18例内源性眼内炎患者的临床特征和纳米孔技术测序结果_Chinese Journal of Ocular Fundus Diseases

Authors：

郝昕蕾 , 袁满 , 陈刘贵 , 王文俊 , 金玮 ,  杨安怀

武汉大学人民医院眼科中心, 武汉 430060金玮和杨安怀对本文有同等贡献;

Corresponding author：

杨安怀, Email: yah0525@126.com

Keywords：

眼内炎; 纳米孔; 疾病特征; 病原体培养

DOI：

10.3760/cma.j.cn511434-20210823-00456

Video：

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Citation： 郝昕蕾, 袁满, 陈刘贵, 王文俊, 金玮, 杨安怀. 18例内源性眼内炎患者的临床特征和纳米孔技术测序结果. Chinese Journal of Ocular Fundus Diseases, 2022, 38(5): 396-399. doi: 10.3760/cma.j.cn511434-20210823-00456 Copy

1.	Durand ML. Bacterial and fungal endophthalmitis[J]. Clin Microbiol Rev, 2017, 30(3): 597-613. DOI: 10.1128/CMR.00113-16.
2.	Doan T, Wilson MR, Crawford ED, et al. Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens[J]. Genome Med, 2016, 8(1): 90. DOI: 10.1186/s13073-016-0344-6.
3.	Deamer D, Akeson M, Branton D. Three decades of nanopore sequencing[J]. Nat Biotechnol, 2016, 34(5): 518-524. DOI: 10.1038/nbt.3423.
4.	Petersen LM, Martin IW, Moschetti WE, et al. Third-generation sequencing in the clinical laboratory: exploring the advantages and challenges of nanopore sequencing[J/OL]. J Clin Microbiol, 2019, 58(1): e1315-1319[2019-12-23]. https://pubmed.ncbi.nlm.nih.gov/31619531/. DOI: 10.1128/JCM.01315-19.
5.	Zhu X, Yan S, Yuan F, et al. The applications of nanopore sequencing technology in pathogenic microorganism detection[J/OL]. Can J Infect Dis Med Microbiol, 2020, 2020: 6675206[2020-12-31]. https://doi.org/10.1155/2020/6675206. DOI: 10.1155/2020/6675206.
6.	Tabatabaei SA, Soleimani M, Mirshahi R, et al. Culture-proven endogenous endophthalmitis: microbiological and clinical survey[J]. Int Ophthalmol, 2020, 40(12): 3521-3528. DOI: 10.1007/s10792-020-01540-z.
7.	Wang M, Fu A, Hu B, et al. Same-day simultaneous diagnosis of bacterial and fungal infections in clinical practice by nanopore targeted sequencing[J/OL]. MedRxiv, 2020, 2020: 1-25[2020-04-11]. https://www.medrxiv.org/content/10.1101/2020.04.08.20057604v1. DOI:10.1101/2020.04.08.20057604.
8.	Lei B, Jiang R, Gu R, et al. Endogenous fungal endophthalmitis associated with genitourinary procedures[J]. Ocul Immunol Inflamm, 2019, 27(5): 747-755. DOI: 10.1080/09273948.2018.1465100.
9.	Cunningham ET, Flynn HW, Relhan N, et al. Endogenous endophthalmitis[J]. Ocul Immunol Inflamm, 2018, 26(4): 491-495. DOI: 10.1080/09273948.2018.1466561.
10.	Yeşiltaş YS, Özcan G, Demirel S, et al. Culture-proven Candida Albicans endogenous endophthalmitis in a patient with onychomycosis[J]. Ocul Immunol Inflamm, 2020, 28(2): 178-181. DOI: 10.1080/09273948.2019.1568503.
11.	Jackson TL, Paraskevopoulos T, Georgalas I. Systematic review of 342 cases of endogenous bacterial endophthalmitis[J]. Surv Ophthalmol, 2014, 59(6): 627-635. DOI: 10.1016/j.survophthal.2014.06.002.
