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Nasser-Ali M, Aja-Macaya P, Conde-Pérez K, Trigo-Tasende N, Rumbo-Feal S, Fernández-González A, Bou G, Poza M, Vallejo JA. Emergence of Carbapenemase Genes in Gram-Negative Bacteria Isolated from the Wastewater Treatment Plant in A Coruña, Spain. Antibiotics (Basel) 2024; 13:194. [PMID: 38391580 PMCID: PMC10886265 DOI: 10.3390/antibiotics13020194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024] Open
Abstract
Wastewater treatment plants (WWTPs) are recognized as important niches of antibiotic-resistant bacteria that can be easily spread to the environment. In this study, we collected wastewater samples from the WWTP of A Coruña (NW Spain) from April 2020 to February 2022 to evaluate the presence of Gram-negative bacteria harboring carbapenemase genes. Bacteria isolated from wastewater were classified and their antimicrobial profiles were determined. In total, 252 Gram-negative bacteria carrying various carbapenemase genes were described. Whole-genome sequencing was conducted on 55 selected carbapenemase producing isolates using Oxford Nanopore technology. This study revealed the presence of a significant population of bacteria carrying carbapenemase genes in WWTP, which constitutes a public health problem due to their risk of dissemination to the environment. This emphasizes the usefulness of WWTP monitoring for combating antibiotic resistance. Data revealed the presence of different types of sequences harboring carbapenemase genes, such as blaKPC-2, blaGES-5, blaGES-6, blaIMP-11, blaIMP-28, blaOXA-24, blaOXA-48, blaOXA-58, blaOXA-217, and blaVIM-2. Importantly, the presence of the blaKPC-2 gene in wastewater, several months before any clinical case was detected in University Hospital of A Coruña, suggests that wastewater-based epidemiology can be used as an early warning system for the surveillance of antibiotic-resistant bacteria.
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Affiliation(s)
- Mohammed Nasser-Ali
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Pablo Aja-Macaya
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Kelly Conde-Pérez
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Noelia Trigo-Tasende
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Soraya Rumbo-Feal
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Ana Fernández-González
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Germán Bou
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
| | - Margarita Poza
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
- Microbiome and Health Group, Faculty of Sciences, Campus da Zapateira, 15071 A Coruna, Spain
| | - Juan A Vallejo
- Microbiology Research Group, Institute of Biomedical Research (INIBIC)-University Hospital of A Coruña (CHUAC)-Interdisciplinary Center for Chemistry and Biology (CICA)-University of A Coruña (UDC)-CIBER de Enfermedades Infecciosas (CIBERINFEC, ISCIII). Servicio de Microbiología, 3° planta, Edificio Sur, Hospital Universitario, As Xubias, 15006 A Coruna, Spain
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Gschwind R, Ugarcina Perovic S, Weiss M, Petitjean M, Lao J, Coelho LP, Ruppé E. ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics. Nucleic Acids Res 2023:7173762. [PMID: 37207327 DOI: 10.1093/nar/gkad384] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023] Open
Abstract
Metagenomics can be used to monitor the spread of antibiotic resistance genes (ARGs). ARGs found in databases such as ResFinder and CARD primarily originate from culturable and pathogenic bacteria, while ARGs from non-culturable and non-pathogenic bacteria remain understudied. Functional metagenomics is based on phenotypic gene selection and can identify ARGs from non-culturable bacteria with a potentially low identity shared with known ARGs. In 2016, the ResFinderFG v1.0 database was created to collect ARGs from functional metagenomics studies. Here, we present the second version of the database, ResFinderFG v2.0, which is available on the Center of Genomic Epidemiology web server (https://cge.food.dtu.dk/services/ResFinderFG/). It comprises 3913 ARGs identified by functional metagenomics from 50 carefully curated datasets. We assessed its potential to detect ARGs in comparison to other popular databases in gut, soil and water (marine + freshwater) Global Microbial Gene Catalogues (https://gmgc.embl.de). ResFinderFG v2.0 allowed for the detection of ARGs that were not detected using other databases. These included ARGs conferring resistance to beta-lactams, cycline, phenicol, glycopeptide/cycloserine and trimethoprim/sulfonamide. Thus, ResFinderFG v2.0 can be used to identify ARGs differing from those found in conventional databases and therefore improve the description of resistomes.
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Affiliation(s)
- Rémi Gschwind
- University of Paris Cité, INSERM UMR 1137 IAME, F-75018Paris, France
| | - Svetlana Ugarcina Perovic
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai200433, China
| | - Maja Weiss
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby 2800, Denmark
| | - Marie Petitjean
- University of Paris Cité, INSERM UMR 1137 IAME, F-75018Paris, France
| | - Julie Lao
- University of Paris Cité, INSERM UMR 1137 IAME, F-75018Paris, France
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai200433, China
| | - Etienne Ruppé
- University of Paris Cité, INSERM UMR 1137 IAME, F-75018Paris, France
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3
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Tang L, Shen W, Zhang Z, Zhang J, Wang G, Xiang L, She J, Hu X, Zou G, Zhu B, Zhou Y. Whole-Genome Analysis of Two Copies of bla NDM-1 Gene Carrying Acinetobacter johnsonii Strain Acsw19 Isolated from Sichuan, China. Infect Drug Resist 2020; 13:855-865. [PMID: 32273730 PMCID: PMC7106997 DOI: 10.2147/idr.s236200] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 03/03/2020] [Indexed: 12/14/2022] Open
Abstract
Purpose To characterize the genetic feature of the carbapenems resistant Acinetobacter johnsonii strain Acsw19 isolated from municipal sludge. This strain was found to carry two copies of bla NDM-1, cmlB1-like gene, and bla OXA-211-like gene along with other 8 antimicrobial resistance genes, 3 plasmids, 15 genomic islands and 8 prophages. Methods A carbapenem-resistant Acinetobacter johnsonii strain Acsw19 isolated from municipal sludge was subjected to whole-genome sequencing (WGS) via the PacBio and Illumina MiSeq platforms. Thereafter, the characteristic was analyzed by a series of bioinformatics software. Results The results showed that the genome of Acsw19 was consisted of a 3,433,749 bp circular chromosome and 3 circular plasmids, pAcsw19-1 (11,161 bp), pAcsw19-2 (351,885 bp) and pAcsw19-3 (38,391bp), respectively. Resistome analysis showed that Acsw19 carried 12 antimicrobial resistance genes, including 6 [cmlB1-like, bla NDM-1, bla OXA-58, aph (3')-VIa, msr(E) and mph(E)] in the plasmid pAcsw19-2 and 6 (bla OXA-211-like, bla NDM-1, aph(3")-Ib, aph(6)-Id, sul2, and floR) in the chromosome genome. Specifically, the cmlB1-like gene shared 86.33%, 71.7% and 71.9% similarities with the cmlB1, cmlA4 and cmlA8 gene, and the bla OXA-211-like gene shared 94.4%, 95.39% and 96.36% similarities with bla OXA-211, bla OXA-643 and bla OXA-652, at the nucleotide level, respectively. Phylogenetic analysis showed that the bla OXA-211-like gene and cmlB1-like gene had the closest evolutionary relationship with bla OXA-643 and cmlB1, respectively. These results indicated that the bla OXA-211-like and cmlB1-like genes identified in the current study should be the novel variant resistance genes. Conclusion Carrying of two copies of bla NDM-1, cmlB1-like, bla OXA-211-like and along with other 8 antimicrobial resistance genes, 3 plasmids, 15 genomic islands and 8 prophages Acinetobacter johnsonii strain might increase the possibility of spreading of resistance genes.
