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

• Published in: Frontiers in microbiology 2022-02, Vol.12, p.780183-780183
• Main Authors: Jin, Yanqi, Xu, Hao, Yao, Qing, Gu, Beiqing, Wang, Zhouhan, Wang, Tianyuan, Yu, Xiaopeng, Lu, Yingfeng, Zheng, Beiwen, Zhang, Yimin
• Format: Article
• Language: English
• Subjects: average nucleotide identity blast; Microbiology; Neisseria mucosa; Neisseria sicca; Neisseria subflava; reclassification; whole-genome sequencing
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2021.780183

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