Genomic Epidemiology and Molecular Resistance Mechanisms of Azithromycin-Resistant Neisseria gonorrhoeae in Canada from 1997 to 2014

Abstract

The emergence of Neisseria gonorrhoeae strains with decreased susceptibility to cephalosporins and azithromycin (AZM) resistance (AZM(r)) represents a public health threat of untreatable gonorrhea infections. Genomic epidemiology through whole-genome sequencing was used to describe the emergence, dissemination, and spread of AZM(r) strains. The genomes of 213 AZM(r) and 23 AZM-susceptible N. gonorrhoeae isolates collected in Canada from 1989 to 2014 were sequenced. Core single nucleotide polymorphism (SNP) phylogenomic analysis resolved 246 isolates into 13 lineages. High-level AZM(r) (MICs ≥ 256 μg/ml) was found in 5 phylogenetically diverse isolates, all of which possessed the A2059G mutation (Escherichia coli numbering) in all four 23S rRNA alleles. One isolate with high-level AZM(r) collected in 2009 concurrently had decreased susceptibility to ceftriaxone (MIC = 0.125 μg/ml). An increase in the number of 23S rRNA alleles with the C2611T mutations (E. coli numbering) conferred low to moderate levels of AZM(r) (MICs = 2 to 4 and 8 to 32 μg/ml, respectively). Low-level AZM(r) was also associated with mtrR promoter mutations, including the -35A deletion and the presence of Neisseria meningitidis-like sequences. Geographic and temporal phylogenetic clustering indicates that emergent AZM(r) strains arise independently and can then rapidly expand clonally in a region through local sexual networks.

Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000–2013

“…We also identify interspecies mosaic variants of the efflux pump–encoding mtr locus (n = 29 [10%]), with 5 isolates containing both the mosaic mtr locus and C2611T mutations. Demczuk et al recently found ermB and ermC in 3 Azi RS isolates in Canada [26], but we found neither of these genes. Notably, many of the mtrR variants reported in the literature to result in Azi RS were not highly associated with resistance in this data set.…”

Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains

“…High-level azithromycin resistance (MIC Ն 256 g/ml) is associated with NG-STAR ST-30, ST-36, ST-69, ST-192, ST-202, ST-223, and ST-225, all of which possess the 23S rRNA A2059G mutation of allele 23S-1. Previous molecular studies have shown that these isolates possessed the A2059G mutation in all 4 alleles (36). Although more than a single mutated 23S rRNA gene in the genome is required to confer elevated azithromycin MICs (28,36), the acquisition of a single mutated allele facilitates the rapid acquisition of a full complement of mutated alleles under selective pressures (3,29); therefore, the presence of a single mutation may be considered a precursor to full resistance, especially if inappropriate treatment adds to this selective pressure.…”

“…Previous molecular studies have shown that these isolates possessed the A2059G mutation in all 4 alleles (36). Although more than a single mutated 23S rRNA gene in the genome is required to confer elevated azithromycin MICs (28,36), the acquisition of a single mutated allele facilitates the rapid acquisition of a full complement of mutated alleles under selective pressures (3,29); therefore, the presence of a single mutation may be considered a precursor to full resistance, especially if inappropriate treatment adds to this selective pressure. It is for this reason that NG-STAR records the presence of a mutation, even if present in a single allele, as being sufficient to identify the potential for full azithromycin resistance and to recommend an alternative treatment.…”

Sexually transmitted infections: challenges ahead

“…Effective STI control will require the political will to prioritise and invest in new 150 rapid molecular methods for predicting AMR (for AMR surveillance but ideally also to inform individualized treatment), [190][191][192] rapid point of care tests for diagnosis of gonorrhoea (ideally with combined prediction of AMR); 190,191 ideal phylogenomics of gonococci and their AMR (also in non-cultured samples); 159,457,[459][460][461][462][463][464] and appropriate models for pharmacokinetics/ pharmacodynamics (urogenital and extragenital sites) and prediction of AMR induction/selection, evolution and biological fitness. -Data are for principal diagnosis, recorded using the ICD-9-CM from 1993-94 to 1997-98, and recording using the ICD-10-AM (Australian modification) from 1998-99.…”