Fig. 2.

Phylogenetic analysis of all the PilE amino acid (aa) sequences from the meningococcal strains used in this study (Supplementary Table S1) as well as five previously sequenced N. meningitidis isolates. All of the PilE aa sequences separated into two main parts: class I and class II PilE. Isolates (n = 63) of class I PilE belonging to seven different clonal complexes (CC) are presented in the blue ellipse. All class II PilE isolates, which split into five groups, are presented in the green ellipse. The strains of CC5 and CC1 are presented separately in pink and orange ellipses (nadA PCR⁺ and PCR⁻, respectively). CC11 strains are presented in yellow and purple ellipses (all nadA PCR⁺). However, the isolates in the yellow ellipse expressed nadA genes containing a whole insertion sequence IS1301. Isolates of CC8 (n = 1) and ST5642 strains (n = 5) are shown in the red ellipse. These strains harboured the same aa sequence as PilE and have no detectable nadA gene.