AUTHOR=Jin Yanqi , Xu Hao , Yao Qing , Gu Beiqing , Wang Zhouhan , Wang Tianyuan , Yu Xiaopeng , Lu Yingfeng , Zheng Beiwen , Zhang Yimin 

TITLE=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

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.780183

DOI=10.3389/fmicb.2021.780183

ISSN=1664-302X

ABSTRACT=<p>The taxonomy of the genus <italic>Neisseria</italic> remains confusing, particularly regarding <italic>Neisseria mucosa</italic> and <italic>Neisseria sicca.</italic> In 2012, ribosomal multi-locus sequence typing reclassified both as <italic>N. mucosa</italic>, but data concerning 17 <italic>N. sicca</italic> 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 <italic>Neisseria</italic> isolate, which caused native-valve endocarditis and multiple embolic brain infarcts in a patient with congenital heart disease, was misidentified as <italic>N. sicca</italic> by VITEK MS. This isolate was reclassified as <italic>N. mucosa</italic> 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 <italic>N. mucosa</italic> (<italic>n</italic> = 13) and <italic>N. sicca</italic> (<italic>n</italic> = 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 <italic>Neisseria</italic> strains (including one <italic>N. sicca</italic> and two <italic>N. mucosa</italic> type strains) as a genomic index. In total, 25 (8 originally identified as <italic>N. mucosa</italic> and 17 originally identified as <italic>N. sicca</italic>) and 7 (1 originally identified as <italic>N. sicca</italic> and 6 originally identified as <italic>N. mucosa</italic>) strains were reclassified into the <italic>N. mucosa</italic> and <italic>Neisseria subflava</italic> groups, respectively; 1 residual <italic>N. mucosa</italic> strain was reclassified as <italic>Neisseria meningitidis</italic>. In conclusion, a combination of ANIb and robust phylogenetic analysis reclassified strains originally identified as <italic>N. mucosa</italic> and <italic>N. sicca</italic> into (principally) the <italic>N. mucosa</italic> group and the <italic>N. subflava</italic> group. The misclassified <italic>N. sicca</italic> and <italic>N. mucosa</italic> strains in the GenBank and MALDI-TOF MS databases were supposed to be corrected. Updated genomic classification strategy for originally identified <italic>N. mucosa</italic> and <italic>N. sicca</italic> strains was recommended to be adopted in GenBank.</p>