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Flannigan KL, Taylor MR, Pereira SK, Rodriguez-Arguello J, Moffat AW, Alston L, Wang X, Poon KK, Beck PL, Rioux KP, Jonnalagadda M, Chelikani PK, Galipeau HJ, Lewis IA, Workentine ML, Greenway SC, Hirota SA. An intact microbiota is required for the gastrointestinal toxicity of the immunosuppressant mycophenolate mofetil. J Heart Lung Transplant 2018; 37:1047-1059. [PMID: 30173823 DOI: 10.1016/j.healun.2018.05.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/04/2018] [Accepted: 05/07/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Mycophenolate mofetil (MMF) is commonly prescribed after transplantation and has major advantages over other immunosuppressive drugs, but frequent gastrointestinal (GI) side-effects limit its use. The mechanism(s) underlying MMF-related GI toxicity have yet to be elucidated. METHODS To investigate MMF-related GI toxicity, experimental mice were fed chow containing MMF (0.563%) and multiple indices of toxicity, including weight loss and colonic inflammation, were measured. Changes in intestinal microbial composition were detected using 16S rRNA Illumina sequencing, and downstream PICRUSt analysis was used to predict metagenomic pathways involved. Germ-free (GF) mice and mice treated with orally administered broad-spectrum antibiotics (ABX) were utilized to interrogate the importance of the microbiota in MMF-induced GI toxicity. RESULTS Mice treated with MMF exhibited significant weight loss, related to loss of body fat and muscle, and marked colonic inflammation. MMF exposure was associated with changes in gut microbial composition, as demonstrated by a loss of overall diversity, expansion of Proteobacteria (specifically Escherichia/Shigella), and enrichment of genes involved in lipopolysaccharide (LPS) biosynthesis, which paralleled increased levels of LPS in the feces and serum. MMF-related GI toxicity was dependent on the intestinal microbiota, as MMF did not induce weight loss or colonic inflammation in GF mice. Furthermore, ABX prevented and reversed MMF-induced weight loss and colonic inflammation. CONCLUSIONS An intact intestinal microbiota is required to initiate and sustain the GI toxicity of MMF. MMF treatment causes dynamic changes in the composition of the intestinal microbiota that may be a targetable driver of the GI side-effects of MMF.
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Affiliation(s)
- Kyle L Flannigan
- Department of Physiology and Pharmacology, Cumming School of Medicine; Snyder Institute for Chronic Diseases.
| | - Michael R Taylor
- Department of Paediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine
| | - Sheldon K Pereira
- Snyder Institute for Chronic Diseases; Department of Paediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine
| | - Jimena Rodriguez-Arguello
- Department of Paediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine
| | - Andrew W Moffat
- Department of Paediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine
| | - Laurie Alston
- Department of Physiology and Pharmacology, Cumming School of Medicine; Snyder Institute for Chronic Diseases
| | - Xuemei Wang
- Department of Paediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine; Department of Cardiac Sciences and the Libin Cardiovascular Institute of Alberta, Cumming School of Medicine
| | - Karen K Poon
- Snyder Institute for Chronic Diseases; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine
| | - Paul L Beck
- Department of Physiology and Pharmacology, Cumming School of Medicine; Snyder Institute for Chronic Diseases; Division of Gastroenterology and Hepatology, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kevin P Rioux
- Snyder Institute for Chronic Diseases; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine; Division of Gastroenterology and Hepatology, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mahesh Jonnalagadda
- Laboratory of Animal Medical Services, University of Cincinnati, Cincinnati, Ohio, USA
| | - Prasanth K Chelikani
- Department of Production, Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Heather J Galipeau
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | | | | | - Steven C Greenway
- Department of Paediatrics and Alberta Children's Hospital Research Institute, Cumming School of Medicine; Department of Cardiac Sciences and the Libin Cardiovascular Institute of Alberta, Cumming School of Medicine; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Simon A Hirota
- Department of Physiology and Pharmacology, Cumming School of Medicine; Snyder Institute for Chronic Diseases; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine
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Freschi L, Jeukens J, Kukavica-Ibrulj I, Boyle B, Dupont MJ, Laroche J, Larose S, Maaroufi H, Fothergill JL, Moore M, Winsor GL, Aaron SD, Barbeau J, Bell SC, Burns JL, Camara M, Cantin A, Charette SJ, Dewar K, Déziel É, Grimwood K, Hancock REW, Harrison JJ, Heeb S, Jelsbak L, Jia B, Kenna DT, Kidd TJ, Klockgether J, Lam JS, Lamont IL, Lewenza S, Loman N, Malouin F, Manos J, McArthur AG, McKeown J, Milot J, Naghra H, Nguyen D, Pereira SK, Perron GG, Pirnay JP, Rainey PB, Rousseau S, Santos PM, Stephenson A, Taylor V, Turton JF, Waglechner N, Williams P, Thrane SW, Wright GD, Brinkman FSL, Tucker NP, Tümmler B, Winstanley C, Levesque RC. Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Front Microbiol 2015; 6:1036. [PMID: 26483767 PMCID: PMC4586430 DOI: 10.3389/fmicb.2015.01036] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/11/2015] [Indexed: 11/24/2022] Open
Abstract
The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care.
