Use of staged molecular analysis to determine causes of unexplained central nervous system infections

Multiplex detection of meningitis and encephalitis pathogens: A study from laboratory to clinic

Introduction

Infectious meningitis and encephalitis (ME) are life-threatening conditions are caused by various pathogens. Conventional laboratory tests with low sensitivity and specificity cannot help with early diagnosis.

Methods

A prospective study using the novel multiplex PCR detection for 18 pathogens of ME (MME-18) was conducted to investigate the clinical utilization and the epidemiology characteristics of ME in southwestern China. Patients with suspected intracranial infection were recruited between May and October 2019 at West China Hospital of Sichuan University. The MME-18 was used to detect cerebrospinal fluid, and conventional experiments including cryptococcal capsular antigen detection, GeneXpert, real-time PCR, and clinical feedback were used to verify the result of MME-18.

Results

Among 581 tested patients, 139 eligible individuals were enrolled in the study. Among them, Mycobacterium tuberculosis was the most common pathogen in mono-infection. Viruses and Cryptococcus neoformans were also frequently detected. Of 139 infected patients, 12 cases were diagnosed by MME-18 only, 57 patients by conventional testing only, and 70 cases by both comparator tests and MME-18. There were 96.3% (79/82) diagnoses made by MME-18 had a favorable outcome, and two of twelve diagnoses, made solely by MME-18, had a likely unclear clinical significance.

Discussion

The MME-18 showed satisfactory consistency with expert clinical consensus for patients presenting with ME. Combined with conventional testing and clinical suspicion, MME-18 may help clinicians with the early identification of pathogens.

Common Etiological Agents in Adult Patients with Gastroenteritis from Central Iran

Aims: This study represents the first analysis from Iran for both the frequency of the most common causes of infectious diarrhoea and their antibiotic resistance patterns in adult patients. Methods: Adult stool specimens (n = 211) were analyzed. Stool specimens were analyzed using standard microbiological, polymerase chain reaction, and reverse transcription polymerase chain reaction tests to identify bacterial, parasitic, and viral enteropathogens. Antibiotic resistance profiles were determined. Results: Enteropathogens were identified in 46.4% (98/211) of the surveyed samples. This included 33.1% (70/211) bacterial infections, including 9.9% (21/211) diarrheagenic Escherichia coli (DEC) and 8.5% (18/211) Shigella spp. We detected 7.1% (15/211) parasitic infections (mostly Giardia lamblia) and 6.1% (13/211) viral infections (mostly adenovirus). The DEC and Shigella spp. isolates included many multi-drug resistant (MDR) isolates (95.2% and 77.7%, respectively), and extended spectrum-β-lactamase (ESBL) genes were often present (57.1% and 61.1%, respectively). The most commonly identified ESBL genes in the DEC and Shigella spp. isolates were bla_TEM (100% in both species), bla_CTX-M15 (91.6% and 100%, respectively), AmpC bla_CIT (80% and 100%, respectively), and bla_DHA (80% and 100%, respectively). Conclusions: Bacterial infection was the primary cause of infectious diarrhea, affecting one-third of the adults. The frequency of DEC and Shigella spp. was higher than for other enteropathogens. The high prevalence of MDR, the elevated incidence of ESBL genes among Shigella spp. and DEC isolates, and the presence of quinolone resistance in the Salmonella spp. isolates represent a significant challenge for gastroenteritis diagnosis and treatment in this region.

Low Frequency of Adenovirus, Rotavirus, and Norovirus in Pediatric Diarrheal Samples from Central Iran

