1
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Murdock A, Bashar S, White D, Uyaguari-Diaz M, Farenhorst A, Kumar A. Bacterial diversity and resistome analysis of drinking water stored in cisterns from two First Nations communities in Manitoba, Canada. Microbiol Spectr 2024; 12:e0314123. [PMID: 38305192 PMCID: PMC10913478 DOI: 10.1128/spectrum.03141-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/05/2024] [Indexed: 02/03/2024] Open
Abstract
The microbiological content of water is an ongoing concern in First Nations communities in Canada. Many communities lack water treatment plants and continue to be under drinking water advisories. However, lack of access to treatment plants is only a part of the problem as poor water distribution systems also contribute to the failure to provide safe drinking water. Here, we studied the microbial diversity and antibiotic resistome from water stored in cisterns from two First Nations communities in Manitoba, Canada. We found that the cistern water contained a high number of bacteria and showed the presence of diverse antimicrobial resistance genes. Interestingly, the bacterial diversity and antimicrobial resistance genes varied considerably from that of the untreated source water, indicating that the origin of contamination in the cistern water came from within the treatment plant or along the delivery route to the homes. Our study highlights the importance of proper maintenance of the water distribution system in addition to access to water treatment facilities to ensure a supply of safe water to First Nations communities in Canada.IMPORTANCEThe work described addresses a critical issue in First Nations communities in Canada-the microbiological content of water. Many of these communities lack access to water treatment plants and frequently experience drinking water advisories. This study focused on the microbial diversity and antibiotic resistome in water stored in cisterns within two First Nations communities in Manitoba, Canada. These findings reveal that cistern water, a common source of drinking water in these communities, contains a high number of bacteria and a wide range of antimicrobial resistance genes. This highlights a serious health risk as exposure to such water can lead to the spread of drug-resistant infections, posing a threat to the well-being of the residents.
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Affiliation(s)
- Anita Murdock
- Departments of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Sabrin Bashar
- Departments of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Dawn White
- Departments of Microbiology, University of Manitoba, Winnipeg, Canada
| | | | | | - Ayush Kumar
- Departments of Microbiology, University of Manitoba, Winnipeg, Canada
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2
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Liang X, Zhang J, Kim Y, Ho J, Liu K, Keenum I, Gupta S, Davis B, Hepp SL, Zhang L, Xia K, Knowlton KF, Liao J, Vikesland PJ, Pruden A, Heath LS. ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization. Front Genet 2023; 14:1219297. [PMID: 37811141 PMCID: PMC10558085 DOI: 10.3389/fgene.2023.1219297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023] Open
Abstract
Antibiotic resistance is of crucial interest to both human and animal medicine. It has been recognized that increased environmental monitoring of antibiotic resistance is needed. Metagenomic DNA sequencing is becoming an attractive method to profile antibiotic resistance genes (ARGs), including a special focus on pathogens. A number of computational pipelines are available and under development to support environmental ARG monitoring; the pipeline we present here is promising for general adoption for the purpose of harmonized global monitoring. Specifically, ARGem is a user-friendly pipeline that provides full-service analysis, from the initial DNA short reads to the final visualization of results. The capture of extensive metadata is also facilitated to support comparability across projects and broader monitoring goals. The ARGem pipeline offers efficient analysis of a modest number of samples along with affordable computational components, though the throughput could be increased through cloud resources, based on the user's configuration. The pipeline components were carefully assessed and selected to satisfy tradeoffs, balancing efficiency and flexibility. It was essential to provide a step to perform short read assembly in a reasonable time frame to ensure accurate annotation of identified ARGs. Comprehensive ARG and mobile genetic element databases are included in ARGem for annotation support. ARGem further includes an expandable set of analysis tools that include statistical and network analysis and supports various useful visualization techniques, including Cytoscape visualization of co-occurrence and correlation networks. The performance and flexibility of the ARGem pipeline is demonstrated with analysis of aquatic metagenomes. The pipeline is freely available at https://github.com/xlxlxlx/ARGem.
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Affiliation(s)
- Xiao Liang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Jingyi Zhang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Yoonjin Kim
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Josh Ho
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kevin Liu
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Ishi Keenum
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Suraj Gupta
- Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Benjamin Davis
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Shannon L. Hepp
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kang Xia
- School of Plant and Environmental Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Katharine F. Knowlton
- Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg, VaA, United States
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Peter J. Vikesland
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Lenwood S. Heath
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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3
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Song Y, Finkelstein R, Rhoads W, Edwards MA, Pruden A. Shotgun Metagenomics Reveals Impacts of Copper and Water Heater Anodes on Pathogens and Microbiomes in Hot Water Plumbing Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13612-13624. [PMID: 37643149 PMCID: PMC10501123 DOI: 10.1021/acs.est.3c03568] [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: 05/10/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023]
Abstract
Hot water building plumbing systems are vulnerable to the proliferation of opportunistic pathogens (OPs), including Legionella pneumophila and Mycobacterium avium. Implementation of copper as a disinfectant could help reduce OPs, but a mechanistic understanding of the effects on the microbial community under real-world plumbing conditions is lacking. Here, we carried out a controlled pilot-scale study of hot water systems and applied shotgun metagenomic sequencing to examine the effects of copper dose (0-2 mg/L), orthophosphate corrosion control agent, and water heater anode materials (aluminum vs magnesium vs powered anode) on the bulk water and biofilm microbiome composition. Metagenomic analysis revealed that, even though a copper dose of 1.2 mg/L was required to reduce Legionella and Mycobacterium numbers, lower doses (e.g., ≤0.6 mg/L) measurably impacted the broader microbial community, indicating that the OP strains colonizing these systems were highly copper tolerant. Orthophosphate addition reduced bioavailability of copper, both to OPs and to the broader microbiome. Functional gene analysis indicated that both membrane damage and interruption of nucleic acid replication are likely at play in copper inactivation mechanisms. This study identifies key factors (e.g., orthophosphate, copper resistance, and anode materials) that can confound the efficacy of copper for controlling OPs in hot water plumbing.
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Affiliation(s)
- Yang Song
- Civil
and Environmental Engineering, Virginia
Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, Virginia 24061, United States
- Utilities
Department, Town of Cary, 316 N. Academy St., Cary, North Carolina 27512, United States
| | - Rachel Finkelstein
- Civil
and Environmental Engineering, Virginia
Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, Virginia 24061, United States
- AECOM, 3101 Wilson Boulevard, Arlington, Virginia 22201, United States
| | - William Rhoads
- Civil
and Environmental Engineering, Virginia
Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, Virginia 24061, United States
- Black
& Veatch, 8400 Ward
Pkwy, Kansas City, Missouri 64114, United States
| | - Marc A. Edwards
- Civil
and Environmental Engineering, Virginia
Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, Virginia 24061, United States
| | - Amy Pruden
- Civil
and Environmental Engineering, Virginia
Tech, 1145 Perry St., 418 Durham Hall, Blacksburg, Virginia 24061, United States
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4
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Di Cesare A, Sabatino R, Sbaffi T, Fontaneto D, Brambilla D, Beghi A, Pandolfi F, Borlandelli C, Fortino D, Biccai G, Genoni P, Corno G. Anthropogenic pollution drives the bacterial resistome in a complex freshwater ecosystem. CHEMOSPHERE 2023; 331:138800. [PMID: 37121282 DOI: 10.1016/j.chemosphere.2023.138800] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/06/2023] [Accepted: 04/27/2023] [Indexed: 05/03/2023]
Abstract
Aquatic ecosystems in anthropogenically impacted areas are important reservoirs of antibiotic resistance genes (ARGs) of allochthonous origin. However, the dynamics of the different ARGs within the bacterial communities of lakes and rivers, as well as the factors that drive their selection, are not completely understood. In this study, we analysed the fate of the bacterial resistome (total content of ARGs and of metal resistance genes, MRGs) for a period of six months (summer-winter) in a continuum lake-river-lake system (Lake Varese, River Bardello, Lake Maggiore) in Northern Italy, by shotgun metagenomics. The metagenomic data were then compared with chemical, physical and microbiological data, to infer the role of anthropogenic pressure in the different sampling stations. ARGs and MRGs were more abundant and diverse in the River Bardello, characterised by the highest anthropogenic pollution. The date of sampling influenced ARGs and MRGs, with higher abundances in summer (August) than in fall or in winter, when the impact of the treated wastewater discharge in the river was limited by a higher water flow from Lake Varese. ARG and MRG abundances were significantly correlated and they co-occurred in the main network analysis modules with potential pathogenic bacteria. Different levels of anthropogenic impact selectively promoted specific ARGs while others, generally abundant in waters, were not affected by anthropogenic pressure. Reducing the level of anthropogenic pressure resulted in a rapid decrease of most ARGs. From our results, the role of anthropogenic pressure in promoting the spread of specific antibiotic resistances and of potential pathogens in aquatic ecosystem becomes clear. Finally we highlight the strict correlation between ARGs and MRGs suggesting their potential co-selection in stressed aquatic bacterial communities.
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Affiliation(s)
- Andrea Di Cesare
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Raffaella Sabatino
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Tomasa Sbaffi
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Diego Fontaneto
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Diego Brambilla
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Andrea Beghi
- Regional Environmental Protection Agency of Lombardia, Italy
| | - Franca Pandolfi
- Regional Environmental Protection Agency of Lombardia, Italy
| | | | - Davide Fortino
- Regional Environmental Protection Agency of Lombardia, Italy
| | - Giovanni Biccai
- Regional Environmental Protection Agency of Lombardia, Italy
| | - Pietro Genoni
- Regional Environmental Protection Agency of Lombardia, Italy
| | - Gianluca Corno
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy.
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5
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Navgire GS, Goel N, Sawhney G, Sharma M, Kaushik P, Mohanta YK, Mohanta TK, Al-Harrasi A. Analysis and Interpretation of metagenomics data: an approach. Biol Proced Online 2022; 24:18. [PMID: 36402995 PMCID: PMC9675974 DOI: 10.1186/s12575-022-00179-7] [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: 07/28/2022] [Accepted: 10/19/2022] [Indexed: 11/20/2022] Open
Abstract
Advances in next-generation sequencing technologies have accelerated the momentum of metagenomic studies, which is increasing yearly. The metagenomics field is one of the versatile applications in microbiology, where any interaction in the environment involving microorganisms can be the topic of study. Due to this versatility, the number of applications of this omics technology reached its horizons. Agriculture is a crucial sector involving crop plants and microorganisms interacting together. Hence, studying these interactions through the lenses of metagenomics would completely disclose a new meaning to crop health and development. The rhizosphere is an essential reservoir of the microbial community for agricultural soil. Hence, we focus on the R&D of metagenomic studies on the rhizosphere of crops such as rice, wheat, legumes, chickpea, and sorghum. These recent developments are impossible without the continuous advancement seen in the next-generation sequencing platforms; thus, a brief introduction and analysis of the available sequencing platforms are presented here to have a clear picture of the workflow. Concluding the topic is the discussion about different pipelines applied to analyze data produced by sequencing techniques and have a significant role in interpreting the outcome of a particular experiment. A plethora of different software and tools are incorporated in the automated pipelines or individually available to perform manual metagenomic analysis. Here we describe 8-10 advanced, efficient pipelines used for analysis that explain their respective workflows to simplify the whole analysis process.
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Affiliation(s)
- Gauri S Navgire
- Department of Microbiology, Savitribai Phule Pune University, Pune, Maharastra, 411007, India
| | - Neha Goel
- Department of Genetics and Tree Improvement, Forest Research Institute, 248006, Dehradun, India
| | - Gifty Sawhney
- Inflammation Pharmacology Division, Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Jammu-180001, Jammu Kashmir, India
| | - Mohit Sharma
- Department of Molecular Medicine, Medical University of Warsaw and Malopolska Center of Biotechnology, Karkow, Poland
| | | | | | - Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman.
