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Timme RE, Karsch-Mizrachi I, Waheed Z, Arita M, MacCannell D, Maguire F, Petit III R, Page AJ, Mendes CI, Nasar MI, Oluniyi P, Tyler AD, Raphenya AR, Guthrie JL, Olawoye I, Rinck G, O’Cathail C, Lees J, Cochrane G, Cummins C, Brister JR, Klimke W, Feldgarden M, Griffiths E. Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications. Microb Genom 2023; 9:001145. [PMID: 38085797 PMCID: PMC10763499 DOI: 10.1099/mgen.0.001145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collaboration (INSDC), have become essential tools for efficient public health decisions. However, these international resources began primarily for academic purposes, rather than for surveillance or interventions. Now, queries need to access not only the whole genomes of multiple pathogens but also make connections using robust contextual metadata to identify issues of public health relevance. Databases that over time developed a patchwork of submission formats and requirements need to be consistently organized and coordinated internationally to allow effective searches.To help resolve these issues, we propose a common pathogen data structure called the Pathogen Data Object Model (DOM) that will formalize the minimum pieces of sequence data and contextual data necessary for general public health uses, while recognizing that submitters will likely withhold a wide range of non-public contextual data. Further, we propose contributors use the Pathogen DOM for all pathogen submissions (bacterial, viral, fungal, and parasites), which will simplify data submissions and provide a consistent and transparent data structure for downstream data analyses. We also highlight how improved submission tools can support the Pathogen DOM, offering users additional easy-to-use methods to ensure this structure is followed.
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Affiliation(s)
- Ruth E. Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Zahra Waheed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Masanori Arita
- DNA Data Bank of Japan, National Institute of Genetics, Mishima, Japan
| | - Duncan MacCannell
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Finlay Maguire
- Department of Community Health & Epidemiology, Faculty of Medicine, Dalhousie University, Halifax, Canada
- Faculty of Computer Science, Dalhousie University, Halifax, Canada
| | | | - Andrew J. Page
- Quadram Institute Bioscience, Norwich, Norfolk, UK
- Theiagen Genomics LLC, Highlands Ranch, CO, USA
| | | | - Muhammad Ibtisam Nasar
- Department of Biology, College of Science, United Arab Emirates University- Al Ain, Abu Dhabi, UAE
| | - Paul Oluniyi
- Chan Zuckerberg Biohub Network, San Francisco, CA, USA
| | - Andrea D. Tyler
- Science Technology Cores and Services, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Amogelang R. Raphenya
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer L. Guthrie
- Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Idowu Olawoye
- Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Gabriele Rinck
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Colman O’Cathail
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - John Lees
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - J. Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Michael Feldgarden
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Emma Griffiths
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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Tyler AD, McAllister J, Stapleton H, Gauci P, Antonation K, Thirkettle-Watts D, Corbett CR. Field-based detection of bacteria using nanopore sequencing: Method evaluation for biothreat detection in complex samples. PLoS One 2023; 18:e0295028. [PMID: 38015952 PMCID: PMC10684088 DOI: 10.1371/journal.pone.0295028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
From pathogen detection to genome or plasmid closure, the utility of the Oxford Nanopore Technologies (ONT) MinION for microbiological analysis has been well documented. The MinION's small footprint, portability, and real-time analytic capability situates it well to address challenges in the field of unbiased pathogen detection, as a component of a security investigation. To this end, a multicenter evaluation of the effect of alternative analytical approaches on the outcome of MinION-based sequencing, using a set of well-characterized samples, was explored in a field-based scenario. Three expert scientific response groups evaluated known bacterial DNA extracts as part of an international first responder (Chemical, Biological, Radiological) training exercise. Samples were prepared independently for analysis using the Rapid and/or Rapid PCR sequencing kits as per the best practices of each of the participating groups. Analyses of sequence data were in turn conducted using varied approaches including ONTs What's in my pot (WIMP) architecture and in-house computational pipelines. Microbial community composition and the ability of each approach to detect pathogens was compared. Each group demonstrated the ability to detect all species present in samples, although several organisms were detected at levels much lower than expected with some organisms even falling below 1% abundance. Several 'contaminant' near neighbor species were also detected, at low abundance. Regardless of the sequencing approach chosen, the observed composition of the bacterial communities diverged from the input composition in each of the analyses, although sequencing conducted using the rapid kit produced the least distortion when compared to PCR-based library preparation methods. One of the participating groups generated drastically lower sequencing output than the other groups, likely attributed to the limited computer hard drive capacity, and occasional disruption of the internet connection. These results provide further consideration for conducting unbiased pathogen identification within a field setting using MinION sequencing. However, the benefits of this approach in providing rapid results and unbiased detection must be considered along with the complexity of sample preparation and data analytics, when compared to more traditional methods. When utilized by trained scientific experts, with appropriate computational resources, the MinION sequencing device is a useful tool for field-based pathogen detection in mixed samples.
