1
|
Romero-González LE, Montelongo-Martínez LF, González-Valdez A, Quiroz-Morales SE, Cocotl-Yañez M, Franco-Cendejas R, Soberón-Chávez G, Pardo-López L, Bustamante VH. Pseudomonas aeruginosa Isolates from Water Samples of the Gulf of Mexico Show Similar Virulence Properties but Different Antibiotic Susceptibility Profiles than Clinical Isolates. Int J Microbiol 2024; 2024:6959403. [PMID: 38784405 PMCID: PMC11115996 DOI: 10.1155/2024/6959403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/14/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen found in a wide variety of environments, including soil, water, and habitats associated with animals, humans, and plants. From a One Health perspective, which recognizes the interconnectedness of human, animal, and environmental health, it is important to study the virulence characteristics and antibiotic susceptibility of environmental bacteria. In this study, we compared the virulence properties and the antibiotic resistance profiles of seven isolates collected from the Gulf of Mexico with those of seven clinical strains of P. aeruginosa. Our results indicate that the marine and clinical isolates tested exhibit similar virulence properties; they expressed different virulence factors and were able to kill Galleria mellonella larvae, an animal model commonly used to analyze the pathogenicity of many bacteria, including P. aeruginosa. In contrast, the clinical strains showed higher antibiotic resistance than the marine isolates. Consistently, the clinical strains exhibited a higher prevalence of class 1 integron, an indicator of anthropogenic impact, compared with the marine isolates. Thus, our results indicate that the P. aeruginosa marine strains analyzed in this study, isolated from the Gulf of Mexico, have similar virulence properties, but lower antibiotic resistance, than those from hospitals.
Collapse
Affiliation(s)
- Luis E. Romero-González
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Luis F. Montelongo-Martínez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Coyoacán, Mexico
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Coyoacán, Mexico
| | - Sara E. Quiroz-Morales
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Coyoacán, Mexico
| | - Miguel Cocotl-Yañez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Coyoacán, Mexico
| | - Rafael Franco-Cendejas
- Instituto Nacional de Rehabilitación “Luis Guillermo Ibarra Ibarra,” Ciudad de México, Mexico
| | - Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Coyoacán, Mexico
| | - Liliana Pardo-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Víctor H. Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| |
Collapse
|
2
|
Qi Q, Ghaly TM, Rajabal V, Gillings MR, Tetu SG. Dissecting molecular evolution of class 1 integron gene cassettes and identifying their bacterial hosts in suburban creeks via epicPCR. J Antimicrob Chemother 2024; 79:100-111. [PMID: 37962091 DOI: 10.1093/jac/dkad353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
OBJECTIVES Our study aimed to sequence class 1 integrons in uncultured environmental bacterial cells in freshwater from suburban creeks and uncover the taxonomy of their bacterial hosts. We also aimed to characterize integron gene cassettes with altered DNA sequences relative to those from databases or literature and identify key signatures of their molecular evolution. METHODS We applied a single-cell fusion PCR-based technique-emulsion, paired isolation and concatenation PCR (epicPCR)-to link class 1 integron gene cassette arrays to the phylogenetic markers of their bacterial hosts. The levels of streptomycin resistance conferred by the WT and altered aadA5 and aadA11 gene cassettes that encode aminoglycoside (3″) adenylyltransferases were experimentally quantified in an Escherichia coli host. RESULTS Class 1 integron gene cassette arrays were detected in Alphaproteobacteria and Gammaproteobacteria hosts. A subset of three gene cassettes displayed signatures of molecular evolution, namely the gain of a regulatory 5'-untranslated region (5'-UTR), the loss of attC recombination sites between adjacent gene cassettes, and the invasion of a 5'-UTR by an IS element. Notably, our experimental testing of a novel variant of the aadA11 gene cassette demonstrated that gaining the observed 5'-UTR contributed to a 3-fold increase in the MIC of streptomycin relative to the ancestral reference gene cassette in E. coli. CONCLUSIONS Dissecting the observed signatures of molecular evolution of class 1 integrons allowed us to explain their effects on antibiotic resistance phenotypes, while identifying their bacterial hosts enabled us to make better inferences on the likely origins of novel gene cassettes and IS that invade known gene cassettes.
Collapse
Affiliation(s)
- Qin Qi
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Timothy M Ghaly
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Vaheesan Rajabal
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Michael R Gillings
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Sasha G Tetu
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| |
Collapse
|
3
|
Givens CE, Kolpin DW, Hubbard LE, Meppelink SM, Cwiertny DM, Thompson DA, Lane RF, Wilson MC. Simultaneous stream assessment of antibiotics, bacteria, antibiotic resistant bacteria, and antibiotic resistance genes in an agricultural region of the United States. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166753. [PMID: 37673265 DOI: 10.1016/j.scitotenv.2023.166753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Antimicrobial resistance (AMR) is now recognized as a leading global threat to human health. Nevertheless, there currently is a limited understanding of the environment's role in the spread of AMR and antibiotic resistance genes (ARGs). In 2019, the U.S. Geological Survey conducted the first statewide assessment of antibiotic resistant bacteria (ARB) and ARGs in surface water and bed sediment collected from 34 stream locations across Iowa. Environmental samples were analyzed for a suite of 29 antibiotics and plated on selective media for 15 types of bacteria growth; DNA was extracted from culture growth and used in downstream polymerase chain reaction (PCR) assays for the detection of 24 ARGs. ARGs encoding resistance to antibiotics of clinical importance to human health and disease prevention were prioritized as their presence in stream systems has the potential for environmental significance. Total coliforms, Escherichia coli (E. coli), and staphylococci were nearly ubiquitous in both stream water and stream bed sediment samples, with enterococci present in 97 % of water samples, and Salmonella spp. growth present in 94 % and 67 % of water and bed sediment samples. Bacteria enumerations indicate that high bacteria loads are common in Iowa's streams, with 23 (68 %) streams exceeding state guidelines for primary contact for E. coli in recreational waters and 6 (18 %) streams exceeding the secondary contact advisory level. Although antibiotic-resistant E. coli growth was detected from 40 % of water samples, vancomycin-resistant enterococci (VRE) and penicillinase-resistant Staphylococcus aureus (MRSA) colony growth was detected from nearly all water samples. A total of 14 different ARGs were detected from viable bacteria cells from 30 Iowa streams (88 %, n = 34). Study results provide the first baseline understanding of the prevalence of ARB and ARGs throughout Iowa's waterways and health risk potential for humans, wildlife, and livestock using these waterways for drinking, irrigating, or recreating.
Collapse
Affiliation(s)
- Carrie E Givens
- U.S. Geological Survey, 5840 Enterprise Drive, Lansing, MI 48911, USA.
| | - Dana W Kolpin
- U.S. Geological Survey, 400 S. Clinton Street, Iowa City, Iowa 52240, USA
| | - Laura E Hubbard
- U.S. Geological Survey, 1 Gifford Pinchot Drive, Madison, WI 53726, USA
| | | | - David M Cwiertny
- University of Iowa Center for Health Effects of Environmental Contamination, The University of Iowa, 251 North Capitol Street, Chemistry Building - Room W195, Iowa City, Iowa 52242, USA
| | - Darrin A Thompson
- University of Iowa Center for Health Effects of Environmental Contamination, The University of Iowa, 251 North Capitol Street, Chemistry Building - Room W195, Iowa City, Iowa 52242, USA
| | - Rachael F Lane
- U.S. Geological Survey, 1217 Biltmore Drive, Lawrence, Kansas 66049, USA
| | - Michaelah C Wilson
- U.S. Geological Survey, 1217 Biltmore Drive, Lawrence, Kansas 66049, USA
| |
Collapse
|
4
|
Okonkwo V, Cholet F, Ijaz UZ, Koottatep T, Pussayanavin T, Polpraset C, Sloan WT, Connelly S, Smith CJ. intI1 gene abundance from septic tanks in Thailand using validated intI1 primers. Appl Environ Microbiol 2023; 89:e0107123. [PMID: 37874304 PMCID: PMC10686061 DOI: 10.1128/aem.01071-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/22/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Antimicrobial resistance is a global crisis, and wastewater treatment, including septic tanks, remains an important source of antimicrobial resistance (AMR) genes. The role of septic tanks in disseminating class 1 integron, and by extension AMR genes, in Thailand, where antibiotic use is unregulated remains understudied. We aimed to monitor gene abundance as a proxy to infer potential AMR from septic tanks in Thailand. We evaluated published intI1 primers due to the lack of consensus on optimal Q-PCR primers and the absence of standardization. Our findings confirmed septic tanks are a source of class 1 integron to the environment. We highlighted the significance of intI1 primer choice, in the context of interpretation of risk associated with AMR spread from septic tanks. We recommend the validated set (F3-R3) for optimal intI1 quantification toward the goal of achieving standardization across studies.
Collapse
Affiliation(s)
- Valentine Okonkwo
- Department of Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Fabien Cholet
- Department of Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Umer Z. Ijaz
- Department of Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Thammarat Koottatep
- School of Environment, Resources and Development, Asian Institute of Technology, Khlong Nueng, Thailand
| | | | - Chongrak Polpraset
- Thammasat School of Engineering, Thammasat University, Bangkok, Thailand
| | - William T. Sloan
- Department of Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Stephanie Connelly
- Department of Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Cindy J. Smith
- Department of Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
5
|
Fry KL, McPherson VJ, Gillings MR, Taylor MP. Tracing the Sources and Prevalence of Class 1 Integrons, Antimicrobial Resistance, and Trace Elements Using European Honey Bees. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:10582-10590. [PMID: 37417314 DOI: 10.1021/acs.est.3c03775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Surveillance of antimicrobial resistance is essential for an effective One Health response. This study explores the efficacy of European honey bees (Apis mellifera) for biomonitoring antimicrobial resistance (AMR) in urban areas. Class 1 integrons (intI1) are investigated as a universal AMR indicator, as well as associated cassette arrays and trace element contaminants at a city-wide scale. Class 1 integrons were found to be pervasive across the urban environment, occurring in 52% (75/144) of the honey bees assessed. The area of waterbodies within the honey bee's foraging radius was associated with intI1 prevalence, indicating an exposure pathway for future investigation to address. Trace element concentrations in honey bees reflected urban sources, supporting the application of this biomonitoring approach. As the first study of intI1 in honey bees, we provide insights into the environmental transfer of bacterial DNA to a keystone species and demonstrate how intI1 biomonitoring can support the surveillance of AMR.
