Work

Molecular typing and characterisation of antimicrobial resistance determinants of Neisseria gonorrhoeae among symptomatic individuals in the Eastern Cape, South Africa

Year: 2026

Type: preprint

Abstract: 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

Source: medRxiv

DOI: 10.64898/2026.11.06.26367404

Authors: Mildred Mandisa Mdingi, Brian Kullin, Hyunsul Jung, Nireshni Mitchev, Remco PH Peters

Institutions: University of Pretoria, University of Cape Town, Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal

Language: English

Topic: Antibiotic Resistance in Bacteria

Subfield: Microbiology (medical)

Field: Medicine

Domain: Health Sciences

SDG: Good health and well-being

Open Access status: green

Funder: University of Pretoria