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Affiliation(s)
- Andrea D. Tyler
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jane McAllister
- Department of Defence, Defence Science and Technology Group, Fishermans Bend, Melbourne, VIC, Australia
| | - Helen Stapleton
- Defence Science and Technology Laboratory, Dstl Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Penny Gauci
- Department of Defence, Defence Science and Technology Group, Fishermans Bend, Melbourne, VIC, Australia
| | - Kym Antonation
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - David Thirkettle-Watts
- Department of Defence, Defence Science and Technology Group, Fishermans Bend, Melbourne, VIC, Australia
| | - Cindi R. Corbett
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
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Rumore J, Walker M, Pagotto F, Forbes JD, Peterson CL, Tyler AD, Graham M, Van Domselaar G, Nadon C, Reimer A, Knox N. Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach. BMC Genomics 2023; 24:361. [PMID: 37370007 DOI: 10.1186/s12864-023-09338-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/02/2022] [Accepted: 04/26/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND The reliability of culture-independent pathogen detection in foods using metagenomics is contingent on the quality and composition of the reference database. The inclusion of microbial sequences from a diverse representation of taxonomies in universal reference databases is recommended to maximize classification precision for pathogen detection. However, these sizable databases have high memory requirements that may be out of reach for some users. In this study, we aimed to assess the performance of a foodborne pathogen (FBP)-specific reference database (taxon-specific) relative to a universal reference database (taxon-agnostic). We tested our FBP-specific reference database's performance for detecting Listeria monocytogenes in two complex food matrices-ready-to-eat (RTE) turkey deli meat and prepackaged spinach-using three popular read-based DNA-to-DNA metagenomic classifiers: Centrifuge, Kraken 2 and KrakenUniq. RESULTS In silico host sequence removal led to substantially fewer false positive (FP) classifications and higher classification precision in RTE turkey deli meat datasets using the FBP-specific reference database. No considerable improvement in classification precision was observed following host filtering for prepackaged spinach datasets and was likely a consequence of a higher microbe-to-host sequence ratio. All datasets classified with Centrifuge using the FBP-specific reference database had the lowest classification precision compared to Kraken 2 or KrakenUniq. When a confidence-scoring threshold was applied, a nearly equivalent precision to the universal reference database was achieved for Kraken 2 and KrakenUniq. Recall was high for both reference databases across all datasets and classifiers. Substantially fewer computational resources were required for metagenomics-based detection of L. monocytogenes using the FBP-specific reference database, especially when combined with Kraken 2. CONCLUSIONS A universal (taxon-agnostic) reference database is not essential for accurate and reliable metagenomics-based pathogen detection of L. monocytogenes in complex food matrices. Equivalent classification performance can be achieved using a taxon-specific reference database when the appropriate quality control measures, classification software, and analysis parameters are applied. This approach is less computationally demanding and more attainable for the broader scientific and food safety communities.
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Affiliation(s)
- Jillian Rumore
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.
- Public Health Agency of Canada, National Microbiology Laboratory, MB, Winnipeg, Canada.