Collapse
Affiliation(s)
- Kara L Fry
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
- EPA Science, Centre for Applied Sciences, Environment Protection Authority Victoria, Ernest Jones Drive, Macleod, Victoria 3085, Australia
| | - Vanessa J McPherson
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Michael R Gillings
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Mark Patrick Taylor
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
- EPA Science, Centre for Applied Sciences, Environment Protection Authority Victoria, Ernest Jones Drive, Macleod, Victoria 3085, Australia
| |
Collapse
|
6
|
Di Pippo F, Crognale S, Levantesi C, Vitanza L, Sighicelli M, Pietrelli L, Di Vito S, Amalfitano S, Rossetti S. Plastisphere in lake waters: Microbial diversity, biofilm structure, and potential implications for freshwater ecosystems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 310:119876. [PMID: 35934149 DOI: 10.1016/j.envpol.2022.119876] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Once dispersed in water, microplastic (MP) particles are rapidly colonised by aquatic microbes, which can adhere and grow onto solid surfaces in the form of biofilms. This study provides new insights on microbial diversity and biofilm structure of plastisphere in lake waters. By combining Fourier Confocal Laser Scanning Microscopy (CLSM), Transform Infrared Spectroscopy (FT-IR) and high-throughput DNA sequencing, we investigated the microbial colonization patterns on floating MPs and, for the first time, the occurrence of eukaryotic core members and their possible relations with biofilm-forming bacterial taxa within the plastisphere of four different lakes. Through PCR-based methods (qPCR, LAMP-PCR), we also evaluated the role of lake plastisphere as long-term dispersal vectors of potentially harmful organisms (including pathogens) and antibiotic resistance genes (ARGs) in freshwater ecosystems. Consistent variation patterns of the microbial community composition occurred between water and among the plastisphere samples of the different lakes. The eukaryotic core microbiome was mainly composed by typical freshwater biofilm colonizers, such as diatoms (Pennales, Bacillariophyceaea) and green algae (Chlorophyceae), which interact with eukaryotic and prokaryotic microbes of different trophic levels. Results also showed that MPs are suitable vectors of biofilm-forming opportunistic pathogens and a hotspot for horizontal gene transfer, likely facilitating antibiotic resistance spread in the environments.
Collapse
Affiliation(s)
- Francesca Di Pippo
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy.
| | - Simona Crognale
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
| | - Caterina Levantesi
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
| | - Luca Vitanza
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
| | - Maria Sighicelli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA) CR Casaccia, Rome, Italy
| | - Loris Pietrelli
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | | | - Stefano Amalfitano
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
| | - Simona Rossetti
- Water Research Institute, CNR-IRSA, National Research Council, Rome, Italy
| |
Collapse
|
7
|
Gao M, Zhang X, Yue Y, Qiu T, Wang J, Wang X. Air path of antimicrobial resistance related genes from layer farms: Emission inventory, atmospheric transport, and human exposure. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128417. [PMID: 35183825 DOI: 10.1016/j.jhazmat.2022.128417] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/26/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Animal husbandry is a significant contributor to increased environmental antimicrobial resistance (AMR), but little is known regarding the dissemination of AMR from animal farms via airborne transmission. Here, we connected the air path of AMR related genes tailored to layer poultry farms from source of escape to end of sedimentation. The emission inventories of 8 AMR related genes from all 163-layer poultry farms around Beijing city were quantified. We developed the atmospheric transport model with a gene degradation module to estimate the spatiotemporal distribution of airborne AMR, and also assessed their corresponding regional exposure and sedimentation. Total emissions of 16 S rDNA and AMR related genes from layer houses ranged from 1015 to 1016 copies year-1. Those layer-sourced genes contributed 1-14.6% of antimicrobial resistant genes, 4.9% of Staphylococcus spp. and 2.2% of CintI1 to the corresponding annual genetic burden of Beijing's urban air. The average exposure of the Beijing residents to layer-sourced airborne 16 S rDNA was 1.39 × 104 copies year-1 person-1, approximately 87% of them would be deposited in the upper respiratory tract. The findings highlight that air medium represents an important dissemination pathway of animal-sourced genes to AMR burden in humans and environment.
Collapse
Affiliation(s)
- Min Gao
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaole Zhang
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland
| | - Yang Yue
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland
| | - Tianlei Qiu
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jing Wang
- Institute of Environmental Engineering (IfU), ETH Zürich, Zürich, CH-8093, Switzerland; Laboratory for Advanced Analytical Technologies, Empa, Dübendorf, CH-8600, Switzerland.
| | - Xuming Wang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| |
Collapse
|
8
|
Rubeck LM, Wells JE, Hanford KJ, Durso LM, Schacht WH, Berry ED. Management-intensive grazing impacts on total Escherichia coli, E. coli O157:H7, and antibiotic resistance genes in a riparian stream. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:152611. [PMID: 34995584 DOI: 10.1016/j.scitotenv.2021.152611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
The impacts of management-intensive grazing (MIG) of cattle on concentrations of total Escherichia coli, total suspended solids (TSS), and nitrate-nitrite nitrogen (NO3 + NO2-N), and occurrence of E. coli O157:H7 and selected antibiotic resistance genes (ARGs) in stream water and/or sediments were evaluated. Cattle were grazed for two-week periods in May in each of three years. Overall, grazing increased total E. coli in downstream water by 0.89 log10 MPN/100 mL (p < 0.0001), and downstream total E. coli concentrations were higher than upstream over all sampling intervals. Downstream TSS levels also increased (p ≤ 0.0294) during grazing. In contrast, there was a main effect of treatment for downstream NO3 + NO2-N to be lower than upstream (3.59 versus 3.70 mg/L; p = 0.0323). Overwintering mallard ducks increased total E. coli and TSS concentrations in January and February (p < 0.05). For precipitation events during the 24 h before sampling, each increase of 1.00 cm of rainfall increased total E. coli by 0.49 log10 MPN/100 mL (p = 0.0005). In contrast, there was no association of previous 24 h precipitation volume on TSS (p = 0.1540), and there was a negative linear effect on NO3 + NO2-N (p = 0.0002). E. coli O157:H7 prevalence was low, but the pathogen was detected downstream up to 2½ months after grazing. Examination of ARGs sul1, ermB, blactx-m-32, and intI1 identified the need for additional research to understand the impact of grazing on the ecology of these resistance determinants in pasture-based cattle production. While E. coli remained higher in downstream water compared to upstream, MIG may reduce the magnitude of the downstream E. coli concentrations. Likewise, the MIG strategy may prevent large increases in TSS and NO3 + NO2-N concentrations during heavy rain events. Results indicate that MIG can limit the negative effects of cattle grazing on stream water quality.
Collapse
Affiliation(s)
- Laura M Rubeck
- University of Nebraska-Lincoln, U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - James E Wells
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Kathryn J Hanford
- University of Nebraska-Lincoln, Department of Statistics, 343A Hardin Hall, Lincoln, NE 68583, USA
| | - Lisa M Durso
- USDA, Agricultural Research Service, Agroecosystem Management Research Unit, 251 Filley Hall, University of Nebraska-Lincoln East Campus, Lincoln, NE 68583, USA
| | - Walter H Schacht
- University of Nebraska-Lincoln, Department of Agronomy and Horticulture, 202 Keim Hall, Lincoln, NE 68583, USA
| | - Elaine D Berry
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA.
| |
Collapse
|
9
|
Sanz C, Casado M, Navarro-Martin L, Cañameras N, Carazo N, Matamoros V, Bayona JM, Piña B. Implications of the use of organic fertilizers for antibiotic resistance gene distribution in agricultural soils and fresh food products. A plot-scale study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:151973. [PMID: 34843769 DOI: 10.1016/j.scitotenv.2021.151973] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
The spread of antibiotic resistance genes (ARG) into agricultural soils, products, and foods severely limits the use of organic fertilizers in agriculture. In order to help designing agricultural practices that minimize the spread of ARG, we fertilized, sown, and harvested lettuces and radish plants in experimental land plots for two consecutive agricultural cycles using four types of fertilizers: mineral fertilization, sewage sludge, pig slurry, or composted organic fraction of municipal solid waste. The analysis of the relative abundances of more than 200,000 ASV (Amplicon Sequence Variants) identified a small, but significant overlap (<10%) between soil's and fertilizer microbiomes. Clinically relevant ARG were found in higher loads (up to 100 fold) in fertilized soils than in the initial soil, particularly in those treated with organic fertilizers, and their loads grossly correlated to the amount of antibiotic residues found in the corresponding fertilizer. Similarly, low, but measurable ARG loads were found in lettuce (tetM, sul1) and radish (sul1), corresponding the lowest values to samples collected from minerally fertilized fields. Comparison of soil samples collected along the total period of the experiment indicated a relatively year-round stability of soil microbiomes in amended soils, whereas ARG loads appeared as unstable and transient. The results indicate that ARG loads in soils and foodstuffs were likely linked to the contribution of bacteria from organic fertilizer to the soil microbiomes, suggesting that an adequate waste management and good pharmacological and veterinarian practices may significantly reduce the presence of these ARGs in agricultural soils and plant products.
