<i>Neisseria gonorrhoeae</i> LIN codes provide a robust, multi-resolution lineage nomenclature.

Abstract

Investigation of the bacterial pathogen <i>Neisseria gonorrhoeae</i> is complicated by extensive horizontal gene transfer: a process which disrupts phylogenetic signals and impedes our understanding of population structure. The ability to consistently identify <i>N. gonorrhoeae</i> lineages is important for surveillance of this increasingly antimicrobial resistant organism, facilitating efficient communication regarding its epidemiology; however, conventional typing systems fail to reflect <i>N. gonorrhoeae</i> strain taxonomy in a reliable and stable manner. Here, a <i>N. gonorrhoeae</i> genomic lineage nomenclature, based on the barcoding system of Life Identification Number (LIN) codes, was developed using a refined 1430 core gene MLST (cgMLST). This hierarchical LIN code nomenclature conveys lineage information at multiple levels of resolution within one code, enabling it to provide immediate context to an isolate's ancestry, and to relate to familiar, previously used typing schemes such as Ng cgMLST v1, 7-locus MLST, or NG-STAR clonal complex (CC). Clustering with LIN codes accurately reflects gonococcal diversity and population structure, providing insight into associations between genotype and phenotype for traits such as antibiotic resistance. These codes are automatically assigned and publicly accessible via the https://pubmlst.org/organisms/neisseria-spp database.