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

Palma, Federica; Hennart, Melanie; Jolley, Keith A.; Crestani, Chiara; Wyres, Kelly L.; Bridel, Sebastien; Yeats, Corin A.; Brancotte, Bryan; Raffestin, Brice; David, Sophia; Lam, Margaret M.C.; Izdebski, Radosław; Passet, Virginie; Rodrigues, Carla; Rethoret-Pasty, Martin; Combary, Audrey; Cottis, Solene; Maiden, Martin C.J.; Aanensen, David M.; Holt, Kathryn E.; Criscuolo, Alexis; Brisse, Sylvain

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

Palma, F; Hennart, M; Jolley, KA; Crestani, C; Wyres, KL

; Bridel, S; Yeats, CA; Brancotte, B; Raffestin, B; David, S; Lam, MM; Izdebski, R; Passet, V; Rodrigues, C; Rethoret-Pasty, M; Combary, A; Cottis, S; Maiden, MC; Aanensen, DM; Holt, KE

; Criscuolo, A and Brisse, S

(2026). Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens. [Dataset]. PLOS Biology. https://doi.org/10.1371/journal.pbio.3003781

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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, covering how LIN codes are implemented and used in practice for precise strain definitions and epidemiological tracking.

Keywords

Genomics; Taxonomy; Bacterial taxonomy; Bacterial genomics; Genomic databases; Genetic epidemiology; Phylogenetics; Epidemiology

Item Type	Dataset
Resource Type	Resource Type Resource Description Dataset Quantitative
Capture method	Experiment
Date	4 June 2026
Language(s) of written materials	English
Creator(s)	Palma, F; Hennart, M; Jolley, KA; Crestani, C; Wyres, KL ; Bridel, S; Yeats, CA; Brancotte, B; Raffestin, B; David, S; Lam, MM; Izdebski, R; Passet, V; Rodrigues, C; Rethoret-Pasty, M; Combary, A; Cottis, S; Maiden, MC; Aanensen, DM; Holt, KE ; Criscuolo, A and Brisse, S
LSHTM Faculty/Department	Faculty of Infectious and Tropical Diseases > Department of Infection Biology
Participating Institutions	London School of Hygiene & Tropical Medicine, London, United Kingdom
Date Deposited	29 Jun 2026 08:40
Last Modified	29 Jun 2026 08:41
Publisher	PLOS Biology