Collapse
Affiliation(s)
- Claudia Sanz
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
| | - Marta Casado
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
| | - Laia Navarro-Martin
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
| | - Núria Cañameras
- Department of Agri-Food Engineering and Biotechnology DEAB-UPC, Esteve Terrades 8, Building 4, Castelldefels 08860, Spain
| | - Núria Carazo
- Department of Agri-Food Engineering and Biotechnology DEAB-UPC, Esteve Terrades 8, Building 4, Castelldefels 08860, Spain
| | - Victor Matamoros
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
| | - Josep Maria Bayona
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain
| | - Benjamin Piña
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain.
| |
Collapse
|
10
|
Ghaly TM, Penesyan A, Pritchard A, Qi Q, Rajabal V, Tetu SG, Gillings MR. Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities. Microb Genom 2022; 8. [PMID: 35298369 PMCID: PMC9176274 DOI: 10.1099/mgen.0.000788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Integrons are microbial genetic elements that can integrate mobile gene cassettes. They are mostly known for spreading antibiotic resistance cassettes among human pathogens. However, beyond clinical settings, gene cassettes encode an extraordinarily diverse range of functions important for bacterial adaptation. The recovery and sequencing of cassettes has promising applications, including: surveillance of clinically important genes, particularly antibiotic resistance determinants; investigating the functional diversity of integron-carrying bacteria; and novel enzyme discovery. Although gene cassettes can be directly recovered using PCR, there are no standardised methods for their amplification and, importantly, for validating sequences as genuine integron gene cassettes. Here, we present reproducible methods for the amplification, sequence processing, and validation of gene cassette amplicons from complex communities. We describe two different PCR assays that either amplify cassettes together with integron integrases, or gene cassettes together within cassette arrays. We compare the performance of Nanopore and Illumina sequencing, and present bioinformatic pipelines that filter sequences to ensure that they represent amplicons from genuine integrons. Using a diverse set of environmental DNAs, we show that our approach can consistently recover thousands of unique cassettes per sample and up to hundreds of different integron integrases. Recovered cassettes confer a wide range of functions, including antibiotic resistance, with as many as 300 resistance cassettes found in a single sample. In particular, we show that class one integrons are collecting and concentrating resistance genes out of the broader diversity of cassette functions. The methods described here can be applied to any environmental or clinical microbiome sample.
Collapse
Affiliation(s)
- Timothy M Ghaly
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Alexander Pritchard
- Division of Food Sciences, University of Nottingham, Loughborough LE12 5RD, Australia
| | - Qin Qi
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Sasha G Tetu
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Michael R Gillings
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia.,ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| |
Collapse
|
11
|
Hernández-Alomia F, Ballesteros I, Castillejo P. Bioremediation potential of glyphosate-degrading microorganisms in eutrophicated Ecuadorian water bodies. Saudi J Biol Sci 2022; 29:1550-1558. [PMID: 35280549 PMCID: PMC8913404 DOI: 10.1016/j.sjbs.2021.11.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 11/20/2022] Open
Abstract
Phosphonate compounds are the basis of many xenobiotic pollutants, such as Glyphosate (N-(phosphonomethyl-glycine). Only procaryotic microorganisms and the lower eukaryotes are capable of phosphonate biodegradation through C–P lyase pathways. Thus, the aim of this study was to determine the presence of C–P lyase genes in Ecuadorian freshwater systems as a first step towards assessing the presence of putative glyphosate degraders. To that end, two Nested PCR assays were designed to target the gene that codifies for the subunit J (phnJ), which breaks the C-P bond that is critical for glyphosate mineralization. The assays designed in this study led to the detection of phnJ genes in 7 out of 8 tested water bodies. The amplified fragments presented 85–100% sequence similarity with phnJ genes that belong to glyphosate-degrading microorganisms. Nine sequences were not reported previously in the GenBank. The presence of phosphonate degraders was confirmed by isolating three strains able to grow using glyphosate as a unique carbon source. According to the 16S sequence, these strains belong to the Pantoea, Pseudomonas, and Klebsiella genera. Performing a Nested PCR amplification of phnJ genes isolated from eutrophicated water bodies, prior to isolation, may be a cost-effective strategy for the bioprospection of new species and/or genes that might have new properties for biotech industries, laying the groundwork for additional research.
Collapse
Affiliation(s)
- Fernanda Hernández-Alomia
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
| | - Isabel Ballesteros
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Pablo Castillejo
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
- Corresponding author.
| |
Collapse
|
12
|
Liu H, Ye X, Chen S, Sun A, Duan X, Zhang Y, Zou H, Zhang Y. Chitosan as additive affects the bacterial community, accelerates the removals of antibiotics and related resistance genes during chicken manure composting. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148381. [PMID: 34146805 DOI: 10.1016/j.scitotenv.2021.148381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
Manures, storages for antibiotic resistance genes (ARGs), pollute soil and water as well as endanger human health. Recently, we have been searching a better solution to remove antibiotics and ARGs during aerobic composting. Here, the dynamics of chitosan addition on the profiles of 71 ARGs, bacterial communities, chlortetracycline (CTC), ofloxacin (OFX) were investigated in chicken manure composting and compared with zeolite addition. Chitosan addition effectively reduces antibiotics contents (CTC under detection limit, OFX 90.96%), amounts (18) and abundance (56.7%, 11.1% higher than zeolite addition) of ARGs and mobile genetic elements (MGEs) after 42 days composting. Network analysis indicated that a total of 27 genera strains assigned into 4 phyla (Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes) were the potential hosts of ARGs. Redundancy analysis (RDA) demonstrated that bacterial community succession is the main contributor in the variation of ARGs. Overall, chitosan addition may effect bacterial composition by influencing physic-chemical properties and the concentration of antibiotics, Cu2+, Zn2+ to reduce the risk of ARG transmission. This study gives a new strategy about antibiotics and ARGs removal from composting on the basis of previous studies.
Collapse
Affiliation(s)
- Hongdou Liu
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Xuhong Ye
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Songling Chen
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Aobo Sun
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Xinying Duan
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| | - Yanqing Zhang
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China; Institute of Agricultural Environment and Sustainable Development, Chinese Academy of Agricultural Sciences, China
| | - Hongtao Zou
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China.
| | - Yulong Zhang
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110866, Liaoning, China; National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang 110866, Liaoning, China; Key Laboratory of Arable Land Conservation (Northeast China), Ministry of Agriculture and Rural Areas, Shenyang 110866, Liaoning, China
| |
Collapse
|
13
|
Sanz C, Casado M, Navarro-Martin L, Tadić Đ, Parera J, Tugues J, Bayona JM, Piña B. Antibiotic and antibiotic-resistant gene loads in swine slurries and their digestates: Implications for their use as fertilizers in agriculture. ENVIRONMENTAL RESEARCH 2021; 194:110513. [PMID: 33242487 DOI: 10.1016/j.envres.2020.110513] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 05/23/2023]
Abstract
The spread of antibiotic resistance in bacteria is a matter of global concern, and the identification of possible sources of the associated genetic elements (antibiotic resistance genes -ARGs-, components of the horizontal gene transfer mechanism), is becoming an urgent need. While the transmission of ARGs in medical settings have been adequately characterized, ARG propagation in agroecosystems remains insufficiently studied. Particularly crucial is the determination of potential risks associated to the use of swine slurries and related products as component of organic fertilizers, an increasingly used farming practice. We determined ARGs and antibiotic loads analysed from swine slurries and digestates from eight farms from Catalonia (NE Spain), and compared the results with their microbiome composition. Both ARGs and antibiotic were conspicuous in farm organic wastes, and the levels of some antibiotics exceeded currently accepted minimum inhibitory concentrations. Particularly, the presence of high loads of fluoroquinolones was directly correlated to the prevalence of the related qnrS1 ARG in the slurry. We also found evidence that ARG loads were directly correlated to the prevalence of determined bacterial taxa (Actinobacteria, Proteobacteria, Spirochaeta), a parameter that could be potentially modulated by the processing of the raw slurry prior to their use as fertilizer.
Collapse
Affiliation(s)
- Claudia Sanz
- IDAEA-CSIC, Jordi Girona, 18, E-08034, Barcelona, Spain
| | - Marta Casado
- IDAEA-CSIC, Jordi Girona, 18, E-08034, Barcelona, Spain
| | | | - Đorđe Tadić
- IDAEA-CSIC, Jordi Girona, 18, E-08034, Barcelona, Spain
| | - Joan Parera
- DARP Catalunya Central, GENCAT, Carrer de La Llotja, S/n (Recinte Firal El Sucre), 08500, Vic, Spain
| | - Jordi Tugues
- DARP Catalunya Central, GENCAT, Carrer de La Llotja, S/n (Recinte Firal El Sucre), 08500, Vic, Spain
| | | | - Benjamin Piña
- IDAEA-CSIC, Jordi Girona, 18, E-08034, Barcelona, Spain.
| |
Collapse
|
14
|
Xu M, Wang F, Sheng H, Stedtfeld RD, Li Z, Hashsham SA, Jiang X, Tiedje JM. Does anaerobic condition play a more positive role in dissipation of antibiotic resistance genes in soil? THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143737. [PMID: 33243511 DOI: 10.1016/j.scitotenv.2020.143737] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 06/11/2023]
Abstract
The persistence of antibiotic resistance genes (ARGs) under the aerobic vs. anaerobic conditions is unknown, especially under different fertilization. Towards this goal, a microcosm experiment was carried out with chemical fertilized and manured soil under aerobic and anaerobic conditions. High throughput qPCR was used to analyze ARGs with 144 primer sets and sequencing for microorganisms. Completely different dynamics of ARGs were observed in soil under aerobic and anaerobic conditions, regardless of the fertilization type. ARGs had different half-lives, even though they confer resistance to the same type of antibiotics. Aminoglycoside, chloramphenicol, macrolide - lincosamide - streptogramin B (MLSB) and tetracycline resistance genes were significantly accumulated in the aerobic soils. Anaerobic soil possessed a higher harboring capacity for exogenous microorganisms and ARGs than aerobic soil. The interaction between ARGs and mobile genetic elements (MGEs) in manured soil under aerobic condition was more pronounced than the anaerobic condition. These findings unveil that anaerobic soil could play a more positive role in reducing potential risk of ARGs in the farmland environment.
