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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...

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Autores principales: Pitashny, Milena, Kadry, Balqees, Shalaginov, Raya, Gazit, Liat, Zohar, Yaniv, Szwarcwort, Moran, Stabholz, Yoav, Paul, Mical
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
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.
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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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