1
|
Jia WL, Gao FZ, Song C, Chen CE, Ma CX, White JC, Ying GG. Swine wastewater co-exposed with veterinary antibiotics enhanced the antibiotic resistance of endophytes in radish (Raphanus sativus L.). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 362:125040. [PMID: 39343351 DOI: 10.1016/j.envpol.2024.125040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 09/21/2024] [Accepted: 09/26/2024] [Indexed: 10/01/2024]
Abstract
The widespread utilization of antibiotics in livestock has promoted the accumulation and diffusion of antibiotics and antibiotic resistance in agricultural soils and crops. Here we investigated the mechanisms of antibiotic uptake and accumulation in swine wastewater (SW)-treated radish (Raphanus sativus L.) and subsequent impacts on endophyte antibiotic resistance. Under SW treatments, exposure to 500 μg/L sulfamethazine (SMZ) and enrofloxacin (EFX) significantly affected radish biomass, with SMZ causing 63.0% increases and EFX causing 36.3% decreases relative to the untreated control. EFX uptake by radish were from 5 to 100-folds over SMZ. Passive diffusion through anion channel proteins on cell membranes was an important route for SMZ uptake, while both passive diffusion and energy-dependent processes contributed to the uptake of EFX. Bacterial community was time-dependent as a function of both antibiotics and SW, the bacterial alpha diversity in liquid solution co-treated with antibiotics and SW increased over time. The abundance of antibiotic resistance genes (ARGs) in the roots was positively correlated with ARGs in the Hoagland's solution under antibiotic-alone treatments. EFX co-exposure with SW enhanced the dissemination of ARGs from swine wastewater into plant roots, and significant correlations existed between ARGs and integrons in both Hoagland's solution and roots. These findings increased our understanding of the fate of antibiotics in crops and their subsequent impacts on antibiotic resistance of endophytic bacteria.
Collapse
Affiliation(s)
- Wei-Li Jia
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, China; School of Environment, South China Normal University, University Town, Guangzhou, 510006, China
| | - Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, China; School of Environment, South China Normal University, University Town, Guangzhou, 510006, China
| | - Chao Song
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, China; School of Environment, South China Normal University, University Town, Guangzhou, 510006, China
| | - Chang-Er Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, China; School of Environment, South China Normal University, University Town, Guangzhou, 510006, China
| | - Chuan-Xin Ma
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven, CT, 06511, USA
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, 510006, China; School of Environment, South China Normal University, University Town, Guangzhou, 510006, China.
| |
Collapse
|
2
|
Yang J, Zhang X, Xu Z, Wang X. Prevalence of antibiotic resistance genes in different drinking water treatment processes in a northwest Chinese city. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:436. [PMID: 39316241 DOI: 10.1007/s10653-024-02212-y] [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: 12/17/2023] [Accepted: 09/02/2024] [Indexed: 09/25/2024]
Abstract
Antibiotic resistance genes (ARGs) are an emerging issue which are receiving increasing concerns in drinking water safety. However, the factors (e.g. treatment processes and water quality) affecting the removal efficiency of ARGs in the drinking water treatment plants (DWTPs) is still unclear. This work investigated the ARG profiles in each treatment process of two DWTPs located in a northwest Chinese city. The results showed that tetracycline and sulfonamide resistance genes were predominant among the 14 targeted ARGs. After the treatment, the Z water treatment plant which demonstrated a higher removal rate of ARGs (ranging from 50 to 80%), compared to the S plant (50-75%). And the average removal rate of tetracycline resistance genes (tetA, tetG, tetQ, tetX) was about 49.18% (S plant) and 67.50% (Z plant), as well as the removal rate of 64.2% and 72.9% for sulfonamide resistance (sul1 and sul2) at S and Z water plants, respectively. It was found that the relative abundance of main microbial communities (such as Bacteroidota, Actinobacteria, Verrucomicrobiota, Roseomonas), α-diversity index, as well as the abundance of pathogenic bacteria were all significantly reduced after different treatment processes. Network co-occurrence analysis revealed that Methylocystis possibly was the potential host for most ARGs, and sul1 was found across a broad spectrum of microorganisms in the drinking water environment. Adonis analysis showed that heavy metals and microbial communities explain solely 44.1% and 35.7% of variances of ARGs within DWTPs. This study provides insights into the contamination status and removal efficiencies of ARGs in DWTPs, offering valuable references for future studies on ARG removal, propagation, and diffusion patterns in drinking water treatment.
