Background The increase in N gonorrhoeae (NG) prevalence since the mid-1990s, increasing antibiotic resistance, and the absence of an effective vaccine, demand more efficient national and international surveillance of the NG epidemiology. Accordingly, objective, robust and discriminatory genotyping is a crucial tool. The performance characteristics of the internationally frequently used NG multiantigen sequence typing (NG-MAST) and the recently developed multi-locus variable-number tandem repeat analysis (NG-MLVA), were compared.

Methods From 2002 to 2003, NG isolates (n=330) were obtained from multiple anatomical locations from the same patient (n=118) and from self reported sexual contacts (54 couples). These isolates, were genotyped using NG-MAST, by sequencing of more polymorphic segments of porB and tbpB, and by NG-MLVA, which examines polymorphisms in five different tandem repeat loci.

Results From the 118 patients with multiple isolates per visit, 97 (82.2%) had identical NG-MAST STs. Of these 97, 68 patients (57.6%) had isolates with identical MLVA types, 22 patients (18.6%) had single-locus variants (SLVs), six patients (5.1%) had double-locus variants (DLVs), and one patient (0.8%) had a multilocus variant. Of the isolates of 13 patients (11.0%) with non-identical NG-MAST STs, nine patients had identical MLVA types, three patients had SLVs, and one patient had a DLV. For the isolates of the remaining eight patients (6.8%), both typing methods identified divergent genotypes. So for 76 patients (64%) fully concordant clustering was obtained. Considering a SLV as an identical MLVA type the concordance between the two techniques increased to 83%. From 44 of the 54 couples (81.5%), the isolates of the patient and the contact had identical NG-MAST STs, while there were 34 MLVA couples (63.0%) with identical MLVA types, seven couples (13.0%) with SLVs, and three couples (5.6%) with DLVs. The isolates of 6 couples (11.1%) had identical MLVA types with different NG-MAST STs. In the isolates of four couples (7.4%) both typing methods identified divergent genotypes. So for 45 couples (83%) the two typing techniques were concordant.

Conclusions For efficient international surveillance of gonorrhoea transmission, objective, highly discriminatory, but stable genotyping is essential. Both NG-MAST and NG-MLVA displayed a high resolution and are sequence-based portable genotyping methods. They can either be used singly or in combination, depending on epidemiological questions.