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Attah V, Milner DS, Fang Y, Yan X, Leonard G, Heitman J, Talbot NJ, Richards TA. Duplication and neofunctionalization of a horizontally transferred xyloglucanase as a facet of the Red Queen coevolutionary dynamic. Proc Natl Acad Sci U S A 2024; 121:e2218927121. [PMID: 38830094 PMCID: PMC11181080 DOI: 10.1073/pnas.2218927121] [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: 11/13/2022] [Accepted: 04/20/2024] [Indexed: 06/05/2024] Open
Abstract
Oomycete protists share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a distant region of the tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-to-oomycetes contributed to the evolution of plant-pathogenic traits. These HGTs are predicted to include secreted proteins that degrade plant cell walls, a barrier to pathogen invasion and a rich source of carbohydrates. Using a combination of phylogenomics and functional assays, we investigate the diversification of a horizontally transferred xyloglucanase gene family in the model oomycete species Phytophthora sojae. Our analyses detect 11 xyloglucanase paralogs retained in P. sojae. Using heterologous expression in yeast, we show consistent evidence that eight of these paralogs have xyloglucanase function, including variants with distinct protein characteristics, such as a long-disordered C-terminal extension that can increase xyloglucanase activity. The functional variants analyzed subtend a phylogenetic node close to the fungi-to-oomycete transfer, suggesting the horizontally transferred gene was a bona fide xyloglucanase. Expression of three xyloglucanase paralogs in Nicotiana benthamiana triggers high-reactive oxygen species (ROS) generation, while others inhibit ROS responses to bacterial immunogens, demonstrating that the paralogs differentially stimulate pattern-triggered immunity. Mass spectrometry of detectable enzymatic products demonstrates that some paralogs catalyze the production of variant breakdown profiles, suggesting that secretion of variant xyloglucanases increases efficiency of xyloglucan breakdown as well as diversifying the damage-associated molecular patterns released. We suggest that this pattern of neofunctionalization and the variant host responses represent an aspect of the Red Queen host-pathogen coevolutionary dynamic.
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Affiliation(s)
- Victoria Attah
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - David S. Milner
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Yufeng Fang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Xia Yan
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNR4 7UH, United Kingdom
| | - Guy Leonard
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC27710
| | - Nicholas J. Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNR4 7UH, United Kingdom
| | - Thomas A. Richards
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
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Attah V, Milner DS, Fang Y, Yan X, Leonard G, Heitman J, Talbot NJ, Richards TA. Duplication and neofunctionalization of a horizontally-transferred xyloglucanase as a facet of the red queen co-evolutionary dynamic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561229. [PMID: 37873201 PMCID: PMC10592688 DOI: 10.1101/2023.10.09.561229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Oomycetes are heterotrophic protists that share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a separate and distant region of the eukaryotic tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-to-oomycetes contributed to the evolution of plant-pathogenic traits. These HGTs are predicted to include secreted proteins that degrade plant cell walls. This is a key trait in the pathology of many oomycetes, as the plant cell wall represents a primary barrier to pathogen invasion and a rich source of carbohydrates. Many of the HGT gene families identified have undergone multiple rounds of duplication. Using a combination of phylogenomic analysis and functional assays, we investigate the diversification of a horizontally-transferred xyloglucanase gene family in the model oomycete species Phytophthora sojae. Our analyses detect 11 genes retained in P. sojae among a complex pattern of gene duplications and losses. Using a phenotype assay, based on heterologous expression in yeast, we show that eight of these paralogs have xyloglucanase function, including variants with distinct protein characteristics, such as a long-disordered C-terminal extension that can increase xyloglucanase activity. The functional xyloglucanase