Neisseria sp. SLRRB23 Genome sequencing

This study reports the whole-genome sequence of Neisseria sp. strain SLRRB23, a novel commensal isolate recovered from a patient undergoing evaluation for possible gonorrhea treatment failure. The strain was initially flagged as Neisseria gonorrhoeae due to a positive result in a commercial nucleic acid amplification test (NAAT) targeting the DR-9 genomic region, a sequence highly specific to N. gonorrhoeae. However, further phenotypic and genomic analyses revealed that strain SLRRB23 is a distinct, non-gonococcal Neisseria species, harboring a gonococcal DR-9 region with 96% nucleotide sequence identity. Remarkably, this commensal strain carries multiple antimicrobial resistance determinants that have been described in N. gonorrhoeae, including a mosaic penA allele (NG-STAR 59.0001), mutations in the mtr efflux pump regulatory region, and an A121D mutation in porB. These findings raise concerns about the potential of commensal Neisseria species to serve as reservoirs and vehicles for the horizontal transfer of resistance genes into pathogenic strains, particularly in the oropharyngeal niche where interspecies exchange is known to occur. Additionally, the presence of gonococcal diagnostic marker sequences in this commensal strain highlights the risk of false-positive results in NAAT-based diagnostic assays and underscores the importance of genomic surveillance and confirmatory testing protocols. The availability of this genome will contribute to efforts to refine molecular diagnostics, improve our understanding of resistance gene ecology in commensal Neisseria, and inform public health strategies for managing gonorrhea and antimicrobial resistance.