Researchers at the Institut Pasteur (Paris) have published an article in PLOS Biology describing the principles and applications of the Life Identification Number (LIN), a numerical nomenclature system based on the comparison of bacterial genomes. Designed to standardize the identification of pathogenic strains worldwide, it is now being implemented in several international epidemiological surveillance platforms.
**AI-assisted translation**
Within a single bacterial species, strains can differ considerably in terms of antibiotic resistance, virulence, and the ability to spread among patients. Accurately identifying them is a major public health challenge.
A still-fragmented classification of bacterial strains
However, there is currently no globally standardized nomenclature. Researchers rely on a variety of systems—MLST typing (which compares a few representative genes), definitions of lineages or clones, and laboratory-assigned names—whose parameters vary from one study to another. With the widespread adoption of whole-genome sequencing, these inconsistencies complicate comparisons between research teams and slow down international surveillance.
What is a LIN code?
The Life Identification Number is a series of digits assigned to each strain based on its genetic proximity to all previously cataloged strains. The closer two bacteria are, the more similar their codes are. The system is hierarchical: the first positions of the code distinguish between species and subspecies, while the subsequent positions identify strains or epidemic clones—much like how Linnaean taxonomy classifies organisms from the phylum down to the species level. This nested structure makes it possible to describe any degree of genetic relatedness using a single, consistent code.
From Concept to Operational Tool
In 2022, an initial study by the Institut Pasteur laid the groundwork for the LIN system by demonstrating its feasibility on Klebsiella pneumoniae, a hospital-acquired bacterium responsible for infections that are sometimes highly resistant to antibiotics. This new work takes another step forward by aiming for large-scale adoption. It introduces human-readable “nicknames” for the most well-known bacterial groups—similar to the names Alpha, Delta, or Omicron for SARS-CoV-2 variants—and ensures continuity with MLST, the gold standard method used for decades.
A Practical Tool for International Surveillance
LIN codes are integrated into two major platforms, BIGSdb-Pasteur and Pathogenwatch, which allows for the automatic assignment of a code based on a sequenced genome. In the event of an outbreak, laboratories in different countries can compare their strains by sharing LIN codes, without exchanging the genomic sequences themselves—a benefit for data confidentiality and cross-border cooperation. Beyond Klebsiella pneumoniae, LIN systems have already been developed for Staphylococcus aureus, Neisseria gonorrhoeae, and Corynebacterium diphtheriae, confirming the method’s universal applicability.
This study received support from the Gates Foundation, the European Union’s Horizon 2020 program, and the French government’s Investments for the Future program (IBEID Laboratory of Excellence, ANR-10-LABX-62-IBEID).
