DOI: 10.5061/dryad.k98sf7mfq
title: Using cerebrospinal fluid nanopore sequencing assay to diagnose tuberculous meningitis: a retrospective cohort study in China

description: This study aimed to evaluate the efficiency of nanopore sequencing for the
 early diagnosis of tuberculous meningitis (TBM) using cerebrospinal fluid
 and compared it with acid-fast bacilli (AFB) smear, mycobacterial growth
 indicator tube (MGIT) culture, and Xpert MTB/Rifampicin (RIF). We
 enrolled 64 adult patients with presumptive TBM admitted to our hospital
 from August 2021 to August 2023. We calculated the sensitivity,
 specificity, positive predictive value (PPV), and negative predictive
 value (NPV) of AFB smear, culture, Xpert MTB/RIF, and nanopore sequencing
 to evaluate their diagnostic efficacy compared with a composite reference
 standard for TBM. Among these 64 patients, all tested negative
 for TBM by AFB smear. The sensitivity, specificity, PPV, and NPV were
 11.11%, 100%, 100%, and 32.2% for culture, 13.33%, 100%, 100%, and 2.76%
 for Xpert MTB/RIF, and 77.78%, 100%, 100% and 65.52% for nanopore
 sequencing, respectively. The diagnostic accuracy of the nanopore
 sequencing test was significantly higher than that of conventional testing
 methods used to detect TBM.
description: We retrospectively screened patients with clinically presumptive
 TBM admitted to the Tuberculosis Diagnosis and Treatment Center of
 Zhejiang Chinese and Western Medicine Integrated Hospital from August 2021
 to August 2023. The inclusion criteria were as follows: (1) patients
 aged 18–80 years; (2) those presenting with the symptoms of presumptive
 TBM (such as headache, high fever, nausea and vomiting, or altered
 consciousness) or signs of neurological disease; (3) those who completed
 lumbar puncture; and (4) those whose CSF samples were used for all four
 tests (AFB smear, culture, Xpert MTB/RIF, and nanopore sequencing).
 Patients whose CSF samples were not obtained for relevant testing and
 those lost to follow-up were excluded.
description: # **Using cerebrospinal fluid nanopore sequencing assay to diagnose
 tuberculous meningitis: a retrospective cohort study in China**
 [https://doi.org/10.5061/dryad.k98sf7mfq](https://doi.org/10.5061/dryad.k98sf7mfq) ## Description of the data and file structure After screening 73 patients, 9 with incomplete data were excluded and 64 patients with complete clinical data were enrolled. The average age of the participants was 47 ± 19 years, and 39 (60.94%) were male. All patients tested negative for blood HIV antibody tests, whereas 53 (82.81%) patients tested positive for T-SPOT.TB assay. Based on international standards, 45 patients were diagnosed with TBM, including 18 definite and 27 probable cases. The remaining 19 patients were not diagnosed with TBM, including 8 possible and 11 non-TBM cases. ### Sheet 1 Shows the medical records of all the enrolled patients that we collected. The specifics are: * column A represents gender (male 1, female 0) * column B represents neurological symptoms (presence of central nervous system symptoms 1, asymptomatic 0) * column C represents the presence of impaired consciousness (presence of impaired consciousness 1, absence of impaired consciousness 0) * column D represents the condition of generalized discomfort (presence of generalized tuberculosis symptoms is 1, absence of symptoms is 0) * column E represents the result of TSPOT (positive is 1, negative is 0) * column F represents the condition of somatoform disorders (presence of symptoms is 1, absence of symptoms is 0) * column G represents the condition of cranial nerve disorders (presence of neurological impairment manifestations is 1, absence of neurological impairment manifestations is 0) * column H represents the appearance of the cerebrospinal fluid (turbidity is 1, clarification is 0) * column I represents the number of cells in the cerebrospinal fluid (each cell indicates a specific cell value, 10*6/L) * column J represents the cerebrospinal fluid lymphocyte ratio (greater than 50% is 1, less than 50% is 0) * column K represents the cerebrospinal fluid glucose content (specific value is recorded in each cell, mmol/L) * column L represents the cerebrospinal fluid chloride content (specific value is recorded in each cell, mmol/L) * column M represents the cerebrospinal fluid protein content (specific value is recorded in each cell, mg/L) * column N represents the cerebrospinal fluid ADA content (specific value is recorded in each cell, U/L) * column O represents the presence of hydrocephalus on cranial MRI (presence is 1, absence is 0) * column P represents the presence of basilar membrane thickening on cranial MRI (presence is 1, absence is 0) * column Q represents the presence of tuberculoma on cranial MRI (presence is 1, absence is 0) * column R represents the presence of cerebral infarction on cranial MRI (presence is 1, absence is 0) * column S represents whether the chest CT image is consistent with tuberculosis (presence is 1, absence is 0) * column T represents whether the chest CT image is consistent with hematogenous disseminated tuberculosis (presence is 1, absence is 0) * column U represents whether *Mycobacterium tuberculosis* was detected by sputum bacteriologic testing (1 for clear tuberculosis, 0 for no bacteriologic basis for tuberculosis) * column V represents the results of cerebrospinal fluid mNGS testing (1 for Mycobacterium tuberculosis, 0 for other bacteria listed as specific bacterial species, and 0 for no pathogenic bacteria detected) * column W represents the number of pathogenic bacterial sequences (with specific values listed in each cell) * column X represents the results of the cerebrospinal fluid Xper test results (1 for positive, 0 for negative) * column Y represents cerebrospinal AFB smear test results (1 for positive, 0 for negative) * column Z represents cerebrospinal fluid *Mycobacterium tuberculosis* culture results (1 for positive, 0 for negative) * column AA represents the final clinical diagnosis (each cell lists the name of the specific meningitis disease, with no CNS lesions indicated by null) * column AB categorizes the diagnosis (1 Confirmed TBM, 2 Possible TBM, 3 Essentially impossible TBM, 4 Ruled out TBM) * column AC stands for eventual tuberculous meningitis (1 for TBM, 0 for non-TBM). ### Sheet 2 In Excel, we used the dataset from sheet 2 for our statistics. The specifics are: * column A represents sex, male recorded as 1 * column B represents TSPOT results, positive recorded as 1 * columns C and D represent nanopore test results, *Mycobacterium tuberculosis* detected recorded as 1 * column E represents the number of *Mycobacterium tuberculosis* sequences * column F represents Xpert test results, positive recorded as 1 * column G represents AFB smear test results, positive recorded as 1 * column H represents MTB culture test results, positive recorded as 1 * column I represents the final clinical diagnostic results, the diagnosis of tuberculous meningitis was recorded as 1 ## Sharing/Access information NA ## Code/Software NA