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Neisseria gonorrhoeae LIN codes provide a robust, multi-resolution lineage nomenclature
Anastasia Unitt1, Made A Krisna2, Kasia M Parfitt2
1Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom.
Elife
|December 31, 2025
Summary
A new genomic lineage nomenclature for the bacterial pathogen Neisseria gonorrhoeae, using Life Identification Number (LIN) codes, improves tracking of antimicrobial resistance and population structure. This system enhances gonococcal surveillance and epidemiological communication.
Area of Science:
- Microbiology
- Genomics
- Epidemiology
Background:
- Neisseria gonorrhoeae investigation is hindered by horizontal gene transfer, complicating phylogenetic analysis and population structure understanding.
- Accurate identification of N. gonorrhoeae lineages is crucial for surveillance of antimicrobial resistance and epidemiological communication.
- Conventional typing systems lack the stability and reliability needed for N. gonorrhoeae strain taxonomy.
Purpose of the Study:
- To develop a stable and reliable genomic lineage nomenclature for Neisseria gonorrhoeae.
- To create a hierarchical nomenclature system that reflects gonococcal diversity and population structure.
- To facilitate improved surveillance and communication regarding N. gonorrhoeae epidemiology.
Main Methods:
- Development of a novel genomic lineage nomenclature based on Life Identification Number (LIN) codes.
- Application of a refined 1430 core gene multilocus sequence typing (cgMLST) scheme.
- Clustering analysis to assess the reflection of gonococcal diversity and population structure.
Main Results:
- A hierarchical LIN code nomenclature was successfully developed for N. gonorrhoeae.
- The LIN code system accurately reflects gonococcal diversity and population structure.
- LIN codes provide context to isolate ancestry and relate to existing typing schemes (Ng cgMLST v1, 7-locus MLST, NG-STAR CC).
- The nomenclature offers insights into genotype-phenotype associations, including antibiotic resistance.
Conclusions:
- The LIN code nomenclature provides a stable and reliable method for identifying N. gonorrhoeae lineages.
- This system enhances the ability to track antimicrobial resistance and understand gonococcal population dynamics.
- LIN codes are automatically assigned and publicly accessible, supporting global surveillance efforts.
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