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6
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Hilaire SS, Chen C, Pan Z, Radolinski J, Stewart RD, Maguire RO, Xia K. Subsurface Manure Injection Reduces Surface Transport of Antibiotic Resistance Genes but May Create Antibiotic Resistance Hotspots in Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14972-14981. [PMID: 35839145 DOI: 10.1021/acs.est.2c00981] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Compared to surface application, manure subsurface injection reduces surface runoff of nutrients, antibiotic resistant microorganisms, and emerging contaminants. Less is known regarding the impact of both manure application methods on surface transport of antibiotic resistance genes (ARGs) in manure-amended fields. We applied liquid dairy manure to field plots by surface application and subsurface injection and simulated rainfall on the first or seventh day following application. The ARG richness, relative abundance (normalized to 16s rRNA), and ARG profiles in soil and surface runoff were monitored using shotgun metagenomic sequencing. Within 1 day of manure application, compared to unamended soils, soils treated with manure had 32.5-70.5% greater ARG richness and higher relative abundances of sulfonamide (6.5-129%) and tetracycline (752-3766%) resistance genes (p ≤ 0.05). On day 7, soil ARG profiles in the surface-applied plots were similar to, whereas subsurface injection profiles were different from, that of the unamended soils. Forty-six days after manure application, the soil ARG profiles in manure injection slits were 37% more diverse than that of the unamended plots. The abundance of manure-associated ARGs were lower in surface runoff from manure subsurface injected plots and carried a lower resistome risk score in comparison to surface-applied plots. This study demonstrated, for the first time, that although manure subsurface injection reduces ARGs in the runoff, it can create potential long-term hotspots for elevated ARGs within injection slits.
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Affiliation(s)
- Sheldon S Hilaire
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Chaoqi Chen
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
- School of Resource and Environmental Science, Wuhan University, Wuhan 430079, China
| | - Zhizhen Pan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jesse Radolinski
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Ecology, University of Innsbruck, Innsbruck 6020, Austria
| | - Ryan D Stewart
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Rory O Maguire
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Kang Xia
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
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7
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Sabatino R, Cabello-Yeves PJ, Eckert EM, Corno G, Callieri C, Brambilla D, Dzhembekova N, Moncheva S, Di Cesare A. Antibiotic resistance genes correlate with metal resistances and accumulate in the deep water layers of the Black Sea. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 312:120033. [PMID: 36030962 DOI: 10.1016/j.envpol.2022.120033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/25/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Seas and oceans are a global reservoir of antibiotic resistance genes (ARGs). Only a few studies investigated the dynamics of ARGs along the water column of the Black Sea, a unique environment, with a peculiar geology, biology and history of anthropogenic pollution. In this study, we analyzed metagenomic data from two sampling campaigns (2013 and 2019) collected across three different sites in the Western Black Sea at depths ranging from 5 to 2000 m. The data were processed to annotate ARGs, metal resistance genes (MRGs) and integron integrase genes. The ARG abundance was significantly higher in the deep water layers and depth was the main driver of beta-diversity both for ARGs and MRGs. Moreover, ARG and MRG abundances strongly correlated (r = 0.95). The integron integrase gene abundances and composition were not influenced by the water depth and did not correlate with ARGs. The analysis of the obtained MAGs showed that some of them harbored intI gene together with several ARGs and MRGs, suggesting the presence of multidrug resistant bacteria and that MRGs and integrons could be involved in the selection of ARGs. These results demonstrate that the Black Sea is not only an important reservoir of ARGs, but also that they accumulate in the deep water layers where co-selection with MRGs could be assumed as a relevant mechanism of their persistence.
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Affiliation(s)
- Raffaella Sabatino
- Water Research Institute - National Research Council of Italy (CNR-IRSA), Molecular Ecology Group (MEG), Largo Tonolli 50, 28922, Verbania (VB), Italy
| | - Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel, Hernández, San Juan de Alicante, Alicante, Spain
| | - Ester M Eckert
- Water Research Institute - National Research Council of Italy (CNR-IRSA), Molecular Ecology Group (MEG), Largo Tonolli 50, 28922, Verbania (VB), Italy
| | - Gianluca Corno
- Water Research Institute - National Research Council of Italy (CNR-IRSA), Molecular Ecology Group (MEG), Largo Tonolli 50, 28922, Verbania (VB), Italy
| | - Cristiana Callieri
- Water Research Institute - National Research Council of Italy (CNR-IRSA), Molecular Ecology Group (MEG), Largo Tonolli 50, 28922, Verbania (VB), Italy
| | - Diego Brambilla
- Water Research Institute - National Research Council of Italy (CNR-IRSA), Molecular Ecology Group (MEG), Largo Tonolli 50, 28922, Verbania (VB), Italy
| | - Nina Dzhembekova
- Institute for Oceanology Fridtj of Nansen, Bulgarian Academy of Sciences, First May Street 40, P.O. Box 152, 9000, Varna, Bulgaria
| | - Snejana Moncheva
- Institute for Oceanology Fridtj of Nansen, Bulgarian Academy of Sciences, First May Street 40, P.O. Box 152, 9000, Varna, Bulgaria
| | - Andrea Di Cesare
- Water Research Institute - National Research Council of Italy (CNR-IRSA), Molecular Ecology Group (MEG), Largo Tonolli 50, 28922, Verbania (VB), Italy.
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8
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Prieto Riquelme M, Garner E, Gupta S, Metch J, Zhu N, Blair MF, Arango-Argoty G, Maile-Moskowitz A, Li AD, Flach CF, Aga DS, Nambi IM, Larsson DGJ, Bürgmann H, Zhang T, Pruden A, Vikesland PJ. Demonstrating a Comprehensive Wastewater-Based Surveillance Approach That Differentiates Globally Sourced Resistomes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14982-14993. [PMID: 35759608 PMCID: PMC9631994 DOI: 10.1021/acs.est.1c08673] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Wastewater-based surveillance (WBS) for disease monitoring is highly promising but requires consistent methodologies that incorporate predetermined objectives, targets, and metrics. Herein, we describe a comprehensive metagenomics-based approach for global surveillance of antibiotic resistance in sewage that enables assessment of 1) which antibiotic resistance genes (ARGs) are shared across regions/communities; 2) which ARGs are discriminatory; and 3) factors associated with overall trends in ARGs, such as antibiotic concentrations. Across an internationally sourced transect of sewage samples collected using a centralized, standardized protocol, ARG relative abundances (16S rRNA gene-normalized) were highest in Hong Kong and India and lowest in Sweden and Switzerland, reflecting national policy, measured antibiotic concentrations, and metal resistance genes. Asian versus European/US resistomes were distinct, with macrolide-lincosamide-streptogramin, phenicol, quinolone, and tetracycline versus multidrug resistance ARGs being discriminatory, respectively. Regional trends in measured antibiotic concentrations differed from trends expected from public sales data. This could reflect unaccounted uses, captured only by the WBS approach. If properly benchmarked, antibiotic WBS might complement public sales and consumption statistics in the future. The WBS approach defined herein demonstrates multisite comparability and sensitivity to local/regional factors.
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Affiliation(s)
| | - Emily Garner
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
- Department
of Civil and Environmental Engineering, West Virginia University, Morgantown, West Virginia26506, United States
| | - Suraj Gupta
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
- The
Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational
Biology, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Jake Metch
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Ni Zhu
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Matthew F. Blair
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Gustavo Arango-Argoty
- Department
of Computer Science, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Ayella Maile-Moskowitz
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - An-dong Li
- Department
of Civil Engineering, The University of
Hong Kong, Pokfulam, Hong Kong
| | - Carl-Fredrik Flach
- Centre for
Antibiotic Resistance Research (CARe), University
of Gothenburg, 405 30Göteborg, Sweden
- Department
of Infectious Diseases, University of Gothenburg, 405 30Göteborg, Sweden
| | - Diana S. Aga
- Department
of Chemistry, University at Buffalo, Buffalo, New York14260, United States
| | - Indumathi M. Nambi
- Department
of Civil Engineering, Indian Institute of
Technology, Madras,
Chennai600036, India
| | - D. G. Joakim Larsson
- Centre for
Antibiotic Resistance Research (CARe), University
of Gothenburg, 405 30Göteborg, Sweden
- Department
of Infectious Diseases, University of Gothenburg, 405 30Göteborg, Sweden
| | - Helmut Bürgmann
- Eawag:
Swiss Federal Institute of Aquatic Science and Technology, CH-6047Kastanienbaum, Switzerland
| | - Tong Zhang
- Department
of Civil Engineering, The University of
Hong Kong, Pokfulam, Hong Kong
| | - Amy Pruden
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
| | - Peter J. Vikesland
- Department
of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia24061, United States
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9
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Sabatino R, Sbaffi T, Corno G, de Carvalho DS, Trovatti Uetanabaro AP, Góes-Neto A, Podolich O, Kozyrovska N, de Vera JP, Azevedo V, Barh D, Di Cesare A. Metagenome Analysis Reveals a Response of the Antibiotic Resistome to Mars-like Extraterrestrial Conditions. ASTROBIOLOGY 2022; 22:1072-1080. [PMID: 35714354 PMCID: PMC9508453 DOI: 10.1089/ast.2021.0176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
The spread of antibiotic resistance is becoming a serious global health concern. Numerous studies have been done to investigate the dynamics of antibiotic resistance genes (ARGs) in both indoor and outdoor environments. Nonetheless, few studies are available about the dynamics of the antibiotic resistome (total content of ARGs in the microbial cultures or communities) under stress in outer space environments. In this study, we aimed to experimentally investigate the dynamics of ARGs and metal resistance genes (MRGs) in Kombucha Mutualistic Community (KMC) samples exposed to Mars-like conditions simulated during the BIOMEX experiment outside the International Space Station with analysis of the metagenomics data previously produced. Thus, we compared them with those of the respective non-exposed KMC samples. The antibiotic resistome responded to the Mars-like conditions by enriching its diversity with ARGs after exposure, which were not found in non-exposed samples (i.e., tet and van genes against tetracycline and vancomycin, respectively). Furthermore, ARGs and MRGs were correlated; therefore, their co-selection could be assumed as a mechanism for maintaining antibiotic resistance in Mars-like environments. Overall, these results highlight the high plasticity of the antibiotic resistome in response to extraterrestrial conditions and in the absence of anthropogenic stresses.
