Skip to content
DraconiticResearch
Search Sources API
203,234 studies31 sourcesUpdated 23 min ago
Peer-reviewedCC BYPLoS Biology

Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens

  • Féderica Palma1,2
  • Mélanie Hennart1
  • Keith A. Jolley3
  • Chiara Crestani1
  • Kelly L. Wyres4,5
  • Sébastien Bridel1
  • Corin Yeats6
  • Bryan Brancotte7
  • Brice Raffestin8
  • Sophia David6
  • Margaret M. C. Lam5
  • Radosław Izdebski9
10 more authors
  • Virginie Passet1
  • Carla Rodrigues1
  • Martin Rethoret-Pasty1
  • Audrey Combary
  • Solène Cottis
  • Martin C. J. Maiden3
  • David M. Aanensen6
  • Kathryn E. Holt10,5
  • Alexis Criscuolo2
  • Sylvain Brisse1,2
10 affiliations
  1. 1Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
  2. 2Institut Pasteur, Université Paris Cité, Biological Resource Center of Institut Pasteur, Paris, France
  3. 3Department of Biology, University of Oxford, Oxford, United Kingdom
  4. 4Centre to Impact AMR, Monash University, Clayton, 3800, Australia
  5. 5Department of Infectious Diseases, School of Translational Medicine, Monash University, Melbourne, Australia
  6. 6Centre for Genomic Pathogen Surveillance, Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
  7. 7Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
  8. 8Institut Pasteur, Université Paris Cité, HPC Core Facility, Paris, France
  9. 9Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
  10. 10Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
Open at sourcePDFDOICite

Abstract

Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cgMLST) holds great promise for standardized high-resolution strain genotyping. However, this approach faces challenges including classification instability and disconnection of new nomenclature from widely adopted classical MLST identifiers. This essay discusses the cgMLST-based Life Identification Number (LIN) method, recently proposed as a stable multilevel strain taxonomy system applicable to most bacterial pathogens. We describe how LIN codes are implemented and used in practice for precise strain definitions and epidemiological tracking. Glossary Multilocus sequence typing (MLST) A genotyping method applied mostly to microbial strains to study population structure and epidemiology, based on comparing the nucleotide sequences of a small number (typically seven) of housekeeping protein-coding genes. In MLST, allele numbers are assigned to each sequence variant (allele) of a given gene. The MLST genotype of a bacterial strain is defined by the combination of the allele numbers observed at the genes that are included in the genotyping scheme. A sequence type (ST) is assigned to each unique combination of alleles, called an MLST profile. MLST was invented in 1998 and became a de-facto standard taxonomy of bacterial strains, albeit at low resolution. Core genome MLST An extension of MLST that analyzes sequence variation across hundreds to thousands of conserved (core) genes, shared by all strains of a species, providing higher resolution typing for genomic epidemiology and evolutionary studies. cgMLST schemes typically comprise 2000 to 4000 genes, depending on the genome size and genetic variation (in terms of presence/absence of genes) within bacterial species. A core genome sequence type (cgST) can be assigned to unique cgMLST profiles, i.e., a unique combination of cgMLST allelic numbers. Whole Genome Sequencing (WGS) A method that determines the complete DNA sequence of an organism’s genome in a single process, providing comprehensive information for comparative genetic analyses based on cgMLST or other analytic methods. Single Nucleotide Polymorphisms (SNPs) Variations at a single base position in the DNA sequence among individuals isolates, strains or species, used as genetic markers for studying for example, evolutionary relationships or strain identity. Average nucleotide identity (ANI) A measure of genomic similarity between two organisms, calculated as the average percentage of identical nucleotides in orthologous genomic regions; commonly used to assess species-level relatedness in prokaryotes. Taxonomy Here, we apply the word taxonomy to bacterial strains as a system of classifying, naming and identifying strains based on shared genetic characteristics as defined by e.g., cgMLST.

Related

  1. Epidemiological surveillance of bacterial pathogens in cultured European sea bass (Dicentrarchus labrax) along the Aegean coast of Türkiye
    Pınar Çelik, Vyron Georgalas, İhsan Çelik
    PLOS OnePeer-reviewedCC BY 4.0EcologyZoology & animal behaviourPLOS
  2. Multimodal genomic surveillance for respiratory pathogens at four U.S. international airports: A comparison of air, wastewater, clinical, and national surveillance data
    Dawn Gratalo, Cindy R. Friedman, Valerie J. Morley +11
    PLOS Global Public HealthPeer-reviewedCC BY 4.0Full textGenetics & genomicsMicrobiologyPLOS
  3. Same-day hybrid capture workflow for diagnosis and surveillance of respiratory pathogens
    L. Buggiotti, A. Busam, L. M. Martin Bernal +15
    medRxivPreprintCC BY-NC-NDFull textInfectious diseasemedRxiv
  4. Evolving priorities in the WHO Bacterial Priority Pathogens List
    Zhenlin Ouyang, Wenbo He, Xiaoyu He +3
    Biosafety and healthPeer-reviewedCC BY-NC-NDFull text1 citedInfectious diseaseEurope PMCPMC
  5. Use of Metagenomic Next-Generation Sequencing to Investigate Respiratory Pathogens in Influenza-Negative Nasopharyngeal Swabs From Cameroon's National Influenza Surveillance.
    Modiyinji Abdou Fatawou, Cappy Pierre, Ly Arnaud +7
    Influenza and other respiratory virusesPeer-reviewedCC BY-NCFull textEpidemiology & public healthEurope PMC

