Tables

Table 1. Clinical demographicsSupplementary Table 1. Subjects not meeting inclusion criteria due to known bacterial or fungal infection Cerebrospinal fluid (CSF) total nucleated cells (TNC) and pathogen classification for the 14 cases excluded from analyses. Supplementary Table 2. Subject-Level Clinical DetailsClinical details that include cerebrospinal fluid white blood cells, duration of infection prior to lumbar puncture and treatment provided for the 68 subjects in study. The number of infectious disease tests include tests performed during a MGH hospitalization; infectious disease tests performed prior to an MGH admission were not included. Abbreviations: AIDS, Acquired immunodeficiency syndrome; ALL, Acute lymphocytic leukemia; ANCA, Antineutrophil cytoplasmic antibodies; CLL, Chronic Lymphocytic Leukemia, CNS, Central Nervous System; CVID, Combined Variable Immunodeficiency; DLBCL, Diffuse large B-cell Lymphoma; GAD-65, glutamic acid decarboxylase 65-kilodalton isoform; HIV, Human Immunodeficiency Virus; HSV, Herpes Simplex Virus; HHV-6, Human Herpesvirus 6; ID, Infectious Disease; anti-NMDA-R, anti- N-methyl-D-aspartate receptor; PML, Progressive Multifocal Leukoencephalopathy; WNV, West Nile Virus; VZV, Varicella Zoster Virus Supplementary Table 3. Clinical Followup for Subjects Listed as Unknown at DischargeChart review for subjects classified as unknown at hospital discharge. Supplementary Table 4. Pathogenic taxa of interest classificationsVirus reads identified by KrakenUniq were manually inspected in Geneious and excluded as "Lab contaminant" if the reads matched a known virus commonly used in the laboratory, or if they matched the virus from a different subject in this study. Table hosted on https://figshare.com/articles/dataset/Tables/13266506Supplementary Table 5. Sequencing Read Counts per Library - Computational StepsNumber of read counts per library identified at each step of computational processing. Table hosted on https://figshare.com/articles/dataset/Tables/13266506Supplementary Table 6. Sequencing Read Counts by Subject - Computational StepsNumber of read counts per subject identified at each step of computational processing. Table hosted on https://figshare.com/articles/dataset/Tables/13266506Supplementary Table 7. Enhanced sequencing metrics for positively identified taxaRPM of positively identified taxa in each cell (without computational depletion). Empty cells correspond to 0 counts. Table hosted on https://figshare.com/articles/dataset/Tables/13266506Supplementary Table 8. Detection of reads matching Blacklegged Tick Picorna-Like Virus (BTPLV)Reads identified by Kaiju were aligned to BTPLV in Geneious and manually inspected. Table hosted on https://figshare.com/articles/dataset/Tables/13266506

表 1. 临床人口统计学补充表 1. 因已知细菌或真菌感染不符合纳入标准而被排除的受试者列表。脑脊液（CSF）总核细胞（TNC）和病原体分类，涉及分析排除的 14 个案例。补充表 2. 受试者层级临床细节包括脑脊液白细胞计数、腰穿前的感染持续时间以及为 68 名研究受试者提供的治疗方案。感染性疾病检测次数包括在 MGH 医院住院期间进行的检测；不包括 MGH 入院前的感染性疾病检测。缩写：AIDS（获得性免疫缺陷综合征）；ALL（急性淋巴细胞白血病）；ANCA（抗中性粒细胞胞质抗体）；CLL（慢性淋巴细胞白血病）；CNS（中枢神经系统）；CVID（联合变量免疫缺陷）；DLBCL（弥漫大B细胞淋巴瘤）；GAD-65（谷氨酸脱羧酶 65-kilodalton 亚型）；HIV（人类免疫缺陷病毒）；HSV（单纯疱疹病毒）；HHV-6（人类疱疹病毒 6）；ID（感染性疾病）；anti-NMDA-R（抗 N-甲基-D-天冬氨酸受体）；PML（进行性多灶性白质脑病）；WNV（西尼罗病毒）；VZV（水痘-带状疱疹病毒）。补充表 3. 列为出院时未知状态受试者的临床随访对出院时被分类为“未知”状态的受试者进行病历审查。补充表 4. 有关病原体分类的兴趣分类由 KrakenUniq 识别的病毒读取结果在 Geneious 中手动检查，如果读取结果与实验室常用已知病毒匹配，或与本研究中不同受试者的病毒匹配，则将其排除为“实验室污染物”。表格托管于 https://figshare.com/articles/dataset/Tables/13266506。补充表 5. 每个库的测序读取计数 - 计算步骤在每个计算处理步骤中识别的每个库的读取计数。表格托管于 https://figshare.com/articles/dataset/Tables/13266506。补充表 6. 每个受试者的测序读取计数 - 计算步骤在每个计算处理步骤中识别的每个受试者的读取计数。表格托管于 https://figshare.com/articles/dataset/Tables/13266506。补充表 7. 针对阳性识别分类的增强测序指标每个细胞中阳性识别分类的 RPM 值（未经计算耗竭）。空单元格对应 0 计数。表格托管于 https://figshare.com/articles/dataset/Tables/13266506。补充表 8. 黑腿蜱 Picorna 类病毒（BTPLV）匹配读取的检测由 Kaiju 识别的读取结果在 Geneious 中与 BTPLV 对齐，并进行手动检查。表格托管于 https://figshare.com/articles/dataset/Tables/13266506。