Background: Acute viral gastroenteritis is a disorder that affects children globally but mostly in developing countries. Adenoviruses, rotaviruses, and noroviruses are the leading viral causes of childhood gastroenteritis. Objectives: This study is the first to investigate the frequency of these viruses in diarrheal samples from pediatric patients living in central Iran. Methods: A total of 173 samples of pediatric diarrhea, from May 2015 to May 2016, were included in this descriptive cross-sectional study. The samples were analyzed using in-house developed PCR and reverse transcription (RT)-PCR methods to investigate the frequency of adenoviruses, rotaviruses, and noroviruses. Results: Out of 173 samples of pediatric diarrhea, eight were shown to contain enteric viruses (4.6%): (1) four with adenoviruses (2.3%); (2) three with rotaviruses (1.7%); and (3) one with a genogroup II norovirus (0.6%). Most of the positive samples were obtained from children under the age of seven. The most common additional clinical symptoms in pediatric patients with viral agents were fever, vomiting, and abdominal pain. Conclusions: In central Iran, adenoviruses and rotaviruses were rarely found as agents responsible for gastroenteritis. Although viral gastroenteritis in this area had less frequency than bacterial gastroenteritis, we need to monitor all enteropathogenic agents for longer periods to understand better real endemicity and the possibility of unexpected viral enteritis outbreaks.

Screening for Viral Infections

This article reviews methods for diagnosis of viral infections including histopathology, culture, nucleic acid tests, and serology. We discuss the principles that underlie individual assays as well as their strengths and limitations. Our intent is to provide insights into selecting strategies for viral diagnosis and discovery that can be pursued by accessing more detailed and granular protocols.

Viruses Causing Aseptic Meningitis: A Tertiary Medical Center Experience With a Multiplex PCR Assay

Background: Central nervous system (CNS) infection is associated with high rates of morbidity and mortality, and despite advancements in molecular testing, aseptic meningitis remains challenging to diagnose. Aseptic meningitis cases are often underreported worldwide, which impacts the quality of patient care. Therefore, we aimed to assess the results of BioFire® FilmArray® meningitis/encephalitis (ME) PCR panel, clinical characteristics, and etiologies of aseptic meningitis patients.

Methods: From January 2018 to January 2020, all pediatric and adult patients in a large tertiary medical center who underwent lumbar puncture and cerebrospinal fluid (CSF) testing by a ME multiplex PCR panel and who fit the aseptic meningitis definition were retrospectively reviewed.

Results: Data were reviewed from 1,607 patients; 240 met the inclusion criteria (54.6% males; 68.8% <4 years of age). The rate of detected viral causes of aseptic meningitis was 40.4%; therefore, 59.6% of the patients remained with unidentified etiology. Among the identified viral meningitis, enterovirus and human herpesvirus 6 (HHV-6) were the most common (25 and 7.9%, respectively). The median length of hospital stay was 6 days, and it was longer in patients with unidentifiable aseptic meningitis (p < 0.0001).

Conclusion: Aseptic meningitis is common among suspected meningitis patients, but most cases remained of unknown etiology. The most common identified viruses were enterovirus followed by HHV-6, and there is predominance in males and the pediatric age group. These results highlight that further research is needed to identify other etiologies and possible additional viral pathogens for aseptic meningitis in the current diagnostic methods.

Usefulness of the FilmArray meningitis/encephalitis (M/E) panel for the diagnosis of infectious meningitis and encephalitis in Taiwan

BACKGROUND/PURPOSE

Early recognition of causative pathogens is critical for the appropriate management of central nervous system infection and improved outcomes. The BioFire^® FilmArray^® Meningitis/Encephalitis Panel (BioFire^® ME Panel, BioFire Diagnostics) is the first U.S. Food and Drug Administration (FDA)-approved multiplex PCR assay that allows the rapid detection of 14 pathogens, including bacteria (n = 6), viruses (n = 7), and fungi (n = 1), from cerebrospinal fluid (CSF). The performance of the panel is expected to be dependent on the epidemiology of M/E in different geographical regions.

METHODS

In this preliminary study, we used the BioFire^® ME Panel in 42 subjects who presented to the emergency department with symptoms of M/E in our hospital. The results were compared to conventional culture, antigen detection, PCR, and various laboratory findings.

RESULTS

The panel detected six positive samples, of which five were viral and one bacterial. We observed an overall agreement rate of 88% between the BioFire^® ME Panel results and the conventional methods. There were no false-positive findings, but five discordant results were observed for enterovirus, herpes simplex virus type 1, Escherichia coli, and Cryptococcus species.

