Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids.
Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids.
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DOI：
10.1038/s41591-020-1105-z
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发表时间：
2021-01
期刊：
影响因子：
82.9
通讯作者：
Chiu, Charles Y.
中科院分区：
文献类型：
--
作者：
Gu, Wei;Deng, Xianding;Lee, Marco;Sucu, Yasemin D.;Arevalo, Shaun;Stryke, Doug;Federman, Scot;Gopez, Allan;Reyes, Kevin;Zorn, Kelsey;Sample, Hannah;Yu, Guixia;Ishpuniani, Gurpreet;Briggs, Benjamin;Chow, Eric D.;Berger, Amy;Wilson, Michael R.;Wang, Candace;Hsu, Elaine;Miller, Steve;DeRisi, Joseph L.;Chiu, Charles Y.
我们开发了一种使用无细胞DNA的宏基因组下一代测序（mNGS）测试，以识别急性病患者中的病原体。使用混合条形码系统对87种体液（包括脓肿、关节、腹膜、胸膜、脑脊液、尿液和支气管肺泡灌洗液）进行平行纳米孔和Illumina测序分析。与基于临床裁定、培养和PCR检测的复合金标准相比，细菌检测的灵敏度/特异性为81-86%/91-95%，真菌检测的灵敏度/特异性为63-70%/92-96%。实时计算分析使病原体鉴定在开始纳米孔测序后的中位数50分钟内。PCR和mNGS检测在8例培养阴性体液中的6例中一致，但mNGS检测到另外2例隐匿性病原体。使用mNGS，在所有5个前瞻性采集的可能感染患者体液中也检测到病原体，但所有常规微生物测定均为阴性。快速mNGS检测是临床诊断体液未知感染的一种有前途的工具。
We developed a metagenomic next-generation sequencing (mNGS) test using cell-free DNA to identify pathogens in acutely ill patients. Parallel nanopore and Illumina sequencing analyses of 87 body fluids (including abscess, joint, peritoneal, pleural, cerebrospinal, urine, and bronchoalveolar lavage fluids) using a hybrid barcoding system were performed. Compared to a composite gold standard based on clinical adjudication, culture, and PCR testing, sensitivities/specificities were 81-86%/91-95% for bacterial detection and 63-70%/92-96% for fungal detection. Real-time computational analysis enabled pathogen identification in a median of 50 minutes after starting nanopore sequencing. PCR and mNGS testing were concordant for 6 of 8 culture-negative body fluids, but mNGS detected 2 additional occult pathogens. Using mNGS, a pathogen was also detected in all 5 prospectively collected body fluids from patients with probable infection, but testing negative by all conventional microbiological assays. Rapid mNGS testing is a promising tool for clinical diagnosis of unknown infections from body fluids.
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影响因子：
14.9
作者：
Klindworth A;Pruesse E;Schweer T;Peplies J;Quast C;Horn M;Glöckner FO
通讯作者：
Glöckner FO
影响因子：
16.6
作者：
Burnham P;Dadhania D;Heyang M;Chen F;Westblade LF;Suthanthiran M;Lee JR;De Vlaminck I
通讯作者：
De Vlaminck I
影响因子：
16.6
作者：
De Mattos-Arruda L;Mayor R;Ng CKY;Weigelt B;Martínez-Ricarte F;Torrejon D;Oliveira M;Arias A;Raventos C;Tang J;Guerini-Rocco E;Martínez-Sáez E;Lois S;Marín O;de la Cruz X;Piscuoglio S;Towers R;Vivancos A;Peg V;Ramon y Cajal S;Carles J;Rodon J;González-Cao M;Tabernero J;Felip E;Sahuquillo J;Berger MF;Cortes J;Reis-Filho JS;Seoane J
通讯作者：
Seoane J
影响因子：
12.3
作者：
Grumaz S;Stevens P;Grumaz C;Decker SO;Weigand MA;Hofer S;Brenner T;von Haeseler A;Sohn K
通讯作者：
Sohn K
影响因子：
12.3
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
通讯作者：
Chiu CY