A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains

Melanie Hennart (1, 2) , Julien Guglielmini (3) , Sébastien Bridel (1) , Martin C J Maiden (4) , Keith A. Jolley (4) , Alexis Criscuolo (3) , Sylvain Brisse (1)

1 Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens
2 SU - Sorbonne Université
3 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB
4 Department of Zoology [Oxford]

Sublineages (SLs) within microbial species can differ widely in their ecology and pathogenicity, and their precise definition is important in basic research and for industrial or public health applications. Widely accepted strategies to define SLs are currently missing, which confuses communication in population biology and epidemiological surveillance. Here, we propose a broadly applicable genomic classification and nomenclature approach for bacterial strains, using the prominent public health threat Klebsiella pneumoniae as a model. Based on a 629-gene core genome multilocus sequence typing (cgMLST) scheme, we devised a dual barcoding system that combines multilevel single linkage (MLSL) clustering and life identification numbers (LINs). Phylogenetic and clustering analyses of >7,000 genome sequences captured population structure discontinuities, which were used to guide the definition of 10 infraspecific genetic dissimilarity thresholds. The widely used 7-gene multilocus sequence typing (MLST) nomenclature was mapped onto MLSL SLs (threshold: 190 allelic mismatches) and clonal group (threshold: 43) identifiers for backwards nomenclature compatibility. The taxonomy is publicly accessible through a community-curated platform (https://bigsdb.pasteur.fr/klebsiella), which also enables external users’ genomic sequences identification. The proposed strain taxonomy combines two phylogenetically informative barcode systems that provide full stability (LIN codes) and nomenclatural continuity with previous nomenclature (MLSL). This species-specific dual barcoding strategy for the genomic taxonomy of microbial strains is broadly applicable and should contribute to unify global and cross-sector collaborative knowledge on the emergence and microevolution of bacterial pathogens.

Mots clés: genomic classification; strain nomenclature; microevolution; pathogen tracking; genomic library; international harmonization

Domaines: Bio-Informatique, Biologie Systémique [q-bio.QM]

Melanie Hennart, Julien Guglielmini, Sébastien Bridel, Martin C J Maiden, Keith A. Jolley, et al.. A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains. Molecular Biology and Evolution, 2022, 39 (7), pp.msac135. ⟨10.1093/molbev/msac135⟩. ⟨pasteur-03759200⟩