Characteristics of the Klebsiella Pneumoniae Strain Isolated from a Positive Blood Culture of a Premature Newborn Baby According to the Results of Whole Genome Sequencing

Abstract

Relevance. K. pneumoniae is a common nosocomial pathogen in pediatric hospitals, often characterized by the presence of a wide range of virulence factors and genetic determinants of antibiotic resistance. Аim. To analyze the results obtained during wholegenome sequencing of a Klebsiella pneumoniae strain isolated from a positive blood culture of a premature newborn. Materials and methods. An ESBL-producing strain of K. pneumoniae isolated from a positive blood culture of a newborn premature infant. Sequencing was performed on the MiSeq platform (Illumina). Analysis of DNA nucleotide sequences of the complete genome of K. pneumoniae was carried out using the website of the Center for Genomic Epidemiology. The search for genetic determinants of antibiotic resistance and virulence was carried out using online services. Results and its discussion. The resulting nucleotide sequence was 5,414,099 bp in length, and the proportion of GC nitrogenous bases was 57.3%. The isolated strain belonged to the sequence type ST3559, had 4 genes encoding the synthesis of enzymes that hydrolyze antibacterial drugs from the beta-lactam group, 2 genes providing resistance to quinolones/fluoroquinolones, 1 resistance gene each to trimethoprim, chloramphenicol, fosfomycin and aminoglycoside antibiotics. Most of the virulence factor genes identified in the studied strain ensure the recognition and absorption of iron ions necessary for the competitive functioning of the bacterial cell. K. pneumoniae possesses the acrA efflux pump gene and its regulators, as well as 4 prophage particles and 1 CRISPCas IE system. Conclusions. Whole-genome sequencing of the K. pneumoniae strain isolated from a positive blood culture of a premature newborn allows us to characterize in detail the causative agent of a generalized infection and detect a wide range of genetic determinants of virulence factors and antibiotic resistance. The ESBL-producing strain of K. pneumoniae, as the etiological agent of neonatal sepsis, was characterized by the presence of virulence genes, multidrug resistance, both due to genes encoding enzymes that hydrolyze antibiotics, and due to the presence of efflux pumps and their regulators. The use of the results of traditional cultural research methods together with high-throughput sequencing data is a promising area of scientific research and has a reserve of practical application in the field of clinical medicine, genetics of microorganisms, molecular epidemiology at the local and global levels

Keywords

• klebsiella pneumoniae
• complete genome sequencing
• virulence factor genes
• antibiotic resistance genes no conflict of interest to declare