Figure 1.

Structure and concept of the multilevel genome typing (MGT) system

cgMLST: core genome multilocus sequence typing; GT: genome type; MGT: multilevel genome typing; MLST: multilocus sequence typing; ST: sequence type.

A. Schematic representation of the nine MLST schemes that make up the MGT levels. The increasing number of loci in each level is represented by increasing length of the coloured horizontal bars. MGT1 is the classic seven-gene MLST scheme. MGT levels 1 to 7 are mutually exclusive and are made up of a subset of MGT8 (cgMLST). MGT9 is made up of all loci including intergenic regions and encompasses all other levels (cgMLST plus clade-specific cgMLST). MGT levels are ordered by size, and loci are selected, so that each level matches the desired size, which confers the desired average mutation rate.

B–E. The relationship between phylogenetic relatedness and the MGT.

B. An example phylogeny depicting the relationship between 11 strains.

C. MGT6–9 STs overlaid onto the phylogeny. Each ST for each MGT level is represented by a triangle with the colour corresponding to the MGT level. As levels increase in resolution (increase in number of loci) smaller subclades are defined by each ST.

D. Example STs for MGT 6–9 are overlaid onto each clade.

E. The relationship between isolates expressed only as MTG 6–9 STs. The relatedness of a group of isolates is represented by the largest level that they share an ST (e.g. isolate A and B share an MGT9 ST and so are more closely related than A and E which only share an MGT7 ST).