| | - Matthew Walker
- Public Health Agency of Canada, National Microbiology Laboratory, MB, Winnipeg, Canada
| | - Franco Pagotto
- Food Directorate, Health Canada, Bureau of Microbial Hazards, Ottawa, ON, Canada
| | - Jessica D Forbes
- Eastern Ontario Regional Laboratory Association, Ottawa, ON, Canada
| | - Christy-Lynn Peterson
- Public Health Agency of Canada, National Microbiology Laboratory, MB, Winnipeg, Canada
| | - Andrea D Tyler
- Public Health Agency of Canada, National Microbiology Laboratory, MB, Winnipeg, Canada
| | - Morag Graham
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Public Health Agency of Canada, National Microbiology Laboratory, MB, Winnipeg, Canada
| | - Gary Van Domselaar
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Public Health Agency of Canada, National Microbiology Laboratory, MB, Winnipeg, Canada
| | - Celine Nadon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Public Health Agency of Canada, National Microbiology Laboratory, MB, Winnipeg, Canada
| | - Aleisha Reimer
- Public Health Agency of Canada, National Microbiology Laboratory, MB, Winnipeg, Canada
| | - Natalie Knox
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Public Health Agency of Canada, National Microbiology Laboratory, MB, Winnipeg, Canada
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Chen JCY, Tyler AD. Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data. Biol Direct 2020; 15:29. [PMID: 33302990 PMCID: PMC7731568 DOI: 10.1186/s13062-020-00287-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 02/17/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Background The advent of metagenomic sequencing provides microbial abundance patterns that can be leveraged for sample origin prediction. Supervised machine learning classification approaches have been reported to predict sample origin accurately when the origin has been previously sampled. Using metagenomic datasets provided by the 2019 CAMDA challenge, we evaluated the influence of variable technical, analytical and machine learning approaches for result interpretation and novel source prediction. Results Comparison between 16S rRNA amplicon and shotgun sequencing approaches as well as metagenomic analytical tools showed differences in normalized microbial abundance, especially for organisms present at low abundance. Shotgun sequence data analyzed using Kraken2 and Bracken, for taxonomic annotation, had higher detection sensitivity. As classification models are limited to labeling pre-trained origins, we took an alternative approach using Lasso-regularized multivariate regression to predict geographic coordinates for comparison. In both models, the prediction errors were much higher in Leave-1-city-out than in 10-fold cross validation, of which the former realistically forecasted the increased difficulty in accurately predicting samples from new origins. This challenge was further confirmed when applying the model to a set of samples obtained from new origins. Overall, the prediction performance of the regression and classification models, as measured by mean squared error, were comparable on mystery samples. Due to higher prediction error rates for samples from new origins, we provided an additional strategy based on prediction ambiguity to infer whether a sample is from a new origin. Lastly, we report increased prediction error when data from different sequencing protocols were included as training data. Conclusions Herein, we highlight the capacity of predicting sample origin accurately with pre-trained origins and the challenge of predicting new origins through both regression and classification models. Overall, this work provides a summary of the impact of sequencing technique, protocol, taxonomic analytical approaches, and machine learning approaches on the use of metagenomics for prediction of sample origin. Supplementary Information The online version contains supplementary material available at 10.1186/s13062-020-00287-y.
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Affiliation(s)
- Julie Chih-Yu Chen
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
| | - Andrea D Tyler
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
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Ashburn JH, Berry S, Bolger J, Coffey JC, Cheah M, Chen M, Eghtesad B, Farraye FA, Fialho A, Fialho A, Fung JJ, Gonzalo DH, Guo B, Hull TL, Kalady MF, Kani HT, Keller DS, Khan F, Khanna R, Kulkarni G, Lan P, Lavryk O, Li Y, Liu X, Mahajan L, Mandelia C, Melmed GY, Navaneethan U, Philpott JR, Kiran PR, Sapci I, Saxena AP, Schroeder T, Shawki S, Shelton C, Shen B, Shen JJ, Silverberg MS, Stocchi L, Syal G, Tyler AD, Veniero JC, Wu XR, Zhu W. Contributors. Pouchitis and Ileal Pouch Disorders 2019:xix-xx. [DOI: 10.1016/b978-0-12-809402-0.09994-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Tyler AD, Mataseje L, Urfano CJ, Schmidt L, Antonation KS, Mulvey MR, Corbett CR. Evaluation of Oxford Nanopore's MinION Sequencing Device for Microbial Whole Genome Sequencing Applications. Sci Rep 2018; 8:10931. [PMID: 30026559 PMCID: PMC6053456 DOI: 10.1038/s41598-018-29334-5] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 07/03/2018] [Indexed: 01/15/2023] Open
Abstract
The MinION sequencer (Oxford Nanopore Technologies) is a paradigm shifting device allowing rapid, real time long read sequencing of nucleic acids. Yet external benchmarking of this technologies' capabilities has not been extensively reported, nor has thorough evaluation of its utility for field-based analysis with sub-optimal sample types been described. The aim of this study was to evaluate the capability of the MinION sequencer for bacterial genomic and metagenomic applications, with specific emphasis placed on the quality, yield, and accuracy of generated sequence data. Two independent laboratories at the National Microbiology Laboratory (Public Health Agency of Canada), sequenced a set of microbes in replicate, using the currently available flowcells, sequencing chemistries, and software available at the time of the experiment. Overall sequencing yield and quality improved through the course of this set of experiments. Sequencing alignment accuracy was high reaching 97% for all 2D experiments, though was slightly lower for 1D sequencing (94%). 1D sequencing provided much longer sequences than 2D. Both sequencing chemistries performed equally well in constructing genomic assemblies. There was evidence of barcode cross-over using both the native and PCR barcoding methods. Despite the sub-optimal nature of samples sequenced in the field, sequences attributable to B. anthracis the target organism used in this scenario, could none-the-less be detected. Together, this report showcases the rapid advancement in this technology and its utility in the context of genomic sequencing of microbial isolates of importance to public health.
