs has an impact on the aquatic environment.
Collapse
Affiliation(s)
- Elodie Aubertheau
- University of Poitiers, UMR CNRS 7285 IC2MP, Department of Water and Geochemistry, ENSIP, 1 Rue Marcel Doré, TSA 41105, 86073 Poitiers Cedex, France
| | - Thibault Stalder
- University of Limoges, INSERM UMR-S1092, Faculté de Médecine, 2 rue du Docteur Marcland, 87065 Limoges Cedex, France; University of Limoges, GRESE EA4330, ENSIL, 16 rue Atlantis, 87068 Limoges Cedex, France
| | - Leslie Mondamert
- University of Poitiers, UMR CNRS 7285 IC2MP, Department of Water and Geochemistry, ENSIP, 1 Rue Marcel Doré, TSA 41105, 86073 Poitiers Cedex, France
| | - Marie-Cécile Ploy
- University of Limoges, INSERM UMR-S1092, Faculté de Médecine, 2 rue du Docteur Marcland, 87065 Limoges Cedex, France
| | - Christophe Dagot
- University of Limoges, INSERM UMR-S1092, Faculté de Médecine, 2 rue du Docteur Marcland, 87065 Limoges Cedex, France; University of Limoges, GRESE EA4330, ENSIL, 16 rue Atlantis, 87068 Limoges Cedex, France
| | - Jérôme Labanowski
- University of Poitiers, UMR CNRS 7285 IC2MP, Department of Water and Geochemistry, ENSIP, 1 Rue Marcel Doré, TSA 41105, 86073 Poitiers Cedex, France.
| |
Collapse
|
726
|
Anjum R, Grohmann E, Krakat N. Anaerobic digestion of nitrogen rich poultry manure: Impact of thermophilic biogas process on metal release and microbial resistances. CHEMOSPHERE 2017; 168:1637-1647. [PMID: 27932039 DOI: 10.1016/j.chemosphere.2016.11.132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 11/16/2016] [Accepted: 11/26/2016] [Indexed: 06/06/2023]
Abstract
Poultry manure is a nitrogen rich fertilizer, which is usually recycled and spread on agricultural fields. Due to its high nutrient content, chicken manure is considered to be one of the most valuable animal wastes as organic fertilizer. However, when chicken litter is applied in its native form, concerns are raised as such fertilizers also include high amounts of antibiotic resistant pathogenic Bacteria and heavy metals. We studied the impact of an anaerobic thermophilic digestion process on poultry manure. Particularly, microbial antibiotic resistance profiles, mobile genetic elements promoting the resistance dissemination in the environment as well as the presence of heavy metals were focused in this study. The initiated heat treatment fostered a community shift from pathogenic to less pathogenic bacterial groups. Phenotypic and molecular studies demonstrated a clear reduction of multiple resistant pathogens and self-transmissible plasmids in the heat treated manure. That treatment also induced a higher release of metals and macroelements. Especially, Zn and Cu exceeded toxic thresholds. Although the concentrations of a few metals reached toxic levels after the anaerobic thermophilic treatment, the quality of poultry manure as organic fertilizer may raise significantly due to the elimination of antibiotic resistance genes (ARG) and self-transmissible plasmids.
Collapse
Affiliation(s)
- Reshma Anjum
- Leibniz Institute for Agricultural Engineering and Bio-Economy Potsdam, Dept. Bioengineering, Max-Eyth-Allee 100, D-14469 Potsdam, Germany
| | - Elisabeth Grohmann
- Faculty of Life Sciences and Technology, Beuth University of Applied Sciences, Berlin, Germany; Division of Infectious Diseases, University Medical Centre Freiburg, Freiburg, Germany
| | - Niclas Krakat
- Leibniz Institute for Agricultural Engineering and Bio-Economy Potsdam, Dept. Bioengineering, Max-Eyth-Allee 100, D-14469 Potsdam, Germany.
| |
Collapse
|
727
|
Lee J, Shin SG, Jang HM, Kim YB, Lee J, Kim YM. Characterization of antibiotic resistance genes in representative organic solid wastes: Food waste-recycling wastewater, manure, and sewage sludge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 579:1692-1698. [PMID: 27923578 DOI: 10.1016/j.scitotenv.2016.11.187] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 11/21/2016] [Accepted: 11/25/2016] [Indexed: 06/06/2023]
Abstract
In this research, the distribution of antibiotic resistance genes (ARGs) was characterized in representative organic solid waste (OSW) in Korea: food waste-recycling wastewater (FRW), manure, and sewage sludge. The amounts of total ARG (gene copies/16S rRNA gene copies) was greatest in manure followed by sewage sludge and FRW. Interestingly, there were significantly different patterns in the diversity and mechanisms of ARGs. For example, a significant proportion of ARGs were tetracycline resistant genes in all the OSW (40.4-78.2%). β-lactam antibiotics resistant genes were higher in the FRW samples than in other types of OSW but sulfonamides resistant genes represented the greatest proportion in sludge. Regarding the characteristics of antibiotic resistance mechanisms, there was a relatively higher proportion of the ribosomal protection mechanism to tetracycline observed in the FRW and manure samples. However, tetracycline resistant genes with direct interaction were relatively higher in the sewage sludge samples. sul1 was the dominant subtype in all the OSW types and detection of ermB was observed although there was no ermC detected in sewage sludge. There were significant correlations between the occurrences of ARG subtypes: tetB and tetG in all OSW (P<0.01); tetE and tetQ only in sludge (P<0.01). The Class 1 integron-integrase gene (intI1) was significantly correlated with total ARGs only in manure and sludge (P<0.05), revealing potential horizontal gene transfer in these OSW.