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Affiliation(s)
- Lingtong Tang
- Department of Clinical Laboratory, The People's Hospital of Gao County, Sichuan 644000, People's Republic of China.,Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Wei Shen
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Department of Clinical Laboratory, The First People's Hospital of Yibin, Yibin 644000, Sichuan, People's Republic of China
| | - Zhikun Zhang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Jingping Zhang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Guangxi Wang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Li Xiang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Junping She
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Xiaoyan Hu
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Guoyuan Zou
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Science, Beijing, People's Republic of China
| | - Baoli Zhu
- Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yingshun Zhou
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
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4
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Gaviria-Figueroa A, Preisner EC, Hoque S, Feigley CE, Norman RS. Emission and dispersal of antibiotic resistance genes through bioaerosols generated during the treatment of municipal sewage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 686:402-412. [PMID: 31181526 DOI: 10.1016/j.scitotenv.2019.05.454] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/27/2019] [Accepted: 05/30/2019] [Indexed: 05/22/2023]
Abstract
Wastewater treatment plants act as socio-ecological couplers through the concentration, treatment, and subsequent environmental release of sewage collected from surrounding communities and are often considered hotspots for antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). While studies have identified the release of ARB/ARGs in treated liquid sewage, little is known about potential dispersal through wastewater bioaerosol emissions. The aim of this study was to better define the contribution of WWTP bioaerosols to potential environmental distribution of ARB/ARGs. Bioaerosols were collected immediately upwind and downwind from the aeration tanks of a municipal wastewater treatment plant and liquid sludge samples were obtained from the aeration tanks. From the bioaerosol and liquid samples, qPCR assays identified 44 ARGs that confer resistance to a wide range of antibiotics. Comparison of the ARG profiles across samples showed that the downwind bioaerosol profile was 68% similar to the profile found in liquid sludge samples. Community 16S rRNA gene sequencing also showed that downwind bioaerosols had similar taxonomic profiles as those generated from liquid sludge while the upwind profiles showed a distinct difference. Preliminary ARG dispersion modeling estimated an ARG emission rate of ~10,620 genes per hour from the liquid sludge and indicated that the bioaerosols have the potential to be carried kilometers away from the WWTP source based on wind speed. The overall results from this study suggest that bioaerosols generated during WWTP processes can aid in the emission and dispersal of bacteria and ARGs, resulting in a possible route of human exposure and deposition into surrounding environments.
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Affiliation(s)
- Andrés Gaviria-Figueroa
- Department of Environmental Health Sciences, University of South Carolina, 921 Assembly Street, Columbia, SC 29208, United States of America
| | - Eva C Preisner
- Department of Environmental Health Sciences, University of South Carolina, 921 Assembly Street, Columbia, SC 29208, United States of America
| | - Shamia Hoque
- Department of Civil and Environmental Engineering, University of South Carolina, 300 Main Street, Columbia, SC 29208, United States of America
| | - Charles E Feigley
- Department of Environmental Health Sciences, University of South Carolina, 921 Assembly Street, Columbia, SC 29208, United States of America
| | - R Sean Norman
- Department of Environmental Health Sciences, University of South Carolina, 921 Assembly Street, Columbia, SC 29208, United States of America.
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5
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Zumstein MT, Helbling DE. Biotransformation of antibiotics: Exploring the activity of extracellular and intracellular enzymes derived from wastewater microbial communities. WATER RESEARCH 2019; 155:115-123. [PMID: 30836263 DOI: 10.1016/j.watres.2019.02.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 05/27/2023]
Abstract
Evaluating the activity of extracellular and intracellular enzymes derived from wastewater microbial communities is essential to improve our fundamental understanding of micropollutant removal during wastewater treatment. To study biotransformations with respect to enzyme biogeography, we developed a method to separate soluble extracellular, extracellular polymeric substance (EPS)-bound, and intracellular enzymes from wastewater microbial communities and assessed the protease and peptidase activity of the resulting enzyme pools. We also evaluated the biotransformation of six antibiotics (amoxicillin, ampicillin, clindamycin, daptomycin, linezolid, and vancomycin) in each enzyme pool because we expect that the kinetics, pathways, and biogeography of antibiotic biotransformations influence the selection of antibiotic resistance within wastewater microbial communities and in downstream environments. Our results demonstrated that biotransformation rate constants varied among the tested antibiotics, and that the observed rank order was consistent across three wastewater treatment plants. Importantly, many of the observed biotransformations eliminated the functional groups associated with antibiotic activity. Furthermore, we found that β-lactam hydrolysis and daptomycin hydrolysis were catalyzed by enzymes extracted from the EPS, while none of the tested antibiotics were biotransformed by soluble extracellular enzymes. Finally, our results demonstrated that the number of enzyme-catalyzed antibiotic transformations was larger for intracellular than for extracellular enzymes. Together, this study provides novel insights on the kinetics, pathways, and biogeography of antibiotic biotransformations performed by wastewater microbial communities and can be used to inform pathway prediction or the development of biodegradable chemicals.
