Detection and genomic characterization of an extensively drug-resistant Neisseria gonorrhoeae ST16406 isolate identified in Italy, 2025

Background: The global emergence of antimicrobial-resistant Neisseria gonorrhoeae represents a major public health concern. In particular, strains carrying the mosaic penA-60.001 allele have been associated with resistance to extended-spectrum cephalosporins and high-level resistance to azithromycin, threatening current treatment strategies. We describe an extensively drug-resistant Neisseria gonorrhoeae (XDR-NG) strain belonging to sequence type (ST) 16406, detected in Northern Italy in April 2025. Methods: The N. gonorrhoeae strain was recovered from a urethral swab collected from a 28-year-old male at the Microbiology Unit of IRCCS Azienda Ospedaliero-Universitaria di Bologna. Antimicrobial susceptibility testing was performed using E-test strips and interpreted according to EUCAST breakpoints. Whole-genome sequencing (WGS) was conducted using Illumina technology, and genomic characterization included MLST, NG-MAST, NG-STAR typing, resistance gene detection, and phylogenetic analysis with publicly available ST16406 genomes. Results: The isolate exhibited high-level resistance to tetracycline (MIC = 16 mg/L) and ciprofloxacin (MIC = 4 mg/L), very high azithromycin MIC (>256 mg/L), and resistance to both injectable and oral ESCs (ceftriaxone MIC = 0.25 mg/L, cefixime MIC = 1 mg/L). WGS assigned the isolate to MLST ST16406 and identified the mosaic penA-60.001 allele, the A2059G mutation in all four 23S rRNA alleles, mutations in gyrA and parC associated with fluoroquinolone resistance, and tetracycline resistance determinants including tet(M). The A39T mutation was identified in the mtrR repressor gene. No plasmids were detected using PlasmidFinder. Phylogenetic analysis demonstrated close genetic relatedness to previously reported ST16406 isolates from Europe and Asia. Conclusions: This study reports the first detection in Italy of an XDR N. gonorrhoeae ST16406 isolate carrying the penA-60.001 allele. The finding highlights the ongoing international dissemination of this resistant lineage and underscores the importance of maintaining culture-based diagnostics to ensure effective antimicrobial resistance surveillance.