Collapse
Affiliation(s)
- Jing Yang
- School of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, People's Republic of China.
| | - Xuan Zhang
- School of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, People's Republic of China
| | - Zekun Xu
- School of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, People's Republic of China
| | - Xueyan Wang
- School of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, People's Republic of China
| |
Collapse
|
3
|
Kang S, Kim I, Vikesland PJ. Discriminatory Detection of ssDNA by Surface-Enhanced Raman Spectroscopy (SERS) and Tree-Based Support Vector Machine (Tr-SVM). Anal Chem 2021; 93:9319-9328. [PMID: 34196541 DOI: 10.1021/acs.analchem.0c04576] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We report label-free detection of 86-base single-stranded DNA (ssDNA) gene segments by surface-enhanced Raman spectroscopy (SERS). The use of a slippery liquid infused porous (SLIP) membrane induced aggregation of 43 nm gold nanoparticles and ssDNA upon pin-free droplet evaporation. The combined SLIPSERS approach generates significant numbers of SERS hot-spots and enabled detection at the 100 nM level of mecA and intI1 gene segments-two genes of interest in the context of antibiotic resistance. Tree-based multiclass support vector machine (Tr-SVM) classifiers were built to discriminate SERS spectra of 12 different gene sequences obtained by SLIPSERS: mecA, intI1, as well as analogues of mecA and intI1, respectively, with 2-10 base mismatches, and two random sequences. The trained predictive Tr-SVM classifiers correctly identified each gene sequence with a prediction accuracy of ∼90%. This study illustrates a novel means for discriminatory label-free SERS detection of ssDNA enabled by Tr-SVM.
Collapse
Affiliation(s)
- Seju Kang
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States.,Virginia Tech Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| | - Inyoung Kim
- Department of Statistics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Peter J Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States.,Virginia Tech Institute of Critical Technology and Applied Science (ICTAS) Sustainable Nanotechnology Center (VTSuN), Blacksburg, Virginia 24061, United States
| |
Collapse
|
4
|
Kim M, Ligaray M, Kwon YS, Kim S, Baek S, Pyo J, Baek G, Shin J, Kim J, Lee C, Kim YM, Cho KH. Designing a marine outfall to reduce microbial risk on a recreational beach: Field experiment and modeling. JOURNAL OF HAZARDOUS MATERIALS 2021; 409:124587. [PMID: 33303212 DOI: 10.1016/j.jhazmat.2020.124587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 10/10/2020] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
A marine outfall can be a wastewater management system that discharges sewage and stormwater into the sea; hence, it is a source of microbial pollution on recreational beaches, including antibiotic resistant genes (ARGs), which lead to an increase in untreatable diseases. In this regard, a marine outfall must be efficiently located to mitigate these risks. This study aimed to 1) investigate the spatiotemporal variability of Escherichia coli (E. coli) and ARGs on a recreational beach and 2) design marine outfalls to reduce microbial risks. For this purpose, E. coli and ARGs with influential environmental variables were intensively monitored on Gwangalli beach, South Korea in this study. Environmental fluid dynamic code (EFDC) was used and calibrated using the monitoring data, and 12 outfall extension scenarios were explored (6 locations at 2 depths). The results revealed that repositioning the marine outfall can significantly reduce the concentrations of E. coli and ARGs on the beach by 46-99%. Offshore extended outfalls at the bottom of the sea reduced concentrations of E. coli and ARGs on the beach more effectively than onshore outfalls at the sea surface. These findings could be helpful in establishing microbial pollution management plans at recreational beaches in the future.
