The Use of Comparative Genomic Analysis for the Development of Subspecies-Specific PCR Assays for Mycobacterium abscessus.
The Use of Comparative Genomic Analysis for the Development of Subspecies-Specific PCR Assays for Mycobacterium abscessus.
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DOI：
10.3389/fcimb.2022.816615
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发表时间：
2022
影响因子：
5.7
通讯作者：
Hingley-Wilson SM
中科院分区：
文献类型：
--
作者：
Akwani WC;van Vliet AHM;Joel JO;Andres S;Diricks M;Maurer FP;Chambers MA;Hingley-Wilson SM
脓肿分枝杆菌复合体(MABC)是免疫功能低下患者的重要病原体。在亚种水平上准确、快速地测定MABC对于最佳的抗生素治疗至关重要。在这里，我们使用比较基因组学来设计MABC亚种特异性的PCR分析。单核苷酸多态性和核心基因组多位点序列分型分析表明，基因组聚为三个不同的簇，分别代表MABC亚种M.abscessus、M.bolletii和M.massiliense。对这三个亚种的318个MABC基因组进行了基因组分析，从而确定了15个MABC亚种特有的基因。在对1663个公开可获得的MABC基因组和66个其他密切相关的分枝杆菌基因组进行的电子检测中，所有的检测方法都具有97%的敏感性和98%的特异性。随后对两个亚种特异性基因的实验验证表明，这两种聚合酶链式反应在个体和多重形式下都能很好地工作，与其他5种临床重要的分枝杆菌没有假阳性。综上所述，我们建立了一种快速、准确、多重的检测MABC亚型的方法，可以提高MABC亚型的检测、诊断和指导正确的治疗选择。
Mycobacterium abscessus complex (MABC) is an important pathogen of immunocompromised patients. Accurate and rapid determination of MABC at the subspecies level is vital for optimal antibiotic therapy. Here we have used comparative genomics to design MABC subspecies-specific PCR assays. Analysis of single nucleotide polymorphisms and core genome multilocus sequence typing showed clustering of genomes into three distinct clusters representing the MABC subspecies M. abscessus, M. bolletii and M. massiliense. Pangenome analysis of 318 MABC genomes from the three subspecies allowed for the identification of 15 MABC subspecies-specific genes. In silico testing of primer sets against 1,663 publicly available MABC genomes and 66 other closely related Mycobacterium genomes showed that all assays had >97% sensitivity and >98% specificity. Subsequent experimental validation of two subspecies-specific genes each showed the PCR assays worked well in individual and multiplex format with no false-positivity with 5 other mycobacteria of clinical importance. In conclusion, we have developed a rapid, accurate, multiplex PCR-assay for discriminating MABC subspecies that could improve their detection, diagnosis and inform correct treatment choice.
DOI：
10.1016/j.jctube.2020.100209
发表时间：
2021-03
影响因子：
2
作者：
Pease C;Alvarez GG
通讯作者：
Alvarez GG