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NGS in the clinical microbiology settings
We hypothesized that targeted NGS sequencing might have an advantage over Sanger sequencing, especially in polymicrobial infections. The study included 55 specimens from 51 patients. We compared targeted NGS to Sanger sequencing in clinical samples submitted for Sanger sequencing. The overall concor...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9627026/ https://www.ncbi.nlm.nih.gov/pubmed/36339334 http://dx.doi.org/10.3389/fcimb.2022.955481 |
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author | Pitashny, Milena Kadry, Balqees Shalaginov, Raya Gazit, Liat Zohar, Yaniv Szwarcwort, Moran Stabholz, Yoav Paul, Mical |
author_facet | Pitashny, Milena Kadry, Balqees Shalaginov, Raya Gazit, Liat Zohar, Yaniv Szwarcwort, Moran Stabholz, Yoav Paul, Mical |
author_sort | Pitashny, Milena |
collection | PubMed |
description | We hypothesized that targeted NGS sequencing might have an advantage over Sanger sequencing, especially in polymicrobial infections. The study included 55 specimens from 51 patients. We compared targeted NGS to Sanger sequencing in clinical samples submitted for Sanger sequencing. The overall concordance rate was 58% (32/55) for NGS vs. Sanger. NGS identified 9 polymicrobial and 2 monomicrobial infections among 19 Sanger-negative samples and 8 polymicrobial infections in 11 samples where a 16S gene was identified by gel electrophoresis, but could not be mapped to an identified pathogen by Sanger. We estimated that NGS could have contributed to patient management in 6/18 evaluated patients and thus has an advantage over Sanger sequencing in certain polymicrobial infections. |
format | Online Article Text |
id | pubmed-9627026 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-96270262022-11-03 NGS in the clinical microbiology settings Pitashny, Milena Kadry, Balqees Shalaginov, Raya Gazit, Liat Zohar, Yaniv Szwarcwort, Moran Stabholz, Yoav Paul, Mical Front Cell Infect Microbiol Cellular and Infection Microbiology We hypothesized that targeted NGS sequencing might have an advantage over Sanger sequencing, especially in polymicrobial infections. The study included 55 specimens from 51 patients. We compared targeted NGS to Sanger sequencing in clinical samples submitted for Sanger sequencing. The overall concordance rate was 58% (32/55) for NGS vs. Sanger. NGS identified 9 polymicrobial and 2 monomicrobial infections among 19 Sanger-negative samples and 8 polymicrobial infections in 11 samples where a 16S gene was identified by gel electrophoresis, but could not be mapped to an identified pathogen by Sanger. We estimated that NGS could have contributed to patient management in 6/18 evaluated patients and thus has an advantage over Sanger sequencing in certain polymicrobial infections. Frontiers Media S.A. 2022-10-19 /pmc/articles/PMC9627026/ /pubmed/36339334 http://dx.doi.org/10.3389/fcimb.2022.955481 Text en Copyright © 2022 Pitashny, Kadry, Shalaginov, Gazit, Zohar, Szwarcwort, Stabholz and Paul https://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) and the copyright owner(s) 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 | Cellular and Infection Microbiology Pitashny, Milena Kadry, Balqees Shalaginov, Raya Gazit, Liat Zohar, Yaniv Szwarcwort, Moran Stabholz, Yoav Paul, Mical NGS in the clinical microbiology settings |
title | NGS in the clinical microbiology settings |
title_full | NGS in the clinical microbiology settings |
title_fullStr | NGS in the clinical microbiology settings |
title_full_unstemmed | NGS in the clinical microbiology settings |
title_short | NGS in the clinical microbiology settings |
title_sort | ngs in the clinical microbiology settings |
topic | Cellular and Infection Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9627026/ https://www.ncbi.nlm.nih.gov/pubmed/36339334 http://dx.doi.org/10.3389/fcimb.2022.955481 |
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