biostudies-literatureUnknown12Jin YThe taxonomy of the genus <i>Neisseria</i> remains confusing, particularly regarding <i>Neisseria mucosa</i> and <i>Neisseria sicca.</i> In 2012, ribosomal multi-locus sequence typing reclassified both as <i>N. mucosa</i>, but data concerning 17 <i>N. sicca</i> 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 <i>Neisseria</i> isolate, which caused native-valve endocarditis and multiple embolic brain infarcts in a patient with congenital heart disease, was misidentified as <i>N. sicca</i> by VITEK MS. This isolate was reclassified as <i>N. mucosa</i> 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 <i>N. mucosa</i> (<i>n</i> = 13) and <i>N. sicca</i> (<i>n</i> = 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 <i>Neisseria</i> strains (including one <i>N. sicca</i> and two <i>N. mucosa</i> type strains) as a genomic index. In total, 25 (8 originally identified as <i>N. mucosa</i> and 17 originally identified as <i>N. sicca</i>) and 7 (1 originally identified as <i>N. sicca</i> and 6 originally identified as <i>N. mucosa</i>) strains were reclassified into the <i>N. mucosa</i> and <i>Neisseria subflava</i> groups, respectively; 1 residual <i>N. mucosa</i> strain was reclassified as <i>Neisseria meningitidis</i>. In conclusion, a combination of ANIb and robust phylogenetic analysis reclassified strains originally identified as <i>N. mucosa</i> and <i>N. sicca</i> into (principally) the <i>N. mucosa</i> group and the <i>N. subflava</i> group. The misclassified <i>N. sicca</i> and <i>N. mucosa</i> strains in the GenBank and MALDI-TOF MS databases were supposed to be corrected. Updated genomic classification strategy for originally identified <i>N. mucosa</i> and <i>N. sicca</i> strains was recommended to be adopted in GenBank.Frontiers in microbiology780183https://www.ebi.ac.uk/biostudies/studies/S-EPMC8909641biostudies-literatureConfirmation of the Need for Reclassification of <i>Neisseria mucosa</i> and <i>Neisseria sicca</i> Using Average Nucleotide Identity Blast and Phylogenetic Analysis of Whole-Genome Sequencing: Hinted by Clinical Misclassification of a <i>Neisseria mucosa</i> Strain.PMC8909641Gu BLu YZhang YWang TZheng BYao QJin YXu HWang ZYu XfalseConfirmation of the Need for Reclassification of <i>Neisseria mucosa</i> and <i>Neisseria sicca</i> Using Average Nucleotide Identity Blast and Phylogenetic Analysis of Whole-Genome Sequencing: Hinted by Clinical Misclassification of a <i>Neisseria mucosa</i> Strain.The taxonomy of the genus <i>Neisseria</i> remains confusing, particularly regarding <i>Neisseria mucosa</i> and <i>Neisseria sicca.</i> In 2012, ribosomal multi-locus sequence typing reclassified both as <i>N. mucosa</i>, but data concerning 17 <i>N. sicca</i> 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 <i>Neisseria</i> isolate, which caused native-valve endocarditis and multiple embolic brain infarcts in a patient with congenital heart disease, was misidentified as <i>N. sicca</i> by VITEK MS. This isolate was reclassified as <i>N. mucosa</i> 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 <i>N. mucosa</i> (<i>n</i> = 13) and <i>N. sicca</i> (<i>n</i> = 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 <i>Neisseria</i> strains (including one <i>N. sicca</i> and two <i>N. mucosa</i> type strains) as a genomic index. In total, 25 (8 originally identified as <i>N. mucosa</i> and 17 originally identified as <i>N. sicca</i>) and 7 (1 originally identified as <i>N. sicca</i> and 6 originally identified as <i>N. mucosa</i>) strains were reclassified into the <i>N. mucosa</i> and <i>Neisseria subflava</i> groups, respectively; 1 residual <i>N. mucosa</i> strain was reclassified as <i>Neisseria meningitidis</i>. In conclusion, a combination of ANIb and robust phylogenetic analysis reclassified strains originally identified as <i>N. mucosa</i> and <i>N. sicca</i> into (principally) the <i>N. mucosa</i> group and the <i>N. subflava</i> group. The misclassified <i>N. sicca</i> and <i>N. mucosa</i> strains in the GenBank and MALDI-TOF MS databases were supposed to be corrected. Updated genomic classification strategy for originally identified <i>N. mucosa</i> and <i>N. sicca</i> strains was recommended to be adopted in GenBank.2021-01-01T00:00:00Z20212026-05-30T20:48:57.853Z2024-11-09T11:56:25.318ZS-EPMC89096413528130610.3389/fmicb.2021.780183