Collapse
Affiliation(s)
- Minjeong Kim
- Division of Radioactive Waste Disposal Research, Korea Atomic Energy Research Institute (KAERI), 989-111, Daedeok-daero, Yuseong-gu, Daejeon 34057, Republic of Korea
| | - Mayzonee Ligaray
- Institute of Environmental Science and Meteorology, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Yong Sung Kwon
- Ecosystem Service Team, Division of Ecological Assessment, National Institute of Ecology, Seocheon 33657, Republic of Korea
| | - Soobin Kim
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Sangsoo Baek
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - JongCheol Pyo
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Gahyun Baek
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jingyeong Shin
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Jaai Kim
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Changsoo Lee
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology, UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Seoul 04763, Republic of Korea.
| | - Kyung Hwa Cho
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology, UNIST-gil 50, Ulsan 44919, Republic of Korea.
| |
Collapse
|
5
|
Wang C, Hu R, Strong PJ, Zhuang W, Huang W, Luo Z, Yan Q, He Z, Shu L. Prevalence of antibiotic resistance genes and bacterial pathogens along the soil-mangrove root continuum. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124985. [PMID: 33421848 DOI: 10.1016/j.jhazmat.2020.124985] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/09/2020] [Accepted: 12/24/2020] [Indexed: 06/12/2023]
Abstract
Plants roots are colonised by soil bacteria that are known to be the reservoir of antibiotic resistance genes (ARGs). ARGs can transfer between these microorganisms and pathogens, but to what extent these ARGs and pathogens disseminate from soil into plant is poorly understood. Here, we examined a high-resolution resistome profile along the soil-root continuum of mangrove saplings using amplicon and metagenomic sequencing. Data revealed that 91.4% of total ARGs were shared across four root-associated compartments (endosphere, episphere, rhizosphere and unplanted soil). Rather than compartment-selective dynamics of microbiota, the resistome was disseminated in a continuous fashion along the soil-root continuum. Such dissemination was independent of underlying root-associated bacterial and fungal microbiota, but might be facilitated by a multiplicity of mobile genetic elements. As the multiple-drug resistant pathogens, Vibrio vulnificus, pathogenic Escherichia coli and Klebsiella pneumoniae consistently predominated across four compartments, indicating the potential dissemination of antibiotic pathogens along the soil-root continuum. Through deciphering the profile and dynamics of the root-associated resistome and pathogens, our study identified the soil-root continuum as an interconnected sink through which certain ARGs and pathogens can flow from soil into the plant.
Collapse
Affiliation(s)
- Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - P J Strong
- School of Biology and Environmental Science, Centre for Agriculture and the Bioeconomy, Queensland University of Technology, GPO Box 2432, 2 George St, Brisbane QLD 4001, Australia
| | - Wei Zhuang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Weiming Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, No.132, East Outer Ring Road, Guangzhou Higher Education Mega Center, Guangzhou 510006, China.
| |
Collapse
|
6
|
Hill D, Morra MJ, Stalder T, Jechalke S, Top E, Pollard AT, Popova I. Dairy manure as a potential source of crop nutrients and environmental contaminants. J Environ Sci (China) 2021; 100:117-130. [PMID: 33279025 DOI: 10.1016/j.jes.2020.07.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 06/12/2023]
Abstract
Although animal manure is applied to agricultural fields for its nutrient value, it may also contain potential contaminants. To determine the variability in such contaminants as well as in valuable nutrients, nine uncomposted manure samples from Idaho dairies collected during 2.5 years were analyzed for macro- and micro-nutrients, hormones, phytoestrogens, antibiotics, veterinary drugs, antibiotic resistance genes, and genetic elements involved in the spread of antibiotic resistance. Total N ranged from 6.8 to 30.7 (C:N of 10 to 21), P from 2.4 to 9.0, and K from 10.2 to 47.7 g/kg manure. Zn (103 - 348 mg/kg) was more abundant than Cu (56 - 127 mg/kg) in all samples. Phytoestrogens were the most prevalent contaminants detected, with concentrations fluctuating over time, reflecting animal diets. This is the first study to document the presence of flunixin, a non-steroidal anti-inflammatory drug, in solid stacked manure from regular dairy operations. Monensin was the most frequently detected antibiotic. Progesterones and sulfonamides were regularly detected. We also investigated the relative abundance of several types of plasmids involved in the spread of antibiotic resistance in clinical settings. Plasmids belonging to the IncI, IncP, and IncQ1 incompatibility groups were found in almost all manure samples. IncQ1 plasmids, class 1 integrons, and sulfonamide resistance genes were the most widespread and abundant genetic element surveyed, emphasizing their potential role in the spread of antibiotic resistance. The benefits associated with amending agricultural soils with dairy manure must be carefully weighed against the potential negative consequences of any manure contaminants.