Collapse
Affiliation(s)
- Min Xu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA.
| | - Hongjie Sheng
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA
| | - Zhongpei Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
| |
Collapse
|
15
|
Wickramanayake MVKS, Dahanayake PS, Hossain S, De Zoysa M, Heo GJ. Aeromonas spp. Isolated from Pacific Abalone (Haliotis discus hannai) Marketed in Korea: Antimicrobial and Heavy-Metal Resistance Properties. Curr Microbiol 2020; 77:1707-1715. [PMID: 32300925 DOI: 10.1007/s00284-020-01982-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 04/06/2020] [Indexed: 01/07/2023]
Abstract
Antimicrobial and heavy-metal resistance of 29 Aeromonas spp. (Aeromonas hydrophila n = 9, Aeromonas enteropelogenes n = 14, Aeromonas veronii n = 3, Aeromonas salmonicida n = 2, and Aeromonas sobria n = 1) isolated from Pacific abalone marketed in Korea were analyzed. All isolates were found to be resistant against ampicillin. High level of resistant to cephalothin (86%), rifampicin (73%), imipenem (42%), and oxytetracycline (35%) were also detected. Thirteen (45%) of the isolates showed multiple antimicrobial resistance (MAR) index ≥ 0.2. The PCR assays implied the presence of qnrS, qnrB, qnrA, tetB, tetA, aac (3')- IIa, aac(6')-Ib, aphAI-IAB, blaCTX, blaTEM, and intI1 genes among 76%, 28%, 14%, 17%, 3%, 3%, 41%, 10%, 41%, 28%, and 66% of the isolates, respectively. Class 1 integron gene cassette profiles aadA1(3%) and aadA2 (3%) were also identified. Lead (Pb) resistance was the highest (69%) among 5 heavy metals tested, whereas 38%, 27%, and 20% of the isolates were resistant to Cadmium (Cd), Chromium (Cr), and Copper (Cu), respectively. Heavy-metal resistance genes, CopA, CzcA, and merA were positive in 83%, 75%, and 41% of the isolates, respectively. In conclusion, observed genotypic and phenotypic resistance profiles of Aeromonas spp. against antimicrobials and heavy metals reveal the ability of serving as a source of antimicrobials and heavy-metal-resistant traits.
Collapse
Affiliation(s)
- M V K S Wickramanayake
- Laboratory of Aquatic Animal Medicine, Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju, Chungbuk, 28644, Republic of Korea
| | - P S Dahanayake
- Laboratory of Aquatic Animal Medicine, Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Sabrina Hossain
- Laboratory of Aquatic Animal Medicine, Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Mahanama De Zoysa
- College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungnam National University, Yuseong-gu, Daejeon, 34134, Republic of Korea
| | - Gang-Joon Heo
- Laboratory of Aquatic Animal Medicine, Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju, Chungbuk, 28644, Republic of Korea.
| |
Collapse
|
16
|
Zheng W, Huyan J, Tian Z, Zhang Y, Wen X. Clinical class 1 integron-integrase gene - A promising indicator to monitor the abundance and elimination of antibiotic resistance genes in an urban wastewater treatment plant. ENVIRONMENT INTERNATIONAL 2020; 135:105372. [PMID: 31838265 DOI: 10.1016/j.envint.2019.105372] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/31/2019] [Accepted: 11/27/2019] [Indexed: 06/10/2023]
Abstract
In this study, 295 antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) from the influent, activated sludge (AS), and membrane bioreactor (MBR) permeate were primarily examined in the wastewater treatment plant (WWTP) biweekly over 13 months. The absolute concentrations of ARGs and MGEs respectively ranged from 1.27 × 1010 to 1.94 × 1011 and 8.00 × 109 to 1.24 × 1011 copies/L in the influent, of which were reduced by 2 to 3 orders of magnitude in the permeate. No significant seasonal variation of ARGs and MGEs was found in the WWTP, except that the absolute abundance of ARGs and MGEs in the AS was peaked during spring. The antibiotics affected neither ARGs nor MGEs significantly, suggesting their concentrations may be not high enough to pose a selective pressure. In contrast, the bacterial community had direct effect on the MGEs variation, meanwhile the MGEs influenced the ARG abundance directly. Class 1 integron-integrase gene (intI1), clinical intI1, and Tn21 associated more frequently with ARGs in the AS over long-term, suggesting the potential of them involved in horizontal gene transfer. Both intI1 and clinical intI1 had significantly positive associations with the overall abundance of ARGs, as well as significantly negative relationships with the overall removal rates of ARGs in the MBR. However, the abundances between intI1 and clinical intI1 were significantly different. Meanwhile, clinical intI1 remained rather consistent proportion with the ARG abundance in the AS and permeate, was stronger correlated with human pathogens, and was associated with greater number of ARGs over time. Moreover, clinical intI1 was significantly associated with the removal efficiency of ARGs from all classes. Taken together, clinical intI1 can be adopted as an indicator for the abundance and removal efficiency of ARGs in the WWTP.
Collapse
Affiliation(s)
- Wanlin Zheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Beijing Enterprises Water Group (China) Investment Limited, Beijing 100102, China
| | - Jiaoqi Huyan
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhe Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xianghua Wen
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
17
|
Zhu L, Zhao Y, Yang K, Chen J, Zhou H, Chen X, Liu Q, Wei Z. Host bacterial community of MGEs determines the risk of horizontal gene transfer during composting of different animal manures. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 250:166-174. [PMID: 30995570 DOI: 10.1016/j.envpol.2019.04.037] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/31/2019] [Accepted: 04/06/2019] [Indexed: 05/12/2023]
Abstract
Mobile genetic elements (MGEs) play critical roles in transferring antibiotic resistance genes (ARGs) among different microorganisms in the environment. This study aimed to explore the fate of MGEs during chicken manure (CM) and bovine manure (BM) composting to assess horizontal transfer risks of ARGs. The results showed that the removal efficiency of MGEs during CM composting was significantly higher than that during BM composting, because the potential host bacteria of MGEs were eliminated largely during CM composting. Meanwhile, these potential host bacterial communities are significantly influenced by pH, NH4+, NO3- and total N, which can be used to regulate host bacterial communities to remove MGEs during composting. Projection pursuit regression further confirmed that composting can effectively reduce the horizontal transfer risk of ARGs, especially for CM composting. These results identified the critical roles of host bacterial communities in MGEs removal during composting of different animal manures.
Collapse
Affiliation(s)
- Longji Zhu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province Science and Technology Department, Northeast Agricultural University, Harbin, 150030, China; College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Yue Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province Science and Technology Department, Northeast Agricultural University, Harbin, 150030, China; College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Kangjie Yang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province Science and Technology Department, Northeast Agricultural University, Harbin, 150030, China; College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Jian Chen
- Beijing Tongzhou Agriculture Products Quality Inspection & Testing Center, Beijing, 101149, China
| | - Haixuan Zhou
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province Science and Technology Department, Northeast Agricultural University, Harbin, 150030, China; College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Xiaomeng Chen
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province Science and Technology Department, Northeast Agricultural University, Harbin, 150030, China; College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Qi Liu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province Science and Technology Department, Northeast Agricultural University, Harbin, 150030, China; College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Zimin Wei
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province Science and Technology Department, Northeast Agricultural University, Harbin, 150030, China; College of Life Science, Northeast Agricultural University, Harbin, 150030, China.
| |
Collapse
|
18
|
Cerqueira F, Matamoros V, Bayona J, Elsinga G, Hornstra LM, Piña B. Distribution of antibiotic resistance genes in soils and crops. A field study in legume plants (Vicia faba L.) grown under different watering regimes. ENVIRONMENTAL RESEARCH 2019; 170:16-25. [PMID: 30554053 DOI: 10.1016/j.envres.2018.12.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
Social concern has raised during the last years due to the development of antibiotic resistance hotspots in different environmental compartments, including the edible parts of crops. To assess the influence of the water quality used for watering, we collected samples from soil, roots, leaves and beans from the legume plant Vicia faba (broad beans) in three agricultural peri-urban plots (Barcelona, NE Spain), irrigated with either groundwater, river water, or reclaimed water. Antibiotic resistance genes (ARGs) sul1, tetM, qnrS1, blaCTX-M-32,blaOXA-58, mecA, and blaTEM were quantified by real-time PCR, along with 16S rDNA and intl1 sequences, as proxies for bacterial abundance and integron prevalence, respectively. Microbiome composition of all samples were analyzed by high-throughput DNA sequencing. Results show a gradient of bacterial species diversity and of ARG prevalence from highly diverse soil samples to microbially-poor beans and leaves, in which Rhizobiales essentially displaced all other groups, and that presented very small loads of ARGs and integron sequences. The data suggest that the microbiome and the associated resistome were likely influenced by agricultural practices and water quality, and that future irrigation water legal standards should consider the specific Physiology of the different crop plants.