variants analysed subtend an ancestral node close to the fungi-oomycetes gene transfer, suggesting the horizontally-transferred gene was a bona fide xyloglucanase. Expression of xyloglucanase paralogs in Nicotiana benthamiana triggers distinct patterns of reactive oxygen species (ROS) generation, demonstrating that enzyme variants differentially stimulate pattern-triggered immunity in plants. Mass spectrometry of detectable enzymatic products demonstrates that some paralogs catalyze production of variant breakdown profiles, suggesting that secretion of multiple xyloglucanase variants increases efficiency of xyloglucan breakdown, as well as potentially diversifying the range of Damage-Associated Molecular Patterns (DAMPs) released during pathogen attack. We suggest that such patterns of protein neofunctionalization, and variant host responses, represent an aspect of the Red Queen host-pathogen co-evolutionary dynamic. Significance Statement The oomycetes are a diverse group of eukaryotic microbes that include some of the most devastating pathogens of plants. Oomycetes perceive, invade, and colonize plants in similar ways to fungi, in part because they acquired the genes to attack and feed on plants from fungi. These genes are predicted to be useful to oomycete plant pathogens because they have undergone multiple rounds of gene duplication. One key enzyme for attacking plant cell wall structures is called xyloglucanase. Xyloglucanase in the oomycetes has undergone multiple rounds of gene duplication, leading to variants including an enzyme with a C-terminal extension that increases activity. Some xyloglucanase variants trigger unique patterns of reactive oxygen species (ROS) in planta, and generate different profiles of cell wall breakdown products - such outcomes could act to mystify and increase the workload of the plant immune system, allowing successful pathogens to proliferate.
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Affiliation(s)
- Victoria Attah
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - David S Milner
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Yufeng Fang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Current address: GreenLight Biosciences Inc., Research Triangle Park, North Carolina, United States of America
| | - Xia Yan
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, United Kingdom
| | - Guy Leonard
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, United Kingdom
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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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Baker M, Williams AD, Hooton SPT, Helliwell R, King E, Dodsworth T, María Baena-Nogueras R, Warry A, Ortori CA, Todman H, Gray-Hammerton CJ, Pritchard ACW, Iles E, Cook R, Emes RD, Jones MA, Kypraios T, West H, Barrett DA, Ramsden SJ, Gomes RL, Hudson C, Millard AD, Raman S, Morris C, Dodd CER, Kreft JU, Hobman JL, Stekel DJ. Antimicrobial resistance in dairy slurry tanks: A critical point for measurement and control. ENVIRONMENT INTERNATIONAL 2022; 169:107516. [PMID: 36122459 DOI: 10.1016/j.envint.2022.107516] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
Waste from dairy production is one of the largest sources of contamination from antimicrobial resistant bacteria (ARB) and genes (ARGs) in many parts of the world. However, studies to date do not provide necessary evidence to inform antimicrobial resistance (AMR) countermeasures. We undertook a detailed, interdisciplinary, longitudinal analysis of dairy slurry waste. The slurry contained a population of ARB and ARGs, with resistances to current, historical and never-used on-farm antibiotics; resistances were associated with Gram-negative and Gram-positive bacteria and mobile elements (ISEcp1, Tn916, Tn21-family transposons). Modelling and experimental work suggested that these populations are in dynamic equilibrium, with microbial death balanced by fresh input. Consequently, storing slurry without further waste input for at least 60 days was predicted to reduce ARB spread onto land, with > 99 % reduction in cephalosporin resistant Escherichia coli. The model also indicated that for farms with low antibiotic use, further reductions are unlikely to reduce AMR further. We conclude that the slurry tank is a critical point for measurement and control of AMR, and that actions to limit the spread of AMR from dairy waste should combine responsible antibiotic use, including low total quantity, avoidance of human critical antibiotics, and choosing antibiotics with shorter half-lives, coupled with appropriate slurry storage.
