Rapid Metagenomic Next-Generation Sequencing during an Investigation of Hospital-Acquired Human Parainfluenza Virus 3 Infections
Rapid Metagenomic Next-Generation Sequencing during an Investigation of Hospital-Acquired Human Parainfluenza Virus 3 Infections
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DOI：
10.1128/jcm.01881-16
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发表时间：
2017-01-01
影响因子：
9.4
通讯作者：
Jerome, Keith R.
中科院分区：
文献类型：
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作者：
Greninger, Alexander L.;Zerr, Danielle M.;Jerome, Keith R.
元基因组下一代测序技术(MNGS)越来越多地被用于对临床样本中的病毒、细菌、真菌和真核寄生虫进行无偏见的检测。临床细菌分离株的全基因组测序(WGS)已被证明可以为医院感染预防实践提供信息，但这项技术尚未在潜在的呼吸道病毒暴发期间使用。在这里，我们报告了如何使用mNGS为一家儿童医院的一群医院获得性人类副流感3型病毒(HPIV3)感染提供实时感染预防反应。分析了3名在综合医疗单位12天内确诊的医院获得性HPIV3患者的样本和10名来自社区获得性HPIV3患者的时间相关样本。我们的样本到测序仪的时间是1次读取HPIV3。系统发育聚类显示，在两名医院获得性感染病例中存在相同的HPIV3基因组序列，这与最近在医疗单位内传播的担忧一致。对于第三种情况，没有恢复足够的序列覆盖。这项工作表明，除了微生物检测外，MNGS还有望为感染预防提供快速信息。
Metagenomic next-generation sequencing (mNGS) is increasingly used for the unbiased detection of viruses, bacteria, fungi, and eukaryotic parasites in clinical samples. Whole-genome sequencing (WGS) of clinical bacterial isolates has been shown to inform hospital infection prevention practices, but this technology has not been utilized during potential respiratory virus outbreaks. Here, we report on the use of mNGS to inform the real-time infection prevention response to a cluster of hospital-acquired human parainfluenza 3 virus (HPIV3) infections at a children's hospital. Samples from 3 patients with hospital-acquired HPIV3 identified over a 12-day period on a general medical unit and 10 temporally associated samples from patients with community-acquired HPIV3 were analyzed. Our sample-tosequencer time was 1 read for HPIV3. Phylogenetic clustering revealed the presence of identical HPIV3 genomic sequence in the two of the cases with hospital-acquired infection, consistent with the concern for recent transmission within the medical unit. Adequate sequence coverage was not recovered for the third case. This work demonstrates the promise of mNGS for providing rapid information for infection prevention in addition to microbial detection.