Meningococcal core and accessory phasomes vary by clonal complex

Neisseria meningitidis are Gram-negative human commensal-pathogens, with extensive phenotypic plasticity afforded by phase variable gene expression. Phase variation is a stochastic switch in gene expression from an ON to an OFF state, mediated by localised hypermutation of simple sequence repeats. Circulating N. meningitidis clones vary in propensity to cause disease with some clonal complexes classified as hypervirulent and others as carriage-associated. We examined the phase-variable gene repertoires, or phasome, of these lineages in order to determine if phase variation contributes to disease propensity. We analysed 3,328 genomes representative of nine circulating meningococcal clonal complexes with PhasomeIt, a tool which identifies phase-variable genes by the presence of simple sequence repeats (SSR) and homologous gene clusters. Presence, absence and functions of all identified phase-variable gene clusters were confirmed by annotation or BLAST searches within the Neisseria pubMLST database. While no significant differences were detected in the number of phase-variable genes or the core, conserved phasome content between hypervirulent and carriage lineages, individual clonal complexes exhibited major variations in phase-variable gene numbers. Phylogenetic clusters produced by phasome or core genome analyses were similar indicating co-evolution of phase-variable genes with the core genome. While conservation of phase-variable clusters is high, with 76% present in all meningococcal isolates, maintenance of an SSR is variable ranging from conserved in all isolates to present only in single clonal complexes, indicating differing evolutionary trajectories for each lineage. Diverse functional groups of PV genes were present across the meningococcal lineages, however, the majority directly or indirectly influence bacterial surface antigens and could impact on future vaccine development. Finally, we observe that meningococci have open pan phasomes, indicating on-going evolution of PV gene content and a significant potential for adaptive changes in this clinically relevant genus.