Clinical performance of nanopore targeted sequencing for diagnosing endophthalmitis
Abstract Purpose Rapid identification of pathogenic bacteria in the vitreous and/or aqueous humor of patients with acute clinical diagnosis of endophthalmitis via nanopore sequencing technology. Methods We recruited a total of 12 patients (12 eyes) who were diagnosed with endophthalmitis at an ophth...
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2025-07-01
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| Online Access: | https://doi.org/10.1186/s12866-025-04132-y |
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| author | Dalan Jing Xiaodan Jiang Xiaotong Ren Ran Hao Jie Su Xuemin Li |
| author_facet | Dalan Jing Xiaodan Jiang Xiaotong Ren Ran Hao Jie Su Xuemin Li |
| author_sort | Dalan Jing |
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| description | Abstract Purpose Rapid identification of pathogenic bacteria in the vitreous and/or aqueous humor of patients with acute clinical diagnosis of endophthalmitis via nanopore sequencing technology. Methods We recruited a total of 12 patients (12 eyes) who were diagnosed with endophthalmitis at an ophthalmic outpatient clinic of Peking University Third Hospital from January 2022 to October 2022. Clinical evaluation is conducted in the order of consultation, symptom evaluation, physical sign evaluation, and ophthalmic special examination, all of which are completed by the same experienced clinical physician. Finally, 19 aqueous humor and/or vitreous samples were obtained via anterior chamber wash, vitreous tap and vitrectomy. The samples were separated for cultivation, biochemical drug sensitivity identification, and targeted nanopore sequencing (NTS), and the results of nanopore sequencing were validated via Sanger sequencing. Results In patients with endophthalmitis, NTS can identify infected pathogens within 8–12 h. Six samples (31.6%) were subjected to culture-based diagnosis, while NTS revealed the presence of pathogenic microorganisms in 19 samples (100%), of which bacteria and fungi were detected in three samples. A total of 19 samples were subjected to Sanger sequencing, of which 16 (84.2%) tested positive, including 6 culture-positive samples and 10 culture-negative samples, of which 5 (26.3%) were positive for two bacterial genera. In culture-positive cases, there is a high-quality match between culture and targeted nanopore sequencing. Conclusions NTS can quickly detect pathogenic bacteria in samples from patients with endophthalmitis. Moreover, the use of vitreous and/or aqueous humor for the NTS has potential. NTS is a promising diagnostic platform for endophthalmitis, especially for mixed infections and culture-negative cases. |
| format | Article |
| id | doaj-art-ddee18bf0e3b47e998f526e45f09d1cb |
| institution | Kabale University |
| issn | 1471-2180 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj-art-ddee18bf0e3b47e998f526e45f09d1cb2025-08-20T03:45:22ZengBMCBMC Microbiology1471-21802025-07-0125111210.1186/s12866-025-04132-yClinical performance of nanopore targeted sequencing for diagnosing endophthalmitisDalan Jing0Xiaodan Jiang1Xiaotong Ren2Ran Hao3Jie Su4Xuemin Li5Department of Ophthalmology, Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityDepartment of Ophthalmology, Peking University Third HospitalDepartment of Ophthalmology, First Affiliated Hospital of Fujian Medical UniversityBeijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key LaboratoryDepartment of Ophthalmology, Peking University Third HospitalDepartment of Ophthalmology, Peking University Third HospitalAbstract Purpose Rapid identification of pathogenic bacteria in the vitreous and/or aqueous humor of patients with acute clinical diagnosis of endophthalmitis via nanopore sequencing technology. Methods We recruited a total of 12 patients (12 eyes) who were diagnosed with endophthalmitis at an ophthalmic outpatient clinic of Peking University Third Hospital from January 2022 to October 2022. Clinical evaluation is conducted in the order of consultation, symptom evaluation, physical sign evaluation, and ophthalmic special examination, all of which are completed by the same experienced clinical physician. Finally, 19 aqueous humor and/or vitreous samples were obtained via anterior chamber wash, vitreous tap and vitrectomy. The samples were separated for cultivation, biochemical drug sensitivity identification, and targeted nanopore sequencing (NTS), and the results of nanopore sequencing were validated via Sanger sequencing. Results In patients with endophthalmitis, NTS can identify infected pathogens within 8–12 h. Six samples (31.6%) were subjected to culture-based diagnosis, while NTS revealed the presence of pathogenic microorganisms in 19 samples (100%), of which bacteria and fungi were detected in three samples. A total of 19 samples were subjected to Sanger sequencing, of which 16 (84.2%) tested positive, including 6 culture-positive samples and 10 culture-negative samples, of which 5 (26.3%) were positive for two bacterial genera. In culture-positive cases, there is a high-quality match between culture and targeted nanopore sequencing. Conclusions NTS can quickly detect pathogenic bacteria in samples from patients with endophthalmitis. Moreover, the use of vitreous and/or aqueous humor for the NTS has potential. NTS is a promising diagnostic platform for endophthalmitis, especially for mixed infections and culture-negative cases.https://doi.org/10.1186/s12866-025-04132-yEndophthalmitisMicrobiome16S rRNANanopore sequencingInfectious pathogens |
| spellingShingle | Dalan Jing Xiaodan Jiang Xiaotong Ren Ran Hao Jie Su Xuemin Li Clinical performance of nanopore targeted sequencing for diagnosing endophthalmitis BMC Microbiology Endophthalmitis Microbiome 16S rRNA Nanopore sequencing Infectious pathogens |
| title | Clinical performance of nanopore targeted sequencing for diagnosing endophthalmitis |
| title_full | Clinical performance of nanopore targeted sequencing for diagnosing endophthalmitis |
| title_fullStr | Clinical performance of nanopore targeted sequencing for diagnosing endophthalmitis |
| title_full_unstemmed | Clinical performance of nanopore targeted sequencing for diagnosing endophthalmitis |
| title_short | Clinical performance of nanopore targeted sequencing for diagnosing endophthalmitis |
| title_sort | clinical performance of nanopore targeted sequencing for diagnosing endophthalmitis |
| topic | Endophthalmitis Microbiome 16S rRNA Nanopore sequencing Infectious pathogens |
| url | https://doi.org/10.1186/s12866-025-04132-y |
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