Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study
Abstract This study aimed to evaluate the usefulness of amplicon-based real-time metagenomic sequencing applied to cerebrospinal fluid (CSF) for identifying the causative agents of bacterial meningitis. We conducted a 16S rRNA amplicon sequencing using a nanopore-based platform, alongside routine po...
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Nature Portfolio
2025-01-01
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| Online Access: | https://doi.org/10.1038/s41598-025-87858-z |
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| author | Yoon Hyun Sung Yong Kuk Ju Hak Jun Lee Seung Min Park Jin Woong Suh Jeong Yeon Kim Jang Wook Sohn Young Kyung Yoon |
| author_facet | Yoon Hyun Sung Yong Kuk Ju Hak Jun Lee Seung Min Park Jin Woong Suh Jeong Yeon Kim Jang Wook Sohn Young Kyung Yoon |
| author_sort | Yoon Hyun Sung |
| collection | DOAJ |
| description | Abstract This study aimed to evaluate the usefulness of amplicon-based real-time metagenomic sequencing applied to cerebrospinal fluid (CSF) for identifying the causative agents of bacterial meningitis. We conducted a 16S rRNA amplicon sequencing using a nanopore-based platform, alongside routine polymerase chain reaction (PCR) testing or bacterial culture, to compare its clinical performance in pathogen detection on CSF samples. Among 17 patients, nanopore-based sequencing, multiplex PCR, and bacterial culture detected potential bacterial pathogens in 47.1%, 0%, and 47.1% samples, respectively. Nanopore-based sequencing demonstrated a sensitivity of 50.0%, specificity of 55.6%, positive predictive value of 50.0%, negative predictive value of 55.6%, and overall accuracy of 47.1%, compared to the gold standard method for bacterial culture. In 44.4% (4/9) of culture-negative cases, nanopore-based sequencing detected potentially causative pathogens, whereas four (23.5%) patients were positive only in culture. Using nanopore-based sequencing alongside bacterial culture increased the positivity rate from 47.1 to 70.6%. However, these values may be overestimated due to challenges in distinguishing significant pathogens from background noise. Meanwhile, the bioinformatics module in EPI2ME reduced the turn-around time to 10 min. Nanopore-based metagenomic sequencing is expected to serve as a complementary tool for pathogen detection in CSF samples by facilitating rapid and accurate diagnosis. |
| format | Article |
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| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
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| spelling | doaj-art-b5a85fb3e0b447a2ac316a39cb1058e82025-02-02T12:21:54ZengNature PortfolioScientific Reports2045-23222025-01-0115111010.1038/s41598-025-87858-zClinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot studyYoon Hyun Sung0Yong Kuk Ju1Hak Jun Lee2Seung Min Park3Jin Woong Suh4Jeong Yeon Kim5Jang Wook Sohn6Young Kyung Yoon7Institute of Emerging Infectious Diseases, Korea UniversityInstitute of Emerging Infectious Diseases, Korea UniversityInstitute of Emerging Infectious Diseases, Korea UniversityInstitute of Emerging Infectious Diseases, Korea UniversityDivision of Infectious Diseases, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of MedicineDivision of Infectious Diseases, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of MedicineInstitute of Emerging Infectious Diseases, Korea UniversityInstitute of Emerging Infectious Diseases, Korea UniversityAbstract This study aimed to evaluate the usefulness of amplicon-based real-time metagenomic sequencing applied to cerebrospinal fluid (CSF) for identifying the causative agents of bacterial meningitis. We conducted a 16S rRNA amplicon sequencing using a nanopore-based platform, alongside routine polymerase chain reaction (PCR) testing or bacterial culture, to compare its clinical performance in pathogen detection on CSF samples. Among 17 patients, nanopore-based sequencing, multiplex PCR, and bacterial culture detected potential bacterial pathogens in 47.1%, 0%, and 47.1% samples, respectively. Nanopore-based sequencing demonstrated a sensitivity of 50.0%, specificity of 55.6%, positive predictive value of 50.0%, negative predictive value of 55.6%, and overall accuracy of 47.1%, compared to the gold standard method for bacterial culture. In 44.4% (4/9) of culture-negative cases, nanopore-based sequencing detected potentially causative pathogens, whereas four (23.5%) patients were positive only in culture. Using nanopore-based sequencing alongside bacterial culture increased the positivity rate from 47.1 to 70.6%. However, these values may be overestimated due to challenges in distinguishing significant pathogens from background noise. Meanwhile, the bioinformatics module in EPI2ME reduced the turn-around time to 10 min. Nanopore-based metagenomic sequencing is expected to serve as a complementary tool for pathogen detection in CSF samples by facilitating rapid and accurate diagnosis.https://doi.org/10.1038/s41598-025-87858-zCerebrospinal fluidNanopore sequencingNext-generation sequencingMeningitisPoint-of-care testing |
| spellingShingle | Yoon Hyun Sung Yong Kuk Ju Hak Jun Lee Seung Min Park Jin Woong Suh Jeong Yeon Kim Jang Wook Sohn Young Kyung Yoon Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study Scientific Reports Cerebrospinal fluid Nanopore sequencing Next-generation sequencing Meningitis Point-of-care testing |
| title | Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study |
| title_full | Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study |
| title_fullStr | Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study |
| title_full_unstemmed | Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study |
| title_short | Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study |
| title_sort | clinical performance of real time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid a pilot study |
| topic | Cerebrospinal fluid Nanopore sequencing Next-generation sequencing Meningitis Point-of-care testing |
| url | https://doi.org/10.1038/s41598-025-87858-z |
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