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Affiliation(s)
- Raffaella Sabatino
- Water Research Institute (IRSA) - MEG Molecular Ecology Group, CNR - National Research Council of Italy, Verbania, Italy
| | - Tomasa Sbaffi
- Water Research Institute (IRSA) - MEG Molecular Ecology Group, CNR - National Research Council of Italy, Verbania, Italy
| | - Gianluca Corno
- Water Research Institute (IRSA) - MEG Molecular Ecology Group, CNR - National Research Council of Italy, Verbania, Italy
| | - Daniel Santana de Carvalho
- Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ana Paula Trovatti Uetanabaro
- Laboratório de Microbiologia Aplicada, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brasil
| | - Aristóteles Góes-Neto
- Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Olga Podolich
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | | | - Jean-Pierre de Vera
- German Aerospace Center (DLR), Space Operations and Astronaut Training, Microgravity User Support Center (MUSC), Cologne, Germany
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Debmalya Barh
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), West Bengal, India
| | - Andrea Di Cesare
- Water Research Institute (IRSA) - MEG Molecular Ecology Group, CNR - National Research Council of Italy, Verbania, Italy
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10
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Yasir M, Al-Zahrani IA, Bibi F, Abd El Ghany M, Azhar EI. New insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteria. Food Res Int 2022; 157:111190. [DOI: 10.1016/j.foodres.2022.111190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 11/04/2022]
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11
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Xie J, Jin L, Wu D, Pruden A, Li X. Inhalable Antibiotic Resistome from Wastewater Treatment Plants to Urban Areas: Bacterial Hosts, Dissemination Risks, and Source Contributions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:7040-7051. [PMID: 35038864 DOI: 10.1021/acs.est.1c07023] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance genes (ARGs) are commonly detected in the atmosphere, but questions remain regarding their sources and relative contributions, bacterial hosts, and corresponding human health risks. Here, we conducted a qPCR- and metagenomics-based investigation of inhalable fine particulate matter (PM2.5) at a large wastewater treatment plant (WWTP) and in the ambient air of Hong Kong, together with an in-depth analysis of published data of other potential sources in the area. PM2.5 was observed with increasing enrichment of total ARGs along the coastal-urban-WWTP gradient and clinically relevant ARGs commonly identified in urban and WWTP sites, illustrating anthropogenic impacts on the atmospheric accumulation of ARGs. With certain kinds of putative antibiotic-resistant pathogens detected in urban and WWTP PM2.5, a comparable proportion of ARGs that co-occurred with MGEs was found between the atmosphere and WWTP matrices. Despite similar emission rates of bacteria and ARGs within each WWTP matrix, about 11-13% of the bacteria and >57% of the relevant ARGs in urban and WWTP PM2.5 were attributable to WWTPs. Our study highlights the importance of WWTPs in disseminating bacteria and ARGs to the ambient air from a quantitative perspective and, thus, the need to control potential sources of inhalation exposure to protect the health of urban populations.
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Affiliation(s)
- Jiawen Xie
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, China
| | - Ling Jin
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Dong Wu
- Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Science, East China Normal University, Shanghai 200241, China
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Xiangdong Li
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, China
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12
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Tiwari A, Gomez-Alvarez V, Siponen S, Sarekoski A, Hokajärvi AM, Kauppinen A, Torvinen E, Miettinen IT, Pitkänen T. Bacterial Genes Encoding Resistance Against Antibiotics and Metals in Well-Maintained Drinking Water Distribution Systems in Finland. Front Microbiol 2022; 12:803094. [PMID: 35197945 PMCID: PMC8859300 DOI: 10.3389/fmicb.2021.803094] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/31/2021] [Indexed: 12/13/2022] Open
Abstract
Information on the co-occurrence of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) among bacterial communities in drinking water distribution systems (DWDSs) is scarce. This study characterized ARGs and MRGs in five well-maintained DWDSs in Finland. The studied DWDSs had different raw water sources and treatment methods. Two of the waterworks employed artificially recharged groundwater (ARGW) and used no disinfection in the treatment process. The other three waterworks (two surface and one groundwater source) used UV light and chlorine during the treatment process. Ten bulk water samples (two from each DWDS) were collected, and environmental DNA was extracted and then sequenced using the Illumina HiSeq platform for high-throughput shotgun metagenome sequencing. A total of 430 ARGs were characterized among all samples with the highest diversity of ARGs identified from samples collected from non-disinfected DWDSs. Furthermore, non-disinfected DWDSs contained the highest diversity of bacterial communities. However, samples from DWDSs using disinfectants contained over double the ratio of ARG reads to 16S rRNA gene reads and most of the MRG (namely mercury and arsenic resistance genes). The total reads and types of ARGs conferring genes associated with antibiotic groups namely multidrug resistance, and bacitracin, beta-lactam, and aminoglycoside and mercury resistance genes increased in waterworks treating surface water with disinfection. The findings of this study contribute toward a comprehensive understanding of ARGs and MRGs in DWDSs. The occurrence of bacteria carrying antibiotic or metal resistance genes in drinking water causes direct exposure to people, and thus, more systematic investigation is needed to decipher the potential effect of these resistomes on human health.
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Affiliation(s)
- Ananda Tiwari
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- *Correspondence: Ananda Tiwari,
| | - Vicente Gomez-Alvarez
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, United States
| | - Sallamaari Siponen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Anniina Sarekoski
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Anna-Maria Hokajärvi
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Ari Kauppinen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Eila Torvinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ilkka T. Miettinen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Tarja Pitkänen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Kuopio, Finland
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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13
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Brooks JP, Durso LM, Ibekwe AM. Editorial: Exposure, Risks, and Drivers of the Mobile Antimicrobial Resistance Genes in the Environment-a Global Perspective. Front Microbiol 2021; 12:803282. [PMID: 34917067 PMCID: PMC8670075 DOI: 10.3389/fmicb.2021.803282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- John P Brooks
- Agricultural Research Service, United States Department of Agriculture, Washington, DC, United States
| | - Lisa M Durso
- Agricultural Research Service, United States Department of Agriculture, Washington, DC, United States
| | - Abasiofiok Mark Ibekwe
- Agricultural Research Service, United States Department of Agriculture, Washington, DC, United States
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14
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Di Cesare A, Pinnell LJ, Brambilla D, Elli G, Sabatino R, Sathicq MB, Corno G, O'Donnell C, Turner JW. Bioplastic accumulates antibiotic and metal resistance genes in coastal marine sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118161. [PMID: 34537596 DOI: 10.1016/j.envpol.2021.118161] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/01/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
The oceans are increasingly polluted with plastic debris, and several studies have implicated plastic as a reservoir for antibiotic resistance genes and a potential vector for antibiotic-resistant bacteria. Bioplastic is widely regarded as an environmentally friendly replacement to conventional petroleum-based plastic, but the effects of bioplastic pollution on marine environments remain largely unknown. Here, we present the first evidence that bioplastic accumulates antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in marine sediments. Biofilms fouling ceramic, polyethylene terephthalate (PET), and polyhydroxyalkanoate (PHA) were investigated by shotgun metagenomic sequencing. Four ARG groups were more abundant in PHA: trimethoprim resistance (TMP), multidrug resistance (MDR), macrolide-lincosamide-streptogramin resistance (MLS), and polymyxin resistance (PMR). One MRG group was more abundant in PHA: multimetal resistance (MMR). The relative abundance of ARGs and MRGs were strongly correlated based on a Mantel test between the Bray-Curtis dissimilarity matrices (R = 0.97, p < 0.05) and a Pearson's analysis (R = 0.96, p < 0.05). ARGs were detected in more than 40% of the 57 metagenome-assembled genomes (MAGs) while MRGs were detected in more than 90% of the MAGs. Further investigation (e.g., culturing, genome sequencing, antibiotic susceptibility testing) revealed that PHA biofilms were colonized by hemolytic Bacillus cereus group bacteria that were resistant to beta-lactams, vancomycin, and bacitracin. Taken together, our findings indicate that bioplastic, like conventional petroleum-based plastic, is a reservoir for resistance genes and a potential vector for antibiotic-resistant bacteria in coastal marine sediments.
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Affiliation(s)
- Andrea Di Cesare
- Water Research Institute, National Research Council of Italy (CNR-IRSA), MEG - Molecular Ecology Group, Largo Tonolli 50, 28922, Verbania, Italy
| | - Lee J Pinnell
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, 78412, United States
| | - Diego Brambilla
- Water Research Institute, National Research Council of Italy (CNR-IRSA), MEG - Molecular Ecology Group, Largo Tonolli 50, 28922, Verbania, Italy
| | - Giulia Elli
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| | - Raffaella Sabatino
- Water Research Institute, National Research Council of Italy (CNR-IRSA), MEG - Molecular Ecology Group, Largo Tonolli 50, 28922, Verbania, Italy
| | - María B Sathicq
- Water Research Institute, National Research Council of Italy (CNR-IRSA), MEG - Molecular Ecology Group, Largo Tonolli 50, 28922, Verbania, Italy
| | - Gianluca Corno
- Water Research Institute, National Research Council of Italy (CNR-IRSA), MEG - Molecular Ecology Group, Largo Tonolli 50, 28922, Verbania, Italy
| | - Colin O'Donnell
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, 78412, United States
| | - Jeffrey W Turner
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, 78412, United States.
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15
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de Medeiros Azevedo T, Aburjaile FF, Ferreira-Neto JRC, Pandolfi V, Benko-Iseppon AM. The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications. World J Microbiol Biotechnol 2021; 37:206. [PMID: 34708327 DOI: 10.1007/s11274-021-03168-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/05/2021] [Indexed: 11/25/2022]
Abstract
Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.
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Affiliation(s)
- Thamara de Medeiros Azevedo
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Flávia Figueira Aburjaile
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - José Ribamar Costa Ferreira-Neto
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Valesca Pandolfi
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil.
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16
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Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. Funct Integr Genomics 2021; 22:3-26. [PMID: 34657989 DOI: 10.1007/s10142-021-00810-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/25/2021] [Accepted: 10/03/2021] [Indexed: 10/20/2022]
Abstract
This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the research area, provides details about major analytical methods, examines the taxonomy and assembly of genomes, emphasizes some tools, and concludes by celebrating the richness of the ecosystem populated by the "metagenome."
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17
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Ghosh S, Zhu NJ, Milligan E, Falkinham JO, Pruden A, Edwards MA. Mapping the Terrain for Pathogen Persistence and Proliferation in Non-potable Reuse Distribution Systems: Interactive Effects of Biofiltration, Disinfection, and Water Age. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:12561-12573. [PMID: 34448580 DOI: 10.1021/acs.est.1c02121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Diverse pathogens can potentially persist and proliferate in reclaimed water distribution systems (RWDSs). The goal of this study was to evaluate interactive effects of reclaimed water treatments and water age on persistence and proliferation of multiple fecal (e.g., Klebsiella, Enterobacter) and non-fecal (e.g., Legionella, mycobacteria) gene markers in RWDSs. Six laboratory-scale RWDSs were operated in parallel receiving the influent with or without biologically active carbon (BAC) filtration + chlorination, chloramination, or no disinfectant residual. After 3 years of operation, the RWDSs were subject to sacrificial sampling and shotgun metagenomic sequencing. We developed an in-house metagenome-derived pathogen quantification pipeline, validated by quantitative polymerase chain reaction and mock community analysis, to estimate changes in abundance of ∼30 genera containing waterborne pathogens. Microbial community composition in the RWDS bulk water, biofilm, and sediments was clearly shaped by BAC filtration, disinfectant conditions, and water age. Key commonalities were noted in the ecological niches occupied by fecal pathogen markers in the RWDSs, while non-fecal pathogen markers were more varied in their distribution. BAC-filtration + chlorine was found to most effectively control the widest range of target genera. However, filtration alone or chlorine secondary disinfection alone resulted in proliferation of some of these genera containing waterborne pathogens.
