RESUMO
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, ß-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.
Assuntos
Antibacterianos/farmacologia , Técnicas de Tipagem Bacteriana/métodos , Primers do DNA/síntese química , DNA Bacteriano/genética , Farmacorresistência Bacteriana Múltipla/genética , Reação em Cadeia da Polimerase/métodos , Aminoglicosídeos/farmacologia , Primers do DNA/genética , Enterococcus faecalis/efeitos dos fármacos , Enterococcus faecalis/genética , Enterococcus faecalis/crescimento & desenvolvimento , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Escherichia coli/crescimento & desenvolvimento , Fluoroquinolonas/farmacologia , Ácido Fusídico/farmacologia , Gardnerella vaginalis/efeitos dos fármacos , Gardnerella vaginalis/genética , Gardnerella vaginalis/crescimento & desenvolvimento , Glicopeptídeos/farmacologia , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/crescimento & desenvolvimento , Lincosamidas/farmacologia , Macrolídeos/farmacologia , Testes de Sensibilidade Microbiana , Família Multigênica , Staphylococcus/efeitos dos fármacos , Staphylococcus/genética , Staphylococcus/crescimento & desenvolvimento , Streptococcus agalactiae/efeitos dos fármacos , Streptococcus agalactiae/genética , Streptococcus agalactiae/crescimento & desenvolvimento , beta-Lactamas/farmacologiaRESUMO
According to the results of analysis of whole genome sequencing, the presence of genes having resistance to ß-lactam antibiotics in hospital-associated strains of Klebsiella pneumoniae was studied. The strains were isolated from neonatal intensive care units. The data obtained were compared with the results of antimicrobial susceptibility testing of isolated microorganisms. Among other strains resistant to cephalosporins, the dominance of genes of CTX-M-type extended-spectrum ß-lactamases was shown. It was revealed that one of eight strains phenotypically resistant and moderately resistant to carbapenems have the blaOXA-48 carbapenemase gene.
Assuntos
Proteínas de Bactérias/genética , Resistência às Cefalosporinas , Klebsiella pneumoniae/genética , beta-Lactamases/genética , Feminino , Humanos , Doença Iatrogênica , Recém-Nascido , Klebsiella pneumoniae/enzimologia , Klebsiella pneumoniae/isolamento & purificação , MasculinoRESUMO
A database of 926 (alpha + beta)-proteins and (alpha + beta)-domains containing abCd-units (among them 401 are nonhomologous) has been compiled from the Protein Data Bank (total 2636 PDB entries). A novel structural tree for this structural class of proteins that is composed of 286 possible polypeptide chain folds has been constructed. The structural classification of (alpha + beta)-proteins containing abCd-unit based on the structural tree has been developed. Both the database and the structural tree are accessible at the web-site (http://strees.protres.ru/).
Assuntos
Bases de Dados de Proteínas , Proteínas/química , Proteínas/classificação , Modelos Moleculares , Conformação Proteica , Dobramento de ProteínaRESUMO
A database of 528 beta-proteins and beta-domains containing abcd-units (among them 244 are nonhomologous) has been compiled from the Protein Data Bank (total 1511 PDB entries). A novel structural tree for this structural class of proteins that is composed of 153 possible polypeptide chain folds has been constructed. The structural classification of beta-proteins containing abcd-unit based on the structural tree has been developed. Both the database and the structural tree are accessible at the web-site (http://strees.protres.ru/).