Shotgun metagenomic sequencing can detect nucleic acids from bacteria, fungi, viruses, and/or parasites in clinical specimens; however, little data exist to guide its optimal application to clinical practice. We retrospectively reviewed results of shotgun metagenomic sequencing testing requested on cerebrospinal fluid samples submitted to an outside reference laboratory from December 2017 through December 2019. Of the 53 samples from Mayo Clinic patients, 47 were requested by neurologists, with infectious diseases consultation in 23 cases. The majority of patients presented with difficult-to-diagnose subacute or chronic conditions. Positive results were reported for 9 (17%) Mayo Clinic patient samples, with 6 interpreted as likely contamination. Potential pathogens reported included bunyavirus, human herpesvirus 7, and enterovirus D-68, ultimately impacting care in two cases. Twenty-seven additional samples were submitted from Mayo Clinic Laboratories reference clients, with positive results reported for three (11%): two with potential pathogens (West Nile virus and Toxoplasma gondii) and one with Streptococcus species with other bacteria below the reporting threshold (considered to represent contamination). Of 68 negative results, 10 included comments on decreased sensitivity due to high DNA background (n = 5), high RNA background (n = 1), insufficient RNA read depth (n = 3), or quality control (QC) failure with an external RNA control (n = 1). The overall positive-result rate was 15% (12/80), with 58% (7/12) of these interpreted as being inconsistent with the patient’s clinical presentation. Overall, potential pathogens were found in a low percentage of cases, and positive results were often of unclear clinical significance. Testing was commonly employed in cases of diagnostic uncertainty and when immunotherapy was being considered.

中文翻译：

---

在美国三级医疗医学中心对脑脊液的Shot弹枪基因组测序测试的临床实用性进行回顾性回顾。

gun弹枪宏基因组测序可以检测来自临床标本中细菌，真菌，病毒和/或寄生虫的核酸；然而，几乎没有数据可指导其在临床实践中的最佳应用。我们回顾性研究了2017年12月至2019年12月提交给外部参考实验室的脑脊液样本的gun弹枪宏基因组测序测试的结果。在梅奥诊所的53份样本中，有47份是神经科医生提出的，其中23例接受了传染病咨询。大多数患者表现出难以诊断的亚急性​​或慢性病。据报道9例（17％）Mayo Clinic患者样品呈阳性结果，其中6例可能被污染。报告的潜在病原体包括布尼亚病毒，人疱疹病毒7和肠病毒D-68，最终在两个案例中影响护理。从Mayo Clinic Laboratories参考客户提交了27个额外的样本，其中三个（11％）报告呈阳性结果：两个具有潜在病原体（西尼罗河病毒和弓形虫）和一种链球菌属细菌，其他细菌低于报告阈值（被认为代表污染）。在68个阴性结果中，有10个评论包括由于高DNA背景（n = 5），高RNA背景（n = 1），RNA读取深度不足（n = 3）或质量控制（QC）失败而导致灵敏度降低的问题。外部RNA对照（ñ= 1）。总体阳性结果率为15％（12/80），其中58％（7/12）被解释为与患者的临床表现不一致。总体而言，在低百分比的病例中发现了潜在的病原体，阳性结果通常没有明确的临床意义。在诊断不确定的情况下以及考虑进行免疫治疗时，通常采用测试。