With the increase in genomic sequences of Bordetella pertussis a method that can use this data to generate a standardised and flexible nomenclature is essential. Standardisation facilitates rapid communication and analysis of datasets across jurisdictions and experiments while flexibility allows the descriptions of clades of interest at a resolution appropriate for the analysis of the clade. In this study we present a multilevel genome typing (MGT) scheme for Bordetella pertussis. The scheme was composed of five levels ranging from 7 gene MLST at level 1 to cgMLST covering 85% of the reference at level 5. Levels 2, 3 and 4 are designed to assign types that reflect the phylogenetic population structure of B. pertussis.
We applied MGT to 4861 publicly available genomes from 31 countries and 67 years and described 4, 20, 110, 271 and 2772 sequence types at MGT levels 1,2,3,4 and 5 respectively. All major alleles in ptxA, ptxP, fim2, fim3, prn and fhaB were specifically and sensitively described by MGT STs at levels 2 and 3, including ptxP3 (MGT2 ST2), prn2 (MGT2 ST2 and ST3) and the Chinese ptxP1-fhaB3 lineage (MGT3 ST30), which contains three erythromycin resistant sublineages. Temporal and spatial trends globally and locally can be described at multiple levels facilitating genomic epidemiological surveillance and monitoring. The public B. pertussis MGT web database provides a flexible and standardised nomenclature system for B. pertussis genomic typing and surveillance.