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Affiliation(s)
- Andrea D Tyler
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
| | - Laura Mataseje
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Chantel J Urfano
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Lisa Schmidt
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Kym S Antonation
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Cindi R Corbett
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
- University of Manitoba, Department of Medical Microbiology and Infectious Diseases, Winnipeg, Manitoba, R3E 0J9, Canada
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Tracz DM, Tyler AD, Cunningham I, Antonation KS, Corbett CR. Custom database development and biomarker discovery methods for MALDI-TOF mass spectrometry-based identification of high-consequence bacterial pathogens. J Microbiol Methods 2017; 134:54-57. [PMID: 28108323 DOI: 10.1016/j.mimet.2017.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/16/2017] [Accepted: 01/16/2017] [Indexed: 11/18/2022]
Abstract
A high-quality custom database of MALDI-TOF mass spectral profiles was developed with the goal of improving clinical diagnostic identification of high-consequence bacterial pathogens. A biomarker discovery method is presented for identifying and evaluating MALDI-TOF MS spectra to potentially differentiate biothreat bacteria from less-pathogenic near-neighbour species.
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Affiliation(s)
- Dobryan M Tracz
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Andrea D Tyler
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Ian Cunningham
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Kym S Antonation
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Cindi R Corbett
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada; University of Manitoba, Department of Medical Microbiology and Infectious Diseases, Winnipeg, Manitoba R3E 0J9, Canada.
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Kelly OB, Rosenberg M, Tyler AD, Stempak JM, Steinhart AH, Cohen Z, Greenberg GR, Silverberg MS. Infliximab to Treat Refractory Inflammation After Pelvic Pouch Surgery for Ulcerative Colitis. J Crohns Colitis 2016; 10:410-7. [PMID: 26721938 PMCID: PMC4946767 DOI: 10.1093/ecco-jcc/jjv225] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 10/08/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Inflammatory pouch complications refractory to first-line therapies remain problematic following ileal pouch-anal anastomosis (IPAA) for ulcerative colitis (UC). We evaluated infliximab efficacy and associations with therapeutic response. METHODS Data from individuals who underwent colectomy and IPAA for UC (2000-2014) were reviewed. Patients with chronic refractory pouchitis (CP) and Crohn's disease (CD)-like outcomes treated with infliximab were included. Pre-treatment parameters and response at median 8 (initial) and 48 weeks (sustained) were measured. Complete response was defined as symptomatic and endoscopic resolution with modified Pouchitis Disease Activity Index (mPDAI) <5. Partial response included mPDAI improvement >2. Serum was analysed for Anti-Saccharomyces cerevisiae antibodies (ASCA), anti-OmpC, anti-CBir1 and perinuclear Anti-Neutrophil Cytoplasmic Antibodies (pANCA). RESULTS One hundred and fifty-two patients with CP or a CD-like phenotype were identified. Forty-two were treated with infliximab (33% male; age 32.6±2.6 years, 28.5% CD-like). Post-induction response was achieved in 74% (48% complete) and sustained response in 62.6% (29.6% complete). Mean mPDAI and C-reactive protein declined from 8.5±0.3 to 2±3.4 (p < 0.002) and from 29.48±6.2 to 5.76±1.6mg/L (p < 0.001), respectively. Female gender, smoking and presence of anti-CBir1 were associated with infliximab use (p < 0.01) but not response. Pre-treatment mPDAI <10 (p < 0.01), resolution of rectal bleeding (p < 0.001 ) and week 8 endoscopic activity were associated with sustained response (p = 0.04; odds ratio [OR] 2.2; 95% confidence interval [CI] 1.1-16.5]). More than 2 positive antimicrobial antibody titres were associated with non-response (p < 0.05), but did not retain significance in multivariate analysis (p = 0.197; OR 0.632; 95% CI 0.31-1.2). CONCLUSIONS Infliximab can effectively treat inflammatory pouch complications. Pre-treatment mPDAI <10 and early endoscopy may identify responders.
