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Cell. Infect. Microbiol."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Nanopore adaptive sequencing and standard sequencing was performed on a same flow cell with a bronchoalveolar lavage fluid sample from a patient with <jats:italic>Chlamydia<\/jats:italic> psittacosis infection, and was compared with the previous mNGS results.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Nanopore adaptive sequencing identified 648 on-target stop receiving reads with the longest median read length(688bp), which account for 72.4% of all <jats:italic>Chlamydia<\/jats:italic> psittaci reads and 0.03% of total reads in enriched group. The read proportion matched to <jats:italic>C. psittaci<\/jats:italic> in the stop receiving group was 99.85%, which was much higher than that of the unblock (&amp;lt;0.01%) and fail to adapt (0.02%) groups. Nanopore adaptive sequencing generated similar data yield of <jats:italic>C. psittaci<\/jats:italic> compared with standard nanopore sequencing. The proportion of <jats:italic>C. psittaci<\/jats:italic> reads in adaptive sequencing is close to that of standard nanopore sequencing and mNGS, but generated lower genome coverage than mNGS.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>Nanopore adaptive sequencing can effectively identify target <jats:italic>C. psittaci<\/jats:italic> reads in real-time, but how to increase the targeted data of pathogens still needs to be further evaluated.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fcimb.2023.1064317","type":"journal-article","created":{"date-parts":[[2023,1,23]],"date-time":"2023-01-23T06:16:14Z","timestamp":1674454574000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":15,"title":["Application of nanopore adaptive sequencing in pathogen detection of a patient with Chlamydia psittaci infection"],"prefix":"10.3389","volume":"13","author":[{"given":"Yanfeng","family":"Lin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Dai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lang","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinhui","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaiying","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming","family":"Ni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zongqian","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leili","family":"Jia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiying","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongbin","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,1,23]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"18505","DOI":"10.1002\/ece3.8447","article-title":"Whole genome sequencing of marine organisms by Oxford nanopore technologies: Assessment and optimization of HMW-DNA extraction protocols","volume":"11","author":"Boughattas","year":"2021","journal-title":"Ecol. 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