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Affiliation(s)
- Sudeshna Ghosh
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Ni Joyce Zhu
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Erin Milligan
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Joseph O Falkinham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Marc A Edwards
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
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18
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Wind L, Keenum I, Gupta S, Ray P, Knowlton K, Ponder M, Hession WC, Pruden A, Krometis LA. Integrated Metagenomic Assessment of Multiple Pre-harvest Control Points on Lettuce Resistomes at Field-Scale. Front Microbiol 2021; 12:683410. [PMID: 34305845 PMCID: PMC8299786 DOI: 10.3389/fmicb.2021.683410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/07/2021] [Indexed: 02/01/2023] Open
Abstract
An integrated understanding of factors influencing the occurrence, distribution, and fate of antibiotic resistance genes (ARGs) in vegetable production systems is needed to inform the design and development of strategies for mitigating the potential for antibiotic resistance propagation in the food chain. The goal of the present study was to holistically track antibiotic resistance and associated microbiomes at three distinct pre-harvest control points in an agroecosystem in order to identify the potential impacts of key agricultural management strategies. Samples were collected over the course of a single growing season (67 days) from field-scale plots amended with various organic and inorganic amendments at agronomic rates. Dairy-derived manure and compost amendment samples (n = 14), soil samples (n = 27), and lettuce samples (n = 12) were analyzed via shotgun metagenomics to assess multiple pre-harvest factors as hypothetical control points that shape lettuce resistomes. Pre-harvest factors of interest included manure collection during/post antibiotic use, manure composting, and soil amended with organic (stockpiled manure/compost) versus chemical fertilizer. Microbial community resistome and taxonomic compositions were unique from amendment to soil to lettuce surface according to dissimilarity analysis. The highest resistome alpha diversity (i.e., unique ARGs, n = 642) was detected in amendment samples prior to soil application, while the composted manure had the lowest total ARG relative abundance (i.e., 16S rRNA gene-normalized). Regardless of amendment type, soils acted as an apparent ecological buffer, i.e., soil resistome and taxonomic profiles returned to background conditions 67 d-post amendment application. Effects of amendment conditions surprisingly re-emerged in lettuce phyllosphere resistomes, with the highest total ARG relative abundances recovered on the surface of lettuce plants grown in organically-fertilized soils (i.e., compost- and manure-amended soils). Co-occurrence analysis identified 55 unique ARGs found both in the soil amendments and on lettuce surfaces. Among these, arnA and pmrF were the most abundant ARGs co-occurring with mobile genetic elements (MGE). Other prominent ARG-MGE co-occurrences throughout this pre-harvest lettuce production chain included: TetM to transposon (Clostridiodies difficile) in the manure amendment and TriC to plasmid (Ralstonia solanacearum) on the lettuce surfaces. This suggests that, even with imposing manure management and post-amendment wait periods in agricultural systems, ARGs originating from manure can still be found on crop surfaces. This study demonstrates a comprehensive approach to identifying key control points for the propagation of ARGs in vegetable production systems, identifying potential ARG-MGE combinations that could inform future surveillance. The findings suggest that additional pre-harvest and potentially post-harvest interventions may be warranted to minimize risk of propagating antibiotic resistance in the food chain.
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Affiliation(s)
- Lauren Wind
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Ishi Keenum
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Suraj Gupta
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
| | - Partha Ray
- Department of Dairy Science, Virginia Tech, Blacksburg, VA, United States.,Department of Animal Sciences, University of Reading, Reading, United Kingdom
| | - Katharine Knowlton
- Department of Dairy Science, Virginia Tech, Blacksburg, VA, United States
| | - Monica Ponder
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
| | - W Cully Hession
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Leigh-Anne Krometis
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, United States
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19
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Zhu NJ, Ghosh S, Edwards MA, Pruden A. Interplay of Biologically Active Carbon Filtration and Chlorine-Based Disinfection in Mitigating the Dissemination of Antibiotic Resistance Genes in Water Reuse Distribution Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8329-8340. [PMID: 34080846 DOI: 10.1021/acs.est.1c01199] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Appropriate management approaches are needed to minimize the proliferation of antibiotic resistance genes (ARGs) in reclaimed water distribution systems (RWDSs). Six laboratory-scale RWDSs were operated over 3 years receiving influent with or without biologically active carbon (BAC) filtration + chlorination, chloramination, or no disinfectant residual. Shotgun metagenomic sequencing was applied toward comprehensive characterization of resistomes, focusing on total ARGs, ARG mobility, and specific ARGs of clinical concern. ARGs such as aadA, bacA, blaOXA, mphE, msrE, sul1, and sul2 were found to be particularly sensitive to varying RWDS conditions. BAC filtration with chlorination most effectively achieved and maintained the lowest levels of nearly all metagenomically derived antibiotic resistance indicators. However, BAC filtration or addition of residual disinfectants alone tended to increase these indicators. Biofilm and sediment compartments harbored ARGs in disinfected systems, presenting a concern for their release to bulk water. Relative and absolute abundances of most ARGs tended to decrease with water age (up to 5 days), with notable exceptions in BAC-filtered chloraminated and no residual systems. Superchlorination of unfiltered water especially raised concerns in terms of elevation of clinically relevant and mobile ARGs. This study revealed that BAC filtration and disinfection must be carefully coordinated in order to effectively mitigate ARG dissemination via RWDSs.
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Affiliation(s)
- Ni Joyce Zhu
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Sudeshna Ghosh
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Marc A Edwards
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
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20
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Structural, functional, resistome and pathogenicity profiling of the Cooum river. Microb Pathog 2021; 158:105048. [PMID: 34139279 DOI: 10.1016/j.micpath.2021.105048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/12/2021] [Accepted: 06/06/2021] [Indexed: 01/26/2023]
Abstract
The microbial community's structure and functions determine the health, quality, and anthropogenic conditions of the river ecosystems. The presence of Bacteria such as Arcobacter spp, Escherichia spp, and Campylobacters spp, have been shown to reflect the poor water quality of rivers. Apprehension of the microbial community in polluted water bodies is significant because it affects human health and the environment. Culture-independent metagenomic and metatranscriptomic approaches employed in the current study of the Cooum river unraveled the taxonomic classification of diverse microbes, including archaea, bacteria, viruses, and phages. The presence of abundant Macellibacteroides fermentans, Arcobacter bivolvorium, Arcobacter butzleri, Methanothrix soenhngeii, and Bacteroides graminisolvens were noted. Viruses and phages like Caudovirales, Human mastadenovirus C, Siphoviridae, Escherichia phage, Erwinia phage, Synechoccus phage, and Vibrio phage were relatively predominant. Various metabolic pathways like methane, sulfur, and nitrogen metabolism adopted by the microbiome confer dangerous gases. Mechanisms such as secretory systems, signal transduction, Chemotaxis, quorum sensing, transportation of chemicals and ions were significantly enriched. The microbes expressed antimicrobial resistance mechanisms as identified from the genes encoding beta-lactamase enzymes and aminoglycoside phosphotransferase enzymes. Metal resistance mechanisms against copper, tellurium, chromium, and cadmium were plentiful. Presence of human pathogens interactions with Yersinia pestis, Campylobacter jejuni, Escherichia coli, Helicobacter pylori, and Francisella tularensis subsp. tularensis suggested the possibilities of transmission of pathogenesis to humans. The current study is the first to apprehend the detailed microbiome composition of one of the highly polluted rivers in South India. The study elaborated the microbiome's structure, functions, and metabolic potential at a specific site of the polluted river.
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21
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Majeed HJ, Riquelme MV, Davis BC, Gupta S, Angeles L, Aga DS, Garner E, Pruden A, Vikesland PJ. Evaluation of Metagenomic-Enabled Antibiotic Resistance Surveillance at a Conventional Wastewater Treatment Plant. Front Microbiol 2021; 12:657954. [PMID: 34054755 PMCID: PMC8155483 DOI: 10.3389/fmicb.2021.657954] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/12/2021] [Indexed: 12/31/2022] Open
Abstract
Wastewater treatment plants (WWTPs) receive a confluence of sewage containing antimicrobials, antibiotic resistant bacteria, antibiotic resistance genes (ARGs), and pathogens and thus are a key point of interest for antibiotic resistance surveillance. WWTP monitoring has the potential to inform with respect to the antibiotic resistance status of the community served as well as the potential for ARGs to escape treatment. However, there is lack of agreement regarding suitable sampling frequencies and monitoring targets to facilitate comparison within and among individual WWTPs. The objective of this study was to comprehensively evaluate patterns in metagenomic-derived indicators of antibiotic resistance through various stages of treatment at a conventional WWTP for the purpose of informing local monitoring approaches that are also informative for global comparison. Relative abundance of total ARGs decreased by ∼50% from the influent to the effluent, with each sampling location defined by a unique resistome (i.e., total ARG) composition. However, 90% of the ARGs found in the effluent were also detected in the influent, while the effluent ARG-pathogen taxonomic linkage patterns identified in assembled metagenomes were more similar to patterns in regional clinical surveillance data than the patterns identified in the influent. Analysis of core and discriminatory resistomes and general ARG trends across the eight sampling events (i.e., tendency to be removed, increase, decrease, or be found in the effluent only), along with quantification of ARGs of clinical concern, aided in identifying candidate ARGs for surveillance. Relative resistome risk characterization further provided a comprehensive metric for predicting the relative mobility of ARGs and likelihood of being carried in pathogens and can help to prioritize where to focus future monitoring and mitigation. Most antibiotics that were subject to regional resistance testing were also found in the WWTP, with the total antibiotic load decreasing by ∼40–50%, but no strong correlations were found between antibiotics and corresponding ARGs. Overall, this study provides insight into how metagenomic data can be collected and analyzed for surveillance of antibiotic resistance at WWTPs, suggesting that effluent is a beneficial monitoring point with relevance both to the local clinical condition and for assessing efficacy of wastewater treatment in reducing risk of disseminating antibiotic resistance.
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Affiliation(s)
- Haniyyah J Majeed
- Department of Civil & Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Maria V Riquelme
- Department of Civil & Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Benjamin C Davis
- Department of Civil & Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Suraj Gupta
- Interdisciplinary Ph.D Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Luisa Angeles
- Department of Chemistry, University at Buffalo, Buffalo, NY, United States
| | - Diana S Aga
- Department of Chemistry, University at Buffalo, Buffalo, NY, United States
| | - Emily Garner
- Department of Civil & Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Peter J Vikesland
- Department of Civil & Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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22
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Wind L, Krometis LA, Hession WC, Pruden A. Cross-comparison of methods for quantifying antibiotic resistance in agricultural soils amended with dairy manure and compost. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:144321. [PMID: 33477102 DOI: 10.1016/j.scitotenv.2020.144321] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 12/02/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Agricultural soils are often amended with livestock manure, making them a key reservoir of antibiotic resistance genes (ARGs). Given that soils are among the most microbially-diverse environments on the planet; effective characterization and quantification of the effects of manure-derived amendments on soil resistomes is a major challenge. This study examined the effects of dairy manure-derived amendments on agricultural soils via two strategies: quantification of anthropogenic ARG markers via qPCR and shotgun metagenomic resistome profiling; and these strategies were compared to a previously published antibiotic resistant fecal coliform dataset. Soil samples were collected throughout a 120 day complete block field experiment to compare the effects of amendment type on antibiotic resistance. Results of all three measurements were consistent with the hypothesis that the application of composted manure reduced antibiotic resistance in soil relative to the application of raw manure, although some differences were noted in comparing the patterns of the three measurements with time. Raw dairy manure-amended soils yielded high sul1 and tet(W) relative abundances on Day 0 (following amendment application), but significantly decreased to background levels by Day 67 (harvest) and Day 120 (study completion). Shotgun metagenomics similarly detected a decrease in the relative abundances of sulfonamide and tetracycline-associated ARGs over time in the raw manure- and compost-amended soils; however, these levels were significantly lower than those estimated by qPCR. Interestingly, although patterns of sulfonamide and tetracycline resistance among culturable fecal coliforms echoed those observed via qPCR and metagenomics; erythromycin resistant coliforms were directly recovered by culture in amended soils, but corresponding ARGs were not detected by qPCR or metagenomics. This study supports both composting and time restrictions as means of reducing the potential for antibiotic resistance in manure to spread via soil application. Results suggest some differences in finer conclusions drawn depending on which antibiotic resistance monitoring target is selected.