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Affiliation(s)
- Orlaith B. Kelly
- Division of Gastroenterology, University of Toronto, Mount Sinai Hospital, Toronto, Canada
| | - Morgan Rosenberg
- Division of Gastroenterology, University of Toronto, Mount Sinai Hospital, Toronto, Canada
| | - Andrea D. Tyler
- Zane Cohen Center for Digestive Disease, Mount Sinai Hospital, Toronto, Canada
| | - Joanne M. Stempak
- Zane Cohen Center for Digestive Disease, Mount Sinai Hospital, Toronto, Canada
| | - A. Hillary Steinhart
- Division of Gastroenterology, University of Toronto, Mount Sinai Hospital, Toronto, Canada
| | - Zane Cohen
- Zane Cohen Center for Digestive Disease, Mount Sinai Hospital, Toronto, Canada
| | - Gordon R. Greenberg
- Division of Gastroenterology, University of Toronto, Mount Sinai Hospital, Toronto, Canada
| | - Mark S. Silverberg
- Division of Gastroenterology, University of Toronto, Mount Sinai Hospital, Toronto, Canada
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Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C. Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biol 2015; 16:67. [PMID: 25887922 PMCID: PMC4414286 DOI: 10.1186/s13059-015-0637-x] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [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: 10/09/2014] [Accepted: 03/18/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Pouchitis is common after ileal pouch-anal anastomosis (IPAA) surgery for ulcerative colitis (UC). Similar to inflammatory bowel disease (IBD), both host genetics and the microbiota are implicated in its pathogenesis. We use the IPAA model of IBD to associate mucosal host gene expression with mucosal microbiomes and clinical outcomes. We analyze host transcriptomic data and 16S rRNA gene sequencing data from paired biopsies from IPAA patients with UC and familial adenomatous polyposis. To achieve power for a genome-wide microbiome-transcriptome association study, we use principal component analysis for transcript and clade reduction, and identify significant co-variation between clades and transcripts. RESULTS Host transcripts co-vary primarily with biopsy location and inflammation, while microbes co-vary primarily with antibiotic use. Transcript-microbe associations are surprisingly modest, but the most strongly microbially-associated host transcript pattern is enriched for complement cascade genes and for the interleukin-12 pathway. Activation of these host processes is inversely correlated with Sutterella, Akkermansia, Bifidobacteria, and Roseburia abundance, and positively correlated with Escherichia abundance. CONCLUSIONS This study quantifies the effects of inflammation, antibiotic use, and biopsy location upon the microbiome and host transcriptome during pouchitis. Understanding these effects is essential for basic biological insights as well as for well-designed and adequately-powered studies. Additionally, our study provides a method for profiling host-microbe interactions with appropriate statistical power using high-throughput sequencing, and suggests that cross-sectional changes in gut epithelial transcription are not a major component of the host-microbiome regulatory interface during pouchitis.
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Affiliation(s)
- Xochitl C Morgan
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA. .,The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
| | - Boyko Kabakchiev
- Mount Sinai Hospital, Zane Cohen Centre for Digestive Diseases, University of Toronto, 600 University Ave, Toronto, ON, M5G 1X5, Canada.
| | - Levi Waldron
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA. .,City University of New York School of Public Health, Hunter College, 2180 3rd Ave Rm 538, New York, NY, 10035-4003, USA.
| | - Andrea D Tyler
- Mount Sinai Hospital, Zane Cohen Centre for Digestive Diseases, University of Toronto, 600 University Ave, Toronto, ON, M5G 1X5, Canada.
| | - Timothy L Tickle
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA. .,The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
| | - Raquel Milgrom
- Mount Sinai Hospital, Zane Cohen Centre for Digestive Diseases, University of Toronto, 600 University Ave, Toronto, ON, M5G 1X5, Canada.
| | - Joanne M Stempak
- Mount Sinai Hospital, Zane Cohen Centre for Digestive Diseases, University of Toronto, 600 University Ave, Toronto, ON, M5G 1X5, Canada.
| | - Dirk Gevers
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
| | - Mark S Silverberg
- Mount Sinai Hospital, Zane Cohen Centre for Digestive Diseases, University of Toronto, 600 University Ave, Toronto, ON, M5G 1X5, Canada.
