Metagenomic sequencing improves detection of uncommon pathogens in CNS infections

A groundbreaking seven-year research reveals how metagenomic sequencing presents a extra correct, complete method to diagnosing troublesome CNS infections—recognizing pathogens that conventional exams typically overlook.

Research: Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections. Picture Credit score: Kateryna Kon / Shutterstock

In a current research revealed within the journal Nature Medicine, researchers analyzed the seven-year efficiency of metagenomic next-generation sequencing (mNGS) testing to diagnose central nervous system (CNS) infections. Encephalitis, meningitis, and myelitis related to CNS infections could cause extreme, life-threatening sicknesses. Delays of their prognosis and remedy have been linked to larger morbidity and mortality. Medical mNGS has emerged as a complete method for diagnosing infectious illnesses, permitting for the detection of numerous microbes with out concentrating on a selected pathogen prematurely. This hypothesis-free and agnostic technique might be helpful in instances of CNS infections for which invasive strategies like mind biopsy and restricted cerebrospinal fluid (CSF) samples are difficult to acquire.

The College of California, San Francisco (UCSF) medical mNGS take a look at was developed as a validated DNA/RNA metagenomic sequencing assay in 2016. Earlier research have proven that mNGS can improve the diagnostic yield, offering actionable data in instances of suspected CNS infections.

a,b, Distribution of exams ordered by state (a) and internationally (b). A complete of 4,075 mNGS exams had been carried out from CSF samples collected from the US, California being probably the most frequent state of origin (n = 2,420 samples). Reference laboratories comparable to Related Regional and College Pathologists, Inc., Labcorp and Mayo Clinic (n = 722) obtain exams from a number of states, so the situation of particular person samples can’t be tracked and thus are excluded from the determine. 14.8% (n = 715) of samples had been despatched from pediatric hospitals. c, Variety of exams carried out by yr and variety of constructive outcomes, excluding outcomes that had been reported doable or seemingly contaminants. *Information proven are samples analyzed as much as April 2023.

Research Overview and Key Findings

Within the current research, researchers assessed the medical applicability of mNGS testing over seven years. In complete, the medical microbiology laboratory at UCSF carried out 4,828 mNGS exams between June 2016 and April 2023. Over 84% of exams had been carried out for sufferers from 46 states in the US. Round 56% of sufferers had been males, and 24.2% had been kids beneath 18.

The median turnaround occasions for non-UCSF and UCSF sufferers had been 11.4 and eight.2 days from pattern assortment to outcome and three.8 and three.6 days from pattern processing to outcome, respectively. Roughly 10.6% of samples contained not less than one environmental or commensal organism and had been reported as contaminants. Contaminants had been extra frequent in non-UCSF samples, probably as a consequence of variations in pattern dealing with, acquisition, and transport strategies.

After excluding samples with contaminants, 14.4% of samples had been constructive for a pathogen. The typical annual positivity fee was estimated at 16%, with UCSF samples exhibiting the next fee (16.2%) than non-UCSF samples (13.9%), which can be attributed to the extra frequent reporting of subthreshold leads to UCSF samples. Pathogens detected at subthreshold ranges included West Nile virus, Powassan virus, Balamuthia mandrillaris, Mycobacterium tuberculosis, Coccidioides sp., and Histoplasma capsulatum. Notably, most subthreshold detections had been later confirmed by orthogonal testing. In complete, 797 organisms had been detected, with DNA viruses being probably the most generally recognized, adopted by RNA viruses, micro organism, fungi, and parasites.

Probably the most often detected RNA viruses had been human immunodeficiency virus, arboviruses, and enteroviruses. Unusual arboviruses, comparable to La Crosse virus, Potosi virus, St. Louis encephalitis virus, and Cache Valley virus, had been additionally detected. Detected parasites included Naegleria fowleri, Angiostrongylus cantonensis, B. mandrillaris, and Toxoplasma gondii. Fungal pathogens included Coccidioides sp., Cryptococcus sp., Fusarium sp., and Histoplasma capsulatum.

Evaluation of Medical Information

Subsequent, the researchers analyzed laboratory and medical metadata from a subset of UCSF affected person samples. This cohort included 1,164 samples from 1,053 people; 55% had been males, 15.2% had been kids, and 35.8% had been immunocompromised. Additional, 87.7% of the cohort had been hospitalized for a median of 12 days; 38.7% required intensive care, and 10.2% died inside two months. This cohort included 18% of instances with CNS an infection, 37.1% with autoimmune illnesses or different non-infectious circumstances, 0.1% with prion illness, and 44.8% with unknown etiology.

Immunocompromised sufferers had the next mNGS positivity fee (16.7%); it was additionally larger in sufferers with meningoencephalitis and meningitis. General, 180 instances had been constructive for not less than one microorganism detected by mNGS testing; amongst these, 227 organisms had been detected. Of those detections, 135 had been true positives, 85 had been incidental detections, and 4 had been false positives. Thirty-five detections had been categorized as subthreshold.

Notably, mNGS testing confirmed decrease sensitivity in detecting fungal pathogens, as 10 fungal infections missed by mNGS testing had been recognized by antigen testing, tradition, or each. The efficiency metrics for mNGS testing in diagnosing CNS infections had been 63.1% sensitivity, 92.9% accuracy, 99.6% specificity, 92.3% unfavorable predictive worth, and 97.1% constructive predictive worth.

Furthermore, the diagnostic yield of mNGS was larger (63.1%) than different strategies, together with CSF direct detection (CSF-DD), non-CSF-DD, and oblique serologic testing. Notably, mNGS testing recognized 60 infections missed by CSF-DD strategies, whereas CSF-DD strategies detected 26 infections that mNGS missed.

Conclusions

In sum, mNGS testing demonstrated excessive sensitivity for detecting pathogens in a cohort with extreme and diagnostically difficult CNS infections. It was the first or sole diagnostic instrument for 30.4% of infections, able to figuring out numerous pathogens, together with rising and surprising microbes, which are sometimes onerous to detect utilizing typical strategies. Whereas the sensitivity of 63.1% signifies that mNGS mustn’t change microbiological testing, this research suggests a number of use instances for mNGS testing: 1) detection of unculturable organisms, 2) identification of uncommon or surprising infections, 3) broad viral diagnostics, and 4) outbreak investigations.

Additional research are wanted to evaluate the cost-effectiveness and total medical influence of mNGS testing.