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April 3rd, 2025
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Nuffield Department of Population Health, University of Oxford
genomics
biorxiv

Neisseria gonorrhoeae LIN codes: a Robust, Multi-Resolution Lineage Nomenclature

Unitt, A.Open in Google Scholar•Krisna, M. A.Open in Google Scholar•Parfitt, K. M.Open in Google Scholar•Jolley, K. A.Open in Google Scholar•Maiden, M. C. J.Open in Google Scholar•Harrison, O. B.Open in Google Scholar

Investigation of the bacterial pathogen Neisseria gonorrhoeae is complicated by extensive horizontal gene transfer: a process which disrupts phylogenetic signals and impedes our understanding of population structure. The ability to identify N. gonorrhoeae lineages in a consistent manner is essential for surveillance of this increasingly antimicrobial resistant organism, and to facilitate efficient communication regarding its epidemiology; however, all current typing systems fail to reflect N. gonorrhoeae strain taxonomy in a way that is both reliable and stable. Here, a N. gonorrhoeae 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 pubmlst.org/organisms/neisseria-spp database.

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