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA. .,The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
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Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med 2014; 6:107. [PMID: 25587358 PMCID: PMC4292994 DOI: 10.1186/s13073-014-0107-1] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/13/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Human genetics and host-associated microbial communities have been associated independently with a wide range of chronic diseases. One of the strongest associations in each case is inflammatory bowel disease (IBD), but disease risk cannot be explained fully by either factor individually. Recent findings point to interactions between host genetics and microbial exposures as important contributors to disease risk in IBD. These include evidence of the partial heritability of the gut microbiota and the conferral of gut mucosal inflammation by microbiome transplant even when the dysbiosis was initially genetically derived. Although there have been several tests for association of individual genetic loci with bacterial taxa, there has been no direct comparison of complex genome-microbiome associations in large cohorts of patients with an immunity-related disease. METHODS We obtained 16S ribosomal RNA (rRNA) gene sequences from intestinal biopsies as well as host genotype via Immunochip in three independent cohorts totaling 474 individuals. We tested for correlation between relative abundance of bacterial taxa and number of minor alleles at known IBD risk loci, including fine mapping of multiple risk alleles in the Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) gene exon. We identified host polymorphisms whose associations with bacterial taxa were conserved across two or more cohorts, and we tested related genes for enrichment of host functional pathways. RESULTS We identified and confirmed in two cohorts a significant association between NOD2 risk allele count and increased relative abundance of Enterobacteriaceae, with directionality of the effect conserved in the third cohort. Forty-eight additional IBD-related SNPs have directionality of their associations with bacterial taxa significantly conserved across two or three cohorts, implicating genes enriched for regulation of innate immune response, the JAK-STAT cascade, and other immunity-related pathways. CONCLUSIONS These results suggest complex interactions between genetically altered host functional pathways and the structure of the microbiome. Our findings demonstrate the ability to uncover novel associations from paired genome-microbiome data, and they suggest a complex link between host genetics and microbial dysbiosis in subjects with IBD across independent cohorts.
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Affiliation(s)
- Dan Knights
- />Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455 USA
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
- />Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
- />Biotechnology Institute, University of Minnesota, St. Paul, Minnesota 55108 USA
| | - Mark S Silverberg
- />Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital IBD Group, University of Toronto, Toronto, Ontario M5G 1X5 Canada
| | - Rinse K Weersma
- />Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9700RB The Netherlands
| | - Dirk Gevers
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
| | - Gerard Dijkstra
- />Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9700RB The Netherlands
| | - Hailiang Huang
- />Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114 USA
| | - Andrea D Tyler
- />Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital IBD Group, University of Toronto, Toronto, Ontario M5G 1X5 Canada
| | - Suzanne van Sommeren
- />Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9700RB The Netherlands
- />Department of Genetics, University Medical Center Groningen, Groningen, 9700RB The Netherlands
| | - Floris Imhann
- />Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9700RB The Netherlands
- />Department of Genetics, University Medical Center Groningen, Groningen, 9700RB The Netherlands
| | - Joanne M Stempak
- />Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital IBD Group, University of Toronto, Toronto, Ontario M5G 1X5 Canada
| | - Hu Huang
- />Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 USA
| | - Pajau Vangay
- />Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 USA
| | - Gabriel A Al-Ghalith
- />Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota 55455 USA
| | - Caitlin Russell
- />Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
- />Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
| | - Jenny Sauk
- />Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
| | - Jo Knight
- />Department of Psychiatry, University of Toronto, Toronto, Ontario M5T 1R8 Canada
| | - Mark J Daly
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
- />Department of Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
- />Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
| | - Curtis Huttenhower
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
- />Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts 02115 USA
| | - Ramnik J Xavier
- />Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 USA
- />Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
- />Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114 USA
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11
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Smith MI, Turpin W, Tyler AD, Silverberg MS, Croitoru K. Microbiome analysis - from technical advances to biological relevance. F1000Prime Rep 2014; 6:51. [PMID: 25184041 PMCID: PMC4108955 DOI: 10.12703/p6-51] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The development of culture-independent techniques and next-generation sequencing has led to a staggering rise in the number of microbiome studies over the last decade. Although it remains important to identify the taxa of microbes present in a variety of environmental samples, including the gut microbiomes of healthy and diseased individuals, the next stage of microbiome research will need to focus on uncovering the role of the microbiome rather than its mere composition. Here, we introduce techniques that go beyond identifying the taxa present within a sample and examine the biological function of the microbiome or the host-microbiome interaction.