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Affiliation(s)
- Michael T Zumstein
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA.
| | - Damian E Helbling
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA
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6
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Lim MY, Cho Y, Rho M. Diverse Distribution of Resistomes in the Human and Environmental Microbiomes. Curr Genomics 2018; 19:701-711. [PMID: 30532649 PMCID: PMC6225452 DOI: 10.2174/1389202919666180911130845] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 04/14/2018] [Accepted: 09/03/2018] [Indexed: 11/22/2022] Open
Abstract
The routine therapeutic use of antibiotics has caused resistance genes to be disseminated across microbial populations. In particular, bacterial strains having antibiotic resistance genes are frequently observed in the human microbiome. Moreover, multidrug-resistant pathogens are now widely spread, threatening public health. Such genes are transferred and spread among bacteria even in different environments. Advances in high throughput sequencing technology and computational algorithms have accelerated investigation into antibiotic resistance genes of bacteria. Such studies have revealed that the antibiotic resistance genes are located close to the mobility-associated genes, which promotes their dissemination. An increasing level of information on genomic sequences of resistome should expedite research on drug-resistance in our body and environment, thereby contributing to the development of public health policy. In this review, the high prevalence of antibiotic resistance genes and their exchange in the human and environmental microbiome is discussed with respect to the genomic contents. The relationships among diverse resistomes, related bacterial species, and the antibiotics are reviewed. In addition, recent advances in bioinformatics approaches to investigate such relationships are discussed.
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Affiliation(s)
- Mi Young Lim
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
| | - Youna Cho
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
| | - Mina Rho
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
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7
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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.
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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
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8
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Tehrani AH, Gilbride KA. A closer look at the antibiotic-resistant bacterial community found in urban wastewater treatment systems. Microbiologyopen 2018; 7:e00589. [PMID: 29484827 PMCID: PMC6079166 DOI: 10.1002/mbo3.589] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 12/13/2017] [Accepted: 12/22/2017] [Indexed: 12/12/2022] Open
Abstract
The conventional biological treatment process can provide a favorable environment for the maintenance and dissemination of antibiotic‐resistant bacteria and the antibiotic resistance genes (ARG) they carry. This study investigated the occurrence of antibiotic resistance in three wastewater treatment plants (WWTP) to determine the role they play in the dissemination of ARGs. Bacterial isolates resistant to tetracycline were collected, and tested against eight antibiotics to determine their resistance profiles and the prevalence of multiple antibiotic resistance. It was found that bacteria resistant to tetracycline were more likely to display resistance to multiple antibiotics compared to those isolates that were not tetracycline resistant. Polymerase chain reaction (PCR) was used to identify the tetracycline resistance determinants present within the bacterial communities of the WWTPs and receiving waters, and it was found that ARGs may not be released from the treatment process. Identification of isolates showed that there was a large diversity of species in both the tetracycline‐resistant and tetracycline‐sensitive populations and that the two groups were significantly different in composition. Antibiotic resistance profiles of each population showed that a large diversity of resistance patterns existed within genera suggesting that transmission of ARG may progress by both horizontal gene and vertical proliferation.
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Affiliation(s)
- Amir H Tehrani
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada
| | - Kimberley A Gilbride
- Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada.,Ryerson Urban Water, Ryerson University, Toronto, ON, Canada
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9
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Burch TR, Sadowsky MJ, LaPara TM. Effect of Different Treatment Technologies on the Fate of Antibiotic Resistance Genes and Class 1 Integrons when Residual Municipal Wastewater Solids are Applied to Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:14225-14232. [PMID: 29148730 DOI: 10.1021/acs.est.7b04760] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Residual wastewater solids are a significant reservoir of antibiotic resistance genes (ARGs). While treatment technologies can reduce ARG levels in residual wastewater solids, the effects of these technologies on ARGs in soil during subsequent land-application are unknown. In this study we investigated the use of numerous treatment technologies (air drying, aerobic digestion, mesophilic anaerobic digestion, thermophilic anaerobic digestion, pasteurization, and alkaline stabilization) on the fate of ARGs and class 1 integrons in wastewater solids-amended soil microcosms. Six ARGs [erm(B), qnrA, sul1, tet(A), tet(W), and tet(X)], the integrase gene of class 1 integrons (intI1), and 16S rRNA genes were quantified using quantitative polymerase chain reaction. The quantities of ARGs and intI1 decreased in all microcosms, but thermophilic anaerobic digestion, alkaline stabilization, and pasteurization led to the most extensive decay of ARGs and intI1, often to levels similar to that of the control microcosms to which no wastewater solids had been applied. In contrast, the rates by which ARGs and intI1 declined using the other treatment technologies were generally similar, typically varying by less than 2 fold. These results demonstrate that wastewater solids treatment technologies can be used to decrease the persistence of ARGs and intI1 during their subsequent application to soil.
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Affiliation(s)
- Tucker R Burch
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Michael J Sadowsky
- Biotechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
- Department of Soil, Water, and Climate, University of Minnesota , St. Paul, Minnesota 55108, United States
- Department of Plant and Microbial Biology, University of Minnesota , St. Paul, Minnesota 55108, United States
| | - Timothy M LaPara
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
- Biotechnology Institute, University of Minnesota , St. Paul, Minnesota 55108, United States
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10
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Impact of point sources on antibiotic resistance genes in the natural environment: a systematic review of the evidence. Anim Health Res Rev 2017; 18:112-127. [DOI: 10.1017/s146625231700007x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractThere is a growing concern about the role of the environment in the dissemination of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG). In this systematic review, we summarize evidence for increases of ARG in the natural environment associated with potential sources of ARB and ARG such as agricultural facilities and wastewater treatment plants. A total of 5247 citations were identified, including studies that ascertained both ARG and ARB outcomes. All studies were screened for relevance to the question and methodology. This paper summarizes the evidence only for those studies with ARG outcomes (n= 24). Sixteen studies were at high (n= 3) or at unclear (n= 13) risk of bias in the estimation of source effects due to lack of information or failure to control for confounders. Statistical methods were used in nine studies; three studies assessed the effect of multiple sources using modeling approaches, and none reported effect measures. Most studies reported higher ARG concentration downstream/near the source, but heterogeneous findings hindered making any sound conclusions. To quantify increases of ARG in the environment due to specific point sources, there is a need for studies that emphasize analytic or design control of confounding, and that provide effect measure estimates.
