Phylogenetic analysis of the Klebsiella pneumoniae uge gene in local microbiological monitoring

Abstract

The aim of the study was to evaluate the data of phylogenetically analyzed nucleotide sequences from the K. pneumoniae strain uge genes carried out in the perinatal center. Materials and methods. Fifty-six sequences of the K. pneumoniae uge gene were analyzed. The uge gene was detected by real-time PCR using DT light amplifier (Russia). Results. The rate of K. pneumoniae strains among patients of obstetric and gynecological departments in 2020–2023 averaged 1.4%. In pediatric hospitals, the isolation of K. pneumoniae strains comprised 12–14% in 2020, 2021 and 2023. In 2022, a fourfold decrease in detected K. pneumoniae strains was recorded. Phylogenetic analysis showed that the nucleotide sequences were significantly grouped into 14 clusters. The K. pneumoniae virulence factor uge gene is found in 64.3% cases. The nucleotide sequences allowed to detect heterogeneous K. pneumoniae strain population isolated from patients at the perinatal center from 2019 to 2023 analyzed by the phylogenetic method. There are clusters that combine K. pneumoniae genovariants isolated in 2019 and not replenished with new isolates, which confirms the effectiveness of ongoing anti-epidemic measures, enhanced during COVID-19 spread, excluding the transmission of an infectious agent from a source to a susceptible organism in nosocomial environment. P249Q, N279L amino acid substitutions within the uge gene were determined, which distinguish hypervirulent strains from those with a lower degree of pathogenicity. Out of five mother-child pairs, in four — nucleotide sequences of K. pneumoniae strain uge gene were genetically closer to each other than to other strains isolated from patients of the Medical Departments suggesting about a high degree of their relationship, highly likely indicating that the source of the strain for the child was the paired mother, and not the patients of the departments or the staff of the institution. In one mother-child pair, K. pneumoniae strains belonged to different clusters. The isolate obtained on 09/06/2021 from neonatal faeces (age: 7 days old) was grouped with strains isolated on 12/12/2020 from a patient in the maternity ward and in Laos in 2013 (CP035196). K. pneumoniae isolated on 06/04/2021 from the urine of a woman, was significantly grouped with strains included in cluster 13. Conclusion. An opportunity for improving local microbiological monitoring by sequencing and phylogenetic analysis of K. pneumoniae uge gene has been demonstrated. Assessment of changes in the intraspecies population pattern of HCAI pathogens is necessary for a timely and reasonable response to the deterioration of the epidemiological situation.

Keywords

• sequencing
• phylogenetic analysis
• uge gene
• klebsiella pneumoniae
• monitoring
• neonatology
• epidemiology