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Affiliation(s)
- Michelle I Smith
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5
| | - Williams Turpin
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5 ; Institute of Medical Science, Department of Medicine University of Toronto, Toronto, ON Canada, M5S 1A8
| | - Andrea D Tyler
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5 ; Institute of Medical Science, Department of Medicine University of Toronto, Toronto, ON Canada, M5S 1A8
| | - Kenneth Croitoru
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5 ; Institute of Medical Science, Department of Medicine University of Toronto, Toronto, ON Canada, M5S 1A8
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12
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Tyler AD, Smith MI, Silverberg MS. Analyzing the human microbiome: a "how to" guide for physicians. Am J Gastroenterol 2014; 109:983-93. [PMID: 24751579 DOI: 10.1038/ajg.2014.73] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 03/11/2014] [Indexed: 02/07/2023]
Abstract
The application of high-throughput next-generation sequencing to the analysis of the human microbiome has led to a shift in our understanding of the etiology of complex diseases. In consequence, a great deal of literature can now be found exploring this complex system, and reviewing recent findings. Observations of alterations in the intestinal microbiome associating with inflammatory bowel disease and other chronic conditions are well supported and have been widely accepted by the research community. Yet, it can be difficult to objectively evaluate the importance of these results, given the wide variety of methodologies applied by different groups in the field. The aim of this review is to focus attention on the basic principles involved in microbiome analyses, and to describe factors that may have an impact on the accurate interpretation of results.
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Affiliation(s)
- Andrea D Tyler
- 1] Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada [2] Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada
| | - Michelle I Smith
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada
| | - Mark S Silverberg
- 1] Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada [2] Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada
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Tyler AD, Milgrom R, Stempak JM, Xu W, Brumell JH, Muise AM, Sehgal R, Cohen Z, Koltun W, Shen B, Silverberg MS. The NOD2insC polymorphism is associated with worse outcome following ileal pouch-anal anastomosis for ulcerative colitis. Gut 2013; 62:1433-9. [PMID: 22879519 DOI: 10.1136/gutjnl-2011-301957] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Inflammatory complications after ileal pouch-anal anastomosis (IPAA) for ulcerative colitis (UC) are common. OBJECTIVE To investigate whether genetic factors are associated with adverse pouch outcomes such as chronic pouchitis (CP) and a Crohn's disease-like (CDL) phenotype. DESIGN 866 patients were recruited from three centres in North America: Mount Sinai Hospital (Toronto, Ontario, Canada), the Cleveland Clinic (Cleveland, Ohio, USA) and Penn State Milton S Hershey Medical Center (Hershey, Pennsylvania, USA). DNA and clinical and demographic information were collected. Subjects were classified into post-surgical outcome groups: no chronic pouchitis (NCP), CP and CDL phenotype. RESULTS Clinical and genetic data were available on 714 individuals. 487 (68.2%) were classified as NCP, 118 (16.5%) CP and 109 (15.3%) CDL. The presence of arthritis or arthropathy (p=0.02), primary sclerosing cholangitis (p=0.009) and duration of time from ileostomy closure to recruitment (p=0.001) were significantly associated with outcome. The NOD2insC (rs2066847) risk variant was the single nucleotide polymorphism (SNP) most significantly associated with pouch outcome (p=7.4×10(-5)). Specifically, it was associated with both CP and CDL in comparison with NCP (OR=3.2 and 4.3, respectively). Additionally, SNPs in NOX3 (rs6557421, rs12661812), DAGLB (rs836518) and NCF4 (rs8137602) were shown to be associated with pouch outcome with slightly weaker effects. A multivariable risk model combining previously identified clinical (smoking status, family history of inflammatory bowel disease), serological (anti-Saccharomyces cerevisiae antibody IgG, perinuclear antineutrophil cytoplasmic antibody and anti-CBir1) and genetic markers was constructed and resulted in an OR of 2.72 (p=8.89×10(-7)) for NCP versus CP/CDL and 3.22 (p=4.11×10(-8)) for NCP versus CDL, respectively. CONCLUSION Genetic polymorphisms, in particular, the NOD2insC risk allele, are associated with chronic inflammatory pouch outcomes among patients with UC and IPAA.
