Diagnosis of Streptococcus suis Meningoencephalitis with metagenomic next-generation sequencing of the cerebrospinal fluid: a case report with literature review

The use of metagenomics to enhance diagnosis of encephalitis

INTRODUCTION

Encephalitis has a broad etiology, including infectious and auto-immune causes. In infectious encephalitis, the breadth of causative organisms results in incomplete testing and low diagnostic yields.Metagenomics sequences all DNA and RNA allowing untargeted detection of all organisms in a single specimen; this is of particular use in diagnosis of encephalitis with a broad etiology.

AREAS COVERED

We review the literature and discuss metagenomics workflows, host depletion and pathogen enrichment methods, bioinformatics analysis and potential analysis of the host transcriptome to aid diagnosis. We discuss the clinical use of metagenomics for diagnosis of neurological infection including time to result, cost, quality assurance, patient cohorts in whom metagenomics adds the most value, recommended specimen types, limitations and review published cases in which metagenomics has been used to diagnose encephalitis.

EXPERT OPINION

There is good evidence for the utility of metagenomics to diagnose infection in encephalitis. Due to infections with rare, unexpected or novel pathogens, metagenomics adds most value to diagnosis in immunocompromised patients and the greatest diagnostic yield is in brain biopsies. Technical advances are needed to reduce the complexity, cost and time to result which will enable wider adoption in clinical laboratories and use as a first-line test.

Streptococcus suis meningoencephalitis diagnosed with metagenomic next-generation sequencing: A case report with literature review

Streptococcus suis is a pathogen of emerging zoonotic diseases and meningoencephalitis is the most frequent clinical symptom of S. suis infection in humans. Rapid diagnosis of S. suis meningoencephalitis is critical for the treatment of the disease. While the current routine microbiological tests including bacterial culture and gram staining are poorly sensitive, diagnosis of S. suis meningoencephalitis by metagenomic next-generation sequencing (mNGS) has been rarely reported. Here, we report a 52-year-old female pork food producer with a broken finger developed S. suis meningoencephalitis. After her admission, no pathogenic bacteria were detected through bacterial culture and Gram staining microscopy in the cerebrospinal fluid obtained via lumbar puncture. However, mNGS identified the presence of S. suis in the sample. mNGS is a promising diagnostic tool for rapid diagnosis of rare infectious diseases in the central nervous system.

Evaluation of metagenomic and pathogen-targeted next-generation sequencing for diagnosis of meningitis and encephalitis in adults: A multicenter prospective observational cohort study in China

BACKGROUND

Next-generation sequencing (NGS) might aid in the identification of causal pathogens. However, the optimal approaches applied to cerebrospinal fluid (CSF) for detection are unclear, and studies evaluating the application of different NGS workflows for the diagnosis of intracranial infections are limited.

METHODS

In this multicenter, prospective observational cohort study, we described the diagnostic efficacy of pathogen-targeted NGS (ptNGS) and metagenomic NGS (mNGS) compared to that of composite microbiologic assays, for infectious meningitis/encephalitis (M/E).

RESULTS

In total, 152 patients diagnosed with clinically suspected M/E at four tertiary hospitals were enrolled; ptNGS and mNGS were used in parallel for pathogen detection in CSF. Among the 89 patients who were diagnosed with definite infectious M/E, 57 and 39 patients had causal microbial detection via ptNGS and mNGS, respectively. The overall accuracy of ptNGS was 65.1%, with a positive percent agreement (PPA) of 64% and a negative percent agreement (NPA) of 66.7%; and the overall accuracy of mNGS was 47.4%, with a PPA of 43.8% and an NPA of 52.4% after discrepancy analysis. There was a significant difference in the detection efficiency between these two methods both for PPA (sensitivity) and overall accuracy for pathogen detection (P < 0.05).

CONCLUSIONS

NGS tests have provided new information in addition to conventional microbiologic tests. ptNGS seems to have superior performance over mNGS for common causative pathogen detection in CSF for infectious M/E.

