Molecular Characterization and Antimicrobial Resistance in Neisseria gonorrhoeae, Nunavut Region of Inuit Nunangat, Canada, 2018-2019

Use of genome sequencing to resolve differences in gradient diffusion and agar dilution antimicrobial susceptibility testing performance of Neisseria gonorrhoeae isolates in Alberta, Canada

Agar dilution is the gold standard method for phenotypic antimicrobial susceptibility testing (AST) for Neisseria gonorrhoeae. However, this method is laborious and requires expertise, so laboratories that perform N. gonorrhoeae AST may choose alternative methods such as disk diffusion and gradient diffusion. In this study, we retrospectively compare the performance of gradient diffusion to agar dilution for 2,394 unique N. gonorrhoeae isolates identified in Alberta from 2017 to 2020 against azithromycin, cefixime, ceftriaxone, ciprofloxacin, penicillin, and tetracycline. Genome sequencing was utilized to resolve discrepancies between AST methods, detect antimicrobial resistance markers, and identify trends between error rates and sequence types (STs) of isolates. Over 90% of N. gonorrhoeae isolates were susceptible to azithromycin, cefixime, and ceftriaxone, whereas decreased susceptibility was observed for ciprofloxacin, penicillin, and tetracycline. Categorical (CA) and essential agreement (EA) was poorest between the two methods for penicillin (CA: 86.02%; EA: 77.69%) and tetracycline (CA: 47.22%; EA: 55.96%); however, the low CA was primarily attributed to minor errors. Antimicrobial agents with errors outside of acceptable limits included azithromycin (very major error: 18.42%; major error: 7.73%) and tetracycline (very major error: 6.17%). Genome sequencing on a subset of isolates resolved 30.3% of the azithromycin major errors and confirmed the azithromycin or tetracycline very major errors. Significant associations between certain STs and error types for azithromycin and tetracycline were also identified. Overall, gradient diffusion compared well to agar dilution for cefixime, ceftriaxone, and ciprofloxacin, and genome sequencing was identified as a useful tool to arbitrate discrepant susceptibility testing results between gradient diffusion and agar dilution for N. gonorrhoeae.

Antimicrobial Resistance Profiling and Genome Analysis of the penA-60.001 Neisseria gonorrhoeae Clinical Isolates in China in 2021

BACKGROUND

Neisseria gonorrhoeae antimicrobial resistance (AMR) is an urgent public health threat. With dissemination of FC428-related clones, the efficacy of ceftriaxone has become controversial.

METHODS

Agar dilution and whole genome sequencing were used to analyze AMR.

RESULTS

High resistance to penicillin (75.2%), tetracycline (87.9%), ciprofloxacin (98.3%), ceftriaxone (8.9%), cefixime (14.3%), and azithromycin (8.6%) was observed among 463 isolates first collected in China in 2021. All penA-60.001 clones exhibited resistance to ceftriaxone or cefixime, and 1 of the 12 cases was resistant to azithromycin. ngMAST and ngSTAR of penA-60.001 isolates showed that single-nucleotide polymorphisms in the porB, tbpB, ponA, gyrA, and parC genes were the major causes of different sequence types. MLST-7365 (n = 5) and MLST-1903 (n = 3) were main genotypes, and the other 4 strains featured MLST-10314, MLST-13871, MLST-7827 and MLST-1600. Furthermore, resistance markers (eg, penA, blaTEM-1, blaTEM-135) and virus factors were detected. Most penA-60.001 strains were fully mixed with global FC428-related clones; 2021-A2 and F89 had the same origin; and 2021-A1 exhibited a unique evolutionary trajectory.

CONCLUSIONS

Results provide the first demonstration of extremely severe AMR rates of N gonorrhoeae in China in 2021, particularly strains with ceftriaxone decreased susceptibility. The sustained transmission of penA-60.001 subclones might further threaten treatment effectiveness.

Molecular Surveillance and Prediction of Antimicrobial Resistance of Neisseria gonorrhoeae in Northern Alberta, Canada, 2015 to 2018

BACKGROUND

The aims of this study was to describe molecular surveillance of Neisseria gonorrhoeae in the North Zone of Alberta (NZ) and to determine its value in predicting antimicrobial resistance.

METHODS

Sequence types (STs) and single-nucleotide polymorphism (SNP) assays were performed on nucleic acid amplification testing (NAAT) samples. Sequence types of NAATs were matched to ST of cultures from across Alberta. Antimicrobial resistance prediction of NAATs for cephalosporins, azithromycin, and ciprofloxacin using SNP was compared with matching ST culture results using agar dilution and whole-genome sequencing.

RESULTS

Of 2755 eligible specimens (2492 cases), 61.9% (1646 specimens) were sent for sequence typing, identifying 196 unique ST. Antimicrobial resistance data for 1307 additional cases were available using matching cultures. Decreased susceptibility (DS) to antimicrobials used for gonorrhea treatment was rare in the NZ; according to the SNP assay, none of the specimens had predicted DS to cephalosporins or azithromycin resistance. However, of the NZ NAAT samples tested in this study, 10.7% (131 of 1220) were predicted to have intermediate cephalosporin minimum inhibitory concentrations and 9.6% (115 of 1204) were resistant to ciprofloxacin. Based on cultures, the proportions of resistance in all of Alberta were as follows: DS to cephalosporins, 0.6% (20 of 3373); DS to intermediate cephalosporin, 16.9% (570 of 3373); azithromycin resistance, 1.2% (41 of 3373); and ciprofloxacin resistance, 32.2% (1087 of 3373).

CONCLUSIONS

Our results highlight our ability to use culture-independent methods to predict antimicrobial resistance in N. gonorrhoeae.