Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicolaReport as inadecuate

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BMC Microbiology

, 15:64

First Online: 13 March 2015Received: 19 August 2014Accepted: 20 February 2015DOI: 10.1186-s12866-015-0396-6

Cite this article as: Garza-Ramos, U., Silva-Sánchez, J., Martínez-Romero, E. et al. BMC Microbiol 2015 15: 64. doi:10.1186-s12866-015-0396-6


BackgroundKlebsiella 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.

ResultThis 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.

ConclusionsThis 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.

KeywordsPathogen Genome comparison Prevalence ESBL Endophytic diazotrophic bacteria Symbiosis Electronic supplementary materialThe online version of this article doi:10.1186-s12866-015-0396-6 contains supplementary material, which is available to authorized users.

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Author: Ulises Garza-Ramos - Jesús Silva-Sánchez - Esperanza Martínez-Romero - Perla Tinoco - Marisol Pina-Gonzales - Humberto Ba


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