Collapse
Affiliation(s)
- Jangwoo Lee
- School of Earth Science and Environmental Engineering, Gwang-ju Institute of Science and Technology (GIST), 123, Cheomdangwagi-ro, Buk-gu, Gwang-ju 61005, Republic of Korea
| | - Seung Gu Shin
- School of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Hyun Min Jang
- School of Earth Science and Environmental Engineering, Gwang-ju Institute of Science and Technology (GIST), 123, Cheomdangwagi-ro, Buk-gu, Gwang-ju 61005, Republic of Korea
| | - Young Beom Kim
- School of Earth Science and Environmental Engineering, Gwang-ju Institute of Science and Technology (GIST), 123, Cheomdangwagi-ro, Buk-gu, Gwang-ju 61005, Republic of Korea
| | - Joonyeob Lee
- School of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Young Mo Kim
- School of Earth Science and Environmental Engineering, Gwang-ju Institute of Science and Technology (GIST), 123, Cheomdangwagi-ro, Buk-gu, Gwang-ju 61005, Republic of Korea.
| |
Collapse
|
728
|
Continental-scale pollution of estuaries with antibiotic resistance genes. Nat Microbiol 2017; 2:16270. [DOI: 10.1038/nmicrobiol.2016.270] [Citation(s) in RCA: 608] [Impact Index Per Article: 86.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 12/16/2016] [Indexed: 12/27/2022]
|
729
|
Hu HW, Wang JT, Li J, Shi XZ, Ma YB, Chen D, He JZ. Long-Term Nickel Contamination Increases the Occurrence of Antibiotic Resistance Genes in Agricultural Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:790-800. [PMID: 27977160 DOI: 10.1021/acs.est.6b03383] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Heavy metal contamination is assumed to be a selection pressure on antibiotic resistance, but to our knowledge, evidence of the heavy metal-induced changes of antibiotic resistance is lacking on a long-term basis. Using quantitative PCR array and Illumina sequencing, we investigated the changes of a wide spectrum of soil antibiotic resistance genes (ARGs) following 4-5 year nickel exposure (0-800 mg kg-1) in two long-term experimental sites. A total of 149 unique ARGs were detected, with multidrug and β-lactam resistance as the most prevailing ARG types. The frequencies and abundance of ARGs tended to increase along the gradient of increasing nickel concentrations, with the highest values recorded in the treatments amended with 400 mg nickel kg-1 soil. The abundance of mobile genetic elements (MGEs) was significantly associated with ARGs, suggesting that nickel exposure might enhance the potential for horizontal transfer of ARGs. Network analysis demonstrated significant associations between ARGs and MGEs, with the integrase intI1 gene having the most frequent interactions with other co-occurring ARGs. The changes of ARGs were mainly driven by nickel bioavailability and MGEs as revealed by structural equation models. Taken together, long-term nickel exposure significantly increased the diversity, abundance, and horizontal transfer potential of soil ARGs.
Collapse
Affiliation(s)
- Hang-Wei Hu
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China Faculty of
- Veterinary and Agricultural Sciences, The University of Melbourne , Parkville, Victoria 3010, Australia
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China Faculty of
| | - Jing Li
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China Faculty of
| | - Xiu-Zhen Shi
- Veterinary and Agricultural Sciences, The University of Melbourne , Parkville, Victoria 3010, Australia
| | - Yi-Bing Ma
- National Soil Fertility and Fertilizer Effects Long-term Monitoring Network, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences , Beijing 100081, China
| | - Deli Chen
- Veterinary and Agricultural Sciences, The University of Melbourne , Parkville, Victoria 3010, Australia
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China Faculty of
- Veterinary and Agricultural Sciences, The University of Melbourne , Parkville, Victoria 3010, Australia
| |
Collapse
|
730
|
Osińska A, Korzeniewska E, Harnisz M, Niestępski S. The prevalence and characterization of antibiotic-resistant and virulent Escherichia coli strains in the municipal wastewater system and their environmental fate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 577:367-375. [PMID: 27816226 DOI: 10.1016/j.scitotenv.2016.10.203] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/26/2016] [Accepted: 10/26/2016] [Indexed: 06/06/2023]
Abstract
Antibiotics are widely used in human and veterinary medicine and in animal production, which increases their concentrations in aquatic ecosystems and contributes to selective pressure on environmental microorganisms. The objective of this study was to identify antibiotic resistance determinants in Escherichia coli strains isolated from untreated and treated wastewater (UWW and TWW) and from river water sampled downstream and upstream (URW and DRW) from the effluent discharge point. The analyzed antibiotic groups were beta-lactams, tetracyclines and fluoroquinolones which are widely used in human and veterinary medicine. The virulence of the isolated E. coli strains was also analyzed, and their clonal relatedness was determined by ERIC (enterobacterial repetitive intergenic consensus sequence) PCR. The highest counts of bacteria resistant to beta-lactams, tetracyclines and fluoroquinolones were noted in UWW at 6.4×104, 4.2×104 and 3.1×103CFU/mL, respectively. A total of 317 E. coli isolates resistant to at least one group of antibiotics were selected among bacterial isolates from river water and wastewater samples. Nearly 38% of those isolates were resistant to all of the tested antibiotics. The highest percent (43%) of multidrug-resistant isolates was noted in UWW samples. Isolates resistant to beta-lactams most frequently harbored blaTEM and blaOXA genes. The group of genes encoding resistance to tetracyclines was most frequently represented by tetA, tetB and tetK, whereas the qnrS gene was noted in isolates resistant to fluoroquinolones. Virulence genes bfpA (65%), ST (56%) and eae (39%) were most widely distributed in all isolates, regardless of their origin. The results of this experiment reveal the dangers associated with environmental contamination by drug-resistant and virulent E. coli strains distributed with treated wastewater. Multidrug resistance was determined more frequently in strains isolated from DRW than in isolates from URW samples. Our findings provide valuable inputs for evaluating public health hazards associated with bacterial contamination.