12.	Luong PM, Tsui E, Batra NN, et al. Endogenous endophthalmitis and other ocular manifestations of injection drug use[J]. Curr Opin Ophthalmol, 2019, 30(6): 506-512. DOI: 10.1097/ICU.0000000000000606.
13.	Quick J, Loman NJ, Duraffour S, et al. Real-time, portable genome sequencing for Ebola surveillance[J]. Nature, 2016, 530(7589): 228-232. DOI: 10.1038/nature16996.
14.	Oude Munnink BB, Munger E, Nieuwenhuijse DF, et al. Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016-2018[J/OL]. Sci Rep, 2020, 10(1): 2798[2020-02-18]. https://pubmed.ncbi.nlm.nih.gov/32071379/. DOI: 10.1038/s41598-020-59692-y.
15.	Lu H, Giordano F, Ning Z. Oxford nanopore MinION sequencing and genome assembly[J]. Genomics Proteomics Bioinformatics, 2016, 14(5): 265-279. DOI: 10.1016/j.gpb.2016.05.004.
16.	Sanderson ND, Street TL, Foster D, et al. Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices[J]. BMC Genomics, 2018, 19(1): 714. DOI: 10.1186/s12864-018-5094-y.
17.	Leggett RM, Alcon-Giner C, Heavens D, et al. Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens[J]. Nat Microbiol, 2020, 5(3): 430-442. DOI: 10.1038/s41564-019-0626-z.
18.	Ashikawa S, Tarumoto N, Imai K, et al. Rapid identification of pathogens from positive blood culture bottles with the MinION nanopore sequencer[J]. J Med Microbiol, 2018, 67(11): 1589-1595. DOI: 10.1099/jmm.0.000855.
19.	Cho H, Shin YU, Siegel NH, et al. Endogenous endophthalmitis in the American and Korean population: an 8-year retrospective study[J]. Ocul Immunol Inflamm, 2018, 26(4): 496-503. DOI: 10.1080/09273948.2016.1195000.
20.	Shields RA, Smith SJ, Pan CK, et al. Endogenous klebsiella pneumoniae endophthalmitis in Northern California[J]. Retina, 2019, 39(3): 614-620. DOI: 10.1097/IAE.0000000000001994.
21.	Gu W, Miller S, Chiu CY. Clinical metagenomic next-generation sequencing for pathogen detection[J]. Annu Rev Pathol, 2019, 14: 319-338. DOI: 10.1146/annurev-pathmechdis-012418-012751.
22.	Wilson MR, O'Donovan BD, Gelfand JM, et al. Chronic meningitis investigated via metagenomic next-generation sequencing[J]. JAMA Neurol, 2018, 75(8): 947-955. DOI: 10.1001/jamaneurol.2018.0463.
23.	Schlaberg R, Chiu CY, Miller S, et al. Validation of metagenomic next-generation sequencing tests for universal pathogen detection[J]. Arch Pathol Lab Med, 2017, 141(6): 776-786. DOI: 10.5858/arpa.2016-0539-RA.
24.	Bukowska-Ośko I, Perlejewski K, Nakamura S, et al. Sensitivity of next-generation sequencing metagenomic analysis for detection of RNA and DNA viruses in cerebrospinal fluid: the confounding effect of background contamination[J]. Adv Exp Med Biol, 2017, 944: 53-62. DOI: 10.1007/5584_2016_42.

