Objective To analyze the etiological characteristics of a case of meningococcal meningitis caused by nongroupable Neisseria meningitidis.

Methods The isolate from the case’s blood sample was analyzed by strain identification, serogroup and genogroup identification, antimicrobial susceptibility test, and whole-genome sequencing.

Results The meningococcal meningitis case was a boy student aged 17-years, and the strain isolated from case’s blood sample was identified as nongroupable N. meningitides, belonging to genogroup Y. The antimicrobial susceptibility test to 12 antibiotics showed that it was resistant to trimethoprim-sulfamethoxazole and sensitive to other antibiotics. The sequence type (ST) was ST-1655, belonging to the ST-23 clonal complex (CC23), and the finetyping antigen profile was P1.5-1,10-1:F4-1. The results of core genome multilocus sequence typing (cgMLST), average nucleotide identity (ANI), and single nucleotide polymorphism (SNP) analysis showed that the isolate was more closely related to some isolates from the United Kingdom, Sweden, Japan and Finland compared with the isolates from Guangdong and Shanghai in China. The analysis on the capsular polysaccharide synthesis locus showed that the arrangement was “D’-E-C-A-D-B” and the underlying mechanism of the failure in serogroup identification of the isolate might be internal stop codons in the cssA and csy genes in region A.

Conclusion This was the first reported case of meningococcal meningitis caused by nongroupable N. meningitides genogroup Y in Fujian, suggesting that further epidemiological and etiological surveillance for nongroupable N. meningitides strains need to be strengthened in the future.