Collapse
Affiliation(s)
- Adriana Osińska
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland.
| | - Ewa Korzeniewska
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland.
| | - Monika Harnisz
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland.
| | - Sebastian Niestępski
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland.
| |
Collapse
|
731
|
Granados-Chinchilla F, Rodríguez C. Tetracyclines in Food and Feedingstuffs: From Regulation to Analytical Methods, Bacterial Resistance, and Environmental and Health Implications. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2017; 2017:1315497. [PMID: 28168081 PMCID: PMC5266830 DOI: 10.1155/2017/1315497] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/17/2016] [Accepted: 11/08/2016] [Indexed: 05/15/2023]
Abstract
Antibiotics are widely used as growth promoters in animal husbandry; among them, the tetracyclines are a chemical group of relevance, due to their wide use in agriculture, surpassing in quantities applied almost every other antibiotic family. Seeing the considerable amounts of tetracyclines used worldwide, monitoring of these antibiotics is paramount. Advances must be made in the analysis of antibiotics to assess correct usage and dosage of tetracyclines in food and feedstuffs and possible residues in pertinent environmental samples. The tetracyclines are still considered a clinically relevant group of antibiotics, though dissemination of tolerance and resistance determinants have limited their use. This review focuses on four different aspects: (i) tetracyclines, usage, dosages, and regulatory issues that govern their food-related application, with particular attention to the prohibitions and restrictions that several countries have enforced in recent years by agencies from both the United States and the European Union, (ii) analytical methods for tetracyclines, determination, and residues thereof in feedstuffs and related matrices with an emphasis on the most relevant and novel techniques, including both screening and confirmatory methods, (iii) tetracycline resistance and tetracycline-resistant bacteria in feedstuff, and (iv) environmental and health risks accompanying the use of tetracyclines in animal nutrition. In the last two cases, we discuss the more relevant undesirable effects that tetracyclines exert over bacterial communities and nontarget species including unwanted effects in farmers.
Collapse
Affiliation(s)
| | - César Rodríguez
- Centro de Investigación en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| |
Collapse
|
732
|
Zhao Z, Wang J, Han Y, Chen J, Liu G, Lu H, Yan B, Chen S. Nutrients, heavy metals and microbial communities co-driven distribution of antibiotic resistance genes in adjacent environment of mariculture. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 220:909-918. [PMID: 27814984 DOI: 10.1016/j.envpol.2016.10.075] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 06/06/2023]
Abstract
With the rapid development of aquaculture, the large amounts of pollutants were discharged into the aquatic environment, where the detected antibiotic resistance genes (ARGs) have drawn increasing attention due to their potential threats to ecological environment and human health. Thus, the impact of mariculture on ARGs was assessed and the underlying mechanism of their propagation was explained. Sediments from eight sampling sites were collected along a mariculture drainage ditch, and the sediment in Yellow River Delta National Park was used as a non-mariculture control. Microbial ARGs qPCR array and illumina sequencing of 16S rRNA gene were applied to examine the changing patterns of ARGs and bacterial communities. Results showed that 18 ARGs (3 fluoroquinolone, 1 aminoglycoside, 3 macrolide-lincosamide-streptogramin B, 2 tetracycline, and 9 beta-lactam resistance genes) were influenced by mariculture, and ARGs abundance and diversity were significantly increased in mariculture sediments (p < 0.05). A remarkable shift in bacterial community structure and composition was also observed. The abundance of most of ARGs were significantly decreased in the estuary samples, implying that seawater had a significant dilution effect on the ARGs emission from the mariculture sites. Partial redundancy analysis showed that nutrients, heavy metals, and bacteria communities might directly and indirectly contribute to ARGs propagation, suggesting that the profile and dissemination of ARGs were driven by the combined effects of multiple factors in mariculture-impacted sites.
Collapse
Affiliation(s)
- Zelong Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Ying Han
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Guangfei Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Hong Lu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bin Yan
- School of Environmental Science and Engineering, Xiamen University of Technology, Xiamen 361024, China
| | - Shiaoshing Chen
- Institute of Environmental Engineering and Management, National Taipei University of Technology, Taipei 106, Taiwan, ROC
| |
Collapse
|
733
|
Zhou X, Qiao M, Wang FH, Zhu YG. Use of commercial organic fertilizer increases the abundance of antibiotic resistance genes and antibiotics in soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:701-710. [PMID: 27752947 DOI: 10.1007/s11356-016-7854-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 10/05/2016] [Indexed: 05/23/2023]
Abstract
The application of manure-based commercial organic fertilizers (COFs) is becoming increasingly extensive because of the expanding market for organic food. The present study examined the effects of repeated applications of chicken or swine manure-based COFs on the fate of antibiotics and antibiotic resistance genes (ARGs) in soil by conducting a soil microcosm experiment. Application of COFs significantly increased antibiotics residues, as well as the relative abundance of ARGs and the integrase gene of class 1 integrons (intΙ1) in soil. Two months after each application, antibiotics and ARGs dissipated in amended soils, but they still remained at an elevated level, compared with the control. And, the accumulation of antibiotics was found due to repeated COF applications. However, the relative abundance of ARGs in most COF-amended soils did not differ significantly between the first application and the repeated application. The results imply that 2 months are not sufficient for ARGs to approach background levels, and that animal manure must be treated more effectively prior to using it in agriculture ecosystems.
Collapse
Affiliation(s)
- Xue Zhou
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Qiao
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Feng-Hua Wang
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Yong-Guan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| |
Collapse
|
734
|
Su JQ, Cui L, Chen QL, An XL, Zhu YG. Application of genomic technologies to measure and monitor antibiotic resistance in animals. Ann N Y Acad Sci 2016; 1388:121-135. [DOI: 10.1111/nyas.13296] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/04/2016] [Accepted: 10/18/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| |
Collapse
|
735
|
Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection. ISME JOURNAL 2016; 11:651-662. [PMID: 27959344 DOI: 10.1038/ismej.2016.155] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/30/2016] [Accepted: 10/07/2016] [Indexed: 12/13/2022]
Abstract
The high frequency of antibiotic resistance is a global public health concern. More seriously, widespread metal pressure in the environment may facilitate the proliferation of antibiotic resistance via coselection of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). Given the lack of comprehensive understanding of the ARG and MRG coselection, in this study both abundance relationship and genetic linkage between ARGs and MRGs were rigorously investigated by performing a genomic analysis of a large complete genome collection. Many more ARGs were enriched in human-associated bacteria compared with those subjected to less anthropogenic interference. The signatures of ARG and MRG co-occurrence were much more frequent and the distance linkages between ARGs and MRGs were much more intimate in human pathogens than those less human-associated bacteria. Moreover, the co-occurrence structures in the habitat divisions were significantly different, which could be attributed to their distinct gene transfer potentials. More exogenous ARGs and MRGs on the genomes of human pathogens indicated the importance of recent resistance acquisition in resistome development of human commensal flora. Overall, the study emphasizes the potential risk associated with ARG and MRG coselection of both environmental and medical relevance.
