{
  "abstract": "Background. Antimicrobial resistance in Neisseria gonorrhoeae threatens gonorrhoea treatment, while surveillance is constrained by limited culture capacity. We evaluated multi-antigen sequence typing (NG-MAST) and targeted real-time PCR for molecular epidemiology and detection of antimicrobial resistance-associated determinants directly from clinical specimens. Methods. We analysed 235 N. gonorrhoeae-positive stored DNA extracts from symptomatic individuals in South Africa. NG-MAST sequence types were obtained directly or from whole-genome sequences (WGS) of paired cultured isolates. Real-time PCR targeted quinolone resistance-associated mutations (RAMs) in parC and gyrA and macrolide RAMs in the 23S rRNA gene. Results were compared with WGS and with phenotypic susceptibility results from paired isolates. Results. NG-MAST sequence types were obtained for 200/235 (85.1%) specimens and were diverse, with ST21253 predominating (n=26). At least one gyrA or parC mutation was detected by real-time PCR in 110/193 (57.0%) specimens. Compared with WGS, positive agreement was 81.2% for parC and 97.0% for gyrA, and negative agreement 100% and 95.8%, respectively. Among 65 ciprofloxacin-resistant isolates, RAMs were detected in 60 (92.3%) by real-time PCR and 61 (93.8%) by WGS; four had no RAM detected by either method. The 23S rRNA C2611T mutation was detected by both methods in one isolate (azithromycin MIC, 8 mg/L); no A2059G mutations were detected. Conclusions. Gonococcal sequence types were diverse, quinolone RAMs were common, and the assessed macrolide RAMs were rare. Real-time PCR applied directly to specimen DNA agreed well with WGS, but the targeted markers did not fully predict ciprofloxacin susceptibility, supporting complementary molecular and phenotypic approaches. Key words: Neisseria gonorrhoeae, NG-MAST, Real-time PCR, WGS; quinolone resistance; ciprofloxacin resistance, macrolide resistance",
  "abstract_shown": true,
  "affiliations": [
    "Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa"
  ],
  "article_type": "PUBLISHAHEADOFPRINT",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "M. M. Mdingi"
    },
    {
      "name": "B. Kullin"
    },
    {
      "name": "H. Jung"
    },
    {
      "name": "N. Mitchev"
    },
    {
      "name": "R. P. Peters"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/arja9ftqabxy3.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.11.06.26367404",
  "fulltext_url": "https://www.medrxiv.org/content/10.64898/2026.11.06.26367404v1.full",
  "id": "arja9ftqabxy3",
  "issns": [],
  "landing_url": "https://www.medrxiv.org/content/10.64898/2026.11.06.26367404v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "medrxiv",
      "infectious diseases"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://www.medrxiv.org/content/10.64898/2026.11.06.26367404v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-06",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/arja9ftqabxy3.ris",
  "sources": [
    {
      "first_seen": "2026-11-09T00:20:54Z",
      "native_id": "10.64898/2026.11.06.26367404",
      "source": "medrxiv",
      "url": "https://www.medrxiv.org/content/10.64898/2026.11.06.26367404v1"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "medrxiv:infectious diseases",
      "subfield": "infectious-disease"
    }
  ],
  "title": "Molecular typing and characterisation of antimicrobial resistance determinants of Neisseria gonorrhoeae among symptomatic individuals in the Eastern Cape, South Africa",
  "title_text": "Molecular typing and characterisation of antimicrobial resistance determinants of Neisseria gonorrhoeae among symptomatic individuals in the Eastern Cape, South Africa",
  "type": "preprint",
  "updated_at": "2026-11-09T00:20:54Z",
  "url": "https://research.draconitic.com/paper/arja9ftqabxy3",
  "venue": "medRxiv",
  "versions": []
}