Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species

Abstract The aim of this study was to develop an easy-to-use culture-free diagnostic method based on next generation sequencing (NGS) of PCR amplification products encompassing whole 16S-23S rRNA region to improve the resolution of bacterial species identification. To determine the resolution of the...

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Autores principales:	Artur J. Sabat, Evert van Zanten, Viktoria Akkerboom, Guido Wisselink, Kees van Slochteren, Richard F. de Boer, Ron Hendrix, Alexander W. Friedrich, John W. A. Rossen, Anna M. D. (Mirjam) Kooistra-Smid
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c3917d4f1aa84d428f1e7e27ec879c46
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spelling	oai:doaj.org-article:c3917d4f1aa84d428f1e7e27ec879c462021-12-02T16:06:22ZTargeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species10.1038/s41598-017-03458-62045-2322https://doaj.org/article/c3917d4f1aa84d428f1e7e27ec879c462017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-03458-6https://doaj.org/toc/2045-2322Abstract The aim of this study was to develop an easy-to-use culture-free diagnostic method based on next generation sequencing (NGS) of PCR amplification products encompassing whole 16S-23S rRNA region to improve the resolution of bacterial species identification. To determine the resolution of the new method 67 isolates were subjected to four identification methods: Sanger sequencing of the 16S rRNA gene; NGS of the 16S-23S rRNA region using MiSeq (Illumina) sequencer; Microflex MS (Bruker) and VITEK MS (bioMérieux). To evaluate the performance of this new method when applied directly on clinical samples, we conducted a proof of principle study with 60 urine samples from patients suspected of urinary tract infections (UTIs), 23 BacT/ALERT (bioMérieux) positive blood culture bottles and 21 clinical orthopedic samples. The resolution power of NGS of the 16S-23S rRNA region was superior to other tested identification methods. Furthermore, the new method correctly identified pathogens established as the cause of UTIs and blood stream infections with conventional culture. NGS of the 16S-23S rRNA region also showed increased detection of bacterial microorganisms in clinical samples from orthopedic patients. Therefore, we conclude that our method has the potential to increase diagnostic yield for detection of bacterial pathogenic species compared to current methods.Artur J. SabatEvert van ZantenViktoria AkkerboomGuido WisselinkKees van SlochterenRichard F. de BoerRon HendrixAlexander W. FriedrichJohn W. A. RossenAnna M. D. (Mirjam) Kooistra-SmidNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Artur J. Sabat Evert van Zanten Viktoria Akkerboom Guido Wisselink Kees van Slochteren Richard F. de Boer Ron Hendrix Alexander W. Friedrich John W. A. Rossen Anna M. D. (Mirjam) Kooistra-Smid Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species
description	Abstract The aim of this study was to develop an easy-to-use culture-free diagnostic method based on next generation sequencing (NGS) of PCR amplification products encompassing whole 16S-23S rRNA region to improve the resolution of bacterial species identification. To determine the resolution of the new method 67 isolates were subjected to four identification methods: Sanger sequencing of the 16S rRNA gene; NGS of the 16S-23S rRNA region using MiSeq (Illumina) sequencer; Microflex MS (Bruker) and VITEK MS (bioMérieux). To evaluate the performance of this new method when applied directly on clinical samples, we conducted a proof of principle study with 60 urine samples from patients suspected of urinary tract infections (UTIs), 23 BacT/ALERT (bioMérieux) positive blood culture bottles and 21 clinical orthopedic samples. The resolution power of NGS of the 16S-23S rRNA region was superior to other tested identification methods. Furthermore, the new method correctly identified pathogens established as the cause of UTIs and blood stream infections with conventional culture. NGS of the 16S-23S rRNA region also showed increased detection of bacterial microorganisms in clinical samples from orthopedic patients. Therefore, we conclude that our method has the potential to increase diagnostic yield for detection of bacterial pathogenic species compared to current methods.
format	article
author	Artur J. Sabat Evert van Zanten Viktoria Akkerboom Guido Wisselink Kees van Slochteren Richard F. de Boer Ron Hendrix Alexander W. Friedrich John W. A. Rossen Anna M. D. (Mirjam) Kooistra-Smid
author_facet	Artur J. Sabat Evert van Zanten Viktoria Akkerboom Guido Wisselink Kees van Slochteren Richard F. de Boer Ron Hendrix Alexander W. Friedrich John W. A. Rossen Anna M. D. (Mirjam) Kooistra-Smid
author_sort	Artur J. Sabat
title	Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species
title_short	Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species
title_full	Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species
title_fullStr	Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species
title_full_unstemmed	Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species
title_sort	targeted next-generation sequencing of the 16s-23s rrna region for culture-independent bacterial identification - increased discrimination of closely related species
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/c3917d4f1aa84d428f1e7e27ec879c46
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Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species

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