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Affiliation(s)
- Michelle Baker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Alexander D Williams
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Steven P T Hooton
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; (a)Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Richard Helliwell
- School of Sociology and Social Policy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK; School of Geography, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK; Ruralis, University Centre Dragvoll, N-7491 Trondheim, Norway
| | - Elizabeth King
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Thomas Dodsworth
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; ResChem Analytical Ltd, 8 Jubilee Parkway, Jubilee Business Park, Stores Road, Derby DE21 4BJ, UK
| | - Rosa María Baena-Nogueras
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Andrew Warry
- Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Catherine A Ortori
- School of Pharmacy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Henry Todman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; School of Mathematical Sciences, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Charlotte J Gray-Hammerton
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Alexander C W Pritchard
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Ethan Iles
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Michael A Jones
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Theodore Kypraios
- School of Mathematical Sciences, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Helen West
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - David A Barrett
- School of Pharmacy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Stephen J Ramsden
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Rachel L Gomes
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Chris Hudson
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Andrew D Millard
- (a)Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Sujatha Raman
- School of Sociology and Social Policy, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK; Centre for Public Awareness of Science, Australian National University, Linnaeus Way, Acton ACT 2601, Canberra, Australia
| | - Carol Morris
- School of Geography, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| | - Christine E R Dodd
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Jan-Ulrich Kreft
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK; Department of Mathematics and Applied Mathematics, University of Johannesburg, Auckland Park Kingsway Campus, Rossmore, Johannesburg, South Africa.
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5
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Olson SW, Turner AMW, Arney JW, Saleem I, Weidmann CA, Margolis DM, Weeks KM, Mustoe AM. Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP. Mol Cell 2022; 82:1708-1723.e10. [PMID: 35320755 PMCID: PMC9081252 DOI: 10.1016/j.molcel.2022.02.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/29/2021] [Accepted: 02/02/2022] [Indexed: 12/17/2022]
Abstract
7SK is a conserved noncoding RNA that regulates transcription by sequestering the transcription factor P-TEFb. 7SK function entails complex changes in RNA structure, but characterizing RNA dynamics in cells remains an unsolved challenge. We developed a single-molecule chemical probing strategy, DANCE-MaP (deconvolution and annotation of ribonucleic conformational ensembles), that defines per-nucleotide reactivity, direct base pairing interactions, tertiary interactions, and thermodynamic populations for each state in RNA structural ensembles from a single experiment. DANCE-MaP reveals that 7SK RNA encodes a large-scale structural switch that couples dissolution of the P-TEFb binding site to structural remodeling at distal release factor binding sites. The 7SK structural equilibrium shifts in response to cell growth and stress and can be targeted to modulate expression of P-TEFbresponsive genes. Our study reveals that RNA structural dynamics underlie 7SK function as an integrator of diverse cellular signals to control transcription and establishes the power of DANCE-MaP to define RNA dynamics in cells.
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Affiliation(s)
- Samuel W Olson
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Anne-Marie W Turner
- Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; UNC HIV Cure Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - J Winston Arney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - Irfana Saleem
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA
| | - Chase A Weidmann
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
| | - David M Margolis
- Department of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; UNC HIV Cure Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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6
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Hassoun-Kheir N, Stabholz Y, Kreft JU, de la Cruz R, Dechesne A, Smets BF, Romalde JL, Lema A, Balboa S, García-Riestra C, Torres-Sangiao E, Neuberger A, Graham D, Quintela-Baluja M, Stekel DJ, Graham J, Pruden A, Nesme J, Sørensen SJ, Hough R, Paul M. EMBRACE-WATERS statement: Recommendations for reporting of studies on antimicrobial resistance in wastewater and related aquatic environments. One Health 2021; 13:100339. [PMID: 34746357 PMCID: PMC8554267 DOI: 10.1016/j.onehlt.2021.100339] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 10/17/2021] [Accepted: 10/17/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND A One Health approach requires integrative research to elucidate antimicrobial resistance (AMR) in the environment and the risks it poses to human health. Research on this topic involves experts from diverse backgrounds and professions. Shortcomings exist in terms of consistent, complete, and transparent reporting in many environmental studies. Standardized reporting will improve the quality of scientific papers, enable meta-analyses and enhance the communication among different experts. In this study, we aimed to generate a consensus of reporting standards for AMR research in wastewater and related aquatic environments. METHODS Based on a risk of bias assessment of the literature in a systematic review, we proposed a set of study quality indicators. We then used a multistep modified Delphi consensus to develop the EMBRACE-WATERS statement (rEporting antiMicroBial ResistAnCE in WATERS), a checklist of recommendations for reporting in studies of AMR in wastewater and related aquatic environments. FINDINGS Consensus was achieved among a multidisciplinary panel of twenty-one experts in three steps. The developed EMBRACE-WATERS statement incorporates 21 items. Each item contains essential elements of high-quality reporting and is followed by an explanation of their rationale and a reporting-example. The EMBRACE-WATERS statement is primarily intended to be used by investigators to ensure transparent and comprehensive reporting of their studies. It can also guide peer-reviewers and editors in evaluation of manuscripts on AMR in the aquatic environment. This statement is not intended to be used to guide investigators on the methodology of their research. INTERPRETATION We are hopeful that this statement will improve the reporting quality of future studies of AMR in wastewater and related aquatic environments. Its uptake would generate a common language to be used among researchers from different disciplines, thus advancing the One Health approach towards understanding AMR spread across aquatic environments. Similar initiatives are needed in other areas of One Health research.