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Affiliation(s)
- Andrea D Tyler
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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Tyler AD, Knox N, Kabakchiev B, Milgrom R, Kirsch R, Cohen Z, McLeod RS, Guttman DS, Krause DO, Silverberg MS. Characterization of the gut-associated microbiome in inflammatory pouch complications following ileal pouch-anal anastomosis. PLoS One 2013; 8:e66934. [PMID: 24086242 PMCID: PMC3782502 DOI: 10.1371/journal.pone.0066934] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/10/2013] [Indexed: 12/29/2022] Open
Abstract
Introduction Inflammatory complications following ileal pouch-anal anastomosis (IPAA) for ulcerative colitis (UC) are common and thought to arise through mechanisms similar to denovo onset inflammatory bowel disease. The aim of this study was to determine whether specific organisms in the tissue-associated microbiota are associated with inflammatory pouch complications. Methods Patients having previously undergone IPAA were recruited from Mount Sinai Hospital. Clinical and demographic information were collected and a pouchoscopy with biopsy of both the pouch and afferent limb was performed. Patients were classified based on post-surgical phenotype into four outcome groups: familial adenomatous polyposis controls (FAP), no pouchitis, pouchitis, and Crohn’s disease-like (CDL). Pyrosequencing of the 16S rRNA V1-V3 hypervariable region, and quantitative PCR for bacteria of interest, were used to identify organisms present in the afferent limb and pouch. Associations with outcomes were evaluated using exact and non-parametric tests of significance. Results Analysis at the phylum level indicated that Bacteroidetes were detected significantly less frequently (P<0.0001) in the inflammatory outcome groups (pouchitis and CDL) compared to both FAP and no pouchitis. Conversely, Proteobacteria were detected more frequently in the inflammatory groups (P=0.01). At the genus level, organisms associated with outcome were detected less frequently among the inflammatory groups compared to those without inflammation. Several of these organisms, including Bacteroides (P<0.0001), Parabacteroides (P≤2.2x10-3), Blautia (P≤3.0x10-3) and Sutterella (P≤2.5x10-3), were associated with outcome in both the pouch and afferent limb. These associations remained significant even following adjustment for antibiotic use, smoking, country of birth and gender. Individuals with quiescent disease receiving antibiotic therapy displayed similar reductions in these organisms as those with active pouch inflammation. Conclusions Specific genera are associated with inflammation of the ileal pouch, with a reduction of typically ubiquitous organisms characterizing the inflammatory phenotypes.
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Affiliation(s)
- Andrea D. Tyler
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada
| | - Natalie Knox
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Boyko Kabakchiev
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada
| | - Raquel Milgrom
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada
| | - Richard Kirsch
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Toronto, Toronto, Ontario, Canada
| | - Zane Cohen
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada
| | - Robin S. McLeod
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Denis O. Krause
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada
- Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Mark S. Silverberg
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital Inflammatory Bowel Disease Group, Toronto, Ontario, Canada
- * E-mail:
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15
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Tyler AD, Milgrom R, Xu W, Stempak JM, Steinhart AH, McLeod RS, Greenberg GR, Cohen Z, Silverberg MS. Antimicrobial antibodies are associated with a Crohn's disease-like phenotype after ileal pouch-anal anastomosis. Clin Gastroenterol Hepatol 2012; 10:507-12.e1. [PMID: 21963956 DOI: 10.1016/j.cgh.2011.09.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 09/13/2011] [Accepted: 09/22/2011] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Pouchitis and Crohn's disease (CD)-like (CDL) complications of the pouch occur at rates near 50% and 20%, respectively, after colectomy with ileal pouch-anal anastomosis (IPAA) for ulcerative colitis (UC). We investigated whether antimicrobial antibodies are associated with pouch outcome after IPAA. METHODS We studied clinical and endoscopic data from 399 individuals with UC who underwent colectomy with IPAA at Mount Sinai Hospital in Toronto, Canada; patients were classified as no pouchitis (NP), chronic pouchitis (CP), or CDL. Serum samples were analyzed from 341 patients for antibodies against Saccharomyces cerevisiae (ASCA), OmpC, CBir1, and perinuclear antineutrophil cytoplasmic antibody (pANCA). RESULTS Of the subjects, 70.7% had NP, 16.8% developed CP, and 12.5% developed CDL. Smoking was associated with CDL (P = .003). Ashkenazi Jewish individuals more commonly had CP (P = .008). Of patients with CDL, 53.5% and 14.0% had positive test results for anti-CBir1 and ASCA (immunoglobulin G), respectively, compared with 21.4% and 3.8% of those with NP and 28.3% and 5.0% of those with CP (P < .0001 and P = .03). Anti-CBir1 was associated with CDL, compared with NP (P = 2.8 × 10(-5); odds ratio [OR], 4.2; 95% confidence interval [CI], 2.2-8.3) or CP (P = .011; OR, 2.9; 95% CI, 1.3-6.6). ASCA immunoglobulin G was associated with CDL, compared with patients with NP (P = .01; OR, 4.1; 95% CI, 1.4-12.3). In a combined model, pANCA and the antimicrobial antibodies were associated with CP (P = .029) and CDL (P = 4.7 × 10(-4)). CONCLUSIONS Antimicrobial antibodies and pANCA are associated with inflammatory complications of the pouch. The CDL phenotype is associated with factors that characterize Crohn's disease, including smoking, anti-CBir1, and ASCA.
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Affiliation(s)
- Andrea D Tyler
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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