Dataset Information

Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Neurocysticercosis.

ABSTRACT: Background: Neurocysticercosis (NCC) is the most common helminthic infection of the central nervous system (CNS). The diagnosis of NCC is sometimes challenging due to its heterogenous clinical manifestations and the variable sensitivity and specificity of neuroimaging and serological tests. Methods: Next-generation sequencing (NGS) of cerebrospinal fluid (CSF) was used to detect pathogens in patients with clinically suspected CNS infections. A series of patients diagnosed with NCC is reviewed here. Results: Using NGS of CSF, four patients were diagnosed with NCC. The reads corresponding to Taenia solium ranged from 478 to 117,362, with genomic coverage of 0.0564-11.15%. Reads corresponding to T. solium were not found in non-template controls and far exceeded those of the background microorganisms in patients with NCC, facilitating the interpretation of the NGS results. Conclusions: This case series demonstrates that NGS of CSF is promising in the diagnosis of NCC in difficult to diagnose cases. Larger studies are needed in the future.

SUBMITTER: Fan S

PROVIDER: S-EPMC6018529 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Neurocysticercosis.

Fan Siyuan S Qiao Xiaodong X Liu Lei L Wu Honglong H Zhou Jiali J Sun Ruixue R Chen Qing Q Huang Yan Y Mao Chenhui C Yuan Jing J Lu Qiang Q Ge Ying Y Li Yongjun Y Ren Haitao H Wang Jiawei J Cui Liying L Zhao Weili W Guan Hongzhi H

Frontiers in neurology 20180619

<b>Background:</b> Neurocysticercosis (NCC) is the most common helminthic infection of the central nervous system (CNS). The diagnosis of NCC is sometimes challenging due to its heterogenous clinical manifestations and the variable sensitivity and specificity of neuroimaging and serological tests. <b>Methods:</b> Next-generation sequencing (NGS) of cerebrospinal fluid (CSF) was used to detect pathogens in patients with clinically suspected CNS infections. A series of patients diagnosed with NCC ...[more]

PMID: 29971042

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Project description:BackgroundRecently, with the rapid progress of metagenomic next-generation sequencing (mNGS), inconsistency between mNGS results and clinical diagnoses has become more common. There is currently no reasonable explanation for this, and the interpretation of mNGS reports still needs to be standardised.MethodsA retrospective analysis was conducted on 47 inpatients with suspected central nervous system (CNS) infections, and clinical data were recorded. The final diagnosis was determined by an expert group based on the patient's clinical manifestation, laboratory examination, and response to treatment. mNGS results were compared with the final diagnosis, and any inconsistencies that occurred were investigated. Finally, the credibility of mNGS results was evaluated using the integral approach, which consists of three parts: typical clinical features, positive results with the traditional method, and cerebrospinal fluid cells ≥ 100 (× 106/L) or protein ≥ 500 mg/L, with one point for each item.ResultsForty-one patients with suspected CNS infection were assigned to infected (ID, 31/41, 75.61%) and non-infected groups (NID, 10/41, 24.39%) after assessment by a panel of experts according to the composite diagnostic criteria. For mNGS-positive results, 20 of the 24 pathogens were regarded as contaminants when the final score was ≤ 1. The remaining 11 pathogens detected by mNGS were all true positives, which was consistent with the clinical diagnosis when the score was ≥ 2. For mNGS negative results, when the score was ≥ 2, the likelihood of infection may be greater than when the score is ≤ 1.ConclusionThe integral method is effective for evaluating mNGS results. Regardless of whether the mNGS result was positive or negative, the possibility of infection was greater when the score was ≥ 2. A negative mNGS result does not necessarily indicate that the patient was not clinically infected, and, therefore, clinical features are more important.