Human Streptococcus suis Infections in Thailand: Epidemiology, Clinical Features, Genotypes, and Susceptibility

Streptococcus suis is a zoonotic pathogen causing substantial economic losses to the pig industry, as well as being a human health burden due to infections worldwide, especially in Southeast Asia. In Thailand, there was high cumulative incidence in humans during 1987-2021, mostly in males. At least five large outbreaks have been documented after the largest outbreak in China in 2005, which was related to the consumption of raw pork or dishes containing pig's blood. The major clinical features are sepsis or meningitis, with hearing loss a major complication of S. suis disease. Thai human S. suis isolates have shown diversity in serotypes and sequence types (STs), with serotype 2 and STs 1 and 104 being major genotypes. β-Lactam antibiotics can be used in empirical treatment for human S. suis infections; however, intermediate resistance to penicillin has been reported. Reducing S. suis incidence in Thailand requires a multidimensional approach, with combined efforts from the government and public health sectors through policy, regulations, education, and active surveillance.

A Streptococcus suis infection causing pneumonia in Indonesia: A case report

Streptococcus suis (S. suis) is a zoonotic pathogen that causes pneumonia, sepsis, endocarditis, and meningitis. S. suis is primarily found in the upper respiratory tract of pigs. To our knowledge, the first case of S. suis infection has resulted in pneumonia in Indonesia. A 40-year-old woman suffered from shortness of breath last month. The complaint worsened one week ago. She also complained of a productive cough with thick white phlegm. She has a history of late-stage cervical cancer. The patient's vital signs were normal, except for tachypnea. Vesicular breath sounds, no wheezing, and coarse lung crackles were discovered during a physical examination. A chest x-ray showed patchy airspace opacities and interstitial thickening throughout both lungs. The following results were obtained from routine laboratory leukocytosis. Gram stain of the sputum showed a few Gram-positive cocci, mostly in pairs. We confirmed this finding by performing the blood agar, and chocolate agar revealed small α-hemolytic and catalase-negative colonies. The strain was positive for penicillin and ceftriaxone in antimicrobial susceptibility testing. A combination of penicillin and ceftriaxone intravenous was utilized for definitive treatment. After completing a 14-day course of oral antibiotic medication, the patient was discharged. Her symptoms had subsided. This case should remind physicians about the possibility of cancer associated with S. suis infected patient and no clear history of exposure to pigs or other animals.

Diagnosis of an Acinetobacter pittii from a patient in China with a multiplex PCR-based targeted gene sequencing platform of the cerebrospinal fluid: A case report with literature review

BACKGROUND

The traditional diagnosis model has great challenges for the etiological diagnosis of the central nervous system (CNS) diseases with similar clinical manifestations, especially for the diagnosis of rare pathogens. It is very important to make rapid and accurate identification of pathogens for guiding clinical choices in administering countermeasures.

CASE SUMMARY

On August 22, 2020, a 49 years old Chinese male patient had a headache for two days, and then the computed tomography (CT) scan of the brain showed subarachnoid hemorrhage. Subsequently, he underwent twice craniotomy and about 3 weeks of hospitalization. Since September 20, the patient was in the local rehabilitation hospital for hyperbaric oxygen therapy for about three weeks. Then the patient developed acute purulent meningoencephalitis. In the absence of diagnosis of specific pathogenic bacteria, vancomycin (1 g every 12 hours), ceftazidime (2 g every 8 hours), mannitol dehydration (125 mL, every 8 hours), and sodium valproate (0.4 g tid) was used timely according to cerebrospinal fluid (CSF) examination and clinical manifestations. CSF smear and routine culture test were negative during hospitalization. We used the metagenomic next-generation sequencing (mNGS) analysis of CSF for quick and accurate diagnosis, which identified human herpesvirus type 4 (EBV), Corynebacterium corynebacterium, Achromobacter xylose oxidation, and Acinetobacter baumannii, But the mapping degree was not high. Then, we used the modified method-multiplex PCR-based targeted gene sequencing platform (ptNGS) to detect CSF samples and found that the sequences detected were Acinetobacter pittii (A. pittii) and Staphylococcus epidermidis. S. epidermidis might come from skin colonization during lumbar puncture, so it was excluded from the etiological diagnosis. Therefore, we highly suspected that A. pittii was the pathogen in this case. After about three weeks of hospitalization treatment, the patient's symptoms were relieved.