Collapse
|
736
|
Xie WY, McGrath SP, Su JQ, Hirsch PR, Clark IM, Shen Q, Zhu YG, Zhao FJ. Long-Term Impact of Field Applications of Sewage Sludge on Soil Antibiotic Resistome. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:12602-12611. [PMID: 27934260 DOI: 10.1021/acs.est.6b02138] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Land applications of municipal sewage sludge may pose a risk of introducing antibiotic resistance genes (ARGs) from urban environments into agricultural systems. However, how the sewage sludge recycling and application method influence soil resistome and mobile genetic elements (MGEs) remains unclear. In the present study, high through-put quantitative PCR was conducted on the resistome of soils from a field experiment with past (between 1994 and 1997) and annual (since 1994) applications of five different sewage sludges. Total inputs of organic carbon were similar between the two modes of sludge applications. Intrinsic soil resistome, defined as the ARGs shared by the soils in the control and sludge-amended plots, consisted of genes conferring resistance to multidrug, β-lactam, Macrolide-Lincosamide-Streptogramin B (MLSB), tetracycline, vancomycin, and aminoglycoside, with multidrug resistance genes as the most abundant members. There was a strong correlation between the abundance of ARGs and MGE marker genes in soils. The composition and diversity of ARGs in the five sludges were substantially different from those in soils. Considerable proportions of ARGs and MGE marker genes in the sludges attenuated following the application, especially aminoglycoside and tetracycline resistance genes. Annual applications posed a more significant impact on the soil resistome, through both continued introduction and stimulation of the soil intrinsic ARGs. In addition, direct introduction of sludge-specific ARGs into soil was observed especially from ARG-rich sludge. These results provide a better insight into the characteristics of ARG dissemination from urban environment to the agricultural system through sewage sludge applications.
Collapse
Affiliation(s)
- Wan-Ying Xie
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University , Nanjing 210095, China
| | - Steve P McGrath
- Rothamsted Research , Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, China
| | - Penny R Hirsch
- Rothamsted Research , Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Ian M Clark
- Rothamsted Research , Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Qirong Shen
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University , Nanjing 210095, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, China
| | - Fang-Jie Zhao
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University , Nanjing 210095, China
- Rothamsted Research , Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| |
Collapse
|
737
|
Garner E, Wallace JS, Argoty GA, Wilkinson C, Fahrenfeld N, Heath LS, Zhang L, Arabi M, Aga DS, Pruden A. Metagenomic profiling of historic Colorado Front Range flood impact on distribution of riverine antibiotic resistance genes. Sci Rep 2016; 6:38432. [PMID: 27917931 PMCID: PMC5137141 DOI: 10.1038/srep38432] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/08/2016] [Indexed: 12/15/2022] Open
Abstract
Record-breaking floods in September 2013 caused massive damage to homes and infrastructure across the Colorado Front Range and heavily impacted the Cache La Poudre River watershed. Given the unique nature of this watershed as a test-bed for tracking environmental pathways of antibiotic resistance gene (ARG) dissemination, we sought to determine the impact of extreme flooding on ARG reservoirs in river water and sediment. We utilized high-throughput DNA sequencing to obtain metagenomic profiles of ARGs before and after flooding, and investigated 23 antibiotics and 14 metals as putative selective agents during post-flood recovery. With 277 ARG subtypes identified across samples, total bulk water ARGs decreased following the flood but recovered to near pre-flood abundances by ten months post-flood at both a pristine site and at a site historically heavily influenced by wastewater treatment plants and animal feeding operations. Network analysis of de novo assembled sequencing reads into 52,556 scaffolds identified ARGs likely located on mobile genetic elements, with up to 11 ARGs per plasmid-associated scaffold. Bulk water bacterial phylogeny correlated with ARG profiles while sediment phylogeny varied along the river’s anthropogenic gradient. This rare flood afforded the opportunity to gain deeper insight into factors influencing the spread of ARGs in watersheds.
Collapse
Affiliation(s)
- Emily Garner
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Joshua S Wallace
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | | | - Caitlin Wilkinson
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Nicole Fahrenfeld
- Department of Civil and Environmental Engineering, Rutgers University, Piscataway, NJ 08854, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Mazdak Arabi
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, 80523, USA
| | - Diana S Aga
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| |
Collapse
|
738
|
Elbehery AHA, Aziz RK, Siam R. Insertion sequences enrichment in extreme Red sea brine pool vent. Extremophiles 2016; 21:271-282. [PMID: 27915389 DOI: 10.1007/s00792-016-0900-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 11/27/2016] [Indexed: 01/24/2023]
Abstract
Mobile genetic elements are major agents of genome diversification and evolution. Limited studies addressed their characteristics, including abundance, and role in extreme habitats. One of the rare natural habitats exposed to multiple-extreme conditions, including high temperature, salinity and concentration of heavy metals, are the Red Sea brine pools. We assessed the abundance and distribution of different mobile genetic elements in four Red Sea brine pools including the world's largest known multiple-extreme deep-sea environment, the Red Sea Atlantis II Deep. We report a gradient in the abundance of mobile genetic elements, dramatically increasing in the harshest environment of the pool. Additionally, we identified a strong association between the abundance of insertion sequences and extreme conditions, being highest in the harshest and deepest layer of the Red Sea Atlantis II Deep. Our comparative analyses of mobile genetic elements in secluded, extreme and relatively non-extreme environments, suggest that insertion sequences predominantly contribute to polyextremophiles genome plasticity.
Collapse
Affiliation(s)
- Ali H A Elbehery
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo, 11835, Cairo, Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Rania Siam
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo, 11835, Cairo, Egypt.
