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Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology
Diagnoses that are both timely and accurate are critically important for patients with life-threatening or drug resistant infections. Technological improvements in High-Throughput Sequencing (HTS) have led to its use in pathogen detection and its application in clinical diagnoses of infectious disea...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823605/ https://www.ncbi.nlm.nih.gov/pubmed/27092134 http://dx.doi.org/10.3389/fmicb.2016.00484 |
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author | Hilton, Sarah K. Castro-Nallar, Eduardo Pérez-Losada, Marcos Toma, Ian McCaffrey, Timothy A. Hoffman, Eric P. Siegel, Marc O. Simon, Gary L. Johnson, W. Evan Crandall, Keith A. |
author_facet | Hilton, Sarah K. Castro-Nallar, Eduardo Pérez-Losada, Marcos Toma, Ian McCaffrey, Timothy A. Hoffman, Eric P. Siegel, Marc O. Simon, Gary L. Johnson, W. Evan Crandall, Keith A. |
author_sort | Hilton, Sarah K. |
collection | PubMed |
description | Diagnoses that are both timely and accurate are critically important for patients with life-threatening or drug resistant infections. Technological improvements in High-Throughput Sequencing (HTS) have led to its use in pathogen detection and its application in clinical diagnoses of infectious diseases. The present study compares two HTS methods, 16S rRNA marker gene sequencing (metataxonomics) and whole metagenomic shotgun sequencing (metagenomics), in their respective abilities to match the same diagnosis as traditional culture methods (culture inference) for patients with ventilator associated pneumonia (VAP). The metagenomic analysis was able to produce the same diagnosis as culture methods at the species-level for five of the six samples, while the metataxonomic analysis was only able to produce results with the same species-level identification as culture for two of the six samples. These results indicate that metagenomic analyses have the accuracy needed for a clinical diagnostic tool, but full integration in diagnostic protocols is contingent on technological improvements to decrease turnaround time and lower costs. |
format | Online Article Text |
id | pubmed-4823605 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-48236052016-04-18 Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology Hilton, Sarah K. Castro-Nallar, Eduardo Pérez-Losada, Marcos Toma, Ian McCaffrey, Timothy A. Hoffman, Eric P. Siegel, Marc O. Simon, Gary L. Johnson, W. Evan Crandall, Keith A. Front Microbiol Public Health Diagnoses that are both timely and accurate are critically important for patients with life-threatening or drug resistant infections. Technological improvements in High-Throughput Sequencing (HTS) have led to its use in pathogen detection and its application in clinical diagnoses of infectious diseases. The present study compares two HTS methods, 16S rRNA marker gene sequencing (metataxonomics) and whole metagenomic shotgun sequencing (metagenomics), in their respective abilities to match the same diagnosis as traditional culture methods (culture inference) for patients with ventilator associated pneumonia (VAP). The metagenomic analysis was able to produce the same diagnosis as culture methods at the species-level for five of the six samples, while the metataxonomic analysis was only able to produce results with the same species-level identification as culture for two of the six samples. These results indicate that metagenomic analyses have the accuracy needed for a clinical diagnostic tool, but full integration in diagnostic protocols is contingent on technological improvements to decrease turnaround time and lower costs. Frontiers Media S.A. 2016-04-07 /pmc/articles/PMC4823605/ /pubmed/27092134 http://dx.doi.org/10.3389/fmicb.2016.00484 Text en Copyright © 2016 Hilton, Castro-Nallar, Pérez-Losada, Toma, McCaffrey, Hoffman, Siegel, Simon, Johnson and Crandall. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Public Health Hilton, Sarah K. Castro-Nallar, Eduardo Pérez-Losada, Marcos Toma, Ian McCaffrey, Timothy A. Hoffman, Eric P. Siegel, Marc O. Simon, Gary L. Johnson, W. Evan Crandall, Keith A. Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology |
title | Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology |
title_full | Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology |
title_fullStr | Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology |
title_full_unstemmed | Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology |
title_short | Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology |
title_sort | metataxonomic and metagenomic approaches vs. culture-based techniques for clinical pathology |
topic | Public Health |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823605/ https://www.ncbi.nlm.nih.gov/pubmed/27092134 http://dx.doi.org/10.3389/fmicb.2016.00484 |
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