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Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola
BACKGROUND: Klebsiella variicola was very recently described as a new bacterial species and is very closely related to Klebsiella pneumoniae; in fact, K. variicola isolates were first identified as K. pneumoniae. Therefore, it might be the case that some isolates, which were initially classified as...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361152/ https://www.ncbi.nlm.nih.gov/pubmed/25886267 http://dx.doi.org/10.1186/s12866-015-0396-6 |
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author | Garza-Ramos, Ulises Silva-Sánchez, Jesús Martínez-Romero, Esperanza Tinoco, Perla Pina-Gonzales, Marisol Barrios, Humberto Martínez-Barnetche, Jesús Gómez-Barreto, Rosa Elena Tellez-Sosa, Juan |
author_facet | Garza-Ramos, Ulises Silva-Sánchez, Jesús Martínez-Romero, Esperanza Tinoco, Perla Pina-Gonzales, Marisol Barrios, Humberto Martínez-Barnetche, Jesús Gómez-Barreto, Rosa Elena Tellez-Sosa, Juan |
author_sort | Garza-Ramos, Ulises |
collection | PubMed |
description | BACKGROUND: Klebsiella variicola was very recently described as a new bacterial species and is very closely related to Klebsiella pneumoniae; in fact, K. variicola isolates were first identified as K. pneumoniae. Therefore, it might be the case that some isolates, which were initially classified as K. pneumoniae, are actually K. variicola. The aim of this study was to devise a multiplex-PCR probe that can differentiate isolates from these sister species. RESULT: This work describes the development of a multiplex-PCR method to identify K. variicola. This development was based on sequencing a K. variicola clinical isolate (801) and comparing it to other K. variicola and K. pneumoniae genomes. The phylogenetic analysis showed that K. variicola isolates form a monophyletic group that is well differentiated from K. pneumoniae. Notably, the isolate K. pneumoniae 342 and K. pneumoniae KP5-1 might have been misclassified because in our analysis, both clustered with K. variicola isolates rather than with K. pneumoniae. The multiplex-PCR (M-PCR-1 to 3) probe system could identify K. variicola with high accuracy using the shared unique genes of K. variicola and K. pneumoniae genomes, respectively. M-PCR-1 was used to assay a collection of multidrug-resistant (503) and antimicrobial-sensitive (557) K. pneumoniae clinical isolates. We found K. variicola with a prevalence of 2.1% (23/1,060), of them a 56.5% (13/23) of the isolates were multidrug resistant, and 43.5% (10/23) of the isolates were antimicrobial sensitive. The phylogenetic analysis of rpoB of K. variicola-positive isolates identified by multiplex-PCR support the correct identification and differentiation of K. variicola from K. pneumoniae clinical isolates. CONCLUSIONS: This multiplex-PCR provides the means to reliably identify and genotype K. variicola. This tool could be very helpful for clinical, epidemiological, and population genetics studies of this species. A low but significant prevalence of K. variicola isolates was found, implying that misclassification had occurred previously. We believe that our multiplex-PCR assay could be of paramount importance to understand the population dynamics of K. variicola in both clinical and environmental settings. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-015-0396-6) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4361152 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-43611522015-03-17 Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola Garza-Ramos, Ulises Silva-Sánchez, Jesús Martínez-Romero, Esperanza Tinoco, Perla Pina-Gonzales, Marisol Barrios, Humberto Martínez-Barnetche, Jesús Gómez-Barreto, Rosa Elena Tellez-Sosa, Juan BMC Microbiol Research Article BACKGROUND: Klebsiella variicola was very recently described as a new bacterial species and is very closely related to Klebsiella pneumoniae; in fact, K. variicola isolates were first identified as K. pneumoniae. Therefore, it might be the case that some isolates, which were initially classified as K. pneumoniae, are actually K. variicola. The aim of this study was to devise a multiplex-PCR probe that can differentiate isolates from these sister species. RESULT: This work describes the development of a multiplex-PCR method to identify K. variicola. This development was based on sequencing a K. variicola clinical isolate (801) and comparing it to other K. variicola and K. pneumoniae genomes. The phylogenetic analysis showed that K. variicola isolates form a monophyletic group that is well differentiated from K. pneumoniae. Notably, the isolate K. pneumoniae 342 and K. pneumoniae KP5-1 might have been misclassified because in our analysis, both clustered with K. variicola isolates rather than with K. pneumoniae. The multiplex-PCR (M-PCR-1 to 3) probe system could identify K. variicola with high accuracy using the shared unique genes of K. variicola and K. pneumoniae genomes, respectively. M-PCR-1 was used to assay a collection of multidrug-resistant (503) and antimicrobial-sensitive (557) K. pneumoniae clinical isolates. We found K. variicola with a prevalence of 2.1% (23/1,060), of them a 56.5% (13/23) of the isolates were multidrug resistant, and 43.5% (10/23) of the isolates were antimicrobial sensitive. The phylogenetic analysis of rpoB of K. variicola-positive isolates identified by multiplex-PCR support the correct identification and differentiation of K. variicola from K. pneumoniae clinical isolates. CONCLUSIONS: This multiplex-PCR provides the means to reliably identify and genotype K. variicola. This tool could be very helpful for clinical, epidemiological, and population genetics studies of this species. A low but significant prevalence of K. variicola isolates was found, implying that misclassification had occurred previously. We believe that our multiplex-PCR assay could be of paramount importance to understand the population dynamics of K. variicola in both clinical and environmental settings. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-015-0396-6) contains supplementary material, which is available to authorized users. BioMed Central 2015-03-13 /pmc/articles/PMC4361152/ /pubmed/25886267 http://dx.doi.org/10.1186/s12866-015-0396-6 Text en © Garza-Ramos et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 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 Article Garza-Ramos, Ulises Silva-Sánchez, Jesús Martínez-Romero, Esperanza Tinoco, Perla Pina-Gonzales, Marisol Barrios, Humberto Martínez-Barnetche, Jesús Gómez-Barreto, Rosa Elena Tellez-Sosa, Juan Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola |
title | Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola |
title_full | Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola |
title_fullStr | Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola |
title_full_unstemmed | Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola |
title_short | Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola |
title_sort | development of a multiplex-pcr probe system for the proper identification of klebsiella variicola |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361152/ https://www.ncbi.nlm.nih.gov/pubmed/25886267 http://dx.doi.org/10.1186/s12866-015-0396-6 |
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