Genomic-enabled classification of three Mycobacteroides abscessus subspecies and an effective subspecies-specific identification method.

IF 5.4 2区 医学 Q1 MICROBIOLOGY
Journal of Clinical Microbiology Pub Date : 2025-08-13 Epub Date: 2025-07-24 DOI:10.1128/jcm.00697-25
Zelin Yu, Ruibai Wang
{"title":"Genomic-enabled classification of three <i>Mycobacteroides abscessus</i> subspecies and an effective subspecies-specific identification method.","authors":"Zelin Yu, Ruibai Wang","doi":"10.1128/jcm.00697-25","DOIUrl":null,"url":null,"abstract":"<p><p><i>Mycobacteroides abscessus</i> (Mab) is a clinically significant non-tuberculous mycobacterium. It comprises three distinct subspecies being considered to have different macrolide susceptibilities, transmission patterns, and treatment outcomes. In this study, systematic analysis was conducted on 2,006 Mab genomes deposited in the National Center for Biotechnology Information genome database, and the taxonomic classification of their subspecies was revised accordingly. The findings revealed that: (i) in terms of three distinct subspecies classification, the analysis based on core genes and average nucleotide identity (ANI) values was completely consistent; (ii) ANI was a reliable criterion for Mab species and subspecies classification, with defined thresholds of 95% ANI for species-level and 98% ANI for subspecies-level differentiations; and (iii) the integrity of the <i>erm</i>(41) gene or the similarity of the <i>rpoB</i> gene was an unreliable characteristic for Mab subspecies, and the assertions that subspecies <i>massiliense</i> lack inducible resistance to macrolides also cannot be sustained. Moreover, through a subspecies re-classification of genomes and pangenome analysis, Mab subspecies-specific genes were successfully identified, and a novel single-gene test with enhanced clinical applicability was developed. Additionally, the impact of reference genome selection on taxonomic classification highlighted the importance of adopting a standardized set of reference genomes in species/subspecies identification to significantly enhance the comparability across different studies.IMPORTANCE<i>Mycobacteroides abscessus</i> (Mab) is a clinically challenging non-tuberculous mycobacteria species. The accurate identification of subspecies is of utmost importance for clinical diagnosis and treatment, as well as for research on pathogenicity, drug resistance, and other related aspects. This study provided a clear average nucleotide identity threshold for Mab subspecies classification, as well as revised options of the three Mab subspecies, new and accurate Mab subspecies-special biomarker, and a detection technique with practical clinical application.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0069725"},"PeriodicalIF":5.4000,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12345259/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Clinical Microbiology","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1128/jcm.00697-25","RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/7/24 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Mycobacteroides abscessus (Mab) is a clinically significant non-tuberculous mycobacterium. It comprises three distinct subspecies being considered to have different macrolide susceptibilities, transmission patterns, and treatment outcomes. In this study, systematic analysis was conducted on 2,006 Mab genomes deposited in the National Center for Biotechnology Information genome database, and the taxonomic classification of their subspecies was revised accordingly. The findings revealed that: (i) in terms of three distinct subspecies classification, the analysis based on core genes and average nucleotide identity (ANI) values was completely consistent; (ii) ANI was a reliable criterion for Mab species and subspecies classification, with defined thresholds of 95% ANI for species-level and 98% ANI for subspecies-level differentiations; and (iii) the integrity of the erm(41) gene or the similarity of the rpoB gene was an unreliable characteristic for Mab subspecies, and the assertions that subspecies massiliense lack inducible resistance to macrolides also cannot be sustained. Moreover, through a subspecies re-classification of genomes and pangenome analysis, Mab subspecies-specific genes were successfully identified, and a novel single-gene test with enhanced clinical applicability was developed. Additionally, the impact of reference genome selection on taxonomic classification highlighted the importance of adopting a standardized set of reference genomes in species/subspecies identification to significantly enhance the comparability across different studies.IMPORTANCEMycobacteroides abscessus (Mab) is a clinically challenging non-tuberculous mycobacteria species. The accurate identification of subspecies is of utmost importance for clinical diagnosis and treatment, as well as for research on pathogenicity, drug resistance, and other related aspects. This study provided a clear average nucleotide identity threshold for Mab subspecies classification, as well as revised options of the three Mab subspecies, new and accurate Mab subspecies-special biomarker, and a detection technique with practical clinical application.

三个脓肿分枝杆菌亚种的基因组分类和一种有效的亚种特异性鉴定方法。
脓肿样分枝杆菌(Mab)是一种临床意义重大的非结核分枝杆菌。它包括三个不同的亚种,被认为具有不同的大环内酯易感性、传播模式和治疗结果。本研究对国家生物技术信息中心基因组数据库中的2006个单抗基因组进行了系统分析,并对其亚种进行了分类修正。结果表明:(1)在三个不同的亚种分类上,基于核心基因的分析与平均核苷酸同一性(ANI)值完全一致;(ii) ANI是单克隆抗体种和亚种分类的可靠标准,定义的阈值为95% ANI用于种级分化,98% ANI用于亚种级分化;(iii) erm(41)基因的完整性或rpoB基因的相似性对Mab亚种来说是一个不可靠的特征,马氏亚种对大环内酯类缺乏诱导抗性的断言也不能成立。此外,通过亚种基因组再分类和泛基因组分析,成功鉴定了单抗亚种特异性基因,并开发了一种新的具有增强临床适用性的单基因检测方法。此外,参考基因组选择对分类学分类的影响突出了采用标准化参考基因组集在种/亚种鉴定中的重要性,以显著提高不同研究之间的可比性。重要性脓肿样杆菌(Mab)是一种具有临床挑战性的非结核分枝杆菌。亚种的准确鉴定对于临床诊断和治疗,以及致病性、耐药性等相关方面的研究至关重要。本研究为单克隆抗体亚种分类提供了明确的平均核苷酸识别阈值,修订了单克隆抗体3个亚种的选择,提供了新的、准确的单克隆抗体亚种特异性生物标志物,提供了具有实际临床应用价值的检测技术。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Journal of Clinical Microbiology
Journal of Clinical Microbiology 医学-微生物学
CiteScore
17.10
自引率
4.30%
发文量
347
审稿时长
3 months
期刊介绍: The Journal of Clinical Microbiology® disseminates the latest research concerning the laboratory diagnosis of human and animal infections, along with the laboratory's role in epidemiology and the management of infectious diseases.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信