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Xu YB, Hou MY, Li YF, Huang L, Ruan JJ, Zheng L, Qiao QX, Du QP. Distribution of tetracycline resistance genes and AmpC β-lactamase genes in representative non-urban sewage plants and correlations with treatment processes and heavy metals. CHEMOSPHERE 2017; 170:274-281. [PMID: 28012421 DOI: 10.1016/j.chemosphere.2016.12.027] [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: 08/24/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 05/21/2023]
Abstract
The mixed development of livestock breeding and industry in non-urban zones is a very general phenomenon in China. Distribution of antibiotic resistance genes (ARGs) in non-urban sewage treatment systems has not been paid enough attentions. In this study, eleven tetracycline resistance genes (tetA, tetB, tetC, tetE, tetG, tetL, tetM, tetO, tetQ, tetS and tetX), four AmpC β-lactamase genes (EBC, MOX, FOX and CIT) and four heavy metals (Cu, Zn, Cd and Pb) were detected and analyzed in four non-urban sewage plants with different sewage sources and different treatment processes in Guangzhou. The results showed that tetA and tetC were the most prevalent tetracycline resistance genes with the same detection frequency of 85% and EBC was the most prevalent AmpC β-lactamase gene with a detection frequency of 75%. The relative abundance of tetracycline resistance genes was approximately 1.6 orders of magnitudes higher than that of AmpC β-lactamase genes in all samples. A/O was the most effective process for the non-urban sewage plant receiving industrial or agricultural wastewater. Sedimentation was the most key process to eliminate ARGs from liquid phase. Most ARGs were carried in excess sludge rather than effluent. Significant correlation was found between the tet gene and Zn (r = 0.881, p < 0.01), followed by the AmpC gene and Cu (r = 0.847, p < 0.01), the tet gene and Cu (r = 0.714, p < 0.05). Therefore, the pollution of ARGs in the sewage treatment systems of non-urban zones co-polluted by heavy metals should be paid more attentions.
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Affiliation(s)
- Yan-Bin Xu
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
| | - Mao-Yu Hou
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Ya-Fei Li
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Lu Huang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Jing-Jing Ruan
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Li Zheng
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Qing-Xia Qiao
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Qing-Ping Du
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
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Aubertheau E, Stalder T, Mondamert L, Ploy MC, Dagot C, Labanowski J. Impact of wastewater treatment plant discharge on the contamination of river biofilms by pharmaceuticals and antibiotic resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 579:1387-1398. [PMID: 27913024 DOI: 10.1016/j.scitotenv.2016.11.136] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/18/2016] [Accepted: 11/19/2016] [Indexed: 06/06/2023]
Abstract
Wastewater treatment plants (WWTPs) are one of the main sources of pharmaceutical residue in surface water. Epilithic biofilms were collected downstream from 12 WWTPs of various types and capacities to study the impacts of their discharge through the changes in biofilm composition (compared to a corresponding upstream biofilm) in terms of pharmaceutical concentrations and bacterial community modifications (microbial diversity and resistance integrons). The biofilm is a promising indicator to evaluate the impacts of WWTPs on the surrounding aquatic environment. Indeed, the use of biofilms reveals contamination hot spots. All of the downstream biofilms present significant concentrations (up to 965ng/g) of five to 11 pharmaceuticals (among the 12 analysed). Moreover, the exposition to the discharge point increases the presence of resistance integrons (three to 31 fold for Class 1) and modifies the diversity of the bacterial communities (for example cyanobacteria). The present study confirms that the discharge from WWTPs has an impact on the aquatic environment.
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Affiliation(s)
- Elodie Aubertheau
- University of Poitiers, UMR CNRS 7285 IC2MP, Department of Water and Geochemistry, ENSIP, 1 Rue Marcel Doré, TSA 41105, 86073 Poitiers Cedex, France
| | - Thibault Stalder
- University of Limoges, INSERM UMR-S1092, Faculté de Médecine, 2 rue du Docteur Marcland, 87065 Limoges Cedex, France; University of Limoges, GRESE EA4330, ENSIL, 16 rue Atlantis, 87068 Limoges Cedex, France
| | - Leslie Mondamert
- University of Poitiers, UMR CNRS 7285 IC2MP, Department of Water and Geochemistry, ENSIP, 1 Rue Marcel Doré, TSA 41105, 86073 Poitiers Cedex, France
| | - Marie-Cécile Ploy
- University of Limoges, INSERM UMR-S1092, Faculté de Médecine, 2 rue du Docteur Marcland, 87065 Limoges Cedex, France
| | - Christophe Dagot
- University of Limoges, INSERM UMR-S1092, Faculté de Médecine, 2 rue du Docteur Marcland, 87065 Limoges Cedex, France; University of Limoges, GRESE EA4330, ENSIL, 16 rue Atlantis, 87068 Limoges Cedex, France
| | - Jérôme Labanowski
- University of Poitiers, UMR CNRS 7285 IC2MP, Department of Water and Geochemistry, ENSIP, 1 Rue Marcel Doré, TSA 41105, 86073 Poitiers Cedex, France.