Collapse
Affiliation(s)
- Danika Hill
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA
| | - Matthew J Morra
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA
| | | | - Sven Jechalke
- Justus Liebig University Giessen, Institute for Phytopathology, 35392 Gießen, Germany
| | - Eva Top
- Department of Biology, University of Idaho, ID 83844-3051, USA
| | - Anne T Pollard
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA
| | - Inna Popova
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA.
| |
Collapse
|
7
|
Nieuwkerk DM, Korajkic A, Valdespino EL, Herrmann MP, Harwood VJ. Critical review of methods for isothermal amplification of nucleic acids for environmental analysis. J Microbiol Methods 2020; 179:106099. [PMID: 33159993 DOI: 10.1016/j.mimet.2020.106099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 10/23/2022]
Abstract
The past 30 years have seen the emergence and proliferation of isothermal amplification methods (IAMs) for rapid, sensitive detection and quantification of nucleic acids in a variety of sample types. These methods share dependence on primers and probes with quantitative PCR, but they differ in the specific enzymes and instruments employed, and are frequently conducted in a binary, rather than quantitative format. IAMs typically rely on simpler instruments than PCR analyses due to the maintenance of a single temperature throughout the amplification reaction, which could facilitate deployment of IAMs in a variety of environmental and field settings. This review summarizes the mechanisms of the most common IAM methods and their use in studies of pathogens, harmful algae and fecal indicators in environmental waters, feces, wastewater, reclaimed water, and tissues of aquatic animals. Performance metrics of sensitivity, specificity and limit of detection are highlighted, and the potential for use in monitoring and regulatory contexts is discussed.
Collapse
Affiliation(s)
- Dana M Nieuwkerk
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Asja Korajkic
- US Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Erika L Valdespino
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Michael P Herrmann
- US Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Valerie J Harwood
- University of South Florida, Department of Integrative Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA.
| |
Collapse
|
8
|
Choi J, Rieke EL, Moorman TB, Soupir ML, Allen HK, Smith SD, Howe A. Practical implications of erythromycin resistance gene diversity on surveillance and monitoring of resistance. FEMS Microbiol Ecol 2019; 94:4810543. [PMID: 29346541 PMCID: PMC5939627 DOI: 10.1093/femsec/fiy006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/12/2018] [Indexed: 12/29/2022] Open
Abstract
Use of antibiotics in human and animal medicine has applied selective pressure for the global dissemination of antibiotic-resistant bacteria. Therefore, it is of interest to develop strategies to mitigate the continued amplification and transmission of resistance genes in environmental reservoirs such as farms, hospitals and watersheds. However, the efficacy of mitigation strategies is difficult to evaluate because it is unclear which resistance genes are important to monitor, and which primers to use to detect those genes. Here, we evaluated the diversity of one type of macrolide antibiotic resistance gene (erm) in one type of environment (manure) to determine which primers would be most informative to use in a mitigation study of that environment. We analyzed all known erm genes and assessed the ability of previously published erm primers to detect the diversity. The results showed that all known erm resistance genes group into 66 clusters, and 25 of these clusters (40%) can be targeted with primers found in the literature. These primers can target 74%–85% of the erm gene diversity in the manures analyzed.
