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Molecular typing of N. meningitidis is used for epidemiological purposes to investigate outbreaks and to examine the population genetic structure of the organism to understand better its variation and evolution.

The polysaccharide capsule defines the meningococcal serogroup (N. meningitidis strains may be unencapsulated, however, the capsule is a major virulence factor and the majority of invasive disease is the result of encapsulated strains) and has long been utilised in outbreak management. There are 13 polysaccharide capsules, with only six of these commonly causing human disease; A; B; C; W135; X and Y (Harrison et al., 2009). Many groups have demonstrated horizontal gene transfer of capsule encoding genes resulting in the switching of capsule groups (Swartley et al., 1997). More recently we’ve seen the emergence of a single nucleotide polymorphism (SNP) in the W135 and Y synF capsule polymerase gene resulting in an amino acid substitution flowing on to dual polysaccharide capsule expressed in a small number of strains observed locally and globally (Claus, et al., 2009). The SNP resulting in dual polysaccharide capsule expression is not detected by PCR serotyping of capsule genes but only recognised when gene is sequenced or serogrouped by antisera agglutination. In addition to the serogroup, characterisation of the the outer membrane proteins; PorA and FetA is useful for short-term epidemiological surveillance whilst MLST is useful for long-term surveillance.

Previously performed by PCR and Sanger sequencing the serogroup, porA and fetA is now derived in silico from whole genome sequence data using Meningotype, a bioinformatic pipeline developed at MDU PHL. Serogroup prediction of N. meningitidis from WGS data is based on the detection of the capsule biosynthesis genes, syn or sia for serogroups B (synD), C (synE), Y (synF) and W (synG) and capsule polymerase genes for serogroup A (sacB), and X (xcbA). porA and fetA allele prediction are based on the detection of their respective genes followed by a comparison of the translated amino acid sequence of the variable regions within the antigens to the pubMLST database. These predictions are based on the sequence produced by the PCR and Sanger sequencing reactions. If an exact match is found, the corresponding allele is returned and a novel result is returned if the gene has no exact match to the database.