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Affiliation(s)
- Lauren Wind
- Department of Biological Systems Engineering, Virginia Tech, 155 Ag. Quad Lane, Seitz Hall RM 200, Blacksburg, VA, USA.
| | - Leigh-Anne Krometis
- Department of Biological Systems Engineering, Virginia Tech, 155 Ag. Quad Lane, Seitz Hall RM 200, Blacksburg, VA, USA
| | - W Cully Hession
- Department of Biological Systems Engineering, Virginia Tech, 155 Ag. Quad Lane, Seitz Hall RM 200, Blacksburg, VA, USA
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, 1145 Perry St, Durham Hall RM 403, Blacksburg, VA 24061, USA
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Liang X, Akers K, Keenum I, Wind L, Gupta S, Chen C, Aldaihani R, Pruden A, Zhang L, Knowlton KF, Xia K, Heath LS. AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata. BMC Bioinformatics 2021; 22:117. [PMID: 33691615 PMCID: PMC7944603 DOI: 10.1186/s12859-021-04035-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/17/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance. RESULTS Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. CONCLUSION AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .
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Affiliation(s)
- Xiao Liang
- Department of Computer Science, Virginia Polytechnic Institute and State University, 24061 Blacksburg, USA
| | - Kyle Akers
- Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, 24061 Blacksburg, USA
| | - Ishi Keenum
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, 24061 Blacksburg, USA
| | - Lauren Wind
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, 24061 Blacksburg, USA
| | - Suraj Gupta
- Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, 24061 Blacksburg, USA
| | - Chaoqi Chen
- School of Resource and Environmental Science, Wuhan University, 430072 Wuhan, China
| | - Reem Aldaihani
- Department of Computer Science, Virginia Polytechnic Institute and State University, 24061 Blacksburg, USA
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, 24061 Blacksburg, USA
| | - Liqing Zhang
- Department of Computer Science, Virginia Polytechnic Institute and State University, 24061 Blacksburg, USA
| | - Katharine F. Knowlton
- Department of Dairy Science, Virginia Polytechnic Institute and State University, 24061 Blacksburg, USA
| | - Kang Xia
- School of Plant and Environmental Science, Virginia Polytechnic Institute and State University, 24061 Blacksburg, USA
| | - Lenwood S. Heath
- Department of Computer Science, Virginia Polytechnic Institute and State University, 24061 Blacksburg, USA
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24
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Tan SM, Ismail MH, Cao B. Biodiversity of magnetotactic bacteria in the tropical marine environment of Singapore revealed by metagenomic analysis. ENVIRONMENTAL RESEARCH 2021; 194:110714. [PMID: 33422504 DOI: 10.1016/j.envres.2021.110714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/22/2020] [Accepted: 01/01/2021] [Indexed: 06/12/2023]
Abstract
Most studies on the diversity of magnetotactic bacteria (MTB) have been conducted on samples obtained from the Northern or the Southern hemispheres. The diversity of MTB in tropical Asia near the geo-equator, with a close-to-zero geomagnetic inclination, weak magnetic field and constantly high seawater temperature has never been explored. This study aims to decipher the diversity of MTB in the marine environment of Singapore through shotgun metagenomics. Although MTB has been acknowledged to be ubiquitous in aquatic environments, we did not observe magnetotactic behaviour in the samples. However, we detected the presence and determined the diversity of MTB through bioinformatic analyses. Metagenomic analysis suggested majority of the MTB in the seafloor sediments represents novel MTB taxa that cannot be classified at the species level. The relative abundance of MTB (~0.2-1.69%) in the samples collected from the marine environment of Singapore was found to be substantially lower than studies for other regions. In contrast to other studies, the genera Magnetovibrio and Desulfamplus, but not Magnetococcus, were the dominant MTB. Additionally, we recovered 3 MTB genomic bins that are unclassified at the species level, with Magnetovibrio blakemorei being the closest-associated genome. All the recovered genomic bins contain homologs of at least 5 of the 7 mam genes but lack homologs for mamI, a membrane protein suggested to take part in the magenetosome invagination. This study fills in the knowledge gap of MTB biodiversity in the tropical marine environment near the geo-equator. Our findings will facilitate future research efforts aiming to unravel the ecological roles of MTB in the tropical marine environments as well as to bioprospecting novel MTB that have been adapted to tropical marine environments for biotechnological applications.
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Affiliation(s)
- Shi Ming Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, 637551, Singapore
| | - Muhammad Hafiz Ismail
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, 637551, Singapore
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, N1-01C-69, 639798, Singapore.
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25
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Norouzi-Beirami MH, Marashi SA, Banaei-Moghaddam AM, Kavousi K. CAMAMED: a pipeline for composition-aware mapping-based analysis of metagenomic data. NAR Genom Bioinform 2021; 3:lqaa107. [PMID: 33575649 PMCID: PMC7787360 DOI: 10.1093/nargab/lqaa107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 10/29/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Metagenomics is the study of genomic DNA recovered from a microbial community. Both assembly-based and mapping-based methods have been used to analyze metagenomic data. When appropriate gene catalogs are available, mapping-based methods are preferred over assembly based approaches, especially for analyzing the data at the functional level. In this study, we introduce CAMAMED as a composition-aware mapping-based metagenomic data analysis pipeline. This pipeline can analyze metagenomic samples at both taxonomic and functional profiling levels. Using this pipeline, metagenome sequences can be mapped to non-redundant gene catalogs and the gene frequency in the samples are obtained. Due to the highly compositional nature of metagenomic data, the cumulative sum-scaling method is used at both taxa and gene levels for compositional data analysis in our pipeline. Additionally, by mapping the genes to the KEGG database, annotations related to each gene can be extracted at different functional levels such as KEGG ortholog groups, enzyme commission numbers and reactions. Furthermore, the pipeline enables the user to identify potential biomarkers in case-control metagenomic samples by investigating functional differences. The source code for this software is available from https://github.com/mhnb/camamed. Also, the ready to use Docker images are available at https://hub.docker.com.
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Affiliation(s)
- Mohammad H Norouzi-Beirami
- Laboratory of Complex Biological systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran 1417614335, Iran
| | - Sayed-Amir Marashi
- Department of Biotechnology, College of Science, University of Tehran, Tehran 1417614411, Iran
| | - Ali M Banaei-Moghaddam
- Laboratory of Genomics and Epigenomics (LGE), Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran 1417614335, Iran
| | - Kaveh Kavousi
- Laboratory of Complex Biological systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran 1417614335, Iran
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26
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Davis BC, Riquelme MV, Ramirez-Toro G, Bandaragoda C, Garner E, Rhoads WJ, Vikesland P, Pruden A. Demonstrating an Integrated Antibiotic Resistance Gene Surveillance Approach in Puerto Rican Watersheds Post-Hurricane Maria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15108-15119. [PMID: 33205660 DOI: 10.1021/acs.est.0c05567] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Comprehensive surveillance approaches are needed to assess sources, clinical relevance, and mobility of antibiotic resistance genes (ARGs) in watersheds. Here, we examined metrics derived from shotgun metagenomic sequencing and relationship to human fecal markers (HFMs; crAssphage, enterococci) and anthropogenic antibiotic resistance markers (AARMs; intI1, sul1) in three distinct Puerto Rican watersheds as a function of adjacent land use and wastewater treatment plant (WWTP) input 6 months after Hurricane Maria, a category V storm. Relative abundance and diversity of total ARGs increased markedly downstream of WWTP inputs, with ARGs unique to WWTP and WWTP-impacted river samples predominantly belonging to the aminoglycoside and β-lactam resistance classes. WWTP and other anthropogenic inputs were similarly associated with elevated resistome risk scores and mobility incidence (M%). Contig analysis indicated a wide variety of mobile β-lactam ARGs associated with pathogens downstream of WWTP discharge that were consistent with regional clinical concern, e.g., Klebsiella pneumoniae contigs containing KPC-2 within an ISKpn6-like transposase. HFMs and AARMs correlated strongly with the absolute abundance of total ARGs, but AARMs better predicted the majority of ARGs in general (85.4 versus <2%) and β-lactam ARGs in particular. This study reveals sensitive, quantitative, mobile, clinically relevant, and comprehensive targets for antibiotic resistance surveillance in watersheds.
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Affiliation(s)
- Benjamin C Davis
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Maria Virginia Riquelme
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Graciela Ramirez-Toro
- Center for Environmental Education, Conservation and Research, Inter American University, San Germán, Puerto Rico 00683, United States
| | - Christina Bandaragoda
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Emily Garner
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - William J Rhoads
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Peter Vikesland
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24060, United States
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27
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Hu A, Wang H, Li J, Mulla SI, Qiu Q, Tang L, Rashid A, Wu Y, Sun Q, Yu CP. Homogeneous selection drives antibiotic resistome in two adjacent sub-watersheds, China. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122820. [PMID: 32502801 DOI: 10.1016/j.jhazmat.2020.122820] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 04/21/2020] [Accepted: 05/07/2020] [Indexed: 05/12/2023]
Abstract
Rivers are a significant reservoir of antibiotic resistance genes (ARGs), yet the biogeographic pattern of riverine ARGs and its underlying driving forces remain poorly understood. Here, we used metagenomic approach to investigate the spatio-temporal variation of ARGs in two adjacent sub-watersheds viz. North River (NR) and West River (WR), China. The results demonstrated that Bacitracin (22.8 % of the total ARGs), multidrug (20.7 %), sulfonamide (15.2 %) and tetracycline (10.9 %) were the dominant ARG types. SourceTracker analysis indicated that sewage treatment plants as the main source of ARGs, while animal feces mainly contributed in spreading the ARGs in the upstream of NR. Random forest and network analyses confirmed that NR was under the influence of fecal pollution. PCoA analysis demonstrated that the composition of ARGs changed along with the anthropogenic gradients, while the Raup-Crick null model showed that homogenizing selection mediated by class 1 integron intI1 resulted in stable ARG communities at whole watershed scale. Structural equation models revealed that microbial community, grassland and several non-antibiotic micropollutants may also play certain roles in influencing the distribution of ARGs. Overall, the observed deterministic formation of ARGs in riverine systems calls effective management strategies to mitigate the risks of antibiotic resistance on public health.
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Affiliation(s)
- Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Hongjie Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiangwei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Sikandar I Mulla
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Department of Biochemistry, School of Applied Sciences, Reva University, Bangalore, 560 064, India
| | - Quanyi Qiu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Lina Tang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Azhar Rashid
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Nuclear Institute for Food and Agriculture, Tarnab, Peshawar, Pakistan
| | - Yang Wu
- Department of Biology and Environmental Engineering, Hefei University, Hefei 230601, China
| | - Qian Sun
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan.
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28
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Flores-Orozco D, Patidar R, Levin DB, Sparling R, Kumar A, Çiçek N. Effect of mesophilic anaerobic digestion on the resistome profile of dairy manure. BIORESOURCE TECHNOLOGY 2020; 315:123889. [PMID: 32717520 DOI: 10.1016/j.biortech.2020.123889] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
The effect of mesophilic anaerobic digestion (AD) on the resistome profile of manures from two different dairy farms was evaluated using a metagenomic approach. A total of 187 unique Antibiotic resistance genes (ARGs) for 17 different classes of antibiotics were detected in raw (undigested) manures. The results indicate that regardless of the origin of the dairy manure, mesophilic AD was capable of reducing or enriching the relative abundance of some ARGs. The main driver of these changes was strongly correlated with the evolution of the microbial community during the AD process. Putative ARG hosts were suggested by analyses of the co-occurrence of microbial groups and ARGs. Finally, network analyses revealed that mesophilic AD could also reduce the co-occurrence of different groups of ARGs potentially located in the same genetic elements. Our results provide valuable insights into the microbial mechanisms driving the diversity and abundance of ARGs during mesophilic AD.
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Affiliation(s)
- Daniel Flores-Orozco
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada.
| | - Rakesh Patidar
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada.
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada.
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada.
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada.
| | - Nazim Çiçek
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba R3T 5V6, Canada.
