Application of nanopore adaptive sequencing in pathogen detection of a patient with Chlamydia psittaci infection.
Application of nanopore adaptive sequencing in pathogen detection of a patient with Chlamydia psittaci infection.
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纳米孔自适应测序在鹦鹉热衣原体感染患者病原检测中的应用
DOI：
10.3389/fcimb.2023.1064317
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发表时间：
2023
影响因子：
5.7
通讯作者：
中科院分区：
文献类型：
--
作者：
纳米孔测序技术具有高度的可移植性和实时性，已广泛应用于临床宏基因组测序，用于病原体检测。牛津纳米孔技术公司最近推出了一种自适应测序功能，它可以通过实时比对来丰富靶向读数，并通过逆转纳米孔上的电压来排出不感兴趣的读数。在这里，我们评估了适应性测序在临床病原体检测中的效用。纳米孔适应性测序和标准测序在同一流动池上进行，该流动池具有来自鹦鹉热衣原体感染患者的支气管肺泡灌洗液样品，并与先前的mNGS结果进行比较。纳米孔适应性测序鉴定出648个具有最长中值读段长度（688 bp）的靶向终止接收读段，其占所有鹦鹉热衣原体读段的72.4%和富集组中总读段的0.03%。读取比例与C匹配。停药组鹦鹉热发生率为99.85%，明显高于未阻断组（<0.01%）和不能适应组（0.02%）。纳米孔适应性测序产生了类似的C.与标准纳米孔测序相比。C.适应性测序中的鹦鹉热读段接近于标准纳米孔测序和mNGS的读段，但产生比mNGS更低的基因组覆盖。纳米孔适应性测序可以有效识别目标C。鹦鹉热实时读取，但如何增加病原体的靶向数据仍需进一步评估。
Nanopore sequencing has been widely used in clinical metagenomic sequencing for pathogen detection with high portability and real-time sequencing. Oxford Nanopore Technologies has recently launched an adaptive sequencing function, which can enrich on-target reads through real-time alignment and eject uninteresting reads by reversing the voltage across the nanopore. Here we evaluated the utility of adaptive sequencing in clinical pathogen detection. Nanopore adaptive sequencing and standard sequencing was performed on a same flow cell with a bronchoalveolar lavage fluid sample from a patient with Chlamydia psittacosis infection, and was compared with the previous mNGS results. Nanopore adaptive sequencing identified 648 on-target stop receiving reads with the longest median read length(688bp), which account for 72.4% of all Chlamydia psittaci reads and 0.03% of total reads in enriched group. The read proportion matched to C. psittaci in the stop receiving group was 99.85%, which was much higher than that of the unblock (<0.01%) and fail to adapt (0.02%) groups. Nanopore adaptive sequencing generated similar data yield of C. psittaci compared with standard nanopore sequencing. The proportion of C. psittaci reads in adaptive sequencing is close to that of standard nanopore sequencing and mNGS, but generated lower genome coverage than mNGS. Nanopore adaptive sequencing can effectively identify target C. psittaci reads in real-time, but how to increase the targeted data of pathogens still needs to be further evaluated.
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影响因子：
3.3
作者：
Ong CT;Ross EM;Boe-Hansen GB;Turni C;Hayes BJ;Tabor AE
通讯作者：
Tabor AE
DOI：
10.3390/v12121358
发表时间：
2020-11-27
期刊：
Viruses
影响因子：
--
作者：
Schuele L;Cassidy H;Lizarazo E;Strutzberg-Minder K;Schuetze S;Loebert S;Lambrecht C;Harlizius J;Friedrich AW;Peter S;Niesters HGM;Rossen JWA;Couto N
通讯作者：
Couto N
影响因子：
9.5
作者：
Cheng, Hang;Sun, Yuhong;Xia, Yu
通讯作者：
Xia, Yu
影响因子：
5.2
作者：
通讯作者：
--
使用Oxford Nanopore的自适应测序评估人类阴道样品中微生物组富集和宿主DNA耗竭的评估。
影响因子：
4.6
作者：
Marquet M;Zöllkau J;Pastuschek J;Viehweger A;Schleußner E;Makarewicz O;Pletz MW;Ehricht R;Brandt C
通讯作者：
Brandt C