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Molecular identification of clinical “difficult-to-identify” microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2

BACKGROUND: Clinical microbiology laboratories have to accurately identify clinical microbes. However, some isolates are difficult to identify by the automated biochemical text platforms, which are called “difficult-to-identify” microbes in this study. Therefore, the ability of 16S ribosomal DNA (16...

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Autores principales: Cheng, Cancan, Sun, Jingjing, Zheng, Fen, Wu, Kuihai, Rui, Yongyu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905965/
https://www.ncbi.nlm.nih.gov/pubmed/24383440
http://dx.doi.org/10.1186/1476-0711-13-1
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author Cheng, Cancan
Sun, Jingjing
Zheng, Fen
Wu, Kuihai
Rui, Yongyu
author_facet Cheng, Cancan
Sun, Jingjing
Zheng, Fen
Wu, Kuihai
Rui, Yongyu
author_sort Cheng, Cancan
collection PubMed
description BACKGROUND: Clinical microbiology laboratories have to accurately identify clinical microbes. However, some isolates are difficult to identify by the automated biochemical text platforms, which are called “difficult-to-identify” microbes in this study. Therefore, the ability of 16S ribosomal DNA (16S rDNA) and internal transcribed spacer 2 (ITS2) sequencing to identify these “difficult-to-identify” bacteria and fungi was assessed in this study. METHODS: Samples obtained from a teaching hospital over the past three years were examined. The 16S rDNA of four standard strains, 18 clinical common isolates, and 47 “difficult-to-identify” clinical bacteria were amplified by PCR and sequenced. The ITS2 of eight standard strains and 31 “difficult-to-identify” clinical fungi were also amplified by PCR and sequenced. The sequences of 16S rDNA and ITS2 were compared to reference data available in GenBank by using the BLASTN program. These microbes were identified according to the percentage of similarity to reference sequences of strains in GenBank. RESULTS: The results from molecular sequencing methods correlated well with automated microbiological identification systems for common clinical isolates. Sequencing results of the standard strains were consistent with their known phenotype. Overall, 47 “difficult-to-identify” clinical bacteria were identified as 35 genera or species by sequence analysis (with 10 of these identified isolates first reported in clinical specimens in China and two first identified in the international literature). 31 “difficult-to-identify” clinical fungi tested could be identified as 15 genera or species by sequence analysis (with two of these first reported in China). CONCLUSIONS: Our results show the importance of 16S rDNA and internal ITS2 sequencing for the molecular identification of “difficult-to-identify” bacteria and fungi. The development of this method with advantages of convenience, availability, and cost-effectiveness will make it worth extending into clinical practice in developing countries.
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spelling pubmed-39059652014-01-30 Molecular identification of clinical “difficult-to-identify” microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2 Cheng, Cancan Sun, Jingjing Zheng, Fen Wu, Kuihai Rui, Yongyu Ann Clin Microbiol Antimicrob Research BACKGROUND: Clinical microbiology laboratories have to accurately identify clinical microbes. However, some isolates are difficult to identify by the automated biochemical text platforms, which are called “difficult-to-identify” microbes in this study. Therefore, the ability of 16S ribosomal DNA (16S rDNA) and internal transcribed spacer 2 (ITS2) sequencing to identify these “difficult-to-identify” bacteria and fungi was assessed in this study. METHODS: Samples obtained from a teaching hospital over the past three years were examined. The 16S rDNA of four standard strains, 18 clinical common isolates, and 47 “difficult-to-identify” clinical bacteria were amplified by PCR and sequenced. The ITS2 of eight standard strains and 31 “difficult-to-identify” clinical fungi were also amplified by PCR and sequenced. The sequences of 16S rDNA and ITS2 were compared to reference data available in GenBank by using the BLASTN program. These microbes were identified according to the percentage of similarity to reference sequences of strains in GenBank. RESULTS: The results from molecular sequencing methods correlated well with automated microbiological identification systems for common clinical isolates. Sequencing results of the standard strains were consistent with their known phenotype. Overall, 47 “difficult-to-identify” clinical bacteria were identified as 35 genera or species by sequence analysis (with 10 of these identified isolates first reported in clinical specimens in China and two first identified in the international literature). 31 “difficult-to-identify” clinical fungi tested could be identified as 15 genera or species by sequence analysis (with two of these first reported in China). CONCLUSIONS: Our results show the importance of 16S rDNA and internal ITS2 sequencing for the molecular identification of “difficult-to-identify” bacteria and fungi. The development of this method with advantages of convenience, availability, and cost-effectiveness will make it worth extending into clinical practice in developing countries. BioMed Central 2014-01-03 /pmc/articles/PMC3905965/ /pubmed/24383440 http://dx.doi.org/10.1186/1476-0711-13-1 Text en Copyright © 2014 Cheng et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Cheng, Cancan
Sun, Jingjing
Zheng, Fen
Wu, Kuihai
Rui, Yongyu
Molecular identification of clinical “difficult-to-identify” microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2
title Molecular identification of clinical “difficult-to-identify” microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2
title_full Molecular identification of clinical “difficult-to-identify” microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2
title_fullStr Molecular identification of clinical “difficult-to-identify” microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2
title_full_unstemmed Molecular identification of clinical “difficult-to-identify” microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2
title_short Molecular identification of clinical “difficult-to-identify” microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2
title_sort molecular identification of clinical “difficult-to-identify” microbes from sequencing 16s ribosomal dna and internal transcribed spacer 2
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905965/
https://www.ncbi.nlm.nih.gov/pubmed/24383440
http://dx.doi.org/10.1186/1476-0711-13-1
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