Project description:BackgroundThe cerebrospinal fluid (CSF) culture is a widely used method for the diagnosis of meningitis, but its detection sensitivity is low. Several new methods have been developed for pathogen detection, including metagenomic next-generation sequencing (mNGS) and pathogen-targeted NGS (ptNGS). In this study, we aimed to evaluate the performance of ptNGS in pathogen detection in CSF.MethodsCSF specimens were acquired from 38 patients with meningitis who were diagnosed at Xuanwu Hospital, Capital Medical University between October 2020 and February 2021. DNA was extracted from the CSF samples, and pathogens were identified using both ptNGS and mNGS. SPSS 22.0 software was used to compare the pathogen detection performance of ptNGS and mNGS in CSF.ResultsAmong the 38 patients with meningitis, 14 had a non-infectious disease (NID) and 24 had an infectious disease (ID). Of the 38 samples, both ptNGS and mNGS detected 9 (23.7%) positive samples, and 12 (31.6%) negative samples. Thirteen (34.2%) samples were detected to be positive by ptNGS only, and 4 (10.5%) were detected to be positive by mNGS only. The positivity rate detected by ptNGS for the ID group was higher than that detected by mNGS (P=0.080), and the positivity rates detected by ptNGS and mNGS for the NID group were comparable. The positive predictive value (PPV) and negative predictive value (NPV) of diagnosing an ID by ptNGS were 77.3% and 56.3%, respectively. While, the PPV and NPV of diagnosing an ID by mNGS were 76.9% and 44.0%, respectively. ptNGS increased the sensitivity rate by approximately 70%. The sensitivity rate of ptNGS was higher than that of mNGS (70.8% vs. 41.7%), while the specificity rate of mNGS was higher than that of ptNGS (78.6% vs. 64.3%). Additionally, ptNGS required a shorter time for pathogen diagnosis (15 vs. 24 hrs) and had lower costs than mNGS.ConclusionsptNGS has a number of advantages over mNGS, including its sensitivity, timeliness, and economy, all factors that are important considerations in clinical use.

Project description:PurposeThe application of metagenomic next-generation sequencing (mNGS) in the diagnosis of tuberculous meningitis (TBM) remains poorly characterized. Here, we retrospectively analyzed data from patients with TBM who had taken both mNGS and conventional tests including culture of Mycobacterium tuberculosis (MTB), polymerase chain reaction (PCR) and acid-fast bacillus (AFB) stain, and the sensitivity and specificity of these methods were compared.MethodsWe retrospectively recruited TBM patients admitted to the hospital between December 2015 and October 2018. The first collection of cerebrospinal fluid (CSF) samples underwent both mNGS and conventional tests. In addition, patients with bacterial/cryptococcal meningitis or viral meningoencephalitis were mNGS positive controls, and a patient with auto-immune encephalitis was an mNGS negative control.ResultsTwenty three TBM patients were classified as 12 definite and 11 clinical diagnoses, which were based on clinical manifestations, pathogen evidence, CSF parameters, brain imaging, and treatment response. The mNGS method identified sequences of Mycobacterium tuberculosis complex (MBTC) from 18 samples (18/23, 78.26%). In patients with definite TBM, the sensitivity of mNGS, AFB, PCR, and culture to detect MTB in the first CSF samples were 66.67, 33.33, 25, and 8.33%, respectively. The specificity of each method was 100%. Among the four negative mNGS cases (4/23, 17.39%), three turned out positive by repeated AFB stain. The agreement of mNGS with the total of conventional methods was 44.44% (8/18). Combination of mNGS and conventional methods increased the detection rate to 95.65%. One patient was diagnosed as complex of TBM and cryptococcal meningitis, in which AFB stain and cryptococcal antigen enzyme immunoassay were positive and the DNA of Cryptococcus neoformans was detected by mNGS.ConclusionOur study indicates that mNGS is an alternative method to detect the presence of mycobacterial DNA in CSF samples from patients with TBM and deserves to be applied as a front-line CSF test.

Dataset Information

Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Neurocysticercosis.

Publications

Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Neurocysticercosis.

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