Microevolution associated with clonal expansion of a hypervirulent, penicillin-resistant lineage of Neisseria meningitidis in Western Australia

<i>Neisseria meningitidis</i> is a colonizer of the human nasopharynx which occasionally causes invasive meningococcal disease. Despite numerous reports of penicillin-resistant isolates, antimicrobial-resistant meningococcal clones have historically not persisted over long time periods or become globally distributed, presumably due to the imposed fitness cost associated with antimicrobial resistance. One exception is a penicillin-resistant clade of serogroup W clonal complex 11 (MenW:cc11) isolates identified in Western Australia in 2013, which has since caused disease globally. Here, we investigated the genomic changes associated with penicillin resistance in MenW:cc11 isolated during the 2013-2020 Western Australian meningococcal outbreak. Seventy-six MenW:cc11 disease-causing isolates underwent short-read whole genome sequencing. Reference genomes were generated for three isolates. In accordance with previous analysis, two phylogenetically distinct clusters were identified: cluster A (12 penicillin-susceptible isolates) and cluster B (63 penicillin-resistant isolates). Genomic comparison of the cluster A and cluster B isolates revealed 128 allelic differences present at the branching point between the two lineages. The differences included polymorphisms in genes associated with cell wall regulation, pilus biogenesis and the MtrR transcriptional regulator. A further 60 allelic changes were identified in the Western Australian isolates which were not identified in globally distributed cluster B isolates. In a search of the PubMLST <i>Neisseria</i> database, all allelic variants associated with the emergence of cluster B were found exclusively in other hypervirulent lineages. Taken together, the data suggest the global success of the penicillin-resistant <i>N. meningitidis</i> is due to compensatory mutations acquired through horizontal exchange from other hypervirulent lineages.