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, SSE (Parcel 7), Second Floor, Office: Room 2194, AUC Avenue, New Cairo, 11835, Cairo, Egypt.
| |
Collapse
|
739
|
Xie WY, Yang XP, Li Q, Wu LH, Shen QR, Zhao FJ. Changes in antibiotic concentrations and antibiotic resistome during commercial composting of animal manures. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 219:182-190. [PMID: 27814534 DOI: 10.1016/j.envpol.2016.10.044] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/11/2016] [Accepted: 10/15/2016] [Indexed: 05/12/2023]
Abstract
The over-use of antibiotics in animal husbandry in China and the concomitant enhanced selection of antibiotic resistance genes (ARGs) in animal manures are of serious concern. Thermophilic composting is an effective way of reducing hazards in organic wastes. However, its effectiveness in antibiotic degradation and ARG reduction in commercial operations remains unclear. In the present study, we determined the concentrations of 15 common veterinary antibiotics and the abundances of 213 ARGs and 10 marker genes for mobile genetic elements (MGEs) in commercial composts made from cattle, poultry and swine manures in Eastern China. High concentrations of fluoroquinolones were found in the poultry and swine composts, suggesting insufficient removal of these antibiotics by commercial thermophilic composting. Total ARGs in the cattle and poultry manures were as high as 1.9 and 5.5 copies per bacterial cell, respectively. After thermophilic composting, the ARG abundance in the mature compost decreased to 9.6% and 31.7% of that in the cattle and poultry manure, respectively. However, some ARGs (e.g. aadA, aadA2, qacEΔ1, tetL) and MGE marker genes (e.g. cintI-1, intI-1 and tnpA-04) were persistent with high abundance in the composts. The antibiotics that were detected at high levels in the composts (e.g. norfloxacin and ofloxacin) might have posed a selection pressure on ARGs. MGE marker genes were found to correlate closely with ARGs at the levels of individual gene, resistance class and total abundance, suggesting that MGEs and ARGs are closely associated in their persistence in the composts under antibiotic selection. Our research shows potential disseminations of antibiotics and ARGs via compost utilization.
Collapse
Affiliation(s)
- Wan-Ying Xie
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin-Ping Yang
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qian Li
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Long-Hua Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qi-Rong Shen
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang-Jie Zhao
- Jiangsu Key Laboratory for Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
| |
Collapse
|
740
|
Rafraf ID, Lekunberri I, Sànchez-Melsió A, Aouni M, Borrego CM, Balcázar JL. Abundance of antibiotic resistance genes in five municipal wastewater treatment plants in the Monastir Governorate, Tunisia. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 219:353-358. [PMID: 27814552 DOI: 10.1016/j.envpol.2016.10.062] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/30/2016] [Accepted: 10/21/2016] [Indexed: 05/23/2023]
Abstract
Antimicrobial resistance is a growing and significant threat to global public health, requiring better understanding of the sources and mechanisms involved in its emergence and spread. We investigated the abundance of antibiotic resistance genes (ARGs) before and after treatment in five wastewater treatment plants (WWTPs) located in different areas of the Monastir Governorate (Tunisia). Three of these WWTPs (Frina, Sahline and Zaouiet) use a conventional activated sludge process as secondary treatment, whereas the WWTP located in Beni Hassen applies an ultraviolet disinfection step after the activated sludge process and the WWTP located in Moknine treats wastewater using naturally aerated lagoons as a secondary treatment process. The abundance of six ARGs (blaCTX-M, blaTEM, qnrA, qnrS, sul I and ermB) and the class 1 integron-integrase gene (intI1) were determined by quantitative PCR. All ARGs and the intI1 gene were detected in the wastewater samples, except the blaCTX-M gene, which was not detected in both influent and effluent samples from Sahline and Beni Hassen WWTPs, and the qnrS gene, which was not detected neither in the WWTP influent in Moknine nor in the WWTP effluent in Beni Hassen. Although the relative concentration of ARGs was generally found to be similar between samples collected before and after the wastewater treatment, the abundance of blaCTX-M, blaTEM, and qnrS genes was higher in the effluent of the Frina WWTP which, unlike other WWTPs, not only receives domestic or industrial sewage but also untreated hospital waste. To the best of our knowledge, this study quantified for the first time the abundance of ARGs in different Tunisian WWTPs, and the results agree with previous studies suggesting that conventional wastewater treatment does not efficiently reduce ARGs. Therefore, these findings could be useful to improve the design or operation of WWTPs.
Collapse
Affiliation(s)
- Ikbel Denden Rafraf
- Laboratory of Transmissible Diseases and Biologically Active Substances, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia; Higher Institute of Biotechnology of Monastir, Monastir, Tunisia
| | - Itziar Lekunberri
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Alexandre Sànchez-Melsió
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Mahjoub Aouni
- Laboratory of Transmissible Diseases and Biologically Active Substances, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
| |
Collapse
|
741
|
Lehmann K, Bell T, Bowes MJ, Amos GCA, Gaze WH, Wellington EMH, Singer AC. Trace levels of sewage effluent are sufficient to increase class 1 integron prevalence in freshwater biofilms without changing the core community. WATER RESEARCH 2016; 106:163-170. [PMID: 27710799 DOI: 10.1016/j.watres.2016.09.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/19/2016] [Accepted: 09/19/2016] [Indexed: 06/06/2023]
Abstract
Most river systems are impacted by sewage effluent. It remains unclear if there is a lower threshold to the concentration of sewage effluent that can significantly change the structure of the microbial community and its mobile genetic elements in a natural river biofilm. We used novel in situ mesocosms to conduct replicated experiments to study how the addition of low-level concentrations of sewage effluent (nominally 2.5 ppm) affects river biofilms in two contrasting Chalk river systems, the Rivers Kennet and Lambourn (high/low sewage impact, respectively). 16S sequencing and qPCR showed that community composition was not significantly changed by the sewage effluent addition, but class 1 integron prevalence (Lambourn control 0.07% (SE ± 0.01), Lambourn sewage effluent 0.11% (SE ± 0.006), Kennet control 0.56% (SE ± 0.01), Kennet sewage effluent 1.28% (SE ± 0.16)) was significantly greater in the communities exposed to sewage effluent than in the control flumes (ANOVA, F = 5.11, p = 0.045) in both rivers. Furthermore, the difference in integron prevalence between the Kennet control (no sewage effluent addition) and Kennet sewage-treated samples was proportionally greater than the difference in prevalence between the Lambourn control and sewage-treated samples (ANOVA (interaction between treatment and river), F = 6.42, p = 0.028). Mechanisms that lead to such differences could include macronutrient/biofilm or phage/bacteria interactions. Our findings highlight the role that low-level exposure to complex polluting mixtures such as sewage effluent can play in the spread of antibiotic resistance genes. The results also highlight that certain conditions, such as macronutrient load, might accelerate spread of antibiotic resistance genes.