Collapse
Affiliation(s)
- Francisco Cerqueira
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, 08034 Barcelona, Spain
| | - Víctor Matamoros
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, 08034 Barcelona, Spain
| | - Josep Bayona
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, 08034 Barcelona, Spain
| | - Goffe Elsinga
- KWR Watercycle Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Luc M Hornstra
- KWR Watercycle Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Benjamin Piña
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, 08034 Barcelona, Spain.
| |
Collapse
|
19
|
Liu Y, Cui E, Neal AL, Zhang X, Li Z, Xiao Y, Du Z, Gao F, Fan X, Hu C. Reducing water use by alternate-furrow irrigation with livestock wastewater reduces antibiotic resistance gene abundance in the rhizosphere but not in the non-rhizosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 648:12-24. [PMID: 30107302 PMCID: PMC6234105 DOI: 10.1016/j.scitotenv.2018.08.101] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 08/07/2018] [Indexed: 05/08/2023]
Abstract
Livestock wastewater is rich in nutrients but may contain antibiotics and antibiotic resistance genes (ARGs). Their discharge to watercourses or soil may result in proliferation of ARGs. Irrigation with wastewater appears to be the most feasible option of disposing of it. One efficient irrigation technology used in arid regions is alternate-furrow irrigation (AFI) by alternately drying part of the plant roots for a prolonged period to physiologically reduce transpiration without compromising yield. However, the extent to which AFI with wastewater influences the concentration of antibiotics and spread of ARGs in soil is poorly understood. The purpose of this paper is to investigate how AFI using swine wastewater alters antibiotic kinetics and ARGs abundance under different irrigation rates, using pepper as the model plant. We examined three AFI treatments using 50%, 65% and 80% of the amount of water employed in sufficient conventional furrow irrigation. Each treatment had a groundwater irrigation control. The results showed that antibiotic concentrations and relative ARGs abundance in the top 20 cm of soil did not increase with the irrigation amount, although they were higher than those in the groundwater-irrigated soils. The relative ARGs abundance in the soil was modulated by irrigation amount and reducing the irrigation amount in AFI reduced ARGs dispersion only in rhizosphere. When the soil moisture was close to field capacity, ARGs were more abundant in rhizosphere than in non-rhizosphere, possibly because the rhizosphere is rich in microbes and increasing antibiotic concentrations due to an increase in irrigation rate favors antibiotic-resistant microbiome in competing for substrates. These, however, were not mirrored in the relative ARGs abundance in the roots. These results have important implications as it revealed that reducing the input of antibiotics and ARGs into soil with AFI does not necessarily reduce ARGs proliferation.
Collapse
Affiliation(s)
- Yuan Liu
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Erping Cui
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Andrew L Neal
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Xiaoxian Zhang
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Zhongyang Li
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China.
| | - Yatao Xiao
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Zhenjie Du
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Feng Gao
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Xiangyang Fan
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Chao Hu
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| |
Collapse
|
20
|
Liu L, Su JQ, Guo Y, Wilkinson DM, Liu Z, Zhu YG, Yang J. Large-scale biogeographical patterns of bacterial antibiotic resistome in the waterbodies of China. ENVIRONMENT INTERNATIONAL 2018; 117:292-299. [PMID: 29891393 DOI: 10.1016/j.envint.2018.05.023] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 05/03/2018] [Accepted: 05/09/2018] [Indexed: 05/26/2023]
Abstract
Antibiotic resistance genes (ARGs) are widespread in aquatic environments, but we know little about their biogeographical distribution and occurrence at national scales. Here we analyzed the patterns of ARGs from 42 natural waterbodies (natural lakes and reservoirs) across China using high-throughput approaches. The major ARGs were multidrug genes and the main resistance mechanism was the efflux pump. Although the absolute abundance of ARGs (gene copies/L) in the south/central waterbodies was similar to the northern waterbodies, the normalized abundance of ARGs (ARGs/16S rRNA gene copy number) was higher in the south/central waterbodies than in the north (mainly because of the aminoglycoside and multidrug resistance genes). Human activities strongly correlated with the normalized abundance of ARGs. The composition of ARGs in the waterbodies of south/central China was different from that in the north, and ARGs showed a distance-decay relationship. Anthropogenic factors had the most significant effects on this spatial distribution of ARG composition, followed by the spatial, bacterial and physicochemical factors. These indicate that the ARGs exhibited biogeographical patterns and that multiple ecological mechanisms - such as environmental selection (human activities and local physicochemical parameters) and dispersal limitation - influence distribution of ARGs in these waters. In general, our results provide a valuable ecological insight to explain the large-scale dispersal patterns in ARGs, thereby having potential applications for both public health and environmental management.
Collapse
Affiliation(s)
- Lemian Liu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Yunyan Guo
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | | | - Zhengwen Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Jun Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China.
| |
Collapse
|
21
|
Peng S, Dolfing J, Feng Y, Wang Y, Lin X. Enrichment of the Antibiotic Resistance Gene tet(L) in an Alkaline Soil Fertilized With Plant Derived Organic Manure. Front Microbiol 2018; 9:1140. [PMID: 29904377 PMCID: PMC5990627 DOI: 10.3389/fmicb.2018.01140] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 05/14/2018] [Indexed: 12/17/2022] Open
Abstract
Fifteen antibiotic resistance genes (ARGs) and intI1, a gene involved in horizontal gene transfer (HGT) of ARGs, were quantified in three different soil samples from a 22 year old field experiment that had received inorganic fertilizer (NPK), organic manure (OM; a mixture of wheat straw, soybean oil cake and cotton cake), and control fields that had received no fertilizer and manure (CK). Tet(L) was the most abundant ARG in OM, which also contained considerable levels of intI1. Molecular analysis of yearly collected archived soils over the past 22 years showed that tet(L) and intI1 were higher in OM soils than in NPK soils. The relative abundance of tet(L) was essentially constant during these years, while the level of intI1 in OM soils decreased over time. The main genotype of tet(L) was the same in archived and in fresh soil, OM, and irrigation water. Phylogenetic analysis of the 16S rRNA genes of tetracycline-resistant bacteria (TRB) isolates indicated that the Firmucutes carrying tet(L) in OM were similar to those in the OM soil, suggesting that OM transferred TRB into the OM soils where they survived. Almost all of the TRB isolated from OM carried tet(L) and belonged to the Firmicutes. Survival of bacteria from the organic manure that carried tet(L) may be the cause of the increased level of tet(L) in OM soil.
Collapse
Affiliation(s)
- Shuang Peng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,College of Environment and Ecology, Jiangsu Open University, Nanjing, China
| | - Jan Dolfing
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Youzhi Feng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yiming Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xiangui Lin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| |
Collapse
|
22
|
Uyaguari-Díaz MI, Croxen MA, Luo Z, Cronin KI, Chan M, Baticados WN, Nesbitt MJ, Li S, Miller KM, Dooley D, Hsiao W, Isaac-Renton JL, Tang P, Prystajecky N. Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia. Front Microbiol 2018; 9:852. [PMID: 29765365 PMCID: PMC5938356 DOI: 10.3389/fmicb.2018.00852] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/13/2018] [Indexed: 01/08/2023] Open
Abstract
The dissemination of antibiotic resistant bacteria from anthropogenic sources into the environment poses an emerging public health threat. Antibiotic resistance genes (ARGs) and gene-capturing systems such as integron-associated integrase genes (intI) play a key role in alterations of microbial communities and the spread of antibiotic resistant bacteria into the environment. In order to assess the effect of anthropogenic activities on watersheds in southwestern British Columbia, the presence of putative antibiotic resistance and integrase genes was analyzed in the microbiome of agricultural, urban influenced, and protected watersheds. A metagenomics approach and high-throughput quantitative PCR (HT qPCR) were used to screen for elements of resistance including ARGs and intI. Metagenomic sequencing of bacterial genomic DNA was used to characterize the resistome of microbial communities present in watersheds over a 1-year period. There was a low prevalence of ARGs relative to the microbial population (<1%). Analysis of the metagenomic sequences detected a total of 60 elements of resistance including 46 ARGs, intI1, and groEL/intI1 genes and 12 quaternary ammonium compounds (qac) resistance genes across all watershed locations. The relative abundance and richness of ARGs was found to be highest in agriculture impacted watersheds compared to urban and protected watersheds. A downstream transport pattern was observed in the impacted watersheds (urban and agricultural) during dry months. Similar to other reports, this study found a strong association between intI1 and ARGs (e.g., sul1), an association which may be used as a proxy for anthropogenic activities. Chemical analysis of water samples for three major groups of antibiotics was below the detection limit. However, the high richness and gene copy numbers (GCNs) of ARGs in impacted sites suggest that the effects of effluents on microbial communities are occurring even at low concentrations of antimicrobials in the water column. Antibiotic resistance and integrase genes in a year-long metagenomic study showed that ARGs were driven mainly by environmental factors from anthropogenized sites in agriculture and urban watersheds. Environmental factors such as land-use and water quality parameters accounted for 45% of the variability observed in watershed locations.
