Recombination mapping identifies a commensal Neisseria subflava origin of mosaic penA 60.001 allele in Neisseria gonorrhoeae

The emergence of ceftriaxone resistance in Neisseria gonorrhoeae (FC428 clone) has been linked to the acquisition of mosaic penA alleles, yet the origin of the mosaic penA 60.001 alleles and the contribution of commensal Neisseria as genetic donors remain incompletely resolved. We analysed the penA gene from 29 commensal Neisseria isolates collected from adults in Tokyo between 2018 and 2023 and compared these sequences with reference N. gonorrhoeae sequences, including penA-60.001 (FC428). Putative recombination events were inferred using the Recombination Detection Program (RDP5), and region-specific phylogenies were reconstructed with the unweighted pair group method with arithmetic mean (UPGMA) to evaluate congruence across breakpoint schemes. A commensal Neisseria subflava isolate (ID 164862) shared extended, high-identity sequence tracts with the FC428 gonococcal isolate; multiple-sequence alignment showed 87.0% nucleotide identity with a 100% identical region spanning positions 910-1733 bp. Concordantly, RDP5 inferred a recombination event in this region, identifying a contiguous imported segment that was 100% identical between the two sequences. These findings provide molecular evidence that a commensal N. subflava lineage contributed to the mosaic core of the penA 60.001 allele in ceftriaxone-resistant N. gonorrhoeae (FC428), and incorporating commensal Neisseria into antimicrobial-resistance surveillance could facilitate early detection of mosaic penA alleles with the potential to disseminate clinically relevant resistance. We mapped a ceftriaxone-resistance penA gene segment in gonorrhoea to a commensal Neisseria lineage, revealing how gene exchange in the throat can seed resistant strains.