Application of nanopore adaptive sequencing in pathogen detection of a patient with Chlamydia psittaci infection
IntroductionNanopore 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 alignm...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2023.1064317/full |
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| author | Yanfeng Lin Yanfeng Lin Yan Dai Shuang Zhang Shuang Zhang Hao Guo Lang Yang Jinhui Li Kaiying Wang Ming Ni Ming Ni Zongqian Hu Zongqian Hu Leili Jia Huiying Liu Peng Li Hongbin Song Hongbin Song |
| author_facet | Yanfeng Lin Yanfeng Lin Yan Dai Shuang Zhang Shuang Zhang Hao Guo Lang Yang Jinhui Li Kaiying Wang Ming Ni Ming Ni Zongqian Hu Zongqian Hu Leili Jia Huiying Liu Peng Li Hongbin Song Hongbin Song |
| author_sort | Yanfeng Lin |
| collection | DOAJ |
| description | IntroductionNanopore 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.MethodsNanopore 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.ResultsNanopore 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.DiscussionNanopore 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. |
| first_indexed | 2024-04-10T20:55:40Z |
| format | Article |
| id | doaj.art-78afdb37beb549b3847df5786e84ca62 |
| institution | Directory Open Access Journal |
| issn | 2235-2988 |
| language | English |
| last_indexed | 2024-04-10T20:55:40Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj.art-78afdb37beb549b3847df5786e84ca622023-01-23T06:16:05ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882023-01-011310.3389/fcimb.2023.10643171064317Application of nanopore adaptive sequencing in pathogen detection of a patient with Chlamydia psittaci infectionYanfeng Lin0Yanfeng Lin1Yan Dai2Shuang Zhang3Shuang Zhang4Hao Guo5Lang Yang6Jinhui Li7Kaiying Wang8Ming Ni9Ming Ni10Zongqian Hu11Zongqian Hu12Leili Jia13Huiying Liu14Peng Li15Hongbin Song16Hongbin Song17Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, ChinaChinese PLA Center for Disease Control and Prevention, Beijing, ChinaState Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, ChinaAcademy of Military Medical Sciences, Academy of Military Sciences, Beijing, ChinaInstitute of Health Service and Transfusion Medicine, Beijing, ChinaState Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, ChinaChinese PLA Center for Disease Control and Prevention, Beijing, ChinaChinese PLA Center for Disease Control and Prevention, Beijing, ChinaChinese PLA Center for Disease Control and Prevention, Beijing, ChinaAcademy of Military Medical Sciences, Academy of Military Sciences, Beijing, ChinaInstitute of Health Service and Transfusion Medicine, Beijing, ChinaAcademy of Military Medical Sciences, Academy of Military Sciences, Beijing, ChinaBeijing Institute of Radiation Medicine, Beijing, ChinaChinese PLA Center for Disease Control and Prevention, Beijing, ChinaCollege of Pulmonary & Critical Care Medicine, 8th Medical Center, Chinese PLA General Hospital, Beijing, ChinaChinese PLA Center for Disease Control and Prevention, Beijing, ChinaAcademy of Military Medical Sciences, Academy of Military Sciences, Beijing, ChinaChinese PLA Center for Disease Control and Prevention, Beijing, ChinaIntroductionNanopore 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.MethodsNanopore 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.ResultsNanopore 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.DiscussionNanopore 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.https://www.frontiersin.org/articles/10.3389/fcimb.2023.1064317/fullnanopore adaptive sequencingmNGSpathogen detectionrespiratory infectionChlamydia psittaci |
| spellingShingle | Yanfeng Lin Yanfeng Lin Yan Dai Shuang Zhang Shuang Zhang Hao Guo Lang Yang Jinhui Li Kaiying Wang Ming Ni Ming Ni Zongqian Hu Zongqian Hu Leili Jia Huiying Liu Peng Li Hongbin Song Hongbin Song Application of nanopore adaptive sequencing in pathogen detection of a patient with Chlamydia psittaci infection Frontiers in Cellular and Infection Microbiology nanopore adaptive sequencing mNGS pathogen detection respiratory infection Chlamydia psittaci |
| title | Application of nanopore adaptive sequencing in pathogen detection of a patient with Chlamydia psittaci infection |
| title_full | Application of nanopore adaptive sequencing in pathogen detection of a patient with Chlamydia psittaci infection |
| title_fullStr | Application of nanopore adaptive sequencing in pathogen detection of a patient with Chlamydia psittaci infection |
| title_full_unstemmed | Application of nanopore adaptive sequencing in pathogen detection of a patient with Chlamydia psittaci infection |
| title_short | Application of nanopore adaptive sequencing in pathogen detection of a patient with Chlamydia psittaci infection |
| title_sort | application of nanopore adaptive sequencing in pathogen detection of a patient with chlamydia psittaci infection |
| topic | nanopore adaptive sequencing mNGS pathogen detection respiratory infection Chlamydia psittaci |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2023.1064317/full |
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