CONCLUSIONS

The BioFire^® ME Panel performed equivalently to the traditional PCR methods for virus detection, and better than bacterial cultures. This revolutionary system represents a paradigm shift in the diagnosis of M/E and may aid in the rapid identification of community-acquired M/E. However, the usefulness of this tool is limited in regions with a high prevalence of infectious M/E caused by microorganisms not included in the panel.

Association of rodent-borne Leptospira spp. with urban environments in Malaysian Borneo

Although leptospirosis is traditionally considered a disease of rural, agricultural and flooded environments, Leptospira spp. are found in a range of habitats and infect numerous host species, with rodents among the most significant reservoirs and vectors. To explore the local ecology of Leptospira spp. in a city experiencing rapid urbanization, we assessed Leptospira prevalence in rodents from three locations in Malaysian Borneo with differing levels of anthropogenic influence: 1) high but stable influence (urban); 2) moderate yet increasing (developing); and 3) low (rural). A total of 116 urban, 122 developing and 78 rural rodents were sampled, with the majority of individuals assigned to either the Rattus rattus lineage R3 (n = 165) or Sundamys muelleri (n = 100). Leptospira spp. DNA was detected in 31.6% of all rodents, with more urban rodents positive (44.8%), than developing (32.0%) or rural rodents (28.1%), and these differences were statistically significant. The majority of positive samples were identified by sequence comparison to belong to known human pathogens L. interrogans (n = 57) and L. borgpetersenii (n = 38). Statistical analyses revealed that both Leptospira species occurred more commonly at sites with higher anthropogenic influence, particularly those with a combination of commercial and residential activity, while L. interrogans infection was also associated with low forest cover, and L. borgpetersenii was more likely to be identified at sites without natural bodies of water. This study suggests that some features associated with urbanization may promote the circulation of Leptospira spp., resulting in a potential public health risk in cities that may be substantially underestimated.

Leptospirosis is a significant zoonotic disease that is found in a range of environments worldwide, most notably tropical regions prone to flooding. The bacterial agents of this disease, Leptospira spp., are most often associated with rodents, including species frequently found in urban areas. In cities, rodent populations are often larger and denser than those found in natural environments, which can lead to higher rates of contact with people and impact human disease risk. To investigate the impacts of urbanization on Leptospira spp., we sampled rodents at locations with differing levels of human influence, from highly urbanized to rural, surrounding a city in Malaysian Borneo. We found that 31.6% of all rodents were positive for Leptospira spp. DNA, and that two primary species were present, L. interrogans and L. borgpetersenii, both of which are known human pathogens. Statistical analyses revealed that infected animals were more common in areas with higher levels of human influence, and were more likely to occur at sites with limited forest cover, and mixed commercial and residential activity. Our study adds to a growing body of evidence suggesting that there is a significant yet underappreciated risk of leptospirosis for people living in urban environments.

Incidence, aetiology, and sequelae of viral meningitis in UK adults: a multicentre prospective observational cohort study

BACKGROUND

Viral meningitis is increasingly recognised, but little is known about the frequency with which it occurs, or the causes and outcomes in the UK. We aimed to determine the incidence, causes, and sequelae in UK adults to improve the management of patients and assist in health service planning.

METHODS

We did a multicentre prospective observational cohort study of adults with suspected meningitis at 42 hospitals across England. Nested within this study, in the National Health Service (NHS) northwest region (now part of NHS England North), was an epidemiological study. Patients were eligible if they were aged 16 years or older, had clinically suspected meningitis, and either underwent a lumbar puncture or, if lumbar puncture was contraindicated, had clinically suspected meningitis and an appropriate pathogen identified either in blood culture or on blood PCR. Individuals with ventricular devices were excluded. We calculated the incidence of viral meningitis using data from patients from the northwest region only and used these data to estimate the population-standardised number of cases in the UK. Patients self-reported quality-of-life and neuropsychological outcomes, using the EuroQol EQ-5D-3L, the 36-Item Short Form Health Survey (SF-36), and the Aldenkamp and Baker neuropsychological assessment schedule, for 1 year after admission.

