Biochemical Atypia in Russian Neisseria gonorrhoeae Clinical Isolates Belonging to the G807 NG-MAST Genogroup/ST1594 MLST

Abstract

Many current gonococcal clinical isolates in Russia show atypical taxonomically significant biochemical activity, which leads to species misidentification. Molecular typing of such cultures according Neisseria gonorrhoeae multiantigen sequence typing (NG-MAST) and multilocus sequence typing (MLST) protocols assigned them to the G807 NG-MAST GENOGROUP/ST1594 MLST that has been predominant in Russia in recent years. The goal of the study was to analyze the molecular mechanisms of biochemical atypia in N. gonorrhoeae clinical isolates characterized as the members of G807 NG-MAST GENOGROUP/ST1594 MLST. Sixteen isolates of this genogroup were included in the study, eight showed defective amino acid metabolism or loss of D-glucose fermentation. Comparative bioinformatic analysis based on WGS data divided these isolates into two clusters strictly associated with typical or atypical biochemical activity. Cultures with defective amino acid metabolism had a 5-nucleotide insertion in the pip-gene that caused a stop codon and led to synthesis of the non-functional enzyme. Comparison of the sequenced genomes with publicly available N. gonorrhoeae genomes showed the rarity of this insertion. In the global N. gonorrhoeae phylogenetic tree the G807 NG-MAST GENOGROUP/ST1594 MLST forms a distinct branch characterized by 170 SNPs, most of which are non-synonymous. We hypothesized a unique strategy for G807 NG-MAST GENOGROUP/ST1594 MLST clone persistence in the global N. gonorrhoeae population via escape of antimicrobial therapy due to diagnostic misidentification.

Keywords: Neisseria gonorrhoeae; biochemical atypia; phylogenetic analysis.

Figure 1

Clustering of Russian strains of N. gonorrhoeae G807 NG-MAST GENOGROUP/ST1594 MLST based on core single nucleotide substitutions.

Figure 2

Localization of a 5 bp deletion at positions 733–737 in the pip gene of Russian atypical strains of N. gonorrhoeae; the gene sequence is provided in reverse complementary form.

Figure 3

Phylogenetic analysis of the global diversity of N. gonorrhoeae was performed using the Maximum likelihood algorithm in Parsnp 1.6. Green triangles mark the Russian strains of the G807 NG-MAST GENOGROUP/ST1594 MLST with biochemical atypia, the cluster of strains from Asian countries are represented by the clones of strain FC428 of the NG-MAST 3435/MLST 1903 and strains of the NG-MAST 1407/MLST 1901 isolated in European countries.