Collapse
Affiliation(s)
- Jinlyung Choi
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA 50011, USA
| | - Elizabeth L Rieke
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA 50011, USA
| | - Thomas B Moorman
- National Laboratory for Agriculture and the Environment, USDA-ARS, 2110 University Blvd, Ames, IA 50011, USA
| | - Michelle L Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA 50011, USA
| | - Heather K Allen
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Ave, Ames, IA, 50010, USA
| | - Schuyler D Smith
- Department of Bioinformatics and Computational Biology, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA 50011, USA
| |
Collapse
|
9
|
Pärnänen KMM, Narciso-da-Rocha C, Kneis D, Berendonk TU, Cacace D, Do TT, Elpers C, Fatta-Kassinos D, Henriques I, Jaeger T, Karkman A, Martinez JL, Michael SG, Michael-Kordatou I, O’Sullivan K, Rodriguez-Mozaz S, Schwartz T, Sheng H, Sørum H, Stedtfeld RD, Tiedje JM, Giustina SVD, Walsh F, Vaz-Moreira I, Virta M, Manaia CM. Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence. SCIENCE ADVANCES 2019; 5:eaau9124. [PMID: 30944853 PMCID: PMC6436925 DOI: 10.1126/sciadv.aau9124] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 02/06/2019] [Indexed: 05/03/2023]
Abstract
Integrated antibiotic resistance (AR) surveillance is one of the objectives of the World Health Organization global action plan on antimicrobial resistance. Urban wastewater treatment plants (UWTPs) are among the most important receptors and sources of environmental AR. On the basis of the consistent observation of an increasing north-to-south clinical AR prevalence in Europe, this study compared the influent and final effluent of 12 UWTPs located in seven countries (Portugal, Spain, Ireland, Cyprus, Germany, Finland, and Norway). Using highly parallel quantitative polymerase chain reaction, we analyzed 229 resistance genes and 25 mobile genetic elements. This first trans-Europe surveillance showed that UWTP AR profiles mirror the AR gradient observed in clinics. Antibiotic use, environmental temperature, and UWTP size were important factors related with resistance persistence and spread in the environment. These results highlight the need to implement regular surveillance and control measures, which may need to be appropriate for the geographic regions.
Collapse
Affiliation(s)
- Katariina M. M. Pärnänen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 University of Helsinki, Finland
| | - Carlos Narciso-da-Rocha
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina–Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - David Kneis
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany
| | | | - Damiano Cacace
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany
| | - Thi Thuy Do
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | | | - Despo Fatta-Kassinos
- Department of Civil and Environmental Engineering and Nireas–International Water Research Centre, University of Cyprus, P.O. Box 20537, CY-1678 Nicosia, Cyprus
| | - Isabel Henriques
- Department of Biology and CESAM, University of Aveiro, Campus Universitário Santiago, 3810-193 Aveiro, Portugal
| | - Thomas Jaeger
- Karlsruhe Institute of Technology (KIT)–Campus North, Institute of Functional Interfaces (IFG), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Antti Karkman
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 University of Helsinki, Finland
| | - Jose Luis Martinez
- Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, 20049 Madrid, Spain
| | - Stella G. Michael
- Department of Civil and Environmental Engineering and Nireas–International Water Research Centre, University of Cyprus, P.O. Box 20537, CY-1678 Nicosia, Cyprus
| | - Irene Michael-Kordatou
- Department of Civil and Environmental Engineering and Nireas–International Water Research Centre, University of Cyprus, P.O. Box 20537, CY-1678 Nicosia, Cyprus
| | - Kristin O’Sullivan
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Food Safety and Infection Biology, Section of Microbiology, Immunology and Parasitology, Post Box 8146 Dep, 0033 Oslo, Norway
| | - Sara Rodriguez-Mozaz
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003 Girona, Spain
| | - Thomas Schwartz
- Karlsruhe Institute of Technology (KIT)–Campus North, Institute of Functional Interfaces (IFG), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Hongjie Sheng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Henning Sørum
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Food Safety and Infection Biology, Section of Microbiology, Immunology and Parasitology, Post Box 8146 Dep, 0033 Oslo, Norway