Collapse
Affiliation(s)
- Miguel I Uyaguari-Díaz
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Matthew A Croxen
- Provincial Laboratory for Public Health, Edmonton, AB, Canada.,Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Zhiyao Luo
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Kirby I Cronin
- Laboratory Services, Public Health Ontario, Toronto, ON, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Michael Chan
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Waren N Baticados
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | | | - Shaorong Li
- Pacific Biological Station, Nanaimo, BC, Canada
| | | | - Damion Dooley
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - William Hsiao
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Judith L Isaac-Renton
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - Natalie Prystajecky
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| |
Collapse
|
23
|
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
|
24
|
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: 67] [Impact Index Per Article: 9.6] [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
|
25
|
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
|
26
|
Chamosa LS, Álvarez VE, Nardelli M, Quiroga MP, Cassini MH, Centrón D. Lateral Antimicrobial Resistance Genetic Transfer is active in the open environment. Sci Rep 2017; 7:513. [PMID: 28364120 PMCID: PMC5428826 DOI: 10.1038/s41598-017-00600-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/27/2017] [Indexed: 12/31/2022] Open
Abstract
Historically, the environment has been viewed as a passive deposit of antimicrobial resistance mechanisms, where bacteria show biological cost for maintenance of these genes. Thus, in the absence of antimicrobial pressure, it is expected that they disappear from environmental bacterial communities. To test this scenario, we studied native IntI1 functionality of 11 class 1 integron-positive environmental strains of distant genera collected in cold and subtropical forests of Argentina. We found natural competence and successful site-specific insertion with no significant fitness cost of both aadB and blaVIM-2 antimicrobial resistance gene cassettes, in a model system without antibiotic pressure. A bidirectional flow of antimicrobial resistance gene cassettes between natural and nosocomial habitats is proposed, which implies an active role of the open environment as a reservoir, recipient and source of antimicrobial resistance mechanisms, outlining an environmental threat where novel concepts of rational use of antibiotics are extremely urgent and mandatory.
Collapse
Affiliation(s)
- Luciana S Chamosa
- Instituto de Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones, Científicas y Tecnológicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Verónica E Álvarez
- Instituto de Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones, Científicas y Tecnológicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Maximiliano Nardelli
- Instituto de Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones, Científicas y Tecnológicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - María Paula Quiroga
- Instituto de Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones, Científicas y Tecnológicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo H Cassini
- Grupo GEMA, Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Buenos Aires, Argentina.,Laboratorio de Biología del Comportamiento, IBYME, Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniela Centrón
- Instituto de Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones, Científicas y Tecnológicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina.
| |
Collapse
|
27
|
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: 137] [Impact Index Per Article: 17.1] [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
|
28
|
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
|
29
|
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
|
30
|
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
|
31
|
Power ML, Samuel A, Smith JJ, Stark JS, Gillings MR, Gordon DM. Escherichia coli out in the cold: Dissemination of human-derived bacteria into the Antarctic microbiome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 215:58-65. [PMID: 27179324 DOI: 10.1016/j.envpol.2016.04.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 03/19/2016] [Accepted: 04/04/2016] [Indexed: 05/12/2023]
Abstract
Discharge of untreated sewage into Antarctic environments presents a risk of introducing non-native microorganisms, but until now, adverse consequences have not been conclusively identified. Here we show that sewage disposal introduces human derived Escherichia coli carrying mobile genetic elements and virulence traits with the potential to affect the diversity and evolution of native Antarctic microbial communities. We compared E. coli recovered from environmental and animal sources in Antarctica to a reference collection of E. coli from humans and non-Antarctic animals. The distribution of phylogenetic groups and frequency of 11 virulence factors amongst the Antarctic isolates were characteristic of E. coli strains more commonly associated with humans. The rapidly emerging E. coli ST131 and ST95 clones were found amongst the Antarctic isolates, and ST95 was the predominant E. coli recovered from Weddell seals. Class 1 integrons were found in 15% of the Antarctic E. coli with 4 of 5 identified gene cassette arrays containing antibiotic resistance genes matching those common in clinical contexts. Disposing untreated sewage into the Antarctic environment does disseminate non-native microorganisms, but the extent of this impact and implications for Antarctic ecosystem health are, as yet, poorly understood.
Collapse
Affiliation(s)
- Michelle L Power
- Biological Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW 2109, Australia.
| | - Angelingifta Samuel
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, 116 Daley Road, Acton, ACT 2601, Australia.
| | - James J Smith
- Queensland University of Technology, Science and Engineering Faculty, School of Earth, Environmental and Biological Sciences, GPO Box 2434, Brisbane, QLD 4001, Australia; JJSC Consulting Ltd., 16 Mullacor St., Ferny Grove, QLD 4055, Australia.
| | - Jonathon S Stark
- Antarctic Conservation and Management, Australian Antarctic Division, 203 Channel Highway, Kingston, Tasmania 7050, Australia.
| | - Michael R Gillings
- Biological Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW 2109, Australia
| | - David M Gordon
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, 116 Daley Road, Acton, ACT 2601, Australia.
| |
Collapse
|
32
|
Sui Q, Zhang J, Chen M, Tong J, Wang R, Wei Y. Distribution of antibiotic resistance genes (ARGs) in anaerobic digestion and land application of swine wastewater. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 213:751-759. [PMID: 27038206 DOI: 10.1016/j.envpol.2016.03.038] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/11/2016] [Accepted: 03/15/2016] [Indexed: 06/05/2023]
Abstract
Swine farm and the adjacent farmland are hot spots of ARGs. However, few studies have investigated the on-site occurrence of ARGs distributed in the process of anaerobic digestion (AD) followed by land application of swine wastewater. Two typical swine farms, in southern and northern China respectively, with AD along with land application were explored on ARG distributions. ARGs were highly abundant in raw swine wastewater, AD effectively reduced the copy number of all detected ARGs (0.21-1.34 logs removal), but the relative abundance with different resistance mechanisms showed distinctive variation trends. The reduction efficiency of ARGs was improved by stable operational temperature and longer solid retention time (SRT) of AD. ARGs in soil characterized the contamination from the irrigation of the digested liquor. The total ARGs quantity in soil fell down by 1.66 logs in idle period of winter compared to application period of summer in the northern region, whereas the total amount was steady with whole-year application in south. Some persistent (sul1 and sul2) and elevated ARGs (tetG and ereA) in AD and land application need more attention.
Collapse
Affiliation(s)
- 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, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, 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, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, 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, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, 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, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, 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, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Energy, Jiangxi Academy of Sciences, Nanchang 330096, China.
| |
Collapse
|
33
|
Hu HW, Han XM, Shi XZ, Wang JT, Han LL, Chen D, He JZ. Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure. FEMS Microbiol Ecol 2015; 92:fiv169. [DOI: 10.1093/femsec/fiv169] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2015] [Indexed: 02/07/2023] Open
|
34
|
Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DGJ. Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics 2015; 16:964. [PMID: 26576951 PMCID: PMC4650350 DOI: 10.1186/s12864-015-2153-5] [Citation(s) in RCA: 450] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/27/2015] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Antibacterial biocides and metals can co-select for antibiotic resistance when bacteria harbour resistance or tolerance genes towards both types of compounds. Despite numerous case studies, systematic and quantitative data on co-occurrence of such genes on plasmids and chromosomes is lacking, as is knowledge on environments and bacterial taxa that tend to carry resistance genes to such compounds. This effectively prevents identification of risk scenarios. Therefore, we aimed to identify general patterns for which biocide/metal resistance genes (BMRGs) and antibiotic resistance genes (ARGs) that tend to occur together. We also aimed to quantify co-occurrence of resistance genes in different environments and taxa, and investigate to what extent plasmids carrying both types of genes are conjugative and/or are carrying toxin-antitoxin systems. RESULTS Co-occurrence patterns of resistance genes were derived from publicly available, fully sequenced bacterial genomes (n = 2522) and plasmids (n = 4582). The only BMRGs commonly co-occurring with ARGs on plasmids were mercury resistance genes and the qacE∆1 gene that provides low-level resistance to quaternary ammonium compounds. Novel connections between cadmium/zinc and macrolide/aminoglycoside resistance genes were also uncovered. Several clinically important bacterial taxa were particularly prone to carry both BMRGs and ARGs. Bacteria carrying BMRGs more often carried ARGs compared to bacteria without (p < 0.0001). BMRGs were found in 86 % of bacterial genomes, and co-occurred with ARGs in 17 % of the cases. In contrast, co-occurrences of BMRGs and ARGs were rare on plasmids from all external environments (<0.7 %) but more common on those of human and domestic animal origin (5 % and 7 %, respectively). Finally, plasmids with both BMRGs and ARGs were more likely to be conjugative (p < 0.0001) and carry toxin-antitoxin systems (p < 0.0001) than plasmids without resistance genes. CONCLUSIONS This is the first large-scale identification of compounds, taxa and environments of particular concern for co-selection of resistance against antibiotics, biocides and metals. Genetic co-occurrences suggest that plasmids provide limited opportunities for biocides and metals to promote horizontal transfer of antibiotic resistance through co-selection, whereas ample possibilities exist for indirect selection via chromosomal BMRGs. Taken together, the derived patterns improve our understanding of co-selection potential between biocides, metals and antibiotics, and thereby provide guidance for risk-reducing actions.
Collapse
Affiliation(s)
- Chandan Pal
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden
| | - Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46, Gothenburg, Sweden.
| |
Collapse
|
35
|
Abella J, Fahy A, Duran R, Cagnon C. Integron diversity in bacterial communities of freshwater sediments at different contamination levels. FEMS Microbiol Ecol 2015; 91:fiv140. [DOI: 10.1093/femsec/fiv140] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2015] [Indexed: 12/29/2022] Open
|
36
|
Abella J, Bielen A, Huang L, Delmont TO, Vujaklija D, Duran R, Cagnon C. Integron diversity in marine environments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015. [PMID: 26213132 DOI: 10.1007/s11356-015-5085-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Integrons are bacterial genetic elements known to be active vectors of antibiotic resistance among clinical bacteria. They are also found in bacterial communities from natural environments. Although integrons have become especially efficient for bacterial adaptation in the particular context of antibiotic usage, their role in natural environments in other contexts is still unknown. Indeed, most studies have focused on integrons and the spread of antibiotic resistance in freshwater or soil impacted by anthropogenic activities, with only few on marine environments. Notably, integrons show a wider diversity of both gene cassettes and integrase gene in natural environments than in clinical environments, suggesting a general role of integrons in bacterial adaptation. This article reviews the current knowledge on integrons in marine environments. We also present conclusions of our studies on polluted and nonpolluted backgrounds.