FINDINGS

1126 patients were enrolled between Sept 30, 2011, and Sept 30, 2014. 638 (57%) patients had meningitis: 231 (36%) cases were viral, 99 (16%) were bacterial, and 267 (42%) had an unknown cause. 41 (6%) cases had other causes. The estimated annual incidence of viral meningitis was 2·73 per 100 000 and that of bacterial meningitis was 1·24 per 100 000. The median length of hospital stay for patients with viral meningitis was 4 days (IQR 3-7), increasing to 9 days (6-12) in those treated with antivirals. Earlier lumbar puncture resulted in more patients having a specific cause identified than did those who had a delayed lumbar puncture. Compared with the age-matched UK population, patients with viral meningitis had a mean loss of 0·2 quality-adjusted life-years (SD 0·04) in that first year.

INTERPRETATION

Viruses are the most commonly identified cause of meningitis in UK adults, and lead to substantial long-term morbidity. Delays in getting a lumbar puncture and unnecessary treatment with antivirals were associated with longer hospital stays. Rapid diagnostics and rationalising treatments might reduce the burden of meningitis on health services.

FUNDING

Meningitis Research Foundation and UK National Institute for Health Research.

Epidemiological surveillance of herpes viral encephalitis in Cordoba, Colombia

Objective To establish an epidemiological surveillance of viral herpes encephalitis in major hospitals of Monteria, Cordoba. Methods From September 2009 to December 2011, a descriptive study of cases of viral encephalitis was made in three hospitals in the city of Monteria. Cerebrospinal fluid (CSF) samples from 118 patients were included in the study. Clinical aspects, as well as cytochemical and microbiological analysis (Gram stain and culture) of CSF, were used for selecting the patients. Virus detection was performed by using multiplex nested PCR for Herpes simplex virus 1 and 2, Epstein Barr virus, Cytomegalovirus and Varicella zoster virus. Results Viral DNA of herpesvirus was detected in the CSFs of 30 (25.4 %) participants, as follows: 22 (18.6 %) Herpes simplex 1 and 2 viruses, 4 (3.3 %) Cytomegalovirus and 1 (0.8 %) Varicella zoster virus. Co-infections were observed in 3 patients (2.5 %), 1 case by HSV-VZV and 2 cases by CMV/HSV. The clinical manifestations of the patients included: headache (18.6 %), fever (14.4 %), asthenia (10.1 %), seizures (9.3 %), vomiting (8.4 %), and stiff neck (5.9 %). Thirty percent of the patients also had HIV-AIDS. A case fatality rate of 20 % was observed for the patients. Conclusions This paper shows that herpesvirus is a cause of infection of the CNS in patients from Cordoba. This study contributes to the epidemiology of encephalitis, as well as to patient management.

Viral meningitis: current issues in diagnosis and treatment

PURPOSE OF REVIEW

The purpose of this review is to give an overview of viral meningitis and then focus in on some of the areas of uncertainty in diagnostics, treatment and outcome.

RECENT FINDINGS

Bacterial meningitis has been declining in incidence over recent years. Over a similar time period molecular diagnostics have increasingly been used. Because of both of these developments viral meningitis is becoming relatively more important. However, there are still many unanswered questions. Despite improvements in diagnostics many laboratories do not use molecular methods and even when they are used many cases still remain without a proven viral aetiology identified. There are also no established treatments for viral meningitis and the one potential treatment, aciclovir, which is effective in vitro for herpes simplex virus, has never been subjected to a clinical trial.

SUMMARY

Viruses are in increasingly important cause of meningitis in the era of declining bacterial disease. The exact viral aetiology varies according to age and country. Molecular diagnostics can not only improve the rate of pathogen detection but also reduce unnecessary antibiotics use and length of hospitalization. Further research is required into treatments for viral meningitis and the impact in terms of longer term sequelae.

Challenges in laboratory diagnosis of acute viral central nervous system infections in the era of emerging infectious diseases: the syndromic approach

INTRODUCTION

Many acute viral infections of the central nervous system (CNS) remain without etiological diagnosis. Specific treatment is available for only few of them; however, accurate diagnosis is essential for patient's life and public health.

