Diagnostic accuracy of VIDISCA-NGS in patients with suspected central nervous system infections

Diagnosis of an immunocompetent adult with acute headache and fever as Epstein-Barr virus encephalitis by mNGS of cerebrospinal fluid

Complicated case with fever or headache of unknown origin is currently one of the main challenges in clinical diagnosis. A retrospective analysis was conducted on a 27-year-old female patient hospitalized with headache and fever, and the pathogen species were ultimately determined by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF). The culture results of CSF showed no bacterial or fungal growth. CSF cytology showed a significant increase in nucleated cells. Pathogenic index (corresponded to human gamma herpesvirus 4) of the microorganism after correcting for human background was 12846.77 with a host index (human resource) of 27822.48 by mNGS of CSF. The patient improved through antiviral treatment with ganciclovir. Epstein-Barr virus encephalitis is rare in immunocompetent adults, which can easily cause misdiagnosis and should be paid attention to. mNGS of CSF has significant advantages in the diagnosis of Epstein-Barr virus encephalitis.

High-throughput sequencing technology facilitates the discovery of novel biomarkers for antiphospholipid syndrome

Antiphospholipid syndrome (APS) is characterized by arterial and venous thrombosis and/or morbid pregnancy, accompanied by persistent antiphospholipid antibody (aPL) positivity. However, due to the complex pathogenesis of APS and the large individual differences in the expression of aPL profiles of patients, the problem of APS diagnosis, prognosis judgment, and risk assessment may not be solved only from the antibody level. It is necessary to use new technologies and multiple dimensions to explore novel APS biomarkers. The application of next-generation sequencing (NGS) technology in diseases with a high incidence of somatic mutations, such as genetic diseases and tumors, has been very mature. Thus, we try to know the research and application progress of APS by NGS technology from genome, transcriptome, epigenome and other aspects. This review will describe the related research of NGS technology in APS and provide more reference for the deep understanding of APS-related screening markers and disease pathogenesis.

A risk score for identifying patients at a low risk of bacterial meningitis amongst adults with cerebrospinal fluid leucocytosis and a negative gram stain result: a derivation and validation study

OBJECTIVES

We aimed to derive and validate a risk score to differentiate patients with bacterial meningitis from those with viral meningitis or encephalitis amongst patients presenting with cerebrospinal fluid (CSF) leucocytosis and a negative Gram staining result.

METHODS

We included adults with bacterial and viral meningitis or encephalitis presenting with CSF leukocyte counts of >10 per mm³ and a negative Gram staining result from cohorts in Houston, Texas (2004-2019), and the Netherlands (2012-2021). Derivation and the first validation were performed in the American patients and further validation in the Dutch patients.

RESULTS

Derivation was performed in 109 American patients with bacterial meningitis (median age, 56 years; interquartile range [IQR], 46-66 years; 46% women) and 194 with viral meningitis or encephalitis (median age, 46 years; IQR, 33-60 years; 53% women). Serum leukocyte counts of >10.0 × 10⁹/L, CSF leukocyte counts of >2000 per mm³, granulocyte counts of >1180 per mm³, protein levels of >2.2 g/L, glucose levels of <1.9 mmol/L and fever on admission were included in the risk score, which was dichotomized into 'low risk' (0 present) and 'high risk' (>0 present). The first validation showed a sensitivity of 100% (95% CI, 96.6-100) and specificity of 34.0% (95% CI, 27.4-41.2). Further validation in 262 Dutch patients with bacterial meningitis (median age, 57 years; IQR 44-70 years; 45% women) and 68 with viral meningitis (median age, 34 years; IQR, 28-45 years; 60% women) showed a sensitivity of 99.6% (95% CI, 97.9-100) and specificity of 41.2% (95% CI, 29.4-53.7).

CONCLUSIONS

Our risk score may be able to rule out bacterial meningitis amongst patients presenting with CSF leucocytosis and a negative Gram staining result. However, it needs prospective testing prior to clinical implementation.

Bacterial ribosomal RNA detection in cerebrospinal fluid using a viromics approach

BACKGROUND

In patients with central nervous system (CNS) infections identification of the causative pathogen is important for treatment. Metagenomic next-generation sequencing techniques are increasingly being applied to identify causes of CNS infections, as they can detect any pathogen nucleic acid sequences present. Viromic techniques that enrich samples for virus particles prior to sequencing may simultaneously enrich ribosomes from bacterial pathogens, which are similar in size to small viruses.