CONCLUSION

In conclusion, empirical medication before the identification of pathogens is very important. The ptNGS may be an effective method for the diagnosis of pathogens.

The Evolving Role of Next Generation Sequencing in Pediatric Neurosurgery: a Call for Action for Research, Clinical Practice, and Optimization of Care

NGS (Next-Generation Sequencing) is one of the most promising technologies that have truly revolutionized many aspects of clinical practice in recent years. It has been and is increasingly applied in many disciplines of medicine; however, it appears that pediatric neurosurgery despite its great potential has not truly embraced this new technology and is hesitant to employ it in its routine practice and guidelines. In this review, we briefly summarized the developments that lead to the establishment of NGS technology, reviewed the current applications and potentials of NGS in the disorders treated by pediatric neurosurgeons, and lastly discuss the steps we need to take to better harness NGS in pediatric neurosurgery.

Direct Metagenomic Diagnosis of Community-Acquired Meningitis: State of the Art

Current routine diagnosis of community-acquired meningitis (CAM) by multiplex real-time polymerase chain reaction (RT-PCR) is limited in the number of tested pathogens and their full characterisation, requiring additional in vitro investigations to disclose genotype and antimicrobial susceptibility. We reviewed 51 studies published through December 2021 reporting metagenomic next generation sequencing (mNGS) directly applied to the cerebrospinal fluid (CSF). This approach, potentially circumventing the above-mentioned limitations, indicated 1,248 investigated patients, and 617 patients dually investigated by routine diagnosis and mNGS, in whom 116 microbes were detected, including 50 by mNGS only, nine by routine methods only, and 57 by both routine methods and mNGS. Of 217 discordant CSF findings, 103 CSF samples were documented by mNGS only, 87 CSF samples by routine methods only, and 27 CSF samples in which the pathogen identified by mNGS was different than that found using routine methods. Overall, mNGS allowed for diagnosis and genomic surveillance of CAM causative pathogens in real-time, with a cost which is competitive with current routine multiplex RT-PCR. mNGS could be implemented at point-of-care (POC) laboratories as a part of routine investigations to improve the diagnosis and molecular epidemiology of CAM, particularly in the event of failure of routine assays.

Next-Generation Sequencing Technology Combined With Multiplex Polymerase Chain Reaction as a Powerful Detection and Semiquantitative Method for Herpes Simplex Virus Type 1 in Adult Encephalitis: A Case Report

Background

Traditional testing for specific microbes or categories of central nervous system (CNS) infectious diseases is often limited in sensitivity and timeliness. However, failure to initiate a timely etiological diagnosis and corresponding treatment in patients with neurologic infections contribute to poor outcomes.

Case Summary

A 58 year-old male presented acutely with fever, abnormal mental behavior, seizures and decreased consciousness. Brain magnetic resonance imaging (MRI) showed an abnormal FLAIR/T2 signal mainly in the left thalamus, temporal lobe, insular lobe, and bilateral hippocampus. To identify the pathogen, the cerebrospinal fluid (CSF) sample of the patient was used for metagenomic next-generation sequencing (mNGS) analysis and multiplex polymerase chain reaction (mPCR). The results showed 188 herpes simplex virus (HSV-1)-specific sequences. After acyclovir and foscarnet sodium treatment, the ratio of HSV-1/internal reference reads decreased from 813/493 to 695/1961, which coincided with clinical remission.

