Cerebrospinal fluid MinION sequencing of 16S rRNA gene for rapid and accurate diagnosis of bacterial meningitis

Hong, Nguyen Thi Thu; Nghia, Ho Dang Trung; Thanh, Tran Tan; Lan, Nguyen Phu Huong; Ny, Nguyen Thi Han; Ngoc, Nghiêm My; Hang, Vu Thi Ty; Chau, Le Thi My; Quynh, Van Xuan; Diem, Le Thi; Hanh, Bui Thi Bich; Hanh, Nguyen Ho Hong; Duc, Du Trong; Man, Dinh Nguyen Huy; Oanh, Pham Kieu Nguyet; Day, Jeremy; Phu, Nguyen Hoan; Châu, Nguyễn Văn Vĩnh; Thwaites, Guy; Tan, Le Van

doi:10.1016/j.jinf.2019.12.011

Cited by 14 publications

(11 citation statements)

References 9 publications

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“…Once again, this result confirmed the superiority of 16S amplicon sequencing over the conventional culture test, even in CSF samples. 18,19,28 Therefore, there is a possibility that the postoperative CNS infection rate might actually be higher than the results of previous studies, which showed 0.3%À8.9% based on culture studies. [29][30][31] In addition, a CNS foreign body, heavy alcohol consumption, and postoperative fever that we analyzed as risk factors for postoperative bacterial meningitis were partly consistent with the known factors for nosocomial bacterial meningitis.…”

Section: Discussionmentioning

confidence: 85%

Nanopore 16S sequencing enhances the detection of bacterial meningitis after neurosurgery

Jang

Kim

et al. 2022

Ann Clin Transl Neurol

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Objective: Nosocomial bacterial meningitis is one of the major complications after neurosurgery. We performed nanopore 16S amplicon sequencing from cerebrospinal fluid (CSF) to evaluate bacterial meningitis in patients who underwent neurosurgery. Methods: Among the patients who visited the neurosurgery department of Seoul National University Hospital between July 2017 and June 2020, those with clinically suspected bacterial meningitis were included. 16S rDNA PCR was performed from the CSF, and nanopore sequencing was performed for up to 3 h. The reads were aligned to the BLAST database. In each case, the culture and the 16S rRNA gene amplicon analysis were simultaneously performed and compared with each other, and we retrospectively reviewed the medical records. Genuine infection was determined by the identical results between conventional culture study and the sequencing, or clinically determined in cases with inconsistent results between the two methods. Results: Of the 285 samples obtained from 178 patients who had 16S rDNA PCR, 41 samples (14.4%) were diagnosed with genuine infection. A total of 56.1% (23/41) of the samples with genuine infection showed a false-negative culture test. In particular, 16S amplicon sequencing was useful in evaluating patients at the initial tests who had infection with intraventricular hemorrhage (Culture false-negative rate = 100%), subarachnoid hemorrhage (Culture falsenegative rate = 77.8%), and systemic cancer (Culture false-negative rate = 100%), which are risk factors for central fever. Moreover, 16S amplicon sequencing could suggest the possibility of persistent bacterial meningitis in empirical antibiotic use. Conclusion: CSF nanopore 16S sequencing was more effective than conventional CSF culture studies in postoperative bacterial meningitis and may contribute to evidence-based decisions for antibiotic maintenance and discontinuation.

