A Metagenomics – Based Diagnostic Approach for Central Nervous System Infections in Hospital Acute Care Setting

Abstract

24The etiology of central nervous system (CNS) infections such as meningitis and 25 encephalitis remains unknown in a large proportion of cases partly because the diversity of 26 pathogens that may cause CNS infections greatly outnumber available test methods. Here we 27 present a metagenomic next generation sequencing (mNGS) based approach for broad-range 28 detection of pathogens associated with CNS infections, which is suitable for application in the 29 acute care hospital setting. Using an Illumina MiSeq benchtop sequencer and the IDseq pipeline 30 for identifying pathogens in metagenomic sequence data, we show that the analytical sensitivity 31 of mNGS to detect pathogens is comparable to that of PCR in simulated cerebrospinal fluid 32 (CSF) specimens. We then applied this method for pathogen detection in 74 CSF specimens 33 from patients with suspected CNS infections that were previously tested by culture and/or PCR. 34Diagnostic accuracy, sensitivity and specificity of mNGS approach with reference to 35 conventional methods were all 95%. Furthermore, confirmatory testing on specimens that gave 36 discrepant results were mostly in favor of the mNGS assay. The clinical application of mNGS 37 holds promise to benefit patients with CNS infections of unknown etiology. 38 39 40 41 42 43 44 45 46 47 Central nervous system (CNS) infections such as meningitis and encephalitis are 48 potentially life threatening diseases caused by a myriad of infectious pathogens. Besides high 49 rates of mortality, meningitis and encephalitis are major causes of morbidity, and permanent 50 disabilities such as brain damage, hearing loss, and learning disabilities can result from CNS 51 infections (1-5). A specific etiologic agent cannot be identified in 15-60% of cases of meningitis 52 and up to 70% of encephalitis (6, 7). Clinical management of meningitis and encephalitis is 53 highly dependent on early and rapid detection of underlying causes of the disease, so that 54 appropriate antimicrobial or anti-viral therapy can be instituted in a timely manner. Specific 55 diagnosis is also important to avoid unnecessary treatment and hospitalization of patients with 56 self-limiting forms of viral meningitis to minimize potential harm and unnecessary cost to 57 patients (6).58 Current diagnostic test methods for CNS infections include CSF Gram staining, CSF cell 59 count, glucose, and protein measurements and biomarkers such as procalcitonin (PCT) and 60 lactate. These tests are generally performed to distinguish between bacterial versus viral 61 infections, and they are not specific for any causative pathogens. Bacteriological culture or PCR 62 testing to detect specific pathogens in cerebrospinal fluid (CSF) are currently the most important 63 methods for the diagnosis of CNS infections. However, a large number pathogens known to 64 cause meningitis and encephalitis cannot be routinely cultured, and most molecular tests are 65 targeted to common pathogens only. A broad-range, unbiased method to identify all pathogens in 66 CSF would m...

IDseq – An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring

“…to obtain relevant microbial information from any sample type (blood, CSF, respiratory fluids, tissue, etc.) [1,[49][50][51]. There are many challenges for data interpretation that are common across mNGS applications, such as impact of PCR amplification on samples with low amounts of input RNA, background contamination, and genomic similarity between short regions of related organisms.…”

Metode Deteksi Molekuler Berbasis Genomik Dan Diagnostik Akurasinya Dalam Pengembangan Diagnostik Klinik Di Indonesia

“…Konfirmasi lanjutan menggunakan sequencig seperti NGS atau DNA microarray dapat menjadi pilihan dengan beberapa target dan sampel. Pendeteksian infeksi pada cairan cerebrospinal dilakukan oleh Hasan et al (2020) mampu mengungkap berbagai macam bakteri dan virus dengan tingkat akurasi yang tinggi dan hasil yang sama dengan Cao et al (2018) menggunakan DNA microarray (Tabel 3). Secara pemeriksaan rutin metode-metode tersebut tergolong sangat mewah, namun kedepannya diperkirakan akan lebih dapat diterima dari segi biaya.…”

Fun(gi)omics: Advanced and Diverse Technologies to Explore Emerging Fungal Pathogens and Define Mechanisms of Antifungal Resistance

“…Furthermore, the adoption of shotgun metagenomic technology for disease diagnostics can permit unbiased sequencing of polymicrobial communities isolated directly from clinical samples, with powerful prediction capabilities of antimicrobial resistance, virulent gene identification, and high resolution if performing molecular typing ( 48 ). For instance, a metagenomic diagnostic-based approach of fungal infections of the central nervous system (CNS), such as C. gattii , would provide relief in medical settings with limited diagnostic capabilities for the high diversity of etiological agents capable of CNS infections ( 49 ).…”