Collapse
Affiliation(s)
- Katja Lehmann
- NERC Centre for Ecology & Hydrology, Wallingford, OX10 8BB, UK.
| | - Thomas Bell
- Imperial College London, Department of Life Sciences, Silwood Park Campus, SL5 7PY, UK
| | - Michael J Bowes
- NERC Centre for Ecology & Hydrology, Wallingford, OX10 8BB, UK
| | | | - Will H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, Truro, UK
| | | | - Andrew C Singer
- NERC Centre for Ecology & Hydrology, Wallingford, OX10 8BB, UK
| |
Collapse
|
742
|
Gadea R, Fernández Fuentes MÁ, Pérez Pulido R, Gálvez A, Ortega E. Effects of exposure to quaternary-ammonium-based biocides on antimicrobial susceptibility and tolerance to physical stresses in bacteria from organic foods. Food Microbiol 2016; 63:58-71. [PMID: 28040182 DOI: 10.1016/j.fm.2016.10.037] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 11/19/2022]
Abstract
In the present study, a collection of 76 biocide-sensitive bacterial strains isolated from organically produced food were adapted by repeated exposure to increasing concentrations of the quaternary ammonium compounds (QACs) benzalkonium chloride (BC) and hexadecylpyridinium chloride (HDP). The sensitivity of both wildtype strains and their corresponding QAC-adapted strains to other biocides and to antibiotics was studied. QAC tolerance increased in 88.2% of strains for BC and in 30.3% of strains for HDP, with increases in minimum inhibitory concentrations between 2 and over 100 fold. Adaptive resistance was stable after 20 subcultures in biocide-free medium for 7 and 5 of the BC- and HDP-adapted strains, respectively. Adaptation to BC and HDP also reduced the susceptibility to other biocides, mainly hexachlorophene (CF), didecyldimethylammonium bromide (AB), triclosan (TC) and chlorhexidine (CH). BC-adapted strains showed increased antibiotic resistance to ampicillin (AM) followed by sulfamethoxazol (SXT) and cefotaxime (CTX), and some showed increased sensitivity to ceftazidime (CAZ), CTX, AM and STX. Changes in antibiotic resistance in HDP-adapted strains were more heterogeneous and strain-dependent. Main efflux pump genes detected in QAC-adapted strains were acrB, sugE, norC, qacE and qacH, as well as antibiotic resistance genes aac(6_)-Ie-aph(2_)-Ia, aph(2_)-Ic, ant(4_)-Ia, lsa, mrsA/B, ereA, ermB and cat. Membrane anisotropy experiments revealed that QAC adaptation induced an increase in membrane rigidity in the case of BC, while response to HDP was more heterogeneous and strain-dependent. Growth capacity was significantly higher in some QAC-adapted strains and strain-dependent changes in heat tolerance were also detected in QAC-adapted strains. Gastric acid or bile resistances do not seem to be influenced by QAC adaptation.
Collapse
Affiliation(s)
- Rebeca Gadea
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071, Jaén, Spain
| | - Miguel Ángel Fernández Fuentes
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071, Jaén, Spain
| | - Rubén Pérez Pulido
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071, Jaén, Spain
| | - Antonio Gálvez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071, Jaén, Spain.
| | - Elena Ortega
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071, Jaén, Spain
| |
Collapse
|
743
|
Gatica J, Tripathi V, Green S, Manaia CM, Berendonk T, Cacace D, Merlin C, Kreuzinger N, Schwartz T, Fatta-Kassinos D, Rizzo L, Schwermer CU, Garelick H, Jurkevitch E, Cytryn E. High Throughput Analysis of Integron Gene Cassettes in Wastewater Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:11825-11836. [PMID: 27689892 DOI: 10.1021/acs.est.6b03188] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Integrons are extensively targeted as a proxy for anthropogenic impact in the environment. We developed a novel high-throughput amplicon sequencing pipeline that enables characterization of thousands of integron gene cassette-associated reads, and applied it to acquire a comprehensive overview of gene cassette composition in effluents from wastewater treatment facilities across Europe. Between 38 100 and 172 995 reads per-sample were generated and functionally characterized by screening against nr, SEED, ARDB and β-lactamase databases. Over 75% of the reads were characterized as hypothetical, but thousands were associated with toxin-antitoxin systems, DNA repair, cell membrane function, detoxification and aminoglycoside and β-lactam resistance. Among the reads characterized as β-lactamases, the carbapenemase blaOXA was dominant in most of the effluents, except for Cyprus and Israel where blaGES was also abundant. Quantitative PCR assessment of blaOXA and blaGES genes in the European effluents revealed similar trends to those displayed in the integron amplicon sequencing pipeline described above, corroborating the robustness of this method and suggesting that these integron-associated genes may be excellent targets for source tracking of effluents in downstream environments. Further application of the above analyses revealed several order-of-magnitude reductions in effluent-associated β-lactamase genes in effluent-saturated soils, suggesting marginal persistence in the soil microbiome.
