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Rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach
In the event of a bioterror attack, a prompt, sensitive and definite identification of the agents involved is of major concern for confirmation of the event and for mitigation of countermeasures. Whether the information from intelligence forces is limited concerning the biothreat identity or one sus...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6538980/ https://www.ncbi.nlm.nih.gov/pubmed/31193701 http://dx.doi.org/10.1016/j.heliyon.2019.e01793 |
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author | Israeli, Ofir Cohen-Gihon, Inbar Zvi, Anat Lazar, Shirley Shifman, Ohad Levy, Haim Tidhar, Avital Beth-Din, Adi |
author_facet | Israeli, Ofir Cohen-Gihon, Inbar Zvi, Anat Lazar, Shirley Shifman, Ohad Levy, Haim Tidhar, Avital Beth-Din, Adi |
author_sort | Israeli, Ofir |
collection | PubMed |
description | In the event of a bioterror attack, a prompt, sensitive and definite identification of the agents involved is of major concern for confirmation of the event and for mitigation of countermeasures. Whether the information from intelligence forces is limited concerning the biothreat identity or one suspects the presence of a novel or engineered agent, the genetic identification of microorganisms in an unknown sample is challenging. High-throughput sequencing (HTS) technologies can sequence a heterogeneous mixture of genetic materials with high sensitivity and speed; nevertheless, despite the enormous advantages of HTS, all previous reports have analyzed unknown samples in a timeframe of a few days to a few weeks. This timeframe might not be relevant to an emergency scenario. Here, we present an HTS-based approach for deciphering the genetic composition of unknown samples within a working day. This outcome is accomplished by a rapid library preparation procedure, short-length sequencing and a prompt bioinformatics comparison against all available microbial genomic sequences. Using this approach, as a proof of concept, we were able to detect two spiked-in biothreat agents, B. anthracis and Y. pestis, in a variety of environmental samples at relevant concentrations and within a short timeframe of eight hours. |
format | Online Article Text |
id | pubmed-6538980 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-65389802019-06-03 Rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach Israeli, Ofir Cohen-Gihon, Inbar Zvi, Anat Lazar, Shirley Shifman, Ohad Levy, Haim Tidhar, Avital Beth-Din, Adi Heliyon Article In the event of a bioterror attack, a prompt, sensitive and definite identification of the agents involved is of major concern for confirmation of the event and for mitigation of countermeasures. Whether the information from intelligence forces is limited concerning the biothreat identity or one suspects the presence of a novel or engineered agent, the genetic identification of microorganisms in an unknown sample is challenging. High-throughput sequencing (HTS) technologies can sequence a heterogeneous mixture of genetic materials with high sensitivity and speed; nevertheless, despite the enormous advantages of HTS, all previous reports have analyzed unknown samples in a timeframe of a few days to a few weeks. This timeframe might not be relevant to an emergency scenario. Here, we present an HTS-based approach for deciphering the genetic composition of unknown samples within a working day. This outcome is accomplished by a rapid library preparation procedure, short-length sequencing and a prompt bioinformatics comparison against all available microbial genomic sequences. Using this approach, as a proof of concept, we were able to detect two spiked-in biothreat agents, B. anthracis and Y. pestis, in a variety of environmental samples at relevant concentrations and within a short timeframe of eight hours. Elsevier 2019-05-27 /pmc/articles/PMC6538980/ /pubmed/31193701 http://dx.doi.org/10.1016/j.heliyon.2019.e01793 Text en © 2019 The Authors http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Article Israeli, Ofir Cohen-Gihon, Inbar Zvi, Anat Lazar, Shirley Shifman, Ohad Levy, Haim Tidhar, Avital Beth-Din, Adi Rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach |
title | Rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach |
title_full | Rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach |
title_fullStr | Rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach |
title_full_unstemmed | Rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach |
title_short | Rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach |
title_sort | rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6538980/ https://www.ncbi.nlm.nih.gov/pubmed/31193701 http://dx.doi.org/10.1016/j.heliyon.2019.e01793 |
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