Conclusion

This study indicates that mNGS combined with mPCR may be an effective method for etiological diagnostic and dynamic clinical surveillance for HSV-1 encephalitis.

Sociocultural Factors Influencing Human Streptococcus suis Disease in Southeast Asia

The public health systems of Southeast Asian countries are financially challenged by a comparatively higher incidence of human S. suis infections than other geographical areas. Efforts to improve practices in production settings, including improved meat inspection regulations, prevention of the slaughtering of non-healthy pigs, and enhanced hygiene practices at processing facilities, along with improvements in the pork supply chain, all appear promising for reducing food cross-contamination with S. suis. However, opportunities for intervention at the societal level are also needed to effect changes, as population behaviors such as the consumption of raw pork, blood, and offal products are important contributors to the increased incidence of human S. suis disease in Southeast Asia. A plethora of factors are associated with the consumption of these high-risk dishes, including traditional culture and knowledge, shared beliefs, socio-economic level, and personal attitudes associated with gender and/or marital status. Education and intervention in behavioral attitudes that are sensible to cultural practices and traditions may provide additional means to reduce the burden of S. suis human disease in Southeast Asia.

Spinal canal infection caused by Streptococcus suis in human: a case report

Background

Streptococcus suis is an emerging zoonotic pathogen that mainly causes meningitis, sepsis, arthritis, endocarditis, and endophthalmitis in human. To the best of our knowledge, Spinal canal infection caused by Streptococcus suis has rarely been reported.

Case presentation

Here we report a case of spinal canal infection caused by Streptococcus suis in a 50-year-old male patient. The patient had a history of close contact with sick pigs days before disease onset. Initially he presented with headache and fever. After admission, the patient began to experience lower back pain, which led physicians to perform a lumber puncture. Meta-genomic next generation sequencing helped identify Streptococcus suis in the cerebrospinal fluid. MRI imaging indicated a spinal canal infection caused by Streptococcus suis.

Conclusions

Spinal canal infection is an uncommon disease of Streptococcus suis infection. This case report indicates that people presented with fever, headache and lower back pain should also be suspected as Streptococcus suis infection, especially for those who have had a history of sick pig contact.

Polymicrobial Anaerobic Meningitis Detected by Next-Generation Sequencing: Case Report and Review of the Literature

Background

Anaerobic meningitis is a severe central nervous system infection associated with significant neurological sequelae and high mortality. However, the precise detection of causative pathogen(s) remains difficult because anaerobic bacteria are difficult to culture. Next-generation sequencing is a technology that was developed recently and has been applied in many fields. To the best of our knowledge, the use of next-generation sequencing for cerebrospinal fluid analysis in the diagnosis of anaerobic meningitis has been rarely reported.

Case presentation

Here, we report a case of polymicrobial anaerobic meningitis diagnosed using next-generation sequencing of cerebrospinal fluid in a 16-year-old girl. Five species of anaerobic bacteria (Porphyromonas gingivalis, Prevotella enoeca, Campylobacter rectus, Fusobacterium uncleatum, and Actinomyces israelii) were detected by next-generation sequencing and treated with antibacterial agents (ceftriaxone, vancomycin, and metronidazole). The patient responded well to antibacterial treatment. Further inspection revealed bone destruction at the base of the skull, which further confirmed that these bacteria had originated from the oral cavity. One month later, the patient's condition improved significantly. At the same time, we performed a literature review on anaerobic meningitis using studies published in the last 20 years.

Conclusions

This case emphasizes the importance of applying metagenomic next-generation sequencing to clinch the clinical diagnosis for patients with central nervous system infection. Metagenomic next-generation sequencing has been reported to be an important diagnostic modality for identifying uncommon pathogens.