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Affiliation(s)
- Nasreen Hassoun-Kheir
- Infectious Diseases Institute, Rambam Health Care Campus, HaAliya HaShniya St 8, Haifa 3109601, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel
| | - Yoav Stabholz
- Infectious Diseases Institute, Rambam Health Care Campus, HaAliya HaShniya St 8, Haifa 3109601, Israel
| | - Jan-Ulrich Kreft
- School of Biosciences, Institute of Microbiology and Infection (IMI), Centre for Computational Biology (CCB), University of Birmingham, Birmingham, UK
| | - Roberto de la Cruz
- School of Biosciences, Institute of Microbiology and Infection (IMI), Centre for Computational Biology (CCB), University of Birmingham, Birmingham, UK
| | - Arnaud Dechesne
- Technical University of Denmark, Department of Environmental Engineering, bygning 115, Bygningstorvet, 2800 Kongens Lyngby, Denmark
| | - Barth F. Smets
- Technical University of Denmark, Department of Environmental Engineering, bygning 115, Bygningstorvet, 2800 Kongens Lyngby, Denmark
| | - Jesús L. Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
- CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Alberto Lema
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Sabela Balboa
- CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Carlos García-Riestra
- Department of Microbiology and Parasitology, University Hospital Complex of Santiago (CHUS), Spain
| | - Eva Torres-Sangiao
- Escherichia coli Group, Research Foundation Institute (FIDIS), University Hospital Complex (CHUS), Santiago de Compostela, ES, Spain
| | - Ami Neuberger
- Infectious Diseases Institute, Rambam Health Care Campus, HaAliya HaShniya St 8, Haifa 3109601, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel
| | - David Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | | | - Dov J. Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough LE12 5RD, UK
| | - Jay Graham
- University of California, Berkeley School of Public Health, Berkeley, CA, USA
| | - Amy Pruden
- The Charles Edward Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Rupert Hough
- Information and Computational Sciences, The James Hutton Institute, Aberdeen AB15 8QH, Scotland, UK
| | - Mical Paul
- Infectious Diseases Institute, Rambam Health Care Campus, HaAliya HaShniya St 8, Haifa 3109601, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel
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7
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Cook R, Hooton S, Trivedi U, King L, Dodd CER, Hobman JL, Stekel DJ, Jones MA, Millard AD. Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens. MICROBIOME 2021; 9:65. [PMID: 33743832 PMCID: PMC7981956 DOI: 10.1186/s40168-021-01010-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/02/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~ 2.7 million dairy cattle in the UK producing 7-8% of their own bodyweight in manure daily, and 28 million tonnes annually. To avoid pollution of UK freshwaters, manure must be stored and spread in accordance with guidelines set by DEFRA. Manures are used as fertiliser, and widely spread over crop fields, yet little is known about their microbial composition. We analysed the virome of agricultural slurry over a 5-month period using short and long-read sequencing. RESULTS Hybrid sequencing uncovered more high-quality viral genomes than long or short-reads alone; yielding 7682 vOTUs, 174 of which were complete viral genomes. The slurry virome was highly diverse and dominated by lytic bacteriophage, the majority of which represent novel genera (~ 98%). Despite constant influx and efflux of slurry, the composition and diversity of the slurry virome was extremely stable over time, with 55% of vOTUs detected in all samples over a 5-month period. Functional annotation revealed a diverse and abundant range of auxiliary metabolic genes and novel features present in the community, including the agriculturally relevant virulence factor VapE, which was widely distributed across different phage genera that were predicted to infect several hosts. Furthermore, we identified an abundance of phage-encoded diversity-generating retroelements, which were previously thought to be rare on lytic viral genomes. Additionally, we identified a group of crAssphages, including lineages that were previously thought only to be found in the human gut. CONCLUSIONS The cattle slurry virome is complex, diverse and dominated by novel genera, many of which are not recovered using long or short-reads alone. Phages were found to encode a wide range of AMGs that are not constrained to particular groups or predicted hosts, including virulence determinants and putative ARGs. The application of agricultural slurry to land may therefore be a driver of bacterial virulence and antimicrobial resistance in the environment. Video abstract.