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Dos Santos DFK, Istvan P, Quirino BF, Kruger RH. Functional Metagenomics as a Tool for Identification of New Antibiotic Resistance Genes from Natural Environments. MICROBIAL ECOLOGY 2017; 73:479-491. [PMID: 27709246 DOI: 10.1007/s00248-016-0866-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 09/19/2016] [Indexed: 05/26/2023]
Abstract
Antibiotic resistance has become a major concern for human and animal health, as therapeutic alternatives to treat multidrug-resistant microorganisms are rapidly dwindling. The problem is compounded by low investment in antibiotic research and lack of new effective antimicrobial drugs on the market. Exploring environmental antibiotic resistance genes (ARGs) will help us to better understand bacterial resistance mechanisms, which may be the key to identifying new drug targets. Because most environment-associated microorganisms are not yet cultivable, culture-independent techniques are essential to determine which organisms are present in a given environmental sample and allow the assessment and utilization of the genetic wealth they represent. Metagenomics represents a powerful tool to achieve these goals using sequence-based and functional-based approaches. Functional metagenomic approaches are particularly well suited to the identification new ARGs from natural environments because, unlike sequence-based approaches, they do not require previous knowledge of these genes. This review discusses functional metagenomics-based ARG research and describes new possibilities for surveying the resistome in environmental samples.
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Affiliation(s)
| | - Paula Istvan
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, Brazil
| | - Betania Ferraz Quirino
- Embrapa-Agroenergia, Brasília, DF, Brazil
- Universidade Católica de Brasília, Genomic Sciences and Biotechnology Program, Brasília, DF, Brazil
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Wallace JC, Port JA, Smith MN, Faustman EM. FARME DB: a functional antibiotic resistance element database. Database (Oxford) 2017; 2017:baw165. [PMID: 28077567 PMCID: PMC5225399 DOI: 10.1093/database/baw165] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 11/22/2016] [Accepted: 11/28/2016] [Indexed: 01/23/2023]
Abstract
Antibiotic resistance (AR) is a major global public health threat but few resources exist that catalog AR genes outside of a clinical context. Current AR sequence databases are assembled almost exclusively from genomic sequences derived from clinical bacterial isolates and thus do not include many microbial sequences derived from environmental samples that confer resistance in functional metagenomic studies. These environmental metagenomic sequences often show little or no similarity to AR sequences from clinical isolates using standard classification criteria. In addition, existing AR databases provide no information about flanking sequences containing regulatory or mobile genetic elements. To help address this issue, we created an annotated database of DNA and protein sequences derived exclusively from environmental metagenomic sequences showing AR in laboratory experiments. Our Functional Antibiotic Resistant Metagenomic Element (FARME) database is a compilation of publically available DNA sequences and predicted protein sequences conferring AR as well as regulatory elements, mobile genetic elements and predicted proteins flanking antibiotic resistant genes. FARME is the first database to focus on functional metagenomic AR gene elements and provides a resource to better understand AR in the 99% of bacteria which cannot be cultured and the relationship between environmental AR sequences and antibiotic resistant genes derived from cultured isolates.Database URL: http://staff.washington.edu/jwallace/farme.
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Affiliation(s)
- James C. Wallace
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Jesse A. Port
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Marissa N. Smith
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Elaine M. Faustman
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
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Sun Y, Shen YX, Liang P, Zhou J, Yang Y, Huang X. Multiple antibiotic resistance genes distribution in ten large-scale membrane bioreactors for municipal wastewater treatment. BIORESOURCE TECHNOLOGY 2016; 222:100-106. [PMID: 27716561 DOI: 10.1016/j.biortech.2016.09.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/25/2016] [Accepted: 09/28/2016] [Indexed: 05/28/2023]
Abstract
Wastewater treatment plants are thought to be potential reservoirs of antibiotic resistance genes. In this study, GeoChip was used for analyzing multiple antibiotic resistance genes, including four multidrug efflux system gene groups and three β-lactamase genes in ten large-scale membrane bioreactors (MBRs) for municipal wastewater treatment. Results revealed that the diversity of antibiotic genes varied a lot among MBRs, but about 40% common antibiotic resistance genes were existent. The average signal intensity of each antibiotic resistance group was similar among MBRs, nevertheless the total abundance of each group varied remarkably and the dominant resistance gene groups were different in individual MBR. The antibiotic resistance genes majorly derived from Proteobacteria and Actinobacteria. Further study indicated that TN, TP and COD of influent, temperature and conductivity of mixed liquor were significant (P<0.05) correlated to the multiple antibiotic resistance genes distribution in MBRs.
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Affiliation(s)
- Yanmei Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Yue-Xiao Shen
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Peng Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China; Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
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16
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Borgogna TR, Borgogna JL, Mielke JA, Brown CJ, Top EM, Botts RT, Cummings DE. High Diversity of CTX-M Extended-Spectrum β-Lactamases in Municipal Wastewater and Urban Wetlands. Microb Drug Resist 2015; 22:312-20. [PMID: 26670020 DOI: 10.1089/mdr.2015.0197] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The CTX-M-type extended-spectrum β-lactamases (ESBLs) present a serious public health threat as they have become nearly ubiquitous among clinical gram-negative pathogens, particularly the enterobacteria. To aid in the understanding and eventual control of the spread of such resistance genes, we sought to determine the diversity of CTX-M ESBLs not among clinical isolates, but in the environment, where weaker and more diverse selective pressures may allow greater enzyme diversification. This was done by examining the CTX-M diversity in municipal wastewater and urban coastal wetlands in southern California, United States, by Sanger sequencing of polymerase chain reaction amplicons. Of the five known CTX-M phylogroups (1, 2, 8, 9, and 25), only genes from groups 1 and 2 were detected in both wastewater treatment plants (WWTPs), and group 1 genes were also detected in one of the two wetlands after a winter rain. The highest relative abundance of blaCTX-M group 1 genes was in the sludge of one WWTP (2.1 × 10(-4) blaCTX-M copies/16S rRNA gene copy). Gene libraries revealed surprisingly high nucleotide sequence diversity, with 157 new variants not found in GenBank, representing 99 novel amino acid sequences. Our results indicate that the resistomes of WWTPs and urban wetlands contain diverse blaCTX-M ESBLs, which may constitute a mobile reservoir of clinically relevant resistance genes.
