Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Dec 14:11:596175.
doi: 10.3389/fmicb.2020.596175. eCollection 2020.

Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of External Ventricular and Lumbar Drainage-Associated Ventriculitis and Meningitis

Lingye Qian  1 , Yijun Shi  1 , Fangqiang Li  1 , Yufei Wang  1 , Miao Ma  1 , Yanfang Zhang  1 , Yang W Shao  2   3 , Guanghui Zheng  1 , Guojun Zhang  1
Affiliations

Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of External Ventricular and Lumbar Drainage-Associated Ventriculitis and Meningitis

Lingye Qian et al. Front Microbiol. .

Abstract

Metagenomic next-generation sequencing (mNGS) has become a widely used technology that can accurately detect individual pathogens. This prospective study was performed between February 2019 and September 2019 in one of the largest clinical neurosurgery centers in China. The study aimed to evaluate the performance of mNGS on cerebrospinal fluid (CSF) from neurosurgical patients for the diagnosis of external ventricular and lumbar drainage (EVD/LD)-associated ventriculitis and meningitis (VM). We collected CSF specimens from neurosurgical patients with EVD/LD for more than 24 h to perform conventional microbiological studies and mNGS analyses in a pairwise manner. We also investigated the usefulness of mNGS of CSF for the diagnosis of EVD/LD-associated VM. In total, 102 patients were enrolled in this study and divided into three groups, including confirmed VM (cVM) (39), suspected VM (sVM) (49), and non-VM (nVM) (14) groups. Of all the patients, mNGS detected 21 Gram-positive bacteria, 20 Gram-negative bacteria, and five fungi. The three primary bacteria detected were Staphylococcus epidermidis (9), Acinetobacter baumannii (5), and Staphylococcus aureus (3). The mNGS-positive coincidence rate of confirmed EVD/LD-associated VM was 61.54% (24/39), and the negative coincidence rate of the nVM group was 100% (14/14). Of 15 VM pathogens not identified by mNGS in the cVM group, eight were negative with mNGS and seven were inconsistent with the conventional microbiological identification results. In addition, mNGS identified pathogens in 22 cases that were negative using conventional methods; of them, 10 patients received a favorable clinical treatment; thus, showing the benefit of mNGS-guided therapy.

Keywords: EVD; LD; diagnosis; metagenomic next-generation sequencing (mNGS); ventriculitis and meningitis.

PubMed Disclaimer

Conflict of interest statement

YWS was employed by Nanjing Geneseeq Technology Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
(A) Schematic of the mNGS workflow. After collecting CSF samples, DNA was extracted using the TIANamp Magnetic DNA Kit (Tiangen). DNA libraries were prepared using the KAPA Hyper Prep kit (KAPA Biosystems) and fragmentation-end repair and a-tail-ligation PCR amplification. Libraries were quantified, pooled, and loaded onto the sequencer. Using an in-house-developed bioinformatics pipeline, high-quality sequencing data were obtained. Reads were aligned to the NCBI microorganism genome database for pathogen identification. Finally, we reported the results of mNGS according to the criteria. (B) Flowchart of study participants.
Figure 2
Figure 2
VM Diagnosed by mNGS. (A) Concurrent diagnosis by mNGS and conventional microbiological testing (24). (B) Diagnosis by mNGS only (22). (C) Diagnosis by conventional testing only (15). (D) The category of pathogens diagnosed by mNGS.
Figure 3
Figure 3
Clinical effect of the results of mNGS (10 of 22 cases diagnosed by mNGS only).
See this image and copyright information in PMC

References

    1. Beer R., Lackner P., Pfausler B., Schmutzhard E. (2008). Nosocomial ventriculitis and meningitis in neurocritical care patients. J. Neurol. 255, 1617–1624. 10.1007/s00415-008-0059-8 - DOI - PubMed
    1. Blauwkamp T. A., Thair S., Rosen M. J., Blair L., Lindner M. S., Vilfan I. D., et al. (2019). Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat. Microbiol. 4, 663–674. 10.1038/s41564-018-0349-6 - DOI - PubMed
    1. Brain Trauma Foundation American Association of Neurological Surgeons Congress of Neurological Surgeons Joint Section on Neurotrauma and Critical Care AANS/CN. Bratton S. L., Chestnut R. M., et al. (2007). Guidelines for the management of severe traumatic brain injury. IV. infection prophylaxis. J. Neurotrauma 24 (Suppl. 1), S26–31. 10.1089/neu.2007.999 - DOI - PubMed
    1. Carney N., Totten A. M., O'Reilly C., Ullman J. S., Hawryluk G. W., Bell M. J., et al. (2017). Guidelines for the management of severe traumatic brain injury, fourth edition. Neurosurgery 80, 6–15. 10.1227/NEU.0000000000001432 - DOI - PubMed
    1. Chiu C. Y., Miller S. A. (2019). Clinical metagenomics. Nat. Rev. Genet. 20, 341–355. 10.1038/s41576-019-0113-7 - DOI - PMC - PubMed