Global distribution of Xpert CT/NG assay Neisseria gonorrhoeae escape variants indicates sporadic emergence with limited clonality between 2016 and 2025

Screening of 54,837 gonococcal genomes identified 12 new variants lacking one (n = 9) or both (n = 3) of the Xpert CT/NG assay's gonococcal targets. In total, 17 diagnostic-escape variants occurred across five countries and multiple genomic lineages; phylogenomic analysis revealed both ancestral and strain-specific recombination events. Xpert CT/NG diagnostic escape remains rare (0.026%) but illustrates recurrent recombination in gonococci. This emphasises the necessity of continuous external quality assessments, supplementary testing of gonococcal-positive molecular screening samples, and appropriate genomic and epidemiologic surveillance.