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Affiliation(s)
- Timothy R Borgogna
- 1 Department of Biology, Point Loma Nazarene University , San Diego, California
| | | | - Jenna A Mielke
- 1 Department of Biology, Point Loma Nazarene University , San Diego, California
| | - Celeste J Brown
- 2 Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho , Moscow, Idaho
| | - Eva M Top
- 2 Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho , Moscow, Idaho
| | - Ryan T Botts
- 3 Department of Mathematics, Information, and Computer Sciences, Point Loma Nazarene University , San Diego, California
| | - David E Cummings
- 1 Department of Biology, Point Loma Nazarene University , San Diego, California
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17
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Antibiotic Resistance Elements in Wastewater Treatment Plants: Scope and Potential Impacts. THE HANDBOOK OF ENVIRONMENTAL CHEMISTRY 2015. [DOI: 10.1007/698_2015_361] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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18
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Sun Y, Shen YX, Liang P, Zhou J, Yang Y, Huang X. Linkages between microbial functional potential and wastewater constituents in large-scale membrane bioreactors for municipal wastewater treatment. WATER RESEARCH 2014; 56:162-71. [PMID: 24675272 DOI: 10.1016/j.watres.2014.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 02/11/2014] [Accepted: 03/02/2014] [Indexed: 05/17/2023]
Abstract
Large-scale membrane bioreactors (MBRs) have been widely used for the municipal wastewater treatment, whose performance relies on microbial communities of activated sludge. Nevertheless, microbial functional structures in MBRs remain little understood. To gain insight into functional genes and their steering environmental factors, we adopted GeoChip, a high-throughput microarray-based tool, to examine microbial genes in four large-scale, in-operation MBRs located in Beijing, China. The results revealed substantial microbial gene heterogeneity (43.7-85.1% overlaps) among different MBRs. Mantel tests indicated that microbial nutrient cycling genes were significantly (P < 0.05) correlated to influent COD, [Formula: see text] -N, TP or sulfate, which signified the importance of microbial mediation of wastewater constituent removal. In addition, functional genes shared by all four MBRs contained a large number of genes involved in antibiotics resistance, metal resistance and organic remediation, suggesting that they were required for degradation or resistance to toxic compounds in wastewater. The linkages between microbial functional structures and environmental variables were also unveiled by the finding of hydraulic retention time, influent COD, [Formula: see text] -N, mixed liquid temperature and humic substances as major factors shaping microbial communities. Together, the results presented demonstrate the utility of GeoChip-based microarray approach in examining microbial communities of wastewater treatment plants and provide insights into the forces driving important processes of element cycling.
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Affiliation(s)
- Yanmei Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Yue-xiao Shen
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Peng Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China; Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
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19
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Burch TR, Sadowsky MJ, LaPara TM. Fate of antibiotic resistance genes and class 1 integrons in soil microcosms following the application of treated residual municipal wastewater solids. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:5620-5627. [PMID: 24762092 DOI: 10.1021/es501098g] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Substantial quantities of antibiotic resistance genes (ARGs) are discharged with treated residual municipal wastewater solids and subsequently applied to soil. The objective of this work was to determine the decay rates for ARGs and class 1 integrons following simulated land application of treated wastewater solids. Treated residual solids from two full-scale treatment plants were applied to sets of triplicate soil microcosms in two independent experiments. Experiment 1 investigated loading rates of 20, 40, and 100 g kg(-1) of residual solids to a sandy soil, while experiment 2 investigated a loading rate of 40 g kg(-1) to a silty-loamy soil. Five ARGs (erm(B), sul1, tet(A), tet(W), and tet(X)), the integrase of class 1 integrons (intI1), 16S rRNA genes, 16S rRNA genes of all Bacteroides spp., and 16S rRNA genes of human-specific Bacteroides spp. were quantified using real-time polymerase chain reaction. ARGs and intI1 quantities declined in most microcosms, with statistically significant (P < 0.05) half-lives varying between 13 d (erm(B), experiment 1, 100 g kg(-1)) and 81 d (intI1, experiment 1, 40 g kg(-1)). These kinetic rates were much slower than have been previously reported for unit operations used to treat wastewater solids (e.g., anaerobic digestion). This research suggests that the design and operation of municipal wastewater treatment facilities with the explicit goal of mitigating the release of ARGs should focus on using technologies within the treatment facility, rather than depending on attenuation subsequent to land application.
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Affiliation(s)
- Tucker R Burch
- Department of Civil Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
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Abstract
Antibiotic resistance is a major threat to human health and well-being. To effectively combat this problem we need to understand the range of different resistance genes that allow bacteria to resist antibiotics. To do this the whole microbiota needs to be investigated. As most bacteria cannot be cultivated in the laboratory, the reservoir of antibiotic resistance genes in the non-cultivatable majority remains relatively unexplored. Currently the only way to study antibiotic resistance in these organisms is to use metagenomic approaches. Furthermore, the only method that does not require any prior knowledge about the resistance genes is functional metagenomics, which involves expressing genes from metagenomic clones in surrogate hosts. In this review the methods and limitations of functional metagenomics to isolate new antibiotic resistance genes and the mobile genetic elements that mediate their spread are explored.
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Affiliation(s)
- Peter Mullany
- Department of Microbial Diseases; UCL Eastman Dental Institute; University College London; London, UK
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21
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Quantitative and qualitative impact of hospital effluent on dissemination of the integron pool. ISME JOURNAL 2013; 8:768-77. [PMID: 24152716 DOI: 10.1038/ismej.2013.189] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 09/19/2013] [Accepted: 09/22/2013] [Indexed: 01/19/2023]
Abstract
There is increasing evidence that human activity, and especially the resulting effluent, has a major role in the dissemination of bacterial antibiotic-resistance determinants in the environment. Hospitals are the major antibiotic consumers and thus facilitate the spread of antibiotic resistance. Questions are increasingly being raised about the management of hospital effluents, but their involvement in antibiotic-resistance dissemination has never been assessed. Integrons are a paradigm of genetic transfer between the environmental resistome and both commensal and pathogenic bacteria. In order to assess the impact of hospital activities on antibiotic-resistance dissemination in the environment, we monitored integrons and their gene cassettes in hospital effluents, and their release in the environment. We found that bacterial communities present in a hospital effluent contained a high proportion of integrons. In terms of both their gene cassette diversity and gene cassette arrays, the urban effluent and municipal wastewater treatment plant (WWTP) influent were most similar, whereas the hospital effluent and recirculation sludge exhibited very specific patterns. We found that anthropogenic activities led to the release of abundant integrons and antibiotic-resistance gene cassettes, but we observed no specific impact of hospital activities on the receiving environment. Furthermore, although the WWTP did not reduce the normalized integron copy number, it reduced the diversity of gene cassette arrays contained in the raw wastewater, underlining the effect of the biological treatment on the anthropogenic integron pool arriving at the WWTP.
