A standardized core genome multilocus sequence typing and life identification number barcoding framework for global Pasteurella multocida surveillance and outbreak investigation

Effective pathogen surveillance requires robust typing systems for outbreak detection and understanding transmission dynamics, evolutionary patterns, host colonization and disease progression. Pasteurella multocida is a globally distributed pathogen that infects mammals and birds, causing a variety of diseases. Despite its significance to public and animal health, genotypic characterization of this species remains limited, impeding effective surveillance and control strategies. To address this, we developed a core genome multilocus sequence typing (cgMLST) scheme and a complementary life identification number (LIN) barcoding system for P. multocida . The cgMLST scheme was developed and validated using 1,233 core genes identified from 1,593 genomes sourced from more than 8 host species across all continents, spanning collections from 1922 to 2024. Genomes included publicly available assemblies from PubMLST, newly sequenced isolates from the Animal and Plant Health Agency (APHA) and assemblies from Iowa State University. The cgMLST scheme assigned core genome sequence types (cgSTs) to 1,554 of the 1,593 genomes (97.55%), identifying 1,304 unique cgSTs and improving resolution compared to the 2 currently available 7-locus MLST schemes. Based on pairwise allelic differences, 12 thresholds were defined to establish the LIN barcoding system, a hierarchical and stable nomenclature enabling multi-level clustering. Application of the cgMLST-based Life Identification number code to independent outbreak datasets confirmed the scheme’s ability to delineate outbreak clusters and distinguish unrelated isolates. This standardized typing framework provides a robust approach for strain classification, population structure analysis, vaccine target identification and global surveillance of P. multocida . Integration into the PubMLST platform ensures open access and facilitates global collaboration in the molecular epidemiology of this pathogen.