Whole-Genome Sequencing to Predict Antimicrobial Susceptibility Profiles in Neisseria gonorrhoeae

Abstract

Background: Neisseria gonorrhoeae is a major public health problem due to increasing incidence and antimicrobial resistance. Genetic markers of reduced susceptibility have been identified; the extent to which those are representative of global antimicrobial resistance is unknown. We evaluated the performance of whole-genome sequencing (WGS) used to predict susceptibility to ciprofloxacin and other antimicrobials using a global collection of N. gonorrhoeae isolates.

Methods: Susceptibility testing of common antimicrobials and the recently developed zolifodacin was performed using agar dilution to determine minimum inhibitory concentrations (MICs). We identified resistance alleles at loci known to contribute to antimicrobial resistance in N. gonorrhoeae from WGS data. We tested the ability of each locus to predict antimicrobial susceptibility.

Results: A total of 481 N. gonorrhoeae isolates, collected between 2004 and 2019 and making up 457 unique genomes, were sourced from 5 countries. All isolates with demonstrated susceptibility to ciprofloxacin (MIC ≤0.06 μg/mL) had a wild-type gyrA codon 91. Multilocus approaches were needed to predict susceptibility to other antimicrobials. All isolates were susceptible to zoliflodacin, defined by an MIC ≤0.25 μg/mL.

Conclusions: Single marker prediction can be used to inform ciprofloxacin treatment of N. gonorrhoeae infection. A combination of molecular markers may be needed to determine susceptibility for other antimicrobials.

Keywords: Neisseria gonorrhoeae; antimicrobial susceptibility testing; whole-genome sequencing.

Figure 1.

The gyrA 91S genotype is associated with ciprofloxacin susceptibility across geographic locations. A maximum likelihood whole-genome phylogeny of 457 Neisseria gonorrhoeae isolates mapped to the NCCP11945 (NC_011035.1) reference genome was generated using Gubbins software. Branch lengths represent nonrecombinant substitutions. Inner annotation ring represents the geographic locations of isolates: Canada (pink), Dominican Republic (green), Hong Kong (blue), South Africa (tan), or Vietnam (teal). Middle ring represents gyrA codon 91: serine, S (green) or phenylalanine, F (blue), and outer ring, the ciprofloxacin minimum inhibitory concentration (MIC) category: ≤0.06 μg/mL (yellow), 0.06 to <1 μg/mL (green), or ≥1 μg/mL (blue). Inset depicts the distribution of ciprofloxacin MICs; isolates with the gyrA 91S genotype have ciprofloxacin MICs ranging from 0.008–0.06 μg/mL, and isolates with the gyrA 91F genotype have ciprofloxacin MICs ranging from 0.25 – >32 μg/mL.

Figure 2.

Histograms indicating the azithromycin, cefixime, ceftriaxone, ciprofloxacin, penicillin, spectinomycin, tetracycline, and zoliflodacin minimum inhibitory concentration (MIC) distribution in the collection of Neisseria gonorrhoeae isolates (N = 457).