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Burch TR, Sadowsky MJ, LaPara TM. Air-drying beds reduce the quantities of antibiotic resistance genes and class 1 integrons in residual municipal wastewater solids. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:9965-9971. [PMID: 23909386 DOI: 10.1021/es4024749] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This study investigated whether air-drying beds reduce antibiotic resistance gene (ARG) concentrations in residual municipal wastewater solids. Three laboratory-scale drying beds were operated for a period of nearly 100 days. Real-time PCR was used to quantify 16S rRNA genes, 16S rRNA genes specific to fecal bacteria (AllBac) and human fecal bacteria (HF183), the integrase gene of class 1 integrons (intI1), and five ARGs representing a cross-section of antibiotic classes and resistance mechanisms (erm(B), sul1, tet(A), tet(W), and tet(X)). Air-drying beds were capable of reducing all gene target concentrations by 1 to 5 orders of magnitude, and the nature of this reduction was consistent with both a net decrease in the number of bacterial cells and a lack of selection within the microbial community. Half-lives varied between 1.5 d (HF183) and 5.4 d (tet(X)) during the first 20 d of treatment. After the first 20 d of treatment, however, half-lives varied between 8.6 d (tet(X)) and 19.3 d (AllBac), and 16S rRNA gene, intI1, and sul1 concentrations did not change (P > 0.05). These results demonstrate that air-drying beds can reduce ARG and intI1 concentrations in residual municipal wastewater solids within timeframes typical of operating practices.
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MESH Headings
- Anti-Bacterial Agents/analysis
- Anti-Bacterial Agents/pharmacology
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/metabolism
- Bacterial Proteins/analysis
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Drug Resistance, Microbial
- Integrons
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
- RNA, Ribosomal, 16S/metabolism
- Real-Time Polymerase Chain Reaction
- Waste Disposal, Fluid/methods
- Wastewater/analysis
- Wastewater/microbiology
- Water Pollutants, Chemical/analysis
- Water Pollutants, Chemical/pharmacology
- Water Pollution, Chemical/prevention & control
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Affiliation(s)
- Tucker R Burch
- Department of Civil Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
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Environmental and Public Health Implications of Water Reuse: Antibiotics, Antibiotic Resistant Bacteria, and Antibiotic Resistance Genes. Antibiotics (Basel) 2013; 2:367-99. [PMID: 27029309 PMCID: PMC4790270 DOI: 10.3390/antibiotics2030367] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/19/2013] [Accepted: 07/24/2013] [Indexed: 12/21/2022] Open
Abstract
Water scarcity is a global problem, and is particularly acute in certain regions like Africa, the Middle East, as well as the western states of America. A breakdown on water usage revealed that 70% of freshwater supplies are used for agricultural irrigation. The use of reclaimed water as an alternative water source for agricultural irrigation would greatly alleviate the demand on freshwater sources. This paradigm shift is gaining momentum in several water scarce countries like Saudi Arabia. However, microbial problems associated with reclaimed water may hinder the use of reclaimed water for agricultural irrigation. Of particular concern is that the occurrence of antibiotic residues in the reclaimed water can select for antibiotic resistance genes among the microbial community. Antibiotic resistance genes can be associated with mobile genetic elements, which in turn allow a promiscuous transfer of resistance traits from one bacterium to another. Together with the pathogens that are present in the reclaimed water, antibiotic resistant bacteria can potentially exchange mobile genetic elements to create the “perfect microbial storm”. Given the significance of this issue, a deeper understanding of the occurrence of antibiotics in reclaimed water, and their potential influence on the selection of resistant microorganisms would be essential. In this review paper, we collated literature over the past two decades to determine the occurrence of antibiotics in municipal wastewater and livestock manure. We then discuss how these antibiotic resistant bacteria may impose a potential microbial risk to the environment and public health, and the knowledge gaps that would have to be addressed in future studies. Overall, the collation of the literature in wastewater treatment and agriculture serves to frame and identify potential concerns with respect to antibiotics, antibiotic resistant bacteria, and antibiotic resistance genes in reclaimed water.
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Burch TR, Sadowsky MJ, Lapara TM. Aerobic digestion reduces the quantity of antibiotic resistance genes in residual municipal wastewater solids. Front Microbiol 2013; 4:17. [PMID: 23407455 PMCID: PMC3569665 DOI: 10.3389/fmicb.2013.00017] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 01/24/2013] [Indexed: 11/13/2022] Open
Abstract
Numerous initiatives have been undertaken to circumvent the problem of antibiotic resistance, including the development of new antibiotics, the use of narrow spectrum antibiotics, and the reduction of inappropriate antibiotic use. We propose an alternative but complimentary approach to reduce antibiotic resistant bacteria (ARB) by implementing more stringent technologies for treating municipal wastewater, which is known to contain large quantities of ARB and antibiotic resistance genes (ARGs). In this study, we investigated the ability of conventional aerobic digestion to reduce the quantity of ARGs in untreated wastewater solids. A bench-scale aerobic digester was fed untreated wastewater solids collected from a full-scale municipal wastewater treatment facility. The reactor was operated under semi-continuous flow conditions for more than 200 days at a residence time of approximately 40 days. During this time, the quantities of tet(A), tet(W), and erm(B) decreased by more than 90%. In contrast, intI1 did not decrease, and tet(X) increased in quantity by 5-fold. Following operation in semi-continuous flow mode, the aerobic digester was converted to batch mode to determine the first-order decay coefficients, with half-lives ranging from as short as 2.8 days for tet(W) to as long as 6.3 days for intI1. These results demonstrated that aerobic digestion can be used to reduce the quantity of ARGs in untreated wastewater solids, but that rates can vary substantially depending on the reactor design (i.e., batch vs. continuous-flow) and the specific ARG.
