WGS to predict antibiotic MICs for Neisseria gonorrhoeae

Abstract

Background: Tracking the spread of antimicrobial-resistant Neisseria gonorrhoeae is a major priority for national surveillance programmes.

Objectives: We investigate whether WGS and simultaneous analysis of multiple resistance determinants can be used to predict antimicrobial susceptibilities to the level of MICs in N. gonorrhoeae.

Methods: WGS was used to identify previously reported potential resistance determinants in 681 N. gonorrhoeae isolates, from England, the USA and Canada, with phenotypes for cefixime, penicillin, azithromycin, ciprofloxacin and tetracycline determined as part of national surveillance programmes. Multivariate linear regression models were used to identify genetic predictors of MIC. Model performance was assessed using leave-one-out cross-validation.

Results: Overall 1785/3380 (53%) MIC values were predicted to the nearest doubling dilution and 3147 (93%) within ±1 doubling dilution and 3314 (98%) within ±2 doubling dilutions. MIC prediction performance was similar across the five antimicrobials tested. Prediction models included the majority of previously reported resistance determinants. Applying EUCAST breakpoints to MIC predictions, the overall very major error (VME; phenotypically resistant, WGS-prediction susceptible) rate was 21/1577 (1.3%, 95% CI 0.8%-2.0%) and the major error (ME; phenotypically susceptible, WGS-prediction resistant) rate was 20/1186 (1.7%, 1.0%-2.6%). VME rates met regulatory thresholds for all antimicrobials except cefixime and ME rates for all antimicrobials except tetracycline. Country of testing was a strongly significant predictor of MIC for all five antimicrobials.

Conclusions: We demonstrate a WGS-based MIC prediction approach that allows reliable MIC prediction for five gonorrhoea antimicrobials. Our approach should allow reasonably precise prediction of MICs for a range of bacterial species.

Figure 1

Distribution of measured MICs by country. EUCAST breakpoints for susceptibility and resistance (shown as dashed lines) are: azithromycin, ≤0.25 and >0.5; cefixime, ≤0.125 and >0.125; ciprofloxacin, ≤0.03 and >0.06; penicillin, ≤0.06 and >1; and tetracycline, ≤0.5 and >1 mg/L.

Figure 2

Accuracy of predicted MICs. The difference between the measured and predicted MICs is shown on a log₂ scale, such that a difference of 1 represents a difference of 1 doubling dilution. A VME is where the predicted susceptibility is susceptible when the measured susceptibility is resistant; an ME is where the predicted susceptibility is resistant, but the measured susceptibility is susceptible; and minor errors denote where the phenotype is susceptible and the prediction intermediate, or the phenotype is intermediate and the prediction is resistant, or vice versa in both cases. S, susceptible; I, intermediate; R, resistant; ME, major error; VME, very major error.