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29
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Yasir M, Bibi F, Hashem AM, Azhar EI. Comparative metagenomics and characterization of antimicrobial resistance genes in pasteurized and homemade fermented Arabian laban. Food Res Int 2020; 137:109639. [PMID: 33233218 DOI: 10.1016/j.foodres.2020.109639] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/18/2020] [Accepted: 08/21/2020] [Indexed: 11/25/2022]
Abstract
The aim of this study was to investigate bacterial diversity and function in a fermented milk drink called laban, which is traditionally served in the Middle East, Africa, and Indian subcontinent. Pasteurized laban (LBP) and unpasteurized, homemade, raw laban (LBR) underwent 16S rRNA gene amplicon and shotgun sequencing to analyze their bacterial community, presence of antimicrobial resistance genes (ARGs), and metabolic pathways. This study highlighted relatively greater diversity in LBR bacterial populations compared to LBP, despite containing similar major taxa that consisted primarily of Firmicutes followed by Proteobacteria, Bacteroidetes, and Actinobacteria. The dominant species, Streptococcus thermophilus, was relatively more abundant in LBP (80.7%) compared to LBR (47.9%). LBR had increased diversity and higher relative abundance of several known probiotic bacteria, such as Streptococcus salivarius and Lactococcus lactis, whereas Lactobacillus acidophilus was detected at a higher abundance in LBP. Pathogens like Acinetobacter baumannii, Streptococcus pneumoniae, Streptococcus pyogenes, and Escherichia coli had lower abundance in LBP compared to LBR. Thirty-three ARGs were detected in LBR compared to nine in LBP and are responsible for resistance to 11 classes of antibiotics. A significant proportion of the metagenomes from both types of laban were assigned to housekeeping functions, such as amino acid metabolism, translation, membrane transport, and carbohydrate metabolism. LBR demonstrated increased diversity in probiotics and metabolic functions compared to LBP. However, the relatively high diversity of pathogenic and opportunistic bacteria and ARGs in LBR raises safety concerns and highlights the need for a more hygienic environment for the processing of homemade fermented dairy foods.
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Affiliation(s)
- Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M Hashem
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia; Vaccines and Immunnotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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30
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Pérez-Cobas AE, Gomez-Valero L, Buchrieser C. Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. Microb Genom 2020; 6:mgen000409. [PMID: 32706331 PMCID: PMC7641418 DOI: 10.1099/mgen.0.000409] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/30/2020] [Indexed: 12/23/2022] Open
Abstract
Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France and CNRS UMR 3525, 675724, Paris, France
| | - Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France and CNRS UMR 3525, 675724, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France and CNRS UMR 3525, 675724, Paris, France
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Ekwanzala MD, Dewar JB, Momba MNB. Environmental resistome risks of wastewaters and aquatic environments deciphered by shotgun metagenomic assembly. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 197:110612. [PMID: 32302860 DOI: 10.1016/j.ecoenv.2020.110612] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
In this paper, we deciphered the core resistome disseminating from hospital wastewater to the aquatic environment by characterising the resistome, plasmidome, mobilome and virulome using metagenomic analysis. This study also elucidated different environmental resistome risks using shotgun-metagenomic assembly. The results showed that clinically relevant taxa were found in assessed matrices (Salmonella spp., Acinetobacter spp, Escherichia-Shigella spp., Pseudomonas spp., Staphylococcus spp. and Vibrio spp.). For the plasmidome, we found 249 core plasmidome sequences that were shared among all assessed matrices. The core mobilome of 2424 mobile genetic elements shared among all assessed matrices was found. Regarding the virulome, we found 148 core virulence factors shared among all assessed samples, and the core virulome content was consistently shared across the most abundant bacterial genera. Although influent of wastewater showed considerable higher relative bacterial abundance (P = 0.008), hospital wastewater showed significant higher environmental resistome risk scores against all other assessed matrices, with an average of 46.34% (P = 0.001). These results suggest hospital wastewater, effluent and sewage sludge should be subjected to stringent mitigating measures to minimise such dissemination.
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Affiliation(s)
- Mutshiene Deogratias Ekwanzala
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Private BagX680, Pretoria, 0001, South Africa.
| | - John Barr Dewar
- Department of Life and Consumer Sciences, University of South Africa, Florida Campus, Johannesburg, South Africa
| | - Maggy Ndombo Benteke Momba
- Department of Environmental, Water and Earth Sciences, Tshwane University of Technology, Arcadia Campus, Private BagX680, Pretoria, 0001, South Africa.
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Gupta S, Arango-Argoty G, Zhang L, Pruden A, Vikesland P. Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm. MICROBIOME 2019; 7:123. [PMID: 31466530 PMCID: PMC6716844 DOI: 10.1186/s40168-019-0735-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/14/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The interconnectivities of built and natural environments can serve as conduits for the proliferation and dissemination of antibiotic resistance genes (ARGs). Several studies have compared the broad spectrum of ARGs (i.e., "resistomes") in various environmental compartments, but there is a need to identify unique ARG occurrence patterns (i.e., "discriminatory ARGs"), characteristic of each environment. Such an approach will help to identify factors influencing ARG proliferation, facilitate development of relative comparisons of the ARGs distinguishing various environments, and help pave the way towards ranking environments based on their likelihood of contributing to the spread of clinically relevant antibiotic resistance. Here we formulate and demonstrate an approach using an extremely randomized tree (ERT) algorithm combined with a Bayesian optimization technique to capture ARG variability in environmental samples and identify the discriminatory ARGs. The potential of ERT for identifying discriminatory ARGs was first evaluated using in silico metagenomic datasets (simulated metagenomic Illumina sequencing data) with known variability. The application of ERT was then demonstrated through analyses using publicly available and in-house metagenomic datasets associated with (1) different aquatic habitats (e.g., river, wastewater influent, hospital effluent, and dairy farm effluent) to compare resistomes between distinct environments and (2) different river samples (i.e., Amazon, Kalamas, and Cam Rivers) to compare resistome characteristics of similar environments. RESULTS The approach was found to readily identify discriminatory ARGs in the in silico datasets. Also, it was not found to be biased towards ARGs with high relative abundance, which is a common limitation of feature projection methods, and instead only captured those ARGs that elicited significant profiles. Analyses of publicly available metagenomic datasets further demonstrated that the ERT approach can effectively differentiate real-world environmental samples and identify discriminatory ARGs based on pre-defined categorizing schemes. CONCLUSIONS Here a new methodology was formulated to characterize and compare variances in ARG profiles between metagenomic data sets derived from similar/dissimilar environments. Specifically, identification of discriminatory ARGs among samples representing various environments can be identified based on factors of interest. The methodology could prove to be a particularly useful tool for ARG surveillance and the assessment of the effectiveness of strategies for mitigating the spread of antibiotic resistance. The python package is hosted in the Git repository: https://github.com/gaarangoa/ExtrARG.
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Affiliation(s)
- Suraj Gupta
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061 USA
| | | | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061 USA
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Peter Vikesland
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
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Chen C, Pankow CA, Oh M, Heath LS, Zhang L, Du P, Xia K, Pruden A. Effect of antibiotic use and composting on antibiotic resistance gene abundance and resistome risks of soils receiving manure-derived amendments. ENVIRONMENT INTERNATIONAL 2019; 128:233-243. [PMID: 31059918 DOI: 10.1016/j.envint.2019.04.043] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 05/12/2023]
Abstract
Manure-derived amendments are commonly applied to soil, raising questions about whether antibiotic use in livestock could influence the soil resistome (collective antibiotic resistance genes (ARGs)) and ultimately contribute to the spread of antibiotic resistance to humans during food production. Here, we examined the metagenomes of soils amended with raw or composted manure generated from dairy cows administered pirlimycin and cephapirin (antibiotic) or no antibiotics (control) relative to unamended soils. Initial amendment (Day 1) with manure or compost significantly increased the diversity (richness) of ARGs in soils (p < 0.01) and resulted in distinct abundances of individual ARG types. Notably, initial amendment with antibiotic-manure significantly increased the total ARG relative abundances (per 16S rRNA gene) in the soils (2.21 × unamended soils, p < 0.001). After incubating 120 days, to simulate a wait period before crop harvest, 282 ARGs reduced 4.33-fold (median) up to 307-fold while 210 ARGs increased 2.89-fold (median) up to 76-fold in the antibiotic-manure-amended soils, resulting in reduced total ARG relative abundances equivalent to those of the unamended soils. We further assembled the metagenomic data and calculated resistome risk scores, which was recently defined as a relative index comparing co-occurrence of sequences corresponding to ARGs, mobile genetic elements, and putative pathogens on the same scaffold. Initial amendment of manure significantly increased the soil resistome risk scores, especially when generated by cows administered antibiotics, while composting reduced the effects and resulted in soil resistomes more similar to the background. The risk scores of manure-amended soils reduced to levels comparable to the unamended soils after 120 days. Overall, this study provides an integrated, high-resolution examination of the effects of prior antibiotic use, composting, and a 120-day wait period on soil resistomes following manure-derived amendment, demonstrating that all three management practices have measurable effects and should be taken into consideration in the development of policy and practice for mitigating the spread of antibiotic resistance.
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Affiliation(s)
- Chaoqi Chen
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, United States
| | - Christine A Pankow
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - Min Oh
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, United States
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, United States
| | - Pang Du
- Department of Statistics, Virginia Tech, Blacksburg, VA 24061, United States
| | - Kang Xia
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, United States.
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, United States
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Bürgmann H, Frigon D, H Gaze W, M Manaia C, Pruden A, Singer AC, F Smets B, Zhang T. Water and sanitation: an essential battlefront in the war on antimicrobial resistance. FEMS Microbiol Ecol 2019; 94:5033400. [PMID: 29878227 DOI: 10.1093/femsec/fiy101] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/06/2018] [Indexed: 12/15/2022] Open
Abstract
Water and sanitation represent a key battlefront in combatting the spread of antimicrobial resistance (AMR). Basic water sanitation infrastructure is an essential first step towards protecting public health, thereby limiting the spread of pathogens and the need for antibiotics. AMR presents unique human health risks, meriting new risk assessment frameworks specifically adapted to water and sanitation-borne AMR. There are numerous exposure routes to AMR originating from human waste, each of which must be quantified for its relative risk to human health. Wastewater treatment plants play a vital role in centralized collection and treatment of human sewage, but there are numerous unresolved issues in terms of the microbial ecological processes occurring within them and the extent to which they attenuate or amplify AMR. Research is needed to advance understanding of the fate of resistant bacteria and antibiotic resistance genes in various waste management systems, depending on the local constraints and intended reuse applications. World Health Organization and national AMR action plans would benefit from a more holistic 'One Water' understanding. In this article we provide a framework for research, policy, practice and public engagement aimed at limiting the spread of AMR from water and sanitation in low-, medium- and high-income countries.
