Genetic Characterization and Antimicrobial Resistance of Neisseria gonorrhoeae in Russia: Insights from Whole-Genome Sequencing

Objective: Monitoring the spread of antimicrobial-resistant Neisseria gonorrhoeae ( N. gonorrhoeae ) is a major priority for national surveillance programs in the Russian Federation. From 2021 to 2022, there has been a trend in which the previously increased sensitivity of N. gonorrhoeae to penicillins, tetracyclines, fluoroquinolones, and macrolides was replaced by an increase in the number of strains resistant to these drugs, including multi-resistant strains. The aim of this study was to analyze the genetic characteristics of the contemporary Russian population of N. gonorrhoeae based on whole-genome sequencing (WGS) data. Methods: A total 19 strains isolated in the Russian Federation in 2022 were sequenced and included in the present study together with the data on the reference strain FA19 and 169 N. gonorrhoeae strains from various countries taken from the NCBI GenBank and PubMLST databases. We used the Parsnp 1.6 to perform phylogenetic analysis of the studied samples. For single nucleotide polymorphisms calling, reads were mapped to the reference genome using Bowtie2. Single nucleotide polymorphisms calling was performed using GATK protocol. The data were shown as number and percentage. Results: In the present study, molecular typing of N. gonorrhoeae strains revealed changes in the genetic structure of the N. gonorrhoeae population, which was long considered to be very conservative; in particular, there was a detection of a significant number of genotypes that have rarely or never been detected before in the Russian population. WGS data showed the formation of a separate cluster consisting of N. gonorrhoeae strains within the MLST10314, MLST9363 and MLST8134 genogroups. Furthermore, a large number of single nucleotide polymorphisms in the genes of the mtrCDE and mtrR efflux system were revealed. Conclusion: The present results indicate the need to enhance measures to control the spread of antibiotic-resistant N. gonorrhoeae strains and to continue WGS of the Russian N. gonorrhoeae population to identify strains with genetic determinants of antimicrobial resistance.