Collapse
Affiliation(s)
- Joao Gatica
- The Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, Bet-Dagan, Israel
- The Department of Soil and Water Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem , Rehovot, Israel
| | - Vijay Tripathi
- The Department of Soil and Water Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem , Rehovot, Israel
| | - Stefan Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Celia M Manaia
- Escola Superior de Biotecnologia, Universidade Católica Portuguesa , Lisboa, Portugal
| | - Thomas Berendonk
- Faculty of Environmental Sciences, Technische Universität Dresden , Dresden, Germany
| | - Damiano Cacace
- Faculty of Environmental Sciences, Technische Universität Dresden , Dresden, Germany
| | - Christophe Merlin
- CNRS, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement (LCPME), UMR 7564, Institut Jean Barriol , 15 Avenue du Charmois, 54500 Vandoeuvre-lès-Nancy, France
- Université de Lorraine, LCPME , UMR 7564, 15 Avenue du Charmois, 54500 Vandoeuvre-lès-Nancy, France
| | - Norbert Kreuzinger
- Institute for Water Quality, Resources and Waste Managment, Technische Universität Wien , Wien, Austria
| | - Thomas Schwartz
- Karlsruhe Institute of Technology , Eggenstein-Leopoldshafen, Germany
| | - Despo Fatta-Kassinos
- Department of Civil and Environmental Engineering and Nireas, International Water Research Center, University of Cyprus , P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Luigi Rizzo
- Department of Civil Engineering, University of Salerno , Salerno, Italy
| | | | - Hemda Garelick
- School of Science and Technology, Middlesex University , London, U.K
| | - Edouard Jurkevitch
- The Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem , Rehovot, Israel
| | - Eddie Cytryn
- The Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agricultural Research Organization, Bet-Dagan, Israel
| |
Collapse
|
744
|
Winkworth-Lawrence C, Lange K. Antibiotic Resistance Genes in Freshwater Biofilms May Reflect Influences from High-Intensity Agriculture. MICROBIAL ECOLOGY 2016; 72:763-772. [PMID: 26932464 DOI: 10.1007/s00248-016-0740-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 02/10/2016] [Indexed: 06/05/2023]
Abstract
Antibiotic resistance is a major public health concern with growing evidence of environmental gene reservoirs, especially in freshwater. However, the presence of antibiotic resistance genes in freshwater, in addition to the wide spectrum of land use contaminants like nitrogen and phosphate, that waterways are subjected to is inconclusive. Using molecular analyses, freshwater benthic rock biofilms were screened for genes conferring resistance to antibiotics used in both humans and farmed animals (aacA-aphD to aminoglycosides; mecA to ß-lactams; ermA and ermB to macrolides; tetA, tetB, tetK, and tetM to tetracyclines; vanA and vanB to glycopeptides). We detected widespread low levels of antibiotic resistance genes from 20 waterways across southern New Zealand throughout the year (1.3 % overall detection rate; 480 samples from three rocks per site, 20 sites, eight occasions; July 2010-May 2011). Three of the ten genes, ermB, tetK, and tetM, were detected in 62 of the 4800 individual screens; representatives confirmed using Sanger sequencing. No distinction could be made between human and agricultural land use contamination sources based on gene presence distribution alone. However, land use pressures are suggested by moderate correlations between antibiotic resistance genes and high-intensity farming in winter. The detection of antibiotic resistance genes at several sites not subject to known agricultural pressures suggests human sources of resistance, like waterway contamination resulting from unsatisfactory toilet facilities at recreational sites.
Collapse
Affiliation(s)
| | - Katharina Lange
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
- Center of Ecology, Evolution and Biochemistry, Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047, Kastanienbaum, Switzerland
| |
Collapse
|
745
|
Farkas A, Crăciunaş C, Chiriac C, Szekeres E, Coman C, Butiuc-Keul A. Exploring the Role of Coliform Bacteria in Class 1 Integron Carriage and Biofilm Formation During Drinking Water Treatment. MICROBIAL ECOLOGY 2016; 72:773-782. [PMID: 27079455 DOI: 10.1007/s00248-016-0758-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 03/22/2016] [Indexed: 06/05/2023]
Abstract
This study investigates the role of coliforms in the carriage of class 1 integron and biocide resistance genes in a drinking water treatment plant and explores the relationship between the carriage of such genes and the biofouling abilities of the strain. The high incidence of class 1 integron and biocide resistance genes (33.3 % of the isolates) highlights the inherent risk of genetic contamination posed by coliform populations during drinking water treatment. The association between the presence of intI1 gene and qac gene cassettes, especially qacH, was greater in biofilm cells. In coliforms recovered from biofilms, a higher frequency of class 1 integron elements and higher diversity of genetic patterns occurred, compared to planktonic cells. The coliform isolates under the study proved to mostly carry non-classical class 1 integrons lacking the typical qacEΔ1/sul1 genes or a complete tni module, but bearing the qacH gene. No link was found between the carriage of integron genes and the biofouling degree of the strain, neither in aerobic or in anaerobic conditions. Coliform bacteria isolated from established biofilms rather adhere in oxygen depleted environments, while the colonization ability of planktonic cells is not significantly affected by oxygen availability.
Collapse
Affiliation(s)
- Anca Farkas
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 1 Kogălniceanu Street, 400084, Cluj-Napoca, Romania.
