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The taxonomy of the genus  Neisseria  remains confusing, particularly regarding  Neisseria mucosa  and  Neisseria sicca.  In 2012, ribosomal multi-locus sequence typing reclassified both as  N. mucosa , but data concerning 17  N. sicca  strains remain available in GenBank. The continuous progress of high-throughput sequencing has facilitated ready accessibility of whole-genome data, promoting vigorous development of average nucleotide identity (ANI) and high-resolution phylogenetic analysis. Here, we report that a  Neisseria  isolate, which caused native-valve endocarditis and multiple embolic brain infarcts in a patient with congenital heart disease, was misidentified as  N. sicca  by VITEK MS. This isolate was reclassified as  N. mucosa  by ANI blast (ANIb) and by phylogenetic analysis using whole-genome data yielded by the PacBio Sequel and Illumina NovaSeq PE150 platforms. The confusion evident in the GenBank and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) databases suggests that  N. mucosa  ( n  = 13) and  N. sicca  ( n  = 16) in GenBank should be reclassified using ANIb and high-resolution phylogenetic analysis. The whole-genome data of 30 strains (including the clinical isolate) were compared with the data of 27 type  Neisseria  strains (including one  N. sicca  and two  N. mucosa  type strains) as a genomic index. In total, 25 (8 originally identified as  N. mucosa  and 17 originally identified as  N. sicca ) and 7 (1 originally identified as  N. sicca  and 6 originally identified as  N. mucosa ) strains were reclassified into the  N. mucosa  and  Neisseria subflava  groups, respectively; 1 residual  N. mucosa  strain was reclassified as  Neisseria meningitidis . In conclusion, a combination of ANIb and robust phylogenetic analysis reclassified strains originally identified as  N. mucosa  and  N. sicca  into (principally) the  N. mucosa  group and the  N. subflava  group. The misclassified  N. sicca  and  N. mucosa  strains in the GenBank and MALDI-TOF MS databases were supposed to be corrected. Updated genomic classification strategy for originally identified  N. mucosa  and  N. sicca  strains was recommended to be adopted in GenBank.

frontiers in microbiology

Confirmation of the Need for Reclassification of Neisseria mucosa and Neisseria sicca Using Average Nucleotide Identity Blast and Phylogenetic Analysis of Whole-Genome Sequencing: Hinted by Clinical Misclassification of a Neisseria mucosa Strain