Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing.
Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing.
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DOI：
10.1186/s13073-015-0235-2
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发表时间：
2015-12-01
期刊：
影响因子：
12.3
通讯作者：
Chiu CY
中科院分区：
文献类型：
--
作者：
Greninger AL;Messacar K;Dunnebacke T;Naccache SN;Federman S;Bouquet J;Mirsky D;Nomura Y;Yagi S;Glaser C;Vollmer M;Press CA;Kleinschmidt-DeMasters BK;Dominguez SR;Chiu CY
原发性阿米巴脑膜脑炎（PAM）是一种罕见的，通常是致命的脑炎原因，早期诊断和迅速开始联合抗微生物药物可以改善临床结果。在这项研究中，我们对一种罕见的PAM幸存者的Balamuthia mandrillaris基因组（44.2 Mb）的完整草图进行了测序，并从另外六个Balamuthia菌株中恢复了线粒体基因组。我们还使用无偏倚的新一代宏基因组测序（NGS）和SURPI生物信息学分析诊断了一名15岁女孩最终致命的曼氏Balamuthia mandrillaris脑炎病例。对另外6个Balamuthia mandrillaris菌株的线粒体基因组和高拷贝数基因的比较分析表明，序列差异显著，最接近的Balamuthia同源物对应于其他变形虫、水螅类、藻类、黏菌和泥煤苔藓。根据国家生物技术信息中心（NCBI） nt参考数据库中存在的16S和18S核糖体RNA序列的高质量命中，对医院第6天脑脊液和脑活检样本进行实时NGS检测，检测出Balamuthia。随后，美国疾病控制和预防中心（CDC）使用balamusia特异性PCR检测证实了脑活检、组织病理学和NGS分析中变形虫可视化对PAM的推定诊断。对第1天脑脊液样本的回顾性分析显示，如果需要获得完整的基因组序列，那么通过宏基因组NGS更及时地识别Balamuthia可能会产生更好的临床结果。这些结果强调了mandrillaris的多样化进化起源，为诊断检测开发提供了新的靶点，并将有助于进一步研究这种真核病原体的生物学和发病机制。在数据库中没有完整测序的Balamuthia基因组的情况下，未能从第1天的样本中鉴定出PAM，这凸显了全基因组参考序列对于宏基因组NGS微生物检测的重要性。本文的在线版本（doi:10.1186/s13073-015-0235-2）包含补充材料，授权用户可以使用。
Primary amoebic meningoencephalitis (PAM) is a rare, often lethal, cause of encephalitis, for which early diagnosis and prompt initiation of combination antimicrobials may improve clinical outcomes. In this study, we sequenced a full draft assembly of the Balamuthia mandrillaris genome (44.2 Mb in size) from a rare survivor of PAM, and recovered the mitochondrial genome from six additional Balamuthia strains. We also used unbiased metagenomic next-generation sequencing (NGS) and SURPI bioinformatics analysis to diagnose an ultimately fatal case of Balamuthia mandrillaris encephalitis in a 15-year-old girl. Comparative analysis of the mitochondrial genome and high-copy number genes from six additional Balamuthia mandrillaris strains demonstrated remarkable sequence variation, and the closest Balamuthia homologs corresponded to other amoebae, hydroids, algae, slime molds, and peat moss. Real-time NGS testing of hospital day 6 CSF and brain biopsy samples detected Balamuthia on the basis of high-quality hits to 16S and 18S ribosomal RNA sequences present in the National Center for Biotechnology Information (NCBI) nt reference database. The presumptive diagnosis of PAM by visualization of amoebae on brain biopsy histopathology and NGS analysis was subsequently confirmed at the US Centers for Disease Control and Prevention (CDC) using a Balamuthia-specific PCR assay. Retrospective analysis of a day 1 CSF sample revealed that more timely identification of Balamuthia by metagenomic NGS, potentially resulting in a better clinical outcome, would have required availability of the complete genome sequence. These results underscore the diverse evolutionary origins of Balamuthia mandrillaris, provide new targets for diagnostic assay development, and will facilitate further investigations of the biology and pathogenesis of this eukaryotic pathogen. The failure to identify PAM from a day 1 sample without a fully sequenced Balamuthia genome in the database highlights the critical importance of whole-genome reference sequences for microbial detection by metagenomic NGS. The online version of this article (doi:10.1186/s13073-015-0235-2) contains supplementary material, which is available to authorized users.