Human Encephalitis Complicated With Ocular Symptoms Associated With Pseudorabies Virus Infection: A Case Report

Pseudorabies virus (PRV) is an alpha herpesvirus found in many wild and domestic animals, and causes neurological diseases in humans. Several cases of PRV-induced human encephalitis accompanied with severe visual impairment have been reported. There is currently no effective treatment for severe visual impairment caused by PRV. We report a case of PRV encephalitis with severe visual impairment. The diagnosis and treatment experience of this patient is summarized to improve the awareness of clinicians. We present a 42-year-old man with PRV infection who was admitted due to intermittent fever for 5 days and unconsciousness for 1 day. He subsequently developed severe visual impairment during hospital stay. Empirical antiviral treatment with ganciclovir and sodium foscarnet was started on the day of admission and continued for > 50 days, which had significant treatment effect. Eye complications caused by PRV infection have been frequently reported in patients with PRV encephalitis. In this patient, based on the patient's condition, antiviral therapy was initiated on admission day, and according to the results of the next-generation sequencing of the cerebrospinal fluid, the duration of antiviral therapy was prolonged, which improved treatment efficacy and alleviated neurological symptoms and eye vision damage. To the best of our knowledge, this is the first report that describes partial restoration of acute vision loss associated with PRV infection after aggressive treatment. Our experience suggests that although prompt treatment cannot prevent the acute vision loss associated with PRV infection, timely anti-viral and anti-inflammatory treatment can alleviate ocular complications.

Laboratory diagnosis of bacterial meningitis by direct detection, serotyping and Next Generation Sequencing: How 10 years of testing in New York State has evolved to improve laboratory diagnosis and public health

Since 2005, the Wadsworth Center (WC) has provided molecular testing on cerebrospinal fluid (CSF) and whole blood specimens in close collaboration with epidemiologists in New York State and New York City. In this study, we analyzed 10 years of data to demonstrate the significant value of utilizing molecular methods to assess patient specimens for etiologic agents of bacterial meningitis. A comprehensive molecular testing algorithm to detect and serotype/serogroup bacterial agents known to cause bacterial meningitis (Neisseria meningitidis, Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus agalactiae) has evolved, and retrospective specimen testing has been essential for each improvement. Over a ten-year span from 2010 to 2019 the WC received 831 specimens from 634 patients with suspected bacterial meningitis. Real-time PCR was positive for at least one of the agents in 223 (27%) specimens from 183 patients (29%). Of the 223 positives, 146 (66%) were further characterized by real-time PCR into serogroup/serotype. Additionally, examination of 131 paired specimens of CSF and whole blood from the same patients found better detection in CSF, but whole blood is a useful alternative for diagnosis when CSF is not available. For specimens initially PCR-negative, 16S rDNA Sanger sequencing was requested by the submitter for 146 cases resulting in the identification of bacterial agents in an additional 24 (16%) specimens. In a retrospective study, Next Generation Sequencing (NGS) was evaluated for the detection of pathogens in 53 previously tested PCR-negative CSF specimens and identified bacteria in 14 (26%) specimens. This molecular testing algorithm has provided clinicians a diagnosis when culture is negative with the potential to guide therapy. It has also aided public health in determining when antibiotic prophylaxis was needed, augmented surveillance data to yield a fuller picture of community prevalence, and highlighted gaps in the spectrum of agents that cause bacterial meningitis.

Development of a recombinase polymerase amplification assay for rapid detection of Streptococcus suis type 2 in nasopharyngeal swab samples

Streptococcus suis serotype 2 (SS2), an emerging zoonotic pathogen, may induce severe infections and symptoms manifested as septicemia, meningitis and even death both in human and pigs. The aim of this article was to develop a new methodology as real-time recombinase polymerase amplification (RT-RPA) assay targeting cps2J gene for the detection of SS2 (or SS1/2). The sensitivity and reproducibility of RT-RPA results were evaluated and compared with a real-time quantitative PCR (RT-qPCR). The established RT-RPA reaction could be completed in 20 minutes with distinguishable specificity against the predominant S. suis infection serotypes of 3, 4, 5, 7, 9, 14, and 31. Lower detection limit for RT-RPA was 10² genomic DNA copies per reaction. The specimen performance of RT-RPA was tested in nasopharyngeal swab samples with the sensitivity and specificity as 97.5% and 100%, respectively. Thus, this RT-RPA method is a rapid and potential molecular diagnostic tool for SS2 detection.

