Comparative phylogenetic analysis of Neisseria gonorrhoeae clinical isolates in Russia, European Union, and Japan

Shaskolskiy BL1, Kandinov ID1, Chestkov AV2, Solomka VS2, Kubanov AA2, Deryabin DG2, Gryadunov DA1, Dementieva EI1
About authors

1 Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia

2 State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, Moscow, Russia

Correspondence should be addressed: Boris L. Shaskolskiy
Vavilova, 32, Moscow, 119991; ur.pihcoib@yiksloksahs.b

About paper

Funding: the study was supported by the Russian Science Foundation (Project 17-75-20039 on the assessment of genetic diversity of sequence types) and the Ministry of Science and Higher Education of the Russian Federation (Agreement № 075-15-2019-1660 on the collection and verification of clinical isolates and the establishment of the association between the unique sequence types and the population size). The isolates were sequenced at the facilities of the Genome center for collective use (Engelhardt Institute of Molecular Biology; http://www.eimb.ru/ru1/ckp/ccu_genome_c.php).

Compliance with ethical standards: the study was approved by the Ethics Committee of the State Research Centre of Dermatovenerology and Cosmetology (Protocol № 11, dated November 29, 2019). Specimens were collected in compliance with the Declaration of Helsinki (2000) and the European Convention on Human Rights and Biomedicine (1999).

Author contribution: Shaskolskiy BL, Dementieva EI, Kandinov ID carried out the study, analyzed the data and wrote the manuscript; Gryadunov DA supervised the study and wrote the manuscript; Chestkov AV, Solomka VS, Kubanov AA, Deryabin DG collected and verified clinical isolates, analyzed the obtained data.

Received: 2020-01-09 Accepted: 2020-02-08 Published online: 2020-02-22

Surveillance of multidrug-resistant infections is a priority task for contemporary epidemiology. The aim of this study was to genotype modern clinical isolates of N. gonorrhoeae using the NG-MAST technique (Neisseria gonorrhoeae multi-antigen sequence typing) and to compare the phylogeny of the gonococcal pathogens coming from Russia, European Union and Japan. We studied a total of 822 isolates collected in Russia from 2013 through 2018. We also used NG-MAST data from the following databases: PathogenWatch (European Union, 1,071 isolates) and PubMLST (Japan, 206 isolates). Russian isolates represented 301 different NG-MAST types. The most common were types 807, 228, 1993, 5714, and 9476 (8.3%, 3.3%, 3.2%, 3.2%, and 2.7%, respectively). There were only 3 isolates (0.4%) from Russia that represented the epidemiologically significant sequence type 1407 prevailing in many countries and characterized by multiple determinants of antimicrobial resistance. A phylogenetic tree for the NG-MAST types found in Russia and European countries was constructed. The cluster analysis of the proportion of isolates belonging to unique sequence types and the country population size allowed us to identify 2 clusters (significance level — 0.01): the first cluster included Russia and Japan, the second, European countries. A distribution pattern was identified for unique sequence types: the greater is the population size, the higher is their proportion. The phylogenetic analysis demonstrated a genetic distance between the most common Russian, European and Japanese sequence types, suggesting that the Russian population of N. gonorrhoeae has been evolving relatively locally.

Keywords: Neisseria gonorrhoeae, NG-MAST, phylogenetic analysis