Preprint
Neisseria gonorrhoeae LIN codes: a robust, multi-resolution lineage nomenclature
- Abstract:
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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 consistently identify N. gonorrhoeae lineages is important for surveillance of this increasingly antimicrobial resistant organism, facilitating efficient communication regarding its epidemiology; however, conventional typing systems fail to reflect N. gonorrhoeae strain taxonomy in a reliable and stable manner. 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.
- Publication status:
- Published
- Peer review status:
- Not peer reviewed
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- Files:
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(Preview, Version of record, pdf, 2.4MB, Terms of use)
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- Preprint server copy:
- 10.1101/2025.03.28.646058
Authors
- Funder identifier:
- https://ror.org/029chgv08
- Funding agency for:
- Jolley, KA
- Maiden, MCJ
- Parfitt, KM
- Harrison, OB
- Grant:
- 218205/Z/19/Z
- 214374/Z/18/Z
- Funder identifier:
- https://ror.org/00cwqg982
- Funding agency for:
- Unitt, A
- Grant:
- BB/M011224/1
- 214374/Z/18/Z
- Funding agency for:
- Krisna, M
- Grant:
- https://ror.org/03sxt1c89
- Preprint server:
- bioRxiv
- Publication date:
- 2025-04-03
- DOI:
- Language:
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English
- Pubs id:
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2117257
- Local pid:
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pubs:2117257
- Deposit date:
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2025-05-12
Terms of use
- Copyright holder:
- Unitt et al.
- Copyright date:
- 2025
- Rights statement:
- © 2025 The Authors. The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
- Licence:
- CC Attribution (CC BY)
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