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.
Keywords:
antibiotic resistance; clusterization; next-generation sequencing technology; polymerase chain reaction (PCR).
MeSH terms
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Aminoglycosides / pharmacology
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Anti-Bacterial Agents / pharmacology*
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Bacterial Typing Techniques / methods*
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DNA Primers / chemical synthesis*
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DNA Primers / genetics
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DNA, Bacterial / genetics*
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Drug Resistance, Multiple, Bacterial / genetics*
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Enterococcus faecalis / drug effects
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Enterococcus faecalis / genetics
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Enterococcus faecalis / growth & development
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Escherichia coli / drug effects
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Escherichia coli / genetics
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Escherichia coli / growth & development
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Fluoroquinolones / pharmacology
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Fusidic Acid / pharmacology
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Gardnerella vaginalis / drug effects
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Gardnerella vaginalis / genetics
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Gardnerella vaginalis / growth & development
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Glycopeptides / pharmacology
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Klebsiella pneumoniae / drug effects
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Klebsiella pneumoniae / genetics
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Klebsiella pneumoniae / growth & development
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Lincosamides / pharmacology
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Macrolides / pharmacology
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Microbial Sensitivity Tests
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Multigene Family
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Polymerase Chain Reaction / methods*
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Staphylococcus / drug effects
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Staphylococcus / genetics
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Staphylococcus / growth & development
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Streptococcus agalactiae / drug effects
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Streptococcus agalactiae / genetics
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Streptococcus agalactiae / growth & development
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beta-Lactams / pharmacology
Substances
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Aminoglycosides
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Anti-Bacterial Agents
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DNA Primers
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DNA, Bacterial
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Fluoroquinolones
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Glycopeptides
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Lincosamides
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Macrolides
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beta-Lactams
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Fusidic Acid