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Affiliation(s)
- Tucker R Burch
- Department of Civil Engineering, University of Minnesota Minneapolis, MN, USA
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Shi P, Jia S, Zhang XX, Zhang T, Cheng S, Li A. Metagenomic insights into chlorination effects on microbial antibiotic resistance in drinking water. WATER RESEARCH 2013; 47:111-20. [PMID: 23084468 DOI: 10.1016/j.watres.2012.09.046] [Citation(s) in RCA: 296] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 09/03/2012] [Accepted: 09/22/2012] [Indexed: 05/21/2023]
Abstract
This study aimed to investigate the chlorination effects on microbial antibiotic resistance in a drinking water treatment plant. Biochemical identification, 16S rRNA gene cloning and metagenomic analysis consistently indicated that Proteobacteria were the main antibiotic resistant bacteria (ARB) dominating in the drinking water and chlorine disinfection greatly affected microbial community structure. After chlorination, higher proportion of the surviving bacteria was resistant to chloramphenicol, trimethoprim and cephalothin. Quantitative real-time PCRs revealed that sulI had the highest abundance among the antibiotic resistance genes (ARGs) detected in the drinking water, followed by tetA and tetG. Chlorination caused enrichment of ampC, aphA2, bla(TEM-1), tetA, tetG, ermA and ermB, but sulI was considerably removed (p < 0.05). Metagenomic analysis confirmed that drinking water chlorination could concentrate various ARGs, as well as of plasmids, insertion sequences and integrons involved in horizontal transfer of the ARGs. Water pipeline transportation tended to reduce the abundance of most ARGs, but various ARB and ARGs were still present in the tap water, which deserves more public health concerns. The results highlighted prevalence of ARB and ARGs in chlorinated drinking water and this study might be technologically useful for detecting the ARGs in water environments.
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Affiliation(s)
- Peng Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046, China
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Leis B, Angelov A, Liebl W. Screening and expression of genes from metagenomes. ADVANCES IN APPLIED MICROBIOLOGY 2013; 83:1-68. [PMID: 23651593 DOI: 10.1016/b978-0-12-407678-5.00001-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Microorganisms are the most abundant and widely spread organisms on earth. They colonize a huge variety of natural and anthropogenic environments, including very specialized ecological niches and even extreme habitats, which are made possible by the immense metabolic diversity and genetic adaptability of microbes. As most of the organisms from environmental samples defy cultivation, cultivation-independent metagenomics approaches have been applied since more than one decade to access and characterize the phylogenetic diversity in microbial communities as well as their metabolic potential and ecological functions. Thereby, metagenomics has fully emerged as an own scientific field for mining new biocatalysts for many industrially relevant processes in biotechnology and pharmaceutics. This review summarizes common metagenomic approaches ranging from sampling, isolation of nucleic acids, construction of metagenomic libraries and their evaluation. Sequence-based screenings implement next-generation sequencing platforms, microarrays or PCR-based methods, while function-based analysis covers heterologous expression of metagenomic libraries in diverse screening setups. Major constraints and advantages of each strategy are described. The importance of alternative host-vector systems is discussed, and in order to underline the role of phylogenetic and physiological distance from the gene donor and the expression host employed, a case study is presented that describes the screening of a genomic library from an extreme thermophilic bacterium in both Escherichia coli and Thermus thermophilus. Metatranscriptomics, metaproteomics and single-cell-based methods are expected to complement metagenomic screening efforts to identify novel biocatalysts from environmental samples.
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Affiliation(s)
- Benedikt Leis
- Lehrstuhl für Mikrobiologie, Technische Universität München, Freising, Bavaria, Germany
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Port JA, Wallace JC, Griffith WC, Faustman EM. Metagenomic profiling of microbial composition and antibiotic resistance determinants in Puget Sound. PLoS One 2012; 7:e48000. [PMID: 23144718 PMCID: PMC3483302 DOI: 10.1371/journal.pone.0048000] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 09/25/2012] [Indexed: 11/26/2022] Open
Abstract
Human-health relevant impacts on marine ecosystems are increasing on both spatial and temporal scales. Traditional indicators for environmental health monitoring and microbial risk assessment have relied primarily on single species analyses and have provided only limited spatial and temporal information. More high-throughput, broad-scale approaches to evaluate these impacts are therefore needed to provide a platform for informing public health. This study uses shotgun metagenomics to survey the taxonomic composition and antibiotic resistance determinant content of surface water bacterial communities in the Puget Sound estuary. Metagenomic DNA was collected at six sites in Puget Sound in addition to one wastewater treatment plant (WWTP) that discharges into the Sound and pyrosequenced. A total of ∼550 Mbp (1.4 million reads) were obtained, 22 Mbp of which could be assembled into contigs. While the taxonomic and resistance determinant profiles across the open Sound samples were similar, unique signatures were identified when comparing these profiles across the open Sound, a nearshore marina and WWTP effluent. The open Sound was dominated by α-Proteobacteria (in particular Rhodobacterales sp.), γ-Proteobacteria and Bacteroidetes while the marina and effluent had increased abundances of Actinobacteria, β-Proteobacteria and Firmicutes. There was a significant increase in the antibiotic resistance gene signal from the open Sound to marina to WWTP effluent, suggestive of a potential link to human impacts. Mobile genetic elements associated with environmental and pathogenic bacteria were also differentially abundant across the samples. This study is the first comparative metagenomic survey of Puget Sound and provides baseline data for further assessments of community composition and antibiotic resistance determinants in the environment using next generation sequencing technologies. In addition, these genomic signals of potential human impact can be used to guide initial public health monitoring as well as more targeted and functionally-based investigations.
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Affiliation(s)
- Jesse A. Port
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
- Institute for Risk Analysis and Risk Communication, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - James C. Wallace
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
- Institute for Risk Analysis and Risk Communication, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - William C. Griffith
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
- Institute for Risk Analysis and Risk Communication, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Elaine M. Faustman
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
- Institute for Risk Analysis and Risk Communication, School of Public Health, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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