| | - Cornelia Crăciunaş
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 1 Kogălniceanu Street, 400084, Cluj-Napoca, Romania
| | - Cecilia Chiriac
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 1 Kogălniceanu Street, 400084, Cluj-Napoca, Romania
- Institute of Biological Research, National Institute of Research and Development for Biological Sciences, 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Edina Szekeres
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 1 Kogălniceanu Street, 400084, Cluj-Napoca, Romania
- Institute of Biological Research, National Institute of Research and Development for Biological Sciences, 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Cristian Coman
- Institute of Biological Research, National Institute of Research and Development for Biological Sciences, 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Anca Butiuc-Keul
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 1 Kogălniceanu Street, 400084, Cluj-Napoca, Romania
| |
Collapse
|
746
|
Wang M, Sun J, Zhong W, Xiong W, Zeng Z, Sun Y. Presence and distribution of Macrolides-Lincosamide-Streptogramin resistance genes and potential indicator ARGs in the university ponds in Guangzhou, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:22937-22946. [PMID: 27578091 DOI: 10.1007/s11356-016-7521-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/25/2016] [Indexed: 05/22/2023]
Abstract
This study aimed to determine the occurrence, abundance, and variation of seven Macrolides-Lincosamide-Streptogramin (MLS) resistance genes (ereB, ermA, ermB, ermF, mefA, vatB, mphA) and six potential indicator ARGs (tet (B), sul1, qnrS, fexA, IntI1, ermB) from three ponds at university by quantitative PCR and assess the impacts on the surroundings. Solid samples (fish feces, soil and sediment) and water samples were tested. All the genes were found at low levels in soil samples. For the MLS resistance genes, only two MLS genes (ermB, ermF) were detected in all samples and significant correlations between ermB and Σ MLS (R = 0.91 in solid samples; R = 0.86 in water samples, p < 0.01) were found. For the potential indicators, intl1 and sul1 were present at high levels in the three different ponds while the other genes showed varying levels. These findings show that the ermB gene can probably be served as an indicator to evaluate the overall level of MLS resistance genes. The fairly low abundance of all the tested resistance genes in soil samples and the moderate levels in other samples suggests that the university ponds kept a good state and did not have a significant impact on their surroundings.
Collapse
Affiliation(s)
- Mianzhi Wang
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory For Antimicrobial Resistance Of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Wushan Road, Guangzhou, China
| | - Jing Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory For Antimicrobial Resistance Of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Wushan Road, Guangzhou, China
| | - Weixin Zhong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory For Antimicrobial Resistance Of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Wushan Road, Guangzhou, China
| | - Wenguang Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory For Antimicrobial Resistance Of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Wushan Road, Guangzhou, China
| | - Zhenling Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory For Antimicrobial Resistance Of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Wushan Road, Guangzhou, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory For Antimicrobial Resistance Of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Wushan Road, Guangzhou, China.
| |
Collapse
|
747
|
Koczura R, Mokracka J, Taraszewska A, Łopacinska N. Abundance of Class 1 Integron-Integrase and Sulfonamide Resistance Genes in River Water and Sediment Is Affected by Anthropogenic Pressure and Environmental Factors. MICROBIAL ECOLOGY 2016; 72:909-916. [PMID: 27599709 PMCID: PMC5080314 DOI: 10.1007/s00248-016-0843-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/17/2016] [Indexed: 05/22/2023]
Abstract
In this study, we determined the presence of class 1 integron-integrase gene in culturable heterotrophic bacteria isolated from river water and sediment sampled upstream and downstream of a wastewater treatment plant effluent discharge. Moreover, we quantified intI1 and sulfonamide resistance genes (sul1 and sul2) in the water and sediment using qPCR. There was no correlation between the results from water and sediment samples, which suggests integron-containing bacteria are differentially retained in these two environmental compartments. The discharge of treated wastewater significantly increased the frequency of intI1 among culturable bacteria and the gene copy number in river water, and increased the number of sul1 genes in the sediment. We also observed seasonal differences in the frequency of the class 1 integron-integrase gene among culturable heterotrophs as well as intI1 copy number in water, but not in sediment. The results suggest that the abundance of class 1 integrons in aquatic habitat depends on anthropogenic pressure and environmental factors.
Collapse
Affiliation(s)
- Ryszard Koczura
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Umultowska 89, 61-614, Poznań, Poland.
| | - Joanna Mokracka
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Umultowska 89, 61-614, Poznań, Poland
| | - Agata Taraszewska
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Umultowska 89, 61-614, Poznań, Poland
| | - Natalia Łopacinska
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Umultowska 89, 61-614, Poznań, Poland
| |
Collapse
|
748
|
Gillings MR, Paulsen IT, Tetu SG. Genomics and the evolution of antibiotic resistance. Ann N Y Acad Sci 2016; 1388:92-107. [DOI: 10.1111/nyas.13268] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
Affiliation(s)
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Sasha G. Tetu
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| |
Collapse
|
749
|
Gillings MR. Lateral gene transfer, bacterial genome evolution, and the Anthropocene. Ann N Y Acad Sci 2016; 1389:20-36. [DOI: 10.1111/nyas.13213] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/20/2016] [Accepted: 07/28/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Michael R. Gillings
- Genes to Geoscience Research Centre, Department of Biological Sciences Macquarie University Sydney New South Wales Australia
| |
Collapse
|
750
|
Borruso L, Harms K, Johnsen PJ, Nielsen KM, Brusetti L. Distribution of class 1 integrons in a highly impacted catchment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 566-567:1588-1594. [PMID: 27312274 DOI: 10.1016/j.scitotenv.2016.06.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/09/2016] [Accepted: 06/09/2016] [Indexed: 05/22/2023]
Abstract
Polluted compounds into freshwater sediments may select and enrich bacteria carrying specific genetic compositions. Here we examine the possible use of class 1 integrons as bioindicators in freshwater environments. Samples were collected from various sediments in an urban area (Zhangye, Gansu province, China), specifically within the city, in the industrial zone, in the surrounding agricultural area and in a nearby national park. Integrons void of gene cassettes were present in all human-impacted sampling sites. A higher diversity of class 1 integrons with various gene cassettes was found in the agricultural area. Class 1 integrons and related gene cassettes were not detected in the national park. These results suggest that the prevalence and composition of class 1 integrons could be further developed as bioindicators in polluted freshwater environments.
Collapse
Affiliation(s)
- Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bozen-Bolzano, Italy
| | - Klaus Harms
- Centre for GeoGenetics, National History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Department of Pharmacy, Faculty of Health Science, University of Tromsø, Tromsø, Norway
| | - Pål Jarle Johnsen
- Department of Pharmacy, Faculty of Health Science, University of Tromsø, Tromsø, Norway
| | - Kaare Magne Nielsen
- Department of Life Sciences and Health Oslo and Akershus University College of Applied Sciences, Oslo, Norway; Genøk-Centre for Biosafety, Tromsø, Norway
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bozen-Bolzano, Italy.
| |
Collapse
|