| | - Robert D. Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - James M. Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | | | - Fiona Walsh
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina–Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 University of Helsinki, Finland
| | - Célia M. Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina–Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| |
Collapse
|
10
|
Nelson MM, Waldron CL, Bracht JR. Rapid molecular detection of macrolide resistance. BMC Infect Dis 2019; 19:144. [PMID: 30755177 PMCID: PMC6373131 DOI: 10.1186/s12879-019-3762-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 01/30/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Emerging antimicrobial resistance is a significant threat to human health. However, methods for rapidly diagnosing antimicrobial resistance generally require multi-day culture-based assays. Macrolide efflux gene A, mef(A), provides resistance against erythromycin and azithromycin and is known to be laterally transferred among a wide range of bacterial species. METHODS We use Recombinase Polymerase Assay (RPA) to detect the antimicrobial resistance gene mef(A) from raw lysates without nucleic acid purification. To validate these results we performed broth dilution assays to assess antimicrobial resistance to erythromycin and ampicillin (a negative control). RESULTS We validate the detection of mef(A) in raw lysates of Streptococcus pyogenes, S. pneumoniae, S. salivarius, and Enterococcus faecium bacterial lysates within 7-10 min of assay time. We show that detection of mef(A) accurately predicts real antimicrobial resistance assessed by traditional culture methods, and that the assay is robust to high levels of spiked-in non-specific nucleic acid contaminant. The assay was unaffected by single-nucleotide polymorphisms within divergent mef(A) gene sequences, strengthening its utility as a robust diagnostic tool. CONCLUSIONS This finding opens the door to implementation of rapid genomic diagnostics in a clinical setting, while providing researchers a rapid, cost-effective tool to track antibiotic resistance in both pathogens and commensal strains.
Collapse
Affiliation(s)
- Megan M. Nelson
- Department of Biology, American University, Washington, DC 20016 USA
| | | | - John R. Bracht
- Department of Biology, American University, Washington, DC 20016 USA
| |
Collapse
|
11
|
Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review. Molecules 2019; 24:molecules24010163. [PMID: 30609875 PMCID: PMC6337382 DOI: 10.3390/molecules24010163] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 12/28/2018] [Accepted: 12/29/2018] [Indexed: 12/12/2022] Open
Abstract
Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGenTM SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.
Collapse
|
12
|
Stedtfeld RD, Guo X, Stedtfeld TM, Sheng H, Williams MR, Hauschild K, Gunturu S, Tift L, Wang F, Howe A, Chai B, Yin D, Cole JR, Tiedje JM, Hashsham SA. Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements. FEMS Microbiol Ecol 2018; 94:5057470. [PMID: 30052926 PMCID: PMC7250373 DOI: 10.1093/femsec/fiy130] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/28/2018] [Indexed: 01/22/2023] Open
Abstract
The high-throughput antibiotic resistance gene (ARG) qPCR array, initially published in 2012, is increasingly used to quantify resistance and mobile determinants in environmental matrices. Continued utility of the array; however, necessitates improvements such as removing or redesigning questionable primer sets, updating targeted genes and coverage of available sequences. Towards this goal, a new primer design tool (EcoFunPrimer) was used to aid in identification of conserved regions of diverse genes. The total number of assays used for diverse genes was reduced from 91 old primer sets to 52 new primer sets, with only a 10% loss in sequence coverage. While the old and new array both contain 384 primer sets, a reduction in old primer sets permitted 147 additional ARGs and mobile genetic elements to be targeted. Results of validating the updated array with a mock community of strains resulted in over 98% of tested instances incurring true positive/negative calls. Common queries related to sensitivity, quantification and conventional data analysis (e.g. Ct cutoff value, and estimated genomic copies without standard curves) were also explored. A combined list of new and previously used primer sets is provided with a recommended set based on redesign of primer sets and results of validation.