METHODS

We studied the performance of a viromic library preparation technique (VIDISCA) combined with low-depth IonTorrent sequencing (median ~ 25,000 reads per sample) for detection of ribosomal RNA from common pathogens, analyzing 89 cerebrospinal fluid samples from patients with culture proven bacterial meningitis.

RESULTS

Sensitivity and specificity to Streptococcus pneumoniae (n = 24) before and after optimizing threshold parameters were 79% and 52%, then 88% and 90%. Corresponding values for Neisseria meningitidis (n = 22) were 73% and 93%, then 67% and 100%, Listeria monocytogenes (n = 24) 21% and 100%, then 27% and 100%, and Haemophilus influenzae (n = 18) 56% and 100%, then 71% and 100%. A higher total sequencing depth, no antibiotic treatment prior to lumbar puncture, increased disease severity, and higher c-reactive protein levels were associated with pathogen detection.

CONCLUSION

We provide proof of principle that a viromic approach can be used to correctly identify bacterial ribosomal RNA in patients with bacterial meningitis. Further work should focus on increasing assay sensitivity, especially for problematic species (e.g. L. monocytogenes), as well as profiling additional pathogens. The technique is most suited to research settings and examination of idiopathic cases, rather than an acute clinical setting.

Dynamics of the Enteric Virome in a Swine Herd Affected by Non-PCV2/PRRSV Postweaning Wasting Syndrome

A commercial pig farm with no history of porcine circovirus 2 (PCV2) or porcine reproductive and respiratory syndrome virus (PRRSV) repeatedly reported a significant reduction in body weight gain and wasting symptoms in approximately 20–30% of the pigs in the period between three and six weeks after weaning. As standard clinical interventions failed to tackle symptomatology, viral metagenomics were used to describe and monitor the enteric virome at birth, 3 weeks, 4 weeks, 6 weeks, and 9 weeks of age. The latter four sampling points were 7 days, 3 weeks, and 6 weeks post weaning, respectively. Fourteen distinct enteric viruses were identified within the herd, which all have previously been linked to enteric diseases. Here we show that wasting is associated with alterations in the enteric virome of the pigs, characterized by: (1) the presence of enterovirus G at 3 weeks of age, followed by a higher prevalence of the virus in wasting pigs at 6 weeks after weaning; (2) rotaviruses at 3 weeks of age; and (3) porcine sapovirus one week after weaning. However, the data do not provide a causal link between specific viral infections and the postweaning clinical problems on the farm. Together, our results offer evidence that disturbances in the enteric virome at the preweaning stage and early after weaning have a determining role in the development of intestinal barrier dysfunctions and nutrient uptake in the postweaning growth phase. Moreover, we show that the enteric viral load sharply increases in the week after weaning in both healthy and wasting pigs. This study is also the first to report the dynamics and co-infection of porcine rotavirus species and porcine astrovirus genetic lineages during the first 9 weeks of the life of domestic pigs.

Virus discovery in chronic inflammatory demyelinating polyneuropathy

The events triggering and/or sustaining the auto-immune response underlying chronic inflammatory demyelinating polyneuropathy (CIDP) are unknown. Similar to Guillain-Barré syndrome (GBS), a viral infection might play a role in CIDP. In this study, an virus detection method (VIDISCA-next generation sequencing) capable of detecting known and unknown viruses, was used to analyze the virome in serum of 47 CIDP patients at different time points of the disease and, when available, in cerebrospinal fluid (CSF) samples (N: 17). Serum samples of GBS patients (N:24) and healthy controls (N:114) were used for comparisons. In 5/47 (10.6%; 95% CI: 4-23) CIDP samples, 10/24 (42%; 95% CI: 22-63) GBS samples and 32/114 (28.1%; 95% CI: 20-37) healthy controls samples, anelloviruses were detected, generally regarded as a non-pathogenic species. Parvovirus B19 and GB virus C were found in two CIDP samples (4%). Parvovirus B19, HIV-1 and GB virus C were found in three GBS samples (13%). In 2/17 CIDP CSF samples, an anellovirus and polyomavirus were detected, probably due to contamination during lumbar puncture. No sequences of other viruses were detected in serum or CSF. A (persistent) viral infection sustaining the auto-immune response in CIDP seems therefore unlikely.