Collapse
Affiliation(s)
- Justine Abella
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
| | - Ana Bielen
- Laboratory for Molecular Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia
| | - Lionel Huang
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
- Euro Engineering, Technopole Hélioparc Bât Newton, 4 rue Jules Ferry, CS N 99207, 64053, Pau, Cedex 09, France
| | - Tom O Delmont
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biology Laboratory, Woods Hole, MA, USA
| | - Dušica Vujaklija
- Laboratory for Molecular Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Robert Duran
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France
| | - Christine Cagnon
- Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013, Pau, Cedex, France.
| |
Collapse
|
37
|
Abstract
Integrons are versatile gene acquisition systems commonly found in bacterial genomes. They are ancient elements that are a hot spot for genomic complexity, generating phenotypic diversity and shaping adaptive responses. In recent times, they have had a major role in the acquisition, expression, and dissemination of antibiotic resistance genes. Assessing the ongoing threats posed by integrons requires an understanding of their origins and evolutionary history. This review examines the functions and activities of integrons before the antibiotic era. It shows how antibiotic use selected particular integrons from among the environmental pool of these elements, such that integrons carrying resistance genes are now present in the majority of Gram-negative pathogens. Finally, it examines the potential consequences of widespread pollution with the novel integrons that have been assembled via the agency of human antibiotic use and speculates on the potential uses of integrons as platforms for biotechnology.
Collapse
|
38
|
Gillings MR, Gaze WH, Pruden A, Smalla K, Tiedje JM, Zhu YG. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME JOURNAL 2014; 9:1269-79. [PMID: 25500508 PMCID: PMC4438328 DOI: 10.1038/ismej.2014.226] [Citation(s) in RCA: 796] [Impact Index Per Article: 79.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 09/18/2014] [Accepted: 10/23/2014] [Indexed: 12/14/2022]
Abstract
Around all human activity, there are zones of pollution with pesticides, heavy metals, pharmaceuticals, personal care products and the microorganisms associated with human waste streams and agriculture. This diversity of pollutants, whose concentration varies spatially and temporally, is a major challenge for monitoring. Here, we suggest that the relative abundance of the clinical class 1 integron-integrase gene, intI1, is a good proxy for pollution because: (1) intI1 is linked to genes conferring resistance to antibiotics, disinfectants and heavy metals; (2) it is found in a wide variety of pathogenic and nonpathogenic bacteria; (3) its abundance can change rapidly because its host cells can have rapid generation times and it can move between bacteria by horizontal gene transfer; and (4) a single DNA sequence variant of intI1 is now found on a wide diversity of xenogenetic elements, these being complex mosaic DNA elements fixed through the agency of human selection. Here we review the literature examining the relationship between anthropogenic impacts and the abundance of intI1, and outline an approach by which intI1 could serve as a proxy for anthropogenic pollution.
Collapse
Affiliation(s)
- Michael R Gillings
- Department of Biological Sciences, Genes to Geoscience Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Royal Cornwall Hospital, Truro, UK
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| |
Collapse
|
39
|
Fate and effects of veterinary antibiotics in soil. Trends Microbiol 2014; 22:536-45. [DOI: 10.1016/j.tim.2014.05.005] [Citation(s) in RCA: 337] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 05/15/2014] [Accepted: 05/21/2014] [Indexed: 12/15/2022]
|
40
|
Jechalke S, Schreiter S, Wolters B, Dealtry S, Heuer H, Smalla K. Widespread dissemination of class 1 integron components in soils and related ecosystems as revealed by cultivation-independent analysis. Front Microbiol 2014; 4:420. [PMID: 24478761 PMCID: PMC3894453 DOI: 10.3389/fmicb.2013.00420] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/20/2013] [Indexed: 01/29/2023] Open
Abstract
Class 1 integrons contribute to the emerging problem of antibiotic resistance in human medicine by acquisition, exchange, and expression of resistance genes embedded within gene cassettes. Besides the clinical setting they were recently reported from environmental habitats and often located on plasmids and transposons, facilitating their transfer and spread within bacterial communities. In this study we aimed to provide insights into the occurrence of genes typically associated with the class 1 integrons in previously not studied environments with or without human impact and their association with IncP-1 plasmids. Total community DNA was extracted from manure-treated and untreated soils, lettuce and potato rhizosphere, digestates, and an on-farm biopurification system and screened by PCR with subsequent Southern blot hybridization for the presence of the class 1 integrase gene intI1 as well as qacE and qacEΔ 1 resistance genes. The results revealed a widespread dissemination of class 1 integrons in the environments analyzed, mainly related to the presence of qacEΔ 1 genes. All 28 IncP-1ε plasmids carrying class 1 integrons, which were captured exogenously in a recent study from piggery manure and soils treated with manure, carried qacEΔ 1 genes. Based on the strong hybridization signals in the rhizosphere of lettuce compared to the potato rhizosphere, the abundances of intI1, qacE/qacEΔ 1, and sul1 genes were quantified relative to the 16S rRNA gene abundance by real-time PCR in the rhizosphere of lettuce planted in three different soils and in the corresponding bulk soil. A significant enrichment of intI1 and qacE/qacEΔ 1 genes was confirmed in the rhizosphere of lettuce compared to bulk soil. Additionally, the relative abundance of korB genes specific for IncP-1 plasmids was enriched in the rhizosphere and correlated to the intI1 gene abundance indicating that IncP-1 plasmids might have contributed to the spread of class 1 integrons in the analyzed soils.
Collapse
Affiliation(s)
- Sven Jechalke
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI)Braunschweig, Germany
| | - Susanne Schreiter
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI)Braunschweig, Germany
| | - Birgit Wolters
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI)Braunschweig, Germany
- Institute of Environmental and Sustainable Chemistry, Technische Universität BraunschweigBraunschweig, Germany
| | - Simone Dealtry
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI)Braunschweig, Germany
| | - Holger Heuer
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI)Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI)Braunschweig, Germany
| |
Collapse
|
41
|
Abstract
Advances in sequencing technologies have made the investigation of microbial ecology and community dynamics more tractable. The critical first step in such analyses is the efficient and representative recovery of PCR-competent DNA from complex environmental samples. All extraction protocols contain inherent biases, meaning that choice of method involves compromise between various factors, including efficiency, yield, universality, and representative extraction. Here, details are given for a routine method used in our laboratory to extract DNA from soils, sediments, biofilms, roots, and fungi.
Collapse
Affiliation(s)
- Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| |
Collapse
|
42
|
Wang FH, Qiao M, Lv ZE, Guo GX, Jia Y, Su YH, Zhu YG. Impact of reclaimed water irrigation on antibiotic resistance in public parks, Beijing, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2014; 184:247-253. [PMID: 24071635 DOI: 10.1016/j.envpol.2013.08.038] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/26/2013] [Accepted: 08/30/2013] [Indexed: 06/02/2023]
Abstract
The abundance and distribution of antibiotics and antibiotic resistance genes (ARGs) in soils from six parks using reclaimed water in Beijing, China, were characterized. Three classes of commonly used antibiotics (tetracycles, quinolones, and sulfonamides) were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The highest concentrations of tetracyclines and quinolones were 145.2 μg kg(-1) and 79.2 μg kg(-1), respectively. Detected tetG, tetW, sulI, and sulII genes were quantified by quantitative PCR. ARGs exhibited various abundances for different park soils. The integrase gene (intI1) as an indicator of horizontal gene transfer potential was also detected in high abundance, and had significant positive correlation with tetG, sulI, and sulII genes, suggesting that intI1 may be involved in ARGs dissemination. Both sulII and intI1 clones had high homology with some classes of pathogenic bacteria, such as Klebsiella oxytoca, Acinetobacter baumannii, Shigella flexneri, which could trigger potential public health concern.
Collapse
Affiliation(s)
- Feng-Hua Wang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | | | | | | | | | | | | |
Collapse
|
43
|
Elsaied H, Stokes HW, Yoshioka H, Mitani Y, Maruyama A. Novel integrons and gene cassettes from a Cascadian submarine gas-hydrate-bearing core. FEMS Microbiol Ecol 2013; 87:343-56. [PMID: 24117886 DOI: 10.1111/1574-6941.12227] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 09/14/2013] [Accepted: 09/16/2013] [Indexed: 11/28/2022] Open
Abstract
To determine whether integrons are present in a submarine gas hydrate community, metagenomic DNA was extracted from a gas-hydrate-bearing core, 150 m below the seafloor, from the Cascadian Margin. Integrons and gene cassettes were recovered by PCR from metagenomic DNA and sequenced. Thirty-seven integron integrase phylotypes were identified. The phylotypes were diverse and included members with homology to integrases from Methylomonas methanica, Desulfuromonas acetoxidans, Thermodesulfatator indicus, and marine uncultured bacteria. The gene cassette composition, 153 gene cassettes, was dominated by two types of encoded putative proteins. The first of these was predicted oxidoreductases, such as iron/sulfur cluster-binding proteins. A second type was alkyl transferases. Some cassette proteins showed homologies with those from methane-related archaea. These observations suggest that integrons may assist in the adaptation of microbial communities in this environment.
