Method of Selection of Bacteria Antibiotic Resistance Genes Based on Clustering of Similar Nucleotide Sequences
- Authors: Balashov I.S.1, Naumov V.A.1, Borovikov P.I.1, Gordeev A.B.1, Dubodelov D.V.1, Lyubasovskaya L.A.1, Rodchenko Y.V.1, Bystritskii A.A.1, Aleksandrova N.V.1, Trofimov D.Y.1, Priputnevich T.V.1
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Affiliations:
- V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation
- Issue: Vol 163, No 6 (2017)
- Pages: 814-817
- Section: Methods
- URL: https://journals.rcsi.science/0007-4888/article/view/239301
- DOI: https://doi.org/10.1007/s10517-017-3910-z
- ID: 239301
Cite item
Abstract
A new method for selection of bacterium antibiotic resistance genes is proposed and tested for solving the problems related to selection of primers for PCR assay. The method implies clustering of similar nucleotide sequences and selection of group primers for all genes of each cluster. Clustering of resistance genes for six groups of antibiotics (aminoglycosides, β-lactams, fluoroquinolones, glycopeptides, macrolides and lincosamides, and fusidic acid) was performed. The method was tested for 81 strains of bacteria of different genera isolated from patients (K. pneumoniae, Staphylococcus spp., S. agalactiae, E. faecalis, E. coli, and G. vaginalis). The results obtained by us are comparable to those in the selection of individual genes; this allows reducing the number of primers necessary for maximum coverage of the known antibiotic resistance genes during PCR analysis.
About the authors
I. S. Balashov
V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation
Email: a_gordeev@oparina4.ru
Russian Federation, Moscow
V. A. Naumov
V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation
Email: a_gordeev@oparina4.ru
Russian Federation, Moscow
P. I. Borovikov
V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation
Email: a_gordeev@oparina4.ru
Russian Federation, Moscow
A. B. Gordeev
V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation
Author for correspondence.
Email: a_gordeev@oparina4.ru
Russian Federation, Moscow
D. V. Dubodelov
V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation
Email: a_gordeev@oparina4.ru
Russian Federation, Moscow
L. A. Lyubasovskaya
V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation
Email: a_gordeev@oparina4.ru
Russian Federation, Moscow
Yu. V. Rodchenko
V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation
Email: a_gordeev@oparina4.ru
Russian Federation, Moscow
A. A. Bystritskii
V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation
Email: a_gordeev@oparina4.ru
Russian Federation, Moscow
N. V. Aleksandrova
V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation
Email: a_gordeev@oparina4.ru
Russian Federation, Moscow
D. Yu. Trofimov
V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation
Email: a_gordeev@oparina4.ru
Russian Federation, Moscow
T. V. Priputnevich
V. I. Kulakov Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Health of the Russian Federation
Email: a_gordeev@oparina4.ru
Russian Federation, Moscow