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Aguayo-Reyes, Alejandro, Quezada-Aguiluz, Mario, Chabouty-García, Henriette, Gonzalez-Muñoz, Paulina, Ilabaca-Carrasco, Franco, Morales-León, Felipe, Matus-Köhler, Maximiliano, Fuller, Sebastian, Aguilera, Felipe, Neil, Matthew, Evans, Benjamin A. 
ORCID: https://orcid.org/0000-0001-6849-9758, González-Rocha, Gerado and Opazo-Capurro, Andrés
(2026)
Genomic characterization and global phylogenomic placement of a high-level azithromycin (HL-AziR) and fluoroquinolone-resistant Neisseria gonorrhoeae ST9363 strain from Chile.
Journal of Global Antimicrobial Resistance, 50.
pp. 91-94.
ISSN 2213-7165
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Abstract
Background: Antibiotic-resistant Neisseria gonorrhoeae (Ng) is a WHO priority pathogen and represents a serious public health threat. This study reports the first Chilean Ng ST9363 isolate (GC11/23) exhibiting dual high-level resistance to azithromycin and fluoroquinolone, recovered from a urethral discharge sample in July 2023. Methods: Antimicrobial susceptibility was assessed using disk diffusion and MIC strip tests. Whole-genome sequencing (WGS) was performed using a hybrid approach, followed by annotation using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). In silico analyses included Staramr, MLST and NG-STAR. Phylogenetic analysis was performed on the core genome of 2417 global ST9363 Ng isolates using IQ-TREE and visualised with TreeViewer. Results: GC11/23 exhibited resistance to ciprofloxacin, tetracycline, penicillin and azithromycin, while remaining susceptible only to ceftriaxone and spectinomycin. The isolate belonged to ST9363 and NG-STAR 3194. Mutations associated with fluoroquinolone resistance were identified in gyrA and parC, while high-level azithromycin resistance (HL-AziR) was linked to mutations in all four copies of the 23S rRNA gene, as well as in mtrD and mtrR. Additional resistance-associated alterations included an insertion (ins346D) in penA and a mutation in rpsJ, conferring resistance to penicillin and tetracycline, respectively. Phylogenetic analysis clustered GC11/23 with isolates from the USA and Europe collected in 2019. Conclusions: GC11/23 represents a multidrug-resistant Ng strain belonging to ST9363/NG-STAR 3194 and carrying mutations conferring resistance to fluoroquinolones, azithromycin, penicillin and tetracycline. Its phylogenetic placement within a European lineage highlights the global dissemination of HL-AziR and fluoroquinolone-resistant strains.
| Item Type: | Article |
|---|---|
| Additional Information: | Data availability: This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JBFSHC000000000. The version described in this paper is version JBFSHC020000000. |
| Uncontrolled Keywords: | neisseria gonorrhoeae,st9363,fluoroquinolone-resistance,high-level azithromycin resistance,who priority pathogen |
| Faculty \ School: | Faculty of Science Faculty of Medicine and Health Sciences > Norwich Medical School |
| UEA Research Groups: | Faculty of Medicine and Health Sciences > Research Groups > Pathogen Biology Group Faculty of Medicine and Health Sciences > Research Groups > Gastroenterology and Gut Biology Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health |
| Depositing User: | LivePure Connector |
| Date Deposited: | 16 Jul 2026 10:08 |
| Last Modified: | 16 Jul 2026 10:08 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/103878 |
| DOI: | 10.1016/j.jgar.2026.06.008 |
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