Collapse
Affiliation(s)
- Hosam Elsaied
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, AIST, Tsukuba, Japan; Genetics and Biotechnology Research Group, National Institute of Oceanography, Cairo, Egypt
| | | | | | | | | |
Collapse
|
44
|
Jechalke S, Focks A, Rosendahl I, Groeneweg J, Siemens J, Heuer H, Smalla K. Structural and functional response of the soil bacterial community to application of manure from difloxacin-treated pigs. FEMS Microbiol Ecol 2013; 87:78-88. [PMID: 23962048 DOI: 10.1111/1574-6941.12191] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 11/28/2022] Open
Abstract
Difloxacin (DIF) belongs to the class of fluoroquinolone antibiotics that have been intensively used for the treatment of bacterial infections in veterinary and human medicine. The aim of this field study was to compare the effect of manure from DIF-treated pigs and untreated pigs on the bacterial community structure and resistance gene abundance in bulk soil and rhizosphere of maize. A significant effect of DIF manure on the bacterial community composition in bulk soil was revealed by denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rRNA gene fragments amplified from total community DNA. In few samples, quinolone resistance genes qnrB and qnrS1/qnrS2 were detected by PCR and subsequent hybridization, while qnrA was not detected. Quantitative PCR revealed an increased abundance of the integrase gene intI1 of class I integrons and sulfonamide resistance genes sul1 and sul2 in DIF manure-treated bulk soil and rhizosphere, relative to 16S rRNA genes, while traN genes specific for LowGC-type plasmids were increased only in bulk soil. Principal component analysis of DGGE profiles suggested a manure effect in soil until day 28, but samples of days 71 and 140 were found close to untreated soil, indicating resilience of soil community compositions from disturbances by manure.
Collapse
Affiliation(s)
- Sven Jechalke
- Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | | | | | | | | | | | | |
Collapse
|
45
|
Diverse gene cassettes in class 1 integrons of facultative oligotrophic bacteria of River Mahananda,West Bengal, India. PLoS One 2013; 8:e71753. [PMID: 23951238 PMCID: PMC3739733 DOI: 10.1371/journal.pone.0071753] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/02/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In this study a large random collection (n=2188) of facultative oligotrophic bacteria, from 90 water samples gathered in three consecutive years (2007-2009) from three different sampling sites of River Mahananda in Siliguri, West Bengal, India, were investigated for the presence of class 1 integrons and sequences of the amplification products. METHODOLOGY/PRINCIPAL FINDINGS Replica plating method was employed for determining the antibiotic resistance profile of the randomly assorted facultative oligotrophic isolates. Genomic DNA from each isolate was analyzed by PCR for the presence of class 1 integron. Amplicons were cloned and sequenced. Numerical taxonomy and 16S rRNA gene sequence analyses were done to ascertain putative genera of the class 1 integron bearing isolates. Out of 2188 isolates, 1667 (76.19%) were antibiotic-resistant comprising of both single-antibiotic resistance (SAR) and multiple-antibiotic resistant (MAR), and 521 (23.81%) were sensitive to all twelve different antibiotics used in this study. Ninety out of 2188 isolates produced amplicon(s) of varying sizes from 0.15 to 3.45 KB. Chi-square (χ(2)) test revealed that the possession of class 1 integron in sensitive, SAR and MAR is not equally probable at the 1% level of significance. Diverse antibiotic-resistance gene cassettes, aadA1, aadA2, aadA4, aadA5, dfrA1, dfrA5, dfrA7, dfrA12, dfrA16, dfrA17, dfrA28, dfrA30, dfr-IIe, blaIMP-9, aacA4, Ac-6'-Ib, oxa1, oxa10 and arr2 were detected in 64 isolates. The novel cassettes encoding proteins unrelated to any known antibiotic resistance gene function were identified in 26 isolates. Antibiotic-sensitive isolates have a greater propensity to carry gene cassettes unrelated to known antibiotic-resistance genes. The integron-positive isolates under the class Betaproteobacteria comprised of only two genera, Comamonas and Acidovorax of family Comamonadaceae, while isolates under class Gammaproteobacteria fell under the families, Moraxellaceae, Pseudomonadaceae, Aeromonadaceae and Enterobacteriaceae. CONCLUSIONS Oligotrophic bacteria are good sources of novel genes as well as potential reservoirs of antibiotic resistance gene casettes.
Collapse
|
46
|
Rizzo L, Manaia C, Merlin C, Schwartz T, Dagot C, Ploy MC, Michael I, Fatta-Kassinos D. Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2013; 447:345-60. [PMID: 23396083 DOI: 10.1016/j.scitotenv.2013.01.032] [Citation(s) in RCA: 1247] [Impact Index Per Article: 113.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/08/2013] [Accepted: 01/08/2013] [Indexed: 05/20/2023]
Abstract
Urban wastewater treatment plants (UWTPs) are among the main sources of antibiotics' release into the environment. The occurrence of antibiotics may promote the selection of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB), which shade health risks to humans and animals. In this paper the fate of ARB and ARGs in UWTPs, focusing on different processes/technologies (i.e., biological processes, advanced treatment technologies and disinfection), was critically reviewed. The mechanisms by which biological processes influence the development/selection of ARB and ARGs transfer are still poorly understood. Advanced treatment technologies and disinfection process are regarded as a major tool to control the spread of ARB into the environment. In spite of intense efforts made over the last years to bring solutions to control antibiotic resistance spread in the environment, there are still important gaps to fill in. In particular, it is important to: (i) improve risk assessment studies in order to allow accurate estimates about the maximal abundance of ARB in UWTPs effluents that would not pose risks for human and environmental health; (ii) understand the factors and mechanisms that drive antibiotic resistance maintenance and selection in wastewater habitats. The final objective is to implement wastewater treatment technologies capable of assuring the production of UWTPs effluents with an acceptable level of ARB.
Collapse
Affiliation(s)
- L Rizzo
- Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy.
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Nardelli M, Scalzo PM, Ramírez MS, Quiroga MP, Cassini MH, Centrón D. Class 1 integrons in environments with different degrees of urbanization. PLoS One 2012; 7:e39223. [PMID: 22761743 PMCID: PMC3382206 DOI: 10.1371/journal.pone.0039223] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 05/17/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Class 1 integrons are one of the most successful elements in the acquisition, expression and spread of antimicrobial resistance genes (ARG) among clinical isolates. Little is known about the gene flow of the components of the genetic platforms of class 1 integrons within and between bacterial communities. Thus it is important to better understand the interactions among "environmental" intI1, its genetic platforms and its distribution with human activities. METHODOLOGY/PRINCIPAL FINDINGS An evaluation of two types of genetic determinants, ARG (sul1 and qacE1/qacEΔ1 genes) and lateral genetic elements (LGE) (intI1, ISCR1 and tniC genes) in a model of a culture-based method without antibiotic selection was conducted in a gradient of anthropogenic disturbances in a Patagonian island recognized as being one of the last regions containing wild areas. The intI1, ISCR1 genes and intI1 pseudogenes that were found widespread throughout natural communities were not associated with urbanization (p>0.05). Each ARG that is embedded in the most common genetic platform of clinical class 1 integrons, showed different ecological and molecular behaviours in environmental samples. While the sul1 gene frequency was associated with urbanization, the qacE1/qacEΔ1 gene showed an adaptive role to several habitats. CONCLUSIONS/SIGNIFICANCE The high frequency of intI1 pseudogenes suggests that, although intI1 has a deleterious impact within several genomes, it can easily be disseminated among natural bacterial communities. The widespread occurrence of ISCR1 and intI1 throughout Patagonian sites with different degree of urbanization, and within different taxa, could be one of the causes of the increasing frequency of multidrug-resistant isolates that have characterized Argentina for decades. The flow of ARG and LGE between natural and clinical communities cannot be explained with a single general process but is a direct consequence of the interaction of multiple factors operating at molecular, ecological, phylogenetic and historical levels.
Collapse
Affiliation(s)
- Maximiliano Nardelli
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Marina Scalzo
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Soledad Ramírez
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Paula Quiroga
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo Hernán Cassini
- Grupo GEMA, Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Buenos Aires, Argentina
- Laboratorio de Biología del Comportamiento, IBYME, Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniela Centrón
- Laboratorio de Investigaciones de los Mecanismos de Resistencia a Antibióticos, Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
| |
Collapse
|
48
|
Stalder T, Barraud O, Casellas M, Dagot C, Ploy MC. Integron involvement in environmental spread of antibiotic resistance. Front Microbiol 2012; 3:119. [PMID: 22509175 PMCID: PMC3321497 DOI: 10.3389/fmicb.2012.00119] [Citation(s) in RCA: 230] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 03/13/2012] [Indexed: 11/13/2022] Open
Abstract
The spread of antibiotic-resistant bacteria is a growing problem and a public health issue. In recent decades, various genetic mechanisms involved in the spread of resistance genes among bacteria have been identified. Integrons - genetic elements that acquire, exchange, and express genes embedded within gene cassettes (GC) - are one of these mechanisms. Integrons are widely distributed, especially in Gram-negative bacteria; they are carried by mobile genetic elements, plasmids, and transposons, which promote their spread within bacterial communities. Initially studied mainly in the clinical setting for their involvement in antibiotic resistance, their role in the environment is now an increasing focus of attention. The aim of this review is to provide an in-depth analysis of recent studies of antibiotic-resistance integrons in the environment, highlighting their potential involvement in antibiotic-resistance outside the clinical context. We will focus particularly on the impact of human activities (agriculture, industries, wastewater treatment, etc.).
Collapse
|
49
|
|
50
|
Metagenomic exploration of antibiotic resistance in soil. Curr Opin Microbiol 2011; 14:229-35. [DOI: 10.1016/j.mib.2011.04.010] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 04/08/2011] [Accepted: 04/12/2011] [Indexed: 11/23/2022]
|