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Affiliation(s)
- Luca Freschi
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Julie Jeukens
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | | | - Brian Boyle
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Marie-Josée Dupont
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Jérôme Laroche
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Stéphane Larose
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Halim Maaroufi
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
| | - Joanne L Fothergill
- Institute of Infection and Global Health, University of Liverpool Liverpool, UK
| | - Matthew Moore
- Institute of Infection and Global Health, University of Liverpool Liverpool, UK
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University Vancouver, BC, Canada
| | - Shawn D Aaron
- Ottawa Hospital Research Institute Ottawa, ON, Canada
| | - Jean Barbeau
- Faculté de Médecine Dentaire, Université de Montréal Montréal, QC, Canada
| | - Scott C Bell
- QIMR Berghofer Medical Research Institute Brisbane, QLD, Australia
| | - Jane L Burns
- Seattle Children's Research Institute, University of Washington School of Medicine Seattle, WA, USA
| | - Miguel Camara
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - André Cantin
- Département de Médecine, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Steve J Charette
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec, QC, Canada ; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec, QC, Canada
| | - Ken Dewar
- Department of Human Genetics, McGill University Montreal, QC, Canada
| | - Éric Déziel
- INRS Institut Armand Frappier Laval, QC, Canada
| | - Keith Grimwood
- School of Medicine, Griffith University Gold Coast, QLD, Australia
| | - Robert E W Hancock
- Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada
| | - Joe J Harrison
- Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Stephan Heeb
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark Lyngby, Denmark
| | - Baofeng Jia
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Dervla T Kenna
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England London, UK
| | - Timothy J Kidd
- Child Health Research Centre, The University of Queensland Brisbane, QLD, Australia ; Centre for Infection and Immunity, Queen's University Belfast Belfast, UK
| | - Jens Klockgether
- Klinische Forschergruppe, Medizinische Hochschule Hannover, Germany
| | - Joseph S Lam
- Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
| | - Iain L Lamont
- Department of Biochemistry, University of Otago Dunedin, New Zealand
| | - Shawn Lewenza
- Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Nick Loman
- Institute for Microbiology and Infection, University of Birmingham Birmingham, UK
| | - François Malouin
- Département de Médecine, Université de Sherbrooke Sherbrooke, QC, Canada
| | - Jim Manos
- Department of Infectious Diseases and Immunology, The University of Sydney Sydney, NSW, Australia
| | - Andrew G McArthur
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Josie McKeown
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Julie Milot
- Department of Pneumology, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval Quebec, QC, Canada
| | - Hardeep Naghra
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Dao Nguyen
- Department of Human Genetics, McGill University Montreal, QC, Canada ; Department of Microbiology and Immunology and Department of Experimental Medicine, McGill University Montreal, QC, Canada
| | - Sheldon K Pereira
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Gabriel G Perron
- Department of Biology, Bard College, Annandale-On-Hudson NY, USA
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital Brussels, Belgium
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University Albany, New Zealand ; Max Planck Institute for Evolutionary Biology Plön, Germany
| | - Simon Rousseau
- Department of Human Genetics, McGill University Montreal, QC, Canada
| | - Pedro M Santos
- Department of Biology, University of Minho Braga, Portugal
| | | | - Véronique Taylor
- Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
| | - Jane F Turton
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England London, UK
| | - Nicholas Waglechner
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Paul Williams
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Sandra W Thrane
- Department of Systems Biology, Technical University of Denmark Lyngby, Denmark
| | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University Hamilton, ON, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University Vancouver, BC, Canada
| | - Nicholas P Tucker
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde Glasgow, UK
| | - Burkhard Tümmler
- Klinische Forschergruppe, Medizinische Hochschule Hannover, Germany
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool Liverpool, UK
| | - Roger C Levesque
- Institute for Integrative and Systems Biology, Université Laval Quebec, QC, Canada
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Dhillon BK, Laird MR, Shay JA, Winsor GL, Lo R, Nizam F, Pereira SK, Waglechner N, McArthur AG, Langille MGI, Brinkman FSL. IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res 2015; 43:W104-8. [PMID: 25916842 PMCID: PMC4489224 DOI: 10.1093/nar/gkv401] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/15/2015] [Indexed: 01/12/2023] Open
Abstract
IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin, and are of high interest since they disproportionately encode genes involved in medically and environmentally important adaptations, including antimicrobial resistance and virulence. We now report a major new release of IslandViewer, since the last release in 2013. IslandViewer 3 incorporates a completely new genome visualization tool, IslandPlot, enabling for the first time interactive genome analysis and gene search capabilities using synchronized circular, horizontal and vertical genome views. In addition, more curated virulence factors and antimicrobial resistance genes have been incorporated, and homologs of these genes identified in closely related genomes using strict filters. Pathogen-associated genes have been re-calculated for all pre-computed complete genomes. For user-uploaded genomes to be analysed, IslandViewer 3 can also now handle incomplete genomes, with an improved queuing system on compute nodes to handle user demand. Overall, IslandViewer 3 represents a significant new version of this GI analysis software, with features that may make it more broadly useful for general microbial genome analysis and visualization.
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Affiliation(s)
- Bhavjinder K Dhillon
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Matthew R Laird
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Julie A Shay
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Raymond Lo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Fazmin Nizam
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Sheldon K Pereira
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Nicholas Waglechner
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Andrew G McArthur
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Morgan G I Langille
- Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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