Cite

BibTeXRIS
BibTeX
@article{palma2026life,
  title = {{Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens}},
  author = {Féderica Palma and Mélanie Hennart and Keith A. Jolley and Chiara Crestani and Kelly L. Wyres and Sébastien Bridel and Corin Yeats and Bryan Brancotte and Brice Raffestin and Sophia David and Margaret M. C. Lam and Radosław Izdebski and Virginie Passet and Carla Rodrigues and Martin Rethoret-Pasty and Audrey Combary and Solène Cottis and Martin C. J. Maiden and David M. Aanensen and Kathryn E. Holt and Alexis Criscuolo and Sylvain Brisse},
  journal = {PLoS Biology},
  year = {2026},
  month = jun,
  doi = {10.1371/journal.pbio.3003781},
  url = {https://doi.org/10.1371/journal.pbio.3003781},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens
AU  - Féderica Palma
AU  - Mélanie Hennart
AU  - Keith A. Jolley
AU  - Chiara Crestani
AU  - Kelly L. Wyres
AU  - Sébastien Bridel
AU  - Corin Yeats
AU  - Bryan Brancotte
AU  - Brice Raffestin
AU  - Sophia David
AU  - Margaret M. C. Lam
AU  - Radosław Izdebski
AU  - Virginie Passet
AU  - Carla Rodrigues
AU  - Martin Rethoret-Pasty
AU  - Audrey Combary
AU  - Solène Cottis
AU  - Martin C. J. Maiden
AU  - David M. Aanensen
AU  - Kathryn E. Holt
AU  - Alexis Criscuolo
AU  - Sylvain Brisse
PY  - 2026
DA  - 2026/06/04
JO  - PLoS Biology
DO  - 10.1371/journal.pbio.3003781
UR  - https://doi.org/10.1371/journal.pbio.3003781
AB  - Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cgMLST) holds great promise for standardized high-resolution strain genotyping. However, this approach faces challenges including classification instability and disconnection of new nomenclature from widely adopted classical MLST identifiers. This essay discusses the cgMLST-based Life Identification Number (LIN) method, recently proposed as a stable multilevel strain taxonomy system applicable to most bacterial pathogens. We describe how LIN codes are implemented and used in practice for precise strain definitions and epidemiological tracking. Glossary Multilocus sequence typing (MLST) A genotyping method applied mostly to microbial strains to study population structure and epidemiology, based on comparing the nucleotide sequences of a small number (typically seven) of housekeeping protein-coding genes. In MLST, allele numbers are assigned to each sequence variant (allele) of a given gene. The MLST genotype of a bacterial strain is defined by the combination of the allele numbers observed at the genes that are included in the genotyping scheme. A sequence type (ST) is assigned to each unique combination of alleles, called an MLST profile. MLST was invented in 1998 and became a de-facto standard taxonomy of bacterial strains, albeit at low resolution. Core genome MLST An extension of MLST that analyzes sequence variation across hundreds to thousands of conserved (core) genes, shared by all strains of a species, providing higher resolution typing for genomic epidemiology and evolutionary studies. cgMLST schemes typically comprise 2000 to 4000 genes, depending on the genome size and genetic variation (in terms of presence/absence of genes) within bacterial species. A core genome sequence type (cgST) can be assigned to unique cgMLST profiles, i.e., a unique combination of cgMLST allelic numbers. Whole Genome Sequencing (WGS) A method that determines the complete DNA sequence of an organism’s genome in a single process, providing comprehensive information for comparative genetic analyses based on cgMLST or other analytic methods. Single Nucleotide Polymorphisms (SNPs) Variations at a single base position in the DNA sequence among individuals isolates, strains or species, used as genetic markers for studying for example, evolutionary relationships or strain identity. Average nucleotide identity (ANI) A measure of genomic similarity between two organisms, calculated as the average percentage of identical nucleotides in orthologous genomic regions; commonly used to assess species-level relatedness in prokaryotes. Taxonomy Here, we apply the word taxonomy to bacterial strains as a system of classifying, naming and identifying strains based on shared genetic characteristics as defined by e.g., cgMLST.
SN  - 1544-9173
SN  - 1545-7885
ER  -