1. Durand ML. Bacterial and fungal endophthalmitis[J]. Clin Microbiol Rev, 2017, 30(3): 597-613. DOI: 10.1128/CMR.00113-16.
2. Doan T, Wilson MR, Crawford ED, et al. Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens[J]. Genome Med, 2016, 8(1): 90. DOI: 10.1186/s13073-016-0344-6.
3. Deamer D, Akeson M, Branton D. Three decades of nanopore sequencing[J]. Nat Biotechnol, 2016, 34(5): 518-524. DOI: 10.1038/nbt.3423.
4. Petersen LM, Martin IW, Moschetti WE, et al. Third-generation sequencing in the clinical laboratory: exploring the advantages and challenges of nanopore sequencing[J/OL]. J Clin Microbiol, 2019, 58(1): e1315-1319[2019-12-23]. https://pubmed.ncbi.nlm.nih.gov/31619531/. DOI: 10.1128/JCM.01315-19.
5. Zhu X, Yan S, Yuan F, et al. The applications of nanopore sequencing technology in pathogenic microorganism detection[J/OL]. Can J Infect Dis Med Microbiol, 2020, 2020: 6675206[2020-12-31]. https://doi.org/10.1155/2020/6675206. DOI: 10.1155/2020/6675206.
6. Tabatabaei SA, Soleimani M, Mirshahi R, et al. Culture-proven endogenous endophthalmitis: microbiological and clinical survey[J]. Int Ophthalmol, 2020, 40(12): 3521-3528. DOI: 10.1007/s10792-020-01540-z.
7. Wang M, Fu A, Hu B, et al. Same-day simultaneous diagnosis of bacterial and fungal infections in clinical practice by nanopore targeted sequencing[J/OL]. MedRxiv, 2020, 2020: 1-25[2020-04-11]. https://www.medrxiv.org/content/10.1101/2020.04.08.20057604v1. DOI:10.1101/2020.04.08.20057604.
8. Lei B, Jiang R, Gu R, et al. Endogenous fungal endophthalmitis associated with genitourinary procedures[J]. Ocul Immunol Inflamm, 2019, 27(5): 747-755. DOI: 10.1080/09273948.2018.1465100.
9. Cunningham ET, Flynn HW, Relhan N, et al. Endogenous endophthalmitis[J]. Ocul Immunol Inflamm, 2018, 26(4): 491-495. DOI: 10.1080/09273948.2018.1466561.
10. Yeşiltaş YS, Özcan G, Demirel S, et al. Culture-proven Candida Albicans endogenous endophthalmitis in a patient with onychomycosis[J]. Ocul Immunol Inflamm, 2020, 28(2): 178-181. DOI: 10.1080/09273948.2019.1568503.
11. Jackson TL, Paraskevopoulos T, Georgalas I. Systematic review of 342 cases of endogenous bacterial endophthalmitis[J]. Surv Ophthalmol, 2014, 59(6): 627-635. DOI: 10.1016/j.survophthal.2014.06.002.
12. Luong PM, Tsui E, Batra NN, et al. Endogenous endophthalmitis and other ocular manifestations of injection drug use[J]. Curr Opin Ophthalmol, 2019, 30(6): 506-512. DOI: 10.1097/ICU.0000000000000606.
13. Quick J, Loman NJ, Duraffour S, et al. Real-time, portable genome sequencing for Ebola surveillance[J]. Nature, 2016, 530(7589): 228-232. DOI: 10.1038/nature16996.
14. Oude Munnink BB, Munger E, Nieuwenhuijse DF, et al. Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016-2018[J/OL]. Sci Rep, 2020, 10(1): 2798[2020-02-18]. https://pubmed.ncbi.nlm.nih.gov/32071379/. DOI: 10.1038/s41598-020-59692-y.
15. Lu H, Giordano F, Ning Z. Oxford nanopore MinION sequencing and genome assembly[J]. Genomics Proteomics Bioinformatics, 2016, 14(5): 265-279. DOI: 10.1016/j.gpb.2016.05.004.
16. Sanderson ND, Street TL, Foster D, et al. Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices[J]. BMC Genomics, 2018, 19(1): 714. DOI: 10.1186/s12864-018-5094-y.
17. Leggett RM, Alcon-Giner C, Heavens D, et al. Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens[J]. Nat Microbiol, 2020, 5(3): 430-442. DOI: 10.1038/s41564-019-0626-z.
18. Ashikawa S, Tarumoto N, Imai K, et al. Rapid identification of pathogens from positive blood culture bottles with the MinION nanopore sequencer[J]. J Med Microbiol, 2018, 67(11): 1589-1595. DOI: 10.1099/jmm.0.000855.
19. Cho H, Shin YU, Siegel NH, et al. Endogenous endophthalmitis in the American and Korean population: an 8-year retrospective study[J]. Ocul Immunol Inflamm, 2018, 26(4): 496-503. DOI: 10.1080/09273948.2016.1195000.
20. Shields RA, Smith SJ, Pan CK, et al. Endogenous klebsiella pneumoniae endophthalmitis in Northern California[J]. Retina, 2019, 39(3): 614-620. DOI: 10.1097/IAE.0000000000001994.
21. Gu W, Miller S, Chiu CY. Clinical metagenomic next-generation sequencing for pathogen detection[J]. Annu Rev Pathol, 2019, 14: 319-338. DOI: 10.1146/annurev-pathmechdis-012418-012751.
22. Wilson MR, O'Donovan BD, Gelfand JM, et al. Chronic meningitis investigated via metagenomic next-generation sequencing[J]. JAMA Neurol, 2018, 75(8): 947-955. DOI: 10.1001/jamaneurol.2018.0463.
23. Schlaberg R, Chiu CY, Miller S, et al. Validation of metagenomic next-generation sequencing tests for universal pathogen detection[J]. Arch Pathol Lab Med, 2017, 141(6): 776-786. DOI: 10.5858/arpa.2016-0539-RA.
24. Bukowska-Ośko I, Perlejewski K, Nakamura S, et al. Sensitivity of next-generation sequencing metagenomic analysis for detection of RNA and DNA viruses in cerebrospinal fluid: the confounding effect of background contamination[J]. Adv Exp Med Biol, 2017, 944: 53-62. DOI: 10.1007/5584_2016_42.

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18例内源性眼内炎患者的临床特征和纳米孔技术测序结果

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