Diagnosis of Enterococcus faecalis meningitis associated with long-term cerebrospinal fluid rhinorrhoea using metagenomics next-generation sequencing: a case report

Background

Enterococcus faecalis (E. faecalis) meningitis is a rare disease, and most of its occurrences are of post-operative origin. Its rapid diagnosis is critical for effective clinical management. Currently, the diagnosis is focused on cerebrospinal fluid (CSF) culture, but this is quite limited. By comparison, metagenomic next-generation sequencing (mNGS) can overcome the deficiencies of conventional diagnostic approaches. To our knowledge, mNGS analysis of the CSF in the diagnosis of E. faecalis meningitis has been not reported.

Case presentation

We report the case of E. faecalis meningitis in a 70-year-old female patient without a preceding history of head injury or surgery, but with an occult sphenoid sinus bone defect. Enterococcus faecalis meningitis was diagnosed using mNGS of CSF, and she recovered satisfactorily following treatment with appropriate antibiotics and surgical repair of the skull bone defect.

Conclusions

Non-post-traumatic or post-surgical E. faecalis meningitis can occur in the presence of occult defects in the cranium, and mNGS technology could be helpful in diagnosis in the absence of a positive CSF culture.

Detection of meningoencephalitis caused by Listeria monocytogenes with ischemic stroke-like onset using metagenomics next-generation sequencing: A case report

RATIONALE

Listeria monocytogenes (L. monocytogenes) is a compatible intracellular bacterial pathogen that can invade different mammalian cells and reach the central nervous system (CNS), leading to meningoencephalitis and brain abscesses. In the diagnosis of L. monocytogenes meningoencephalitis (LMM), conventional tests are often reported as negative due to antibiotic therapy or low bacterial content in cerebrospinal fluid. To date, prompt diagnosis and accurate treatment remain a challenge for patients with Listeria infections.

PATIENT CONCERNS

Here, we report a case of a 64-year-old male diagnosed with LMM by using metagenomics next-generation sequencing (mNGS).

DIAGNOSIS

LMM was confirmed by mNGS analysis of cerebrospinal fluid.

INTERVENTIONS

The patient was treated with piperacillin and sensitive antibiotics.

OUTCOMES

The patient could walk independently about 1 month after admission and was discharged from the hospital.

LESSONS

This case highlights the value of mNGS in the diagnosis of LMM and emphasizes the inadequate sensitivity of conventional diagnostic methods for Listeria infection.

Developing Diagnostic and Therapeutic Approaches to Bacterial Infections for a New Era: Implications of Globalization

In just a few months, the current coronavirus pandemic has exposed the need for a more global approach to human health. Indeed, the quick spread of infectious diseases and their unpredictable consequences, in terms of human lives and economic losses, will require a change in our strategy, both at the clinical and the research level. Ultimately, we should be ready to fight against infectious diseases affecting a huge number of people in different parts of the world. This new scenario will require rapid, inexpensive diagnostic systems, applicable anywhere in the world and, preferably, without the need for specialized personnel. Also, treatments for these diseases must be versatile, easily scalable, cheap, and easy to apply. All this will only be possible with joint support of the governments, which will have to make the requirements for the approval of new therapies more flexible. Meanwhile, the pharmaceutical sector must commit to prioritizing products of global interest over the most profitable ones. Extreme circumstances demand a vehement response, and any profit losses may well pay dividends going forward. Here, we summarize the developing technologies destined to face the current and future health challenges derived from infectious diseases and discuss which ones have more possibilities of being implemented.