Bioinformation analysis of polymorphism of the blaTEM gene coding regions in Escherichia coli strains

Abstract

Bioinformation analysis of the bacterial genome with screening of genetic elements to detect variability of nucleotide sequences is one of the methods of antibiotic resistance evolution fundamental research. Comparative analysis of the molecular genetic variability or genome sequence conservatism is used as a convenient tool for understanding patterns of the evolutionary process through definition of the phylogenetic relationships. The aim of the study was to conduct a bioinformation analysis of the variability of the antibiotic resistance blaTEM gene in E. coli strains. Materials and methods. The GenBank nucleic acid search database was used for bioinformation analysis. The search for nucleotide sequences of the blaTEM gene was performed in fasta-format. "Vector NTI Advance 11.0" software package was used to analyze the nucleotide sequences of the blaTEM gene. Multiple alignment and its statistical analysis to determine conservative and variable regions of the blaTEM gene was performed using software component module “AlignX”. Nucleotide sequences of the 21 blaTEM gene sequences isolated from E. coli strains in 11 countries and registered in the GenBank database from 1996 to 2019 were analyzed. Research results and discussion. Multiple alignment of the nucleotide sequences of the studied blaTEM gene sequences allowed to determine both conservative and variable regions of the gene. 12 conservative regions of the blaTEM gene with a length of at least 30 nucleotide sequences were identified. The longest homologous region of the gene (144 nucleotide sequences) was found at the 529 - 672 nn position. blaTEM gene variability was evidenced by point mutations at 41 positions of the nucleotide sequences. The most heterogeneous region was found at the 697-717 nn and 773-813 nn positions. Mutations in the analyzed E. coli blaTEM genes were caused by transitions (60,5%), transversions (37,2%) and deletions (2,3%). The degree of relatedness of the analyzed blaTEM gene sequences is presented in the form of a dendrogram. The phylogenetic tree shows three conditional genetic clusters. The top position of the dendrogram is occupied by the cluster that includes eight blaTEM gene sequences, isolated in European countries: 2 - in France and one each - in Poland, Germany, England, Portugal, Italy and the Netherlands. This cluster was characterized by a significant number of evolutionary events (from 4 to 9) associated with nucleotide sequence substitutions, which is represented on the dendrogram by the divergence of the phylogenetic tree branches. The cluster which occupies the middle position of the dendrogram is represented by five phylogenetic branches. This cluster includes blaTEM gene sequences isolated in Korea, China, Germany and India. 1-2 nucleotide substitutions were identified in the majority of the sequences in this cluster. The lower position of the dendrogram consists of blaTEM gene sequences characterized by a high degree of relatedness and a small number of nucleotide sequence substitutions, a significant number of sequences were isolated in the United States and China (75%). Conclusions. Results of the bioinformation analysis showed that the nucleotide sequences of the E. coli blaTEM gene have historically undergone several evolutionary divergences and acquired signs of heterogeneity, which apparently causes the emergence of a large number of species of the blaTEM gene.