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Affiliation(s)
- Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, Kastanienbaum, 6047, Switzerland
| | - Dominic Frigon
- Department of Civil Engineering, McGill University, 817 Sherbrooke Street West, Room 492, Montreal, Quebec, H3A 0C3, Canada
| | - William H Gaze
- European Center for Environment and Human Health, University of Exeter Medical School, Truro, TR1 3HD, UK
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBFQ- Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Robão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - Amy Pruden
- Via Department of Civil & Environmental Engineering, Virginia Tech, 418 Durham Hall, 1145 Perry Street, Blacksburg, Virginia, 24061, USA
| | - Andrew C Singer
- Centre for Ecology & Hydrology, NERC Centre for Ecology & Hydrology, Maclean Building, Benson Lane, Wallingford, OX10 8BB, UK
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej, DK 2800 Kgs., Lyngby, Denmark
| | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, Environmental Biotechnology Laboratory, The University of Hong Kong, Hong Kong
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Arango-Argoty GA, Dai D, Pruden A, Vikesland P, Heath LS, Zhang L. NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes. MICROBIOME 2019; 7:88. [PMID: 31174603 PMCID: PMC6555988 DOI: 10.1186/s40168-019-0703-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/28/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Direct and indirect selection pressures imposed by antibiotics and co-selective agents and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. Therefore, effective environmental monitoring tools should ideally capture not only antibiotic resistance genes (ARGs), but also mobile genetic elements (MGEs) and indicators of co-selective forces, such as metal resistance genes (MRGs). A major challenge towards characterizing the potential human health risk of antibiotic resistance is the ability to identify ARG-carrying microorganisms, of which human pathogens are arguably of greatest risk. Historically, short reads produced by next-generation sequencing technologies have hampered confidence in assemblies for achieving these purposes. RESULTS Here, we introduce NanoARG, an online computational resource that takes advantage of the long reads produced by nanopore sequencing technology. Specifically, long nanopore reads enable identification of ARGs in the context of relevant neighboring genes, thus providing valuable insight into mobility, co-selection, and pathogenicity. NanoARG was applied to study a variety of nanopore sequencing data to demonstrate its functionality. NanoARG was further validated through characterizing its ability to correctly identify ARGs in sequences of varying lengths and a range of sequencing error rates. CONCLUSIONS NanoARG allows users to upload sequence data online and provides various means to analyze and visualize the data, including quantitative and simultaneous profiling of ARGs, MRGs, MGEs, and putative pathogens. A user-friendly interface allows users the analysis of long DNA sequences (including assembled contigs), facilitating data processing, analysis, and visualization. NanoARG is publicly available and freely accessible at https://bench.cs.vt.edu/nanoarg .
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Affiliation(s)
| | - D. Dai
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA USA
| | - A. Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA USA
| | - P. Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA USA
| | - L. S. Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA USA
| | - L. Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA USA
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Guron GKP, Arango-Argoty G, Zhang L, Pruden A, Ponder MA. Effects of Dairy Manure-Based Amendments and Soil Texture on Lettuce- and Radish-Associated Microbiota and Resistomes. mSphere 2019; 4:e00239-19. [PMID: 31068435 PMCID: PMC6506619 DOI: 10.1128/msphere.00239-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/14/2019] [Indexed: 11/20/2022] Open
Abstract
Dairy cattle are routinely treated with antibiotics, and the resulting manure or composted manure is commonly used as a soil amendment for crop production, raising questions regarding the potential for antibiotic resistance to propagate from "farm to fork." The objective of this study was to compare the microbiota and "resistomes" (i.e., carriage of antibiotic resistance genes [ARGs]) associated with lettuce leaf and radish taproot surfaces grown in different soils amended with dairy manure, compost, or chemical fertilizer only (control). Manure was collected from antibiotic-free dairy cattle (DC) or antibiotic-treated dairy cattle (DA), with a portion composted for parallel comparison. Amendments were applied to loamy sand or silty clay loam, and lettuce and radishes were cultivated to maturity in a greenhouse. Metagenomes were profiled via shotgun Illumina sequencing. Radishes carried a distinct ARG composition compared to that of lettuce, with greater relative abundance of total ARGs. Taxonomic species richness was also greater for radishes by 1.5-fold. The resistomes of lettuce grown with DC compost were distinct from those grown with DA compost, DC manure, or fertilizer only. Further, compost applied to loamy sand resulted in twofold-greater relative abundance of total ARGs on lettuce than when applied to silty clay loam. The resistomes of radishes grown with biological amendments were distinct from the corresponding fertilizer controls, but effects of composting or antibiotic use were not measureable. Cultivation in loamy sand resulted in higher species richness for both lettuce and radishes than when grown in silty clay loam by 2.2-fold and 1.2-fold, respectively, when amended with compost.IMPORTANCE A controlled, integrated, and replicated greenhouse study, along with comprehensive metagenomic analysis, revealed that multiple preharvest factors, including antibiotic use during manure collection, composting, biological soil amendment, and soil type, influence vegetable-borne resistomes. Here, radishes, a root vegetable, carried a greater load of ARGs and species richness than lettuce, a leafy vegetable. However, the lettuce resistome was more noticeably influenced by upstream antibiotic use and composting. Network analysis indicated that cooccurring ARGs and mobile genetic elements were almost exclusively associated with conditions receiving raw manure amendments, suggesting that composting could alleviate the mobility of manure-derived resistance traits. Effects of preharvest factors on associated microbiota and resistomes of vegetables eaten raw are worthy of further examination in terms of potential influence on human microbiomes and spread of antibiotic resistance. This research takes a step toward identifying on-farm management practices that can help mitigate the spread of agricultural sources of antibiotic resistance.
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Affiliation(s)
- Giselle K P Guron
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - Monica A Ponder
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
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Vikesland P, Garner E, Gupta S, Kang S, Maile-Moskowitz A, Zhu N. Differential Drivers of Antimicrobial Resistance across the World. Acc Chem Res 2019; 52:916-924. [PMID: 30848890 DOI: 10.1021/acs.accounts.8b00643] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Antimicrobial resistance (AMR) is one of the greatest threats faced by humankind. The development of resistance in clinical and hospital settings has been well documented ever since the initial discovery of penicillin and the subsequent introduction of sulfonamides as clinical antibiotics. In contrast, the environmental (i.e., community-acquired) dimensions of resistance dissemination have been only more recently delineated. The global spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) between air, water, soil, and food is now well documented, while the factors that affect ARB and ARG dissemination (e.g., water and air quality, antibiotic fluxes, urbanization, sanitation practices) in these and other environmental matrices are just now beginning to be more fully appreciated. In this Account, we discuss how the global perpetuation of resistance is dictated by highly interconnected socioeconomic risk factors and illustrate that development status should be more fully considered when developing global strategies to address AMR. We first differentiate low to middle income countries (LMICs) and high-income countries (HICs), then we summarize the modes of action of commercially available antibiotics, and then discuss the four primary mechanisms by which bacteria develop resistance to those antibiotics. Resistance is disseminated via both vertical gene transfer (VGT; parent to offspring) as well as by horizontal gene transfer (HGT; cell to cell transference of genetic material). A key challenge hindering attempts to control resistance dissemination is the presence of native, environmental bacteria that can harbor ARGs. Such environmental "resistomes" have potential to transfer resistance to pathogens via HGT. Of particular concern is the development of resistance to antibiotics of last-resort such as the cephalosporins, carbapenems, and polymyxins. We then illustrate how antibiotic use differs in LMICs relative to HICs in terms of the volumes of antibiotics used and their fate within local environments. Antibiotic use in HICs has remained flat over the past 15 years, while in LMICs use over the same period has increased substantially as a result of economic improvements and changes in diet. These use and fate differences impact local citizens and thus the local dissemination of AMR. Various physical, social, and economic circumstances within LMICs potentially favor AMR dissemination. We focus on three physical factors: changing population density, sanitation infrastructure, and solid-waste disposal. We show that high population densities in cities within LMICs that suffer from poor sanitation and solid-waste disposal can potentially impact the dissemination of resistance. In the final section, we discuss potential monitoring approaches to quantify the spread of resistance both within LMICs as well as in HICs. We posit that culture-based approaches, molecular approaches, and cutting-edge nanotechnology-based methods for monitoring ARB and ARGs should be considered both within HICs and, as appropriate, within LMICs.
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Affiliation(s)
- Peter Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia Tech Global Change Center and Virginia Tech Institute of Critical Technology and Applied Science, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Emily Garner
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Suraj Gupta
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Seju Kang
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Ayella Maile-Moskowitz
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Ni Zhu
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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Fogler K, Guron GKP, Wind LL, Keenum IM, Hession WC, Krometis LA, Strawn LK, Pruden A, Ponder MA. Microbiota and Antibiotic Resistome of Lettuce Leaves and Radishes Grown in Soils Receiving Manure-Based Amendments Derived From Antibiotic-Treated Cows. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00022] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Dharmarha V, Guron G, Boyer RR, Niemira BA, Pruden A, Strawn LK, Ponder MA. Gamma Irradiation Influences the Survival and Regrowth of Antibiotic-Resistant Bacteria and Antibiotic-Resistance Genes on Romaine Lettuce. Front Microbiol 2019; 10:710. [PMID: 31024491 PMCID: PMC6465624 DOI: 10.3389/fmicb.2019.00710] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/21/2019] [Indexed: 02/01/2023] Open
Abstract
Contamination of romaine lettuce with human pathogens, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs) occurs during production. Post-harvest interventions are emplaced to mitigate pathogens, but could also mitigate ARB and ARGs on vegetables. The objective of this research was to determine changes to lettuce phyllosphere microbiota, inoculated ARB, and the resistome (profile of ARGs) following washing with a sanitizer, gamma irradiation, and cold storage. To simulate potential sources of pre-harvest contamination, romaine lettuce leaves were inoculated with compost slurry containing antibiotic-resistant strains of pathogenic (Escherichia coli O157:H7) and representative of spoilage bacteria (Pseudomonas aeruginosa). Various combinations of washing with sodium hypochlorite (50 ppm free chlorine), packaging under modified atmosphere (98% nitrogen), irradiating (1.0 kGy) and storing at 4°C for 1 day versus 14 days were compared. Effects of post-harvest treatments on the resistome were profiled by shotgun metagenomic sequencing. Bacterial 16S rRNA gene amplicon sequencing was performed to determine changes to the phyllosphere microbiota. Survival and regrowth of inoculated ARB were evaluated by enumeration on selective media. Washing lettuce in water containing sanitizer was associated with reduced abundance of ARG classes that confer resistance to glycopeptides, β-lactams, phenicols, and sulfonamides (Wilcoxon, p < 0.05). Washing followed by irradiation resulted in a different resistome chiefly due to reductions in multidrug, triclosan, polymyxin, β-lactam, and quinolone ARG classes (Wilcoxon, p < 0.05). Irradiation followed by storage at 4°C for 14 days led to distinct changes to the β-diversity of the host bacteria of ARGs compared to 1 day after treatment (ANOSIM, R = 0.331; p = 0.003). Storage of washed and irradiated lettuce at 4°C for 14 days increased the relative abundance of Pseudomonadaceae and Carnobacteriaceae (Wilcoxon, p < 0.05), two groups whose presence correlated with detection of 10 ARG classes on the lettuce phyllosphere (p < 0.05). Irradiation resulted in a significant reduction (∼3.5 log CFU/g) of inoculated strains of E. coli O157:H7 and P. aeruginosa (ANOVA, p < 0.05). Results indicate that washing, irradiation and storage of modified atmosphere packaged lettuce at 4°C are effective strategies to reduce antibiotic-resistant E. coli O157:H7 and P. aeruginosa and relative abundance of various ARG classes.
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Affiliation(s)
- Vaishali Dharmarha
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
| | - Giselle Guron
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Renee R. Boyer
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
| | - Brendan A. Niemira
- Food Safety and Intervention Technologies Research Unit, USDA-ARS Eastern Regional Research Center, Wyndmoor, PA, United States
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Laura K. Strawn
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
| | - Monica A. Ponder
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
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40
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Shaw LM, Blanchard A, Chen Q, An X, Davies P, Tötemeyer S, Zhu YG, Stekel DJ. DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples. Sci Rep 2019; 9:2373. [PMID: 30787410 PMCID: PMC6382752 DOI: 10.1038/s41598-019-38873-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
High throughput genomics technologies are applied widely to microbiomes in humans, animals, soil and water, to detect changes in bacterial communities or the genes they carry, between different environments or treatments. We describe a method to test the statistical significance of differences in bacterial population or gene composition, applicable to metagenomic or quantitative polymerase chain reaction data. Our method goes beyond previous published work in being universally most powerful, thus better able to detect statistically significant differences, and through being more reliable for smaller sample sizes. It can also be used for experimental design, to estimate how many samples to use in future experiments, again with the advantage of being universally most powerful. We present three example analyses in the area of antimicrobial resistance. The first is to published data on bacterial communities and antimicrobial resistance genes (ARGs) in the environment; we show that there are significant changes in both ARG and community composition. The second is to new data on seasonality in bacterial communities and ARGs in hooves from four sheep. While the observed differences are not significant, we show that a minimum group size of eight sheep would provide sufficient power to observe significance of similar changes in further experiments. The third is to published data on bacterial communities surrounding rice crops. This is a much larger data set and is used to verify the new method. Our method has broad uses for statistical testing and experimental design in research on changing microbiomes, including studies on antimicrobial resistance.
