Jin Yanqi, Xu Hao, Yao Qing, Gu Beiqing, Wang Zhouhan, Wang Tianyuan, Yu Xiaopeng, Lu Yingfeng, Zheng Beiwen, Zhang Yimin
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
Department of Infectious Diseases, Haining People's Hospital, Haining, China.
Front Microbiol. 2022 Feb 21;12:780183. doi: 10.3389/fmicb.2021.780183. eCollection 2021.
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.
该属的分类仍然令人困惑，特别是在[具体方面1]和[具体方面2]。2012年，核糖体多位点序列分型将两者重新分类为[新分类名称]，但关于17株[菌株名称]的相关数据在GenBank中仍然可用。高通量测序的不断进步促进了全基因组数据的便捷获取，推动了平均核苷酸同一性（ANI）和高分辨率系统发育分析的蓬勃发展。在此，我们报告一例[菌株名称]分离株，它在一名先天性心脏病患者中引起了自体瓣膜心内膜炎和多发性栓塞性脑梗死，VITEK MS将其误鉴定为[错误鉴定名称]。通过ANI比对（ANIb）以及使用PacBio Sequel和Illumina NovaSeq PE150平台产生的全基因组数据进行系统发育分析，该分离株被重新分类为[正确分类名称]。GenBank和基质辅助激光解吸/电离飞行时间质谱（MALDI-TOF MS）数据库中明显存在的混淆表明，GenBank中的[菌株名称1]（= 13）和[菌株名称2]（= 16）应使用ANIb和高分辨率系统发育分析进行重新分类。将30株菌株（包括临床分离株）的全基因组数据与27株模式菌株（包括1株[模式菌株名称1]和2株[模式菌株名称2]）的数据作为基因组索引进行比较。总共，25株（8株最初鉴定为[错误鉴定名称1]和17株最初鉴定为[错误鉴定名称2]）和7株（1株最初鉴定为[错误鉴定名称3]和6株最初鉴定为[错误鉴定名称4]）菌株分别重新分类到[分类组1]和[分类组2]组；1株残留的[菌株名称3]菌株被重新分类为[新分类名称3]。总之，ANIb和强大的系统发育分析相结合，将最初鉴定为[错误鉴定名称1]和[错误鉴定名称2]的菌株重新分类（主要）到[分类组1]组和[分类组2]组。GenBank和MALDI-TOF MS数据库中误分类的[菌株名称1]和[菌株名称2]菌株应予以纠正。建议在GenBank中采用针对最初鉴定为[错误鉴定名称1]和[错误鉴定名称2]菌株的更新后的基因组分类策略。