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Section: Discussionmentioning

confidence: 85%

Nanopore 16S sequencing enhances the detection of bacterial meningitis after neurosurgery

Jang

Kim

et al. 2022

Ann Clin Transl Neurol

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“…The reads produced by nanopore sequencing were much longer than those produced by NGS. Thus, nanopore sequencing can sequence repetitive regions and structural variants, and provide comprehensive genomic information, such as the phenotype of antimicrobial resistance-encoding genes to help clinicians optimize the selection of antifungal agents for treatment ( 11 , 12 , 14 , 18 , 19 ).…”

Section: Conclusion and Discussionmentioning

confidence: 99%

Nanopore sequencing of cerebrospinal fluid of three patients with cryptococcal meningitis

et al. 2022

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Background Cryptococcal meningitis (CM) has a high morbidity and mortality due to the low detection of Cryptococcus in cerebrospinal fluid (CSF) during the early stage of the disease with traditional methods. Case presentation In addition to the traditional methods of India ink staining and cryptococcal antigen (CrAg), we used nanopore sequencing and next-generation sequencing (NGS) to detect pathogenic DNA in CSF samples of three patients with CM. The CSF samples of all three patients were positive by India ink staining and CrAg. NGS also detected Cryptococcus in all three CSF samples. Nanopore sequencing detected Cryptococcus in two CSF samples. Conclusion Nanopore sequencing may be useful in assisting with the clinical diagnosis of CM. Further research is needed to determine the sensitivity and specificity of nanopore sequencing of CSF.

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“…Acute meningitis may be caused by bacteria or viruses, while fungi, mycobacteria, or atypical bacteria are usually involved in chronic meningitis [ 17 ]. The rapid identification of the pathogen is essential for the process of antimicrobial therapy and its impact on clinical outcomes [ 18 ]. More than 100 pathogens, commonly viruses, have been reported as causative agents of encephalitis; however, most of the cases remain undiagnosed or even underestimated and the selection of an appropriate diagnostic method must be the ultimate objective [ 19 , 20 ].…”

Section: Cns Infectionsmentioning

confidence: 99%

Evaluating Infectious, Neoplastic, Immunological, and Degenerative Diseases of the Central Nervous System with Cerebrospinal Fluid-Based Next-Generation Sequencing

et al. 2021

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Cerebrospinal fluid (CSF) is a clear and paucicellular fluid that circulates within the ventricular system and the subarachnoid space of the central nervous system (CNS), and diverse CNS disorders can impact its composition, volume, and flow. As conventional CSF testing suffers from suboptimal sensitivity, this review aimed to evaluate the role of next-generation sequencing (NGS) in the work-up of infectious, neoplastic, neuroimmunological, and neurodegenerative CNS diseases. Metagenomic NGS showed improved sensitivity—compared to traditional methods—to detect bacterial, viral, parasitic, and fungal infections, while the overall performance was maximized in some studies when all diagnostic modalities were used. In patients with primary CNS cancer, NGS findings in the CSF were largely concordant with the molecular signatures derived from tissue-based molecular analysis; of interest, additional mutations were identified in the CSF in some glioma studies, reflecting intratumoral heterogeneity. In patients with metastasis to the CNS, NGS facilitated diagnosis, prognosis, therapeutic management, and monitoring, exhibiting higher sensitivity than neuroimaging, cytology, and plasma-based molecular analysis. Although evidence is still rudimentary, NGS could enhance the diagnosis and pathogenetic understanding of multiple sclerosis in addition to Alzheimer and Parkinson disease. To conclude, NGS has shown potential to aid the research, facilitate the diagnostic approach, and improve the management outcomes of all the aforementioned CNS diseases. However, to establish its role in clinical practice, the clinical validity and utility of each NGS protocol should be determined. Lastly, as most evidence has been derived from small and retrospective studies, results from randomized control trials could be of significant value.

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Cerebrospinal fluid MinION sequencing of 16S rRNA gene for rapid and accurate diagnosis of bacterial meningitis

Cited by 14 publications

References 9 publications

Nanopore 16S sequencing enhances the detection of bacterial meningitis after neurosurgery

Nanopore 16S sequencing enhances the detection of bacterial meningitis after neurosurgery

Nanopore sequencing of cerebrospinal fluid of three patients with cryptococcal meningitis

Evaluating Infectious, Neoplastic, Immunological, and Degenerative Diseases of the Central Nervous System with Cerebrospinal Fluid-Based Next-Generation Sequencing

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