Collapse
Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | - Xueping Guo
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | - Hongjie Sheng
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Maggie R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | - Kristin Hauschild
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Santosh Gunturu
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Leo Tift
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Fang Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa 50010, USA
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Daqiang Yin
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - James R Cole
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
| |
Collapse
|
13
|
Li Y, Yang L, Fu J, Yan M, Chen D, Zhang L. Genotyping and high flux sequencing of the bacterial pathogenic elements - integrons. Microb Pathog 2018; 116:22-25. [PMID: 29306009 DOI: 10.1016/j.micpath.2017.12.073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 10/31/2017] [Accepted: 12/30/2017] [Indexed: 01/09/2023]
Abstract
Regarded as a common genetic element responsible for horizontal gene transfer and wide spread of antimicrobial resistance among a large variety of bacteria, integrons are commonly distributed and considered as a determinant in the acquisition and evolution of virulence and antibiotic resistance. To date, the surveillances of integrons have been widely conducted in clinic, community even husbandry. For exact and accurate integron screening, as well as resistant cassettes, reliable monitoring methods is need. Current methods applied on integron screening are mainly conducted by the screening of integrases, followed by the detection of various gene cassettes inserted into integrons. PCR and PCR-related methods (such as RFLP) are mainly employed under such circumstances. Matured LAMP and Sequencing technology have lowered cost and dramatically increased throughput in integron screening and possessed the advantages in similarity analysis of mutated resistant cassettes. This review focused on the classification and characterization of integrons, antimicrobial resistance of integron and genotyping methods for integrons. In methodology, PCR, LAMP and Sequencing technology were mainly introduced for the screening of various classes' integrons and the detection of resistant gene cassettes. Staphylococcus, Pseudomonas and Enterococcus were selected as typical integron-positive clinical and environmental pathogens screened with three methods mentioned above. With the surveillance of the occurrence of integron and resistance gene cassettes conducted in South China, the review also summarized the occurrence, pathogenicity and virulence mediated by integrons.
Collapse
Affiliation(s)
- Yanmei Li
- Department of Haematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Ling Yang
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Jie Fu
- Department of Haematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Muxia Yan
- Department of Haematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Dingqiang Chen
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China.
| | - Li Zhang
- Department of Haematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China.
| |
Collapse
|
14
|
Chen DQ, Jiang YT, Feng DH, Wen SX, Su DH, Yang L. Integron mediated bacterial resistance and virulence on clinical pathogens. Microb Pathog 2017; 114:453-457. [PMID: 29241766 DOI: 10.1016/j.micpath.2017.12.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/09/2017] [Accepted: 12/09/2017] [Indexed: 02/07/2023]
Abstract
Integron was recognized as mobile elements responsible for the emergence and diffusion of antibiotic resistance, virulence and pathogenicity. The existence of resistant integron in pathogens may consequently lead to the increasing number of clinical failures in bacterial mediated diseases, as well as the expenses. In this study, a total of 22 clinical pathogens (including E. faecalis, S. aureus, K. pneumoniae, Enterobacter, P. aeruginosa and Acinetobacter) were subjected to the identification of class 1-class 3 integrons and drug resistant gene cassettes by high flux LAMP method. According to the results, the clinical isolates were screened as carrying class 1 integron with dfrA12-orfF-aadA2 cassette array, class 1 integron with dfrA17-aadA5 cassette array, class 1 integron with aadA2 cassette, class 1 integron with blaVIM2 cassette, class 1 and class 2 integron with dfrA1-sat1-aadA1 and dfrA12-orfF-aadA2 cassette arrays simultaneously, which was accordantly with the previous data. The optimized high flux LAMP assay was proceeded in water bath at 65 °C for 60 min and determined by naked eye, with the time consumption restricted within 2.5 h. Prior to conventional PCR method, the high flux LAMP assay was demonstrated as a highly-specific and highly-sensitive method. This study offered a valid LAMP method in resistance integrons detection for laboratory use, which was time-saving and easy-determination.
Collapse
Affiliation(s)
- Ding-Qiang Chen
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China; Centre for Translational Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Yue-Ting Jiang
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Dong-Hua Feng
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China; Centre for Translational Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Shu-Xian Wen
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China; Centre for Translational Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Dan-Hong Su
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Ling Yang
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China; Centre for Translational Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China.
| |
Collapse
|