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Affiliation(s)
- Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Steve Hooton
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Liz King
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Christine E R Dodd
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Michael A Jones
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK.
| | - Andrew D Millard
- Dept Genetics and Genome Biology, University of Leicester, University Road, Leicester, Leicestershire, LE1 7RH, UK.
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8
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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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9
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Flaujac Lafontaine GM, Richards PJ, Connerton PL, O’Kane PM, Ghaffar NM, Cummings NJ, Fish NM, Connerton IF. Prebiotic Driven Increases in IL-17A Do Not Prevent Campylobacter jejuni Colonization of Chickens. Front Microbiol 2020; 10:3030. [PMID: 32010094 PMCID: PMC6972505 DOI: 10.3389/fmicb.2019.03030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/17/2019] [Indexed: 01/13/2023] Open
Abstract
Worldwide Campylobacter jejuni is a leading cause of foodborne disease. Contamination of chicken meat with digesta from C. jejuni-positive birds during slaughter and processing is a key route of transmission to humans through the food chain. Colonization of chickens with C. jejuni elicits host innate immune responses that may be modulated by dietary additives to provide a reduction in the number of campylobacters colonizing the gastrointestinal tract and thereby reduce the likelihood of human exposure to an infectious dose. Here we report the effects of prebiotic galacto-oligosaccharide (GOS) on broiler chickens colonized with C. jejuni when challenged at either an early stage in development at 6 days of age or 20 days old when campylobacters are frequently detected in commercial flocks. GOS-fed birds had increased growth performance, but the levels of C. jejuni colonizing the cecal pouches were unchanged irrespective of the age of challenge. Dietary GOS modulated the immune response to C. jejuni by increasing cytokine IL-17A expression at colonization. Correspondingly, reduced diversity of the cecal microbiota was associated with Campylobacter colonization in GOS-fed birds. In birds challenged at 6 days-old the reduction in microbial diversity was accompanied by an increase in the relative abundance of Escherichia spp. Whilst immuno-modulation of the Th17 pro-inflammatory response did not prevent C. jejuni colonization of the intestinal tract of broiler chickens, the study highlights the potential for combinations of prebiotics, and specific competitors (synbiotics) to engage with the host innate immunity to reduce pathogen burdens.
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Affiliation(s)
- Geraldine M. Flaujac Lafontaine
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Philip J. Richards
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Phillippa L. Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Peter M. O’Kane
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Nacheervan M. Ghaffar
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Nicola J. Cummings
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Neville M. Fish
- Saputo Dairy UK, Dairy Crest Innovation Centre, Harper Adams University, Newport, United Kingdom
| | - Ian F. Connerton
- Division of Microbiology, Brewing and Biotechnology, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
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