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Affiliation(s)
- Laurence M Shaw
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK.,School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Adam Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, LE12 5RD, UK.,School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Brackenhurst, NG25 0FQ, UK
| | - Qinglin Chen
- Chinese Academy of Sciences, Institute of Urban Environment, Xiamen, 361021, China
| | - Xinli An
- Chinese Academy of Sciences, Institute of Urban Environment, Xiamen, 361021, China
| | - Peers Davies
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, LE12 5RD, UK.,Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Sabine Tötemeyer
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Yong-Guan Zhu
- Chinese Academy of Sciences, Institute of Urban Environment, Xiamen, 361021, China
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK.
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Dai D, Rhoads WJ, Edwards MA, Pruden A. Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation. Front Microbiol 2018; 9:2695. [PMID: 30542327 PMCID: PMC6277882 DOI: 10.3389/fmicb.2018.02695] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 10/23/2018] [Indexed: 12/20/2022] Open
Abstract
Hot water premise plumbing has emerged as a critical nexus of energy, water, and public health. The composition of hot water microbiomes is of special interest given daily human exposure to resident flora, especially opportunistic pathogens (OPs), which rely on complex microbial ecological interactions for their proliferation. Here, we applied shotgun metagenomic sequencing to characterize taxonomic and functional shifts in microbiomes as a function of water heater temperature setting, stagnation in distal pipes, and associated shifts in water chemistry. A cross-section of samples from controlled, replicated, pilot-scale hot water plumbing rigs representing different temperature settings (39, 42, and 51°C), stagnation periods (8 h vs. 7 days), and time-points, were analyzed. Temperature setting exhibited an overarching impact on taxonomic and functional gene composition. Further, distinct taxa were selectively enriched by specific temperature settings (e.g., Legionella at 39°C vs. Deinococcus at 51°C), while relative abundances of genes encoding corresponding cellular functions were highly consistent with expectations based on the taxa driving these shifts. Stagnation in distal taps diminished taxonomic and functional differences induced by heating the cold influent water to hot water in recirculating line. In distal taps relative to recirculating hot water, reads annotated as being involved in metabolism and growth decreased, while annotations corresponding to stress response (e.g., virulence disease and defense, and specifically antibiotic resistance) increased. Reads corresponding to OPs were readily identified by metagenomic analysis, with L. pneumophila reads in particular correlating remarkably well with gene copy numbers measured by quantitative polymerase chain reaction. Positive correlations between L. pneumophila reads and those of known protozoan hosts were also identified. Elevated proportions of genes encoding metal resistance and hydrogen metabolism were noted, which was consistent with elevated corrosion-induced metal concentrations and hydrogen generation. This study provided new insights into real-world factors influencing taxonomic and functional compositions of hot water microbiomes. Here metagenomics is demonstrated as an effective tool for screening for potential presence, and even quantities, of pathogens, while also providing diagnostic capabilities for assessing functional responses of microbiomes to various operational conditions. These findings can aid in informing future monitoring and intentional control of hot water microbiomes.
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Affiliation(s)
| | | | | | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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Oh M, Pruden A, Chen C, Heath LS, Xia K, Zhang L. MetaCompare: a computational pipeline for prioritizing environmental resistome risk. FEMS Microbiol Ecol 2018; 94:4987204. [PMID: 29718191 PMCID: PMC5995210 DOI: 10.1093/femsec/fiy079] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 12/27/2022] Open
Abstract
The spread of antibiotic resistance is a growing public health concern. While numerous studies have highlighted the importance of environmental sources and pathways of the spread of antibiotic resistance, a systematic means of comparing and prioritizing risks represented by various environmental compartments is lacking. Here, we introduce MetaCompare, a publicly available tool for ranking 'resistome risk', which we define as the potential for antibiotic resistance genes (ARGs) to be associated with mobile genetic elements (MGEs) and mobilize to pathogens based on metagenomic data. A computational pipeline was developed in which each ARG is evaluated based on relative abundance, mobility, and presence within a pathogen. This is determined through the assembly of shotgun sequencing data and analysis of contigs containing ARGs to determine if they contain sequence similarity to MGEs or human pathogens. Based on the assembled metagenomes, samples are projected into a 3-dimensionalhazard space and assigned resistome risk scores. To validate, we tested previously published metagenomic data derived from distinct aquatic environments. Based on unsupervised machine learning, the test samples clustered in the hazard space in a manner consistent with their origin. The derived scores produced a well-resolved ascending resistome risk ranking of: wastewater treatment plant effluent, dairy lagoon, and hospital sewage.
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Affiliation(s)
- Min Oh
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Chaoqi Chen
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Kang Xia
- Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
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Garner E, Chen C, Xia K, Bowers J, Engelthaler DM, McLain J, Edwards MA, Pruden A. Metagenomic Characterization of Antibiotic Resistance Genes in Full-Scale Reclaimed Water Distribution Systems and Corresponding Potable Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6113-6125. [PMID: 29741366 DOI: 10.1021/acs.est.7b05419] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Water reclamation provides a valuable resource for meeting nonpotable water demands. However, little is known about the potential for wastewater reuse to disseminate antibiotic resistance genes (ARGs). Here, samples were collected seasonally in 2014-2015 from four U.S. utilities' reclaimed and potable water distribution systems before treatment, after treatment, and at five points of use (POU). Shotgun metagenomic sequencing was used to profile the resistome (i.e., full contingent of ARGs) of a subset ( n = 38) of samples. Four ARGs ( qnrA, blaTEM, vanA, sul1) were quantified by quantitative polymerase chain reaction. Bacterial community composition (via 16S rRNA gene amplicon sequencing), horizontal gene transfer (via quantification of intI1 integrase and plasmid genes), and selection pressure (via detection of metals and antibiotics) were investigated as potential factors governing the presence of ARGs. Certain ARGs were elevated in all ( sul1; p ≤ 0.0011) or some ( blaTEM, qnrA; p ≤ 0.0145) reclaimed POU samples compared to corresponding potable samples. Bacterial community composition was weakly correlated with ARGs (Adonis, R2 = 0.1424-0.1734) and associations were noted between 193 ARGs and plasmid-associated genes. This study establishes that reclaimed water could convey greater abundances of certain ARGs than potable waters and provides observations regarding factors that likely control ARG occurrence in reclaimed water systems.
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Affiliation(s)
- Emily Garner
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Chaoqi Chen
- Department of Crop and Soil Environmental Sciences , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Kang Xia
- Department of Crop and Soil Environmental Sciences , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Jolene Bowers
- Translational Genomics Research Institute , Flagstaff , Arizona 86005 , United States
| | - David M Engelthaler
- Translational Genomics Research Institute , Flagstaff , Arizona 86005 , United States
| | - Jean McLain
- Water Resources Research Center , University of Arizona , Tucson , Arizona 85719 , United States
| | - Marc A Edwards
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
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Metch JW, Burrows ND, Murphy CJ, Pruden A, Vikesland PJ. Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design. NATURE NANOTECHNOLOGY 2018; 13:253-259. [PMID: 29335567 DOI: 10.1038/s41565-017-0029-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 11/14/2017] [Indexed: 05/27/2023]
Abstract
Next-generation DNA sequencing and metagenomic analysis provide powerful tools for the environmentally friendly design of nanoparticles. Herein we demonstrate this approach using a model community of environmental microbes (that is, wastewater-activated sludge) dosed with gold nanoparticles of varying surface coatings and morphologies. Metagenomic analysis was highly sensitive in detecting the microbial community response to gold nanospheres and nanorods with either cetyltrimethylammonium bromide or polyacrylic acid surface coatings. We observed that the gold-nanoparticle morphology imposes a stronger force in shaping the microbial community structure than does the surface coating. Trends were consistent in terms of the compositions of both taxonomic and functional genes, which include antibiotic resistance genes, metal resistance genes and gene-transfer elements associated with cell stress that are relevant to public health. Given that nanoparticle morphology remained constant, the potential influence of gold dissolution was minimal. Surface coating governed the nanoparticle partitioning between the bioparticulate and aqueous phases.
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Affiliation(s)
- Jacob W Metch
- Via Department of Civil and Environmental Engineering and Institute for Critical Technology and Applied Science (ICTAS), Virginia Tech, Blacksburg, VA, USA
| | - Nathan D Burrows
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering and Institute for Critical Technology and Applied Science (ICTAS), Virginia Tech, Blacksburg, VA, USA.
| | - Peter J Vikesland
- Via Department of Civil and Environmental Engineering and Institute for Critical Technology and Applied Science (ICTAS), Virginia Tech, Blacksburg, VA, USA.
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Reusing Treated Wastewater: Consideration of the Safety Aspects Associated with Antibiotic-Resistant Bacteria and Antibiotic Resistance Genes. WATER 2018. [DOI: 10.3390/w10030244] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Arango-Argoty G, Garner E, Pruden A, Heath LS, Vikesland P, Zhang L. DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data. MICROBIOME 2018; 6:23. [PMID: 29391044 PMCID: PMC5796597 DOI: 10.1186/s40168-018-0401-z] [Citation(s) in RCA: 364] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/10/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Growing concerns about increasing rates of antibiotic resistance call for expanded and comprehensive global monitoring. Advancing methods for monitoring of environmental media (e.g., wastewater, agricultural waste, food, and water) is especially needed for identifying potential resources of novel antibiotic resistance genes (ARGs), hot spots for gene exchange, and as pathways for the spread of ARGs and human exposure. Next-generation sequencing now enables direct access and profiling of the total metagenomic DNA pool, where ARGs are typically identified or predicted based on the "best hits" of sequence searches against existing databases. Unfortunately, this approach produces a high rate of false negatives. To address such limitations, we propose here a deep learning approach, taking into account a dissimilarity matrix created using all known categories of ARGs. Two deep learning models, DeepARG-SS and DeepARG-LS, were constructed for short read sequences and full gene length sequences, respectively. RESULTS Evaluation of the deep learning models over 30 antibiotic resistance categories demonstrates that the DeepARG models can predict ARGs with both high precision (> 0.97) and recall (> 0.90). The models displayed an advantage over the typical best hit approach, yielding consistently lower false negative rates and thus higher overall recall (> 0.9). As more data become available for under-represented ARG categories, the DeepARG models' performance can be expected to be further enhanced due to the nature of the underlying neural networks. Our newly developed ARG database, DeepARG-DB, encompasses ARGs predicted with a high degree of confidence and extensive manual inspection, greatly expanding current ARG repositories. CONCLUSIONS The deep learning models developed here offer more accurate antimicrobial resistance annotation relative to current bioinformatics practice. DeepARG does not require strict cutoffs, which enables identification of a much broader diversity of ARGs. The DeepARG models and database are available as a command line version and as a Web service at http://bench.cs.vt.edu/deeparg .
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Affiliation(s)
| | - Emily Garner
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA USA
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA USA
| | - Lenwood S. Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA USA
| | - Peter Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA USA
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA USA
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