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DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples
We describe DAMIAN, an open source bioinformatics tool designed for the identification of pathogenic microorganisms in diagnostic samples. By using authentic clinical samples and comparing our results to those from established analysis pipelines as well as conventional diagnostics, we demonstrate th...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856179/ https://www.ncbi.nlm.nih.gov/pubmed/31727957 http://dx.doi.org/10.1038/s41598-019-52881-4 |
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author | Alawi, Malik Burkhardt, Lia Indenbirken, Daniela Reumann, Kerstin Christopeit, Maximilian Kröger, Nicolaus Lütgehetmann, Marc Aepfelbacher, Martin Fischer, Nicole Grundhoff, Adam |
author_facet | Alawi, Malik Burkhardt, Lia Indenbirken, Daniela Reumann, Kerstin Christopeit, Maximilian Kröger, Nicolaus Lütgehetmann, Marc Aepfelbacher, Martin Fischer, Nicole Grundhoff, Adam |
author_sort | Alawi, Malik |
collection | PubMed |
description | We describe DAMIAN, an open source bioinformatics tool designed for the identification of pathogenic microorganisms in diagnostic samples. By using authentic clinical samples and comparing our results to those from established analysis pipelines as well as conventional diagnostics, we demonstrate that DAMIAN rapidly identifies pathogens in different diagnostic entities, and accurately classifies viral agents down to the strain level. We furthermore show that DAMIAN is able to assemble full-length viral genomes even in samples co-infected with multiple virus strains, an ability which is of considerable advantage for the investigation of outbreak scenarios. While DAMIAN, similar to other pipelines, analyzes single samples to perform classification of sequences according to their likely taxonomic origin, it also includes a tool for cohort-based analysis. This tool uses cross-sample comparisons to identify sequence signatures that are frequently present in a sample group of interest (e.g., a disease-associated cohort), but occur less frequently in control cohorts. As this approach does not require homology searches in databases, it principally allows the identification of not only known, but also completely novel pathogens. Using samples from a meningitis outbreak, we demonstrate the feasibility of this approach in identifying enterovirus as the causative agent. |
format | Online Article Text |
id | pubmed-6856179 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-68561792019-12-17 DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples Alawi, Malik Burkhardt, Lia Indenbirken, Daniela Reumann, Kerstin Christopeit, Maximilian Kröger, Nicolaus Lütgehetmann, Marc Aepfelbacher, Martin Fischer, Nicole Grundhoff, Adam Sci Rep Article We describe DAMIAN, an open source bioinformatics tool designed for the identification of pathogenic microorganisms in diagnostic samples. By using authentic clinical samples and comparing our results to those from established analysis pipelines as well as conventional diagnostics, we demonstrate that DAMIAN rapidly identifies pathogens in different diagnostic entities, and accurately classifies viral agents down to the strain level. We furthermore show that DAMIAN is able to assemble full-length viral genomes even in samples co-infected with multiple virus strains, an ability which is of considerable advantage for the investigation of outbreak scenarios. While DAMIAN, similar to other pipelines, analyzes single samples to perform classification of sequences according to their likely taxonomic origin, it also includes a tool for cohort-based analysis. This tool uses cross-sample comparisons to identify sequence signatures that are frequently present in a sample group of interest (e.g., a disease-associated cohort), but occur less frequently in control cohorts. As this approach does not require homology searches in databases, it principally allows the identification of not only known, but also completely novel pathogens. Using samples from a meningitis outbreak, we demonstrate the feasibility of this approach in identifying enterovirus as the causative agent. Nature Publishing Group UK 2019-11-14 /pmc/articles/PMC6856179/ /pubmed/31727957 http://dx.doi.org/10.1038/s41598-019-52881-4 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Alawi, Malik Burkhardt, Lia Indenbirken, Daniela Reumann, Kerstin Christopeit, Maximilian Kröger, Nicolaus Lütgehetmann, Marc Aepfelbacher, Martin Fischer, Nicole Grundhoff, Adam DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples |
title | DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples |
title_full | DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples |
title_fullStr | DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples |
title_full_unstemmed | DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples |
title_short | DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples |
title_sort | damian: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856179/ https://www.ncbi.nlm.nih.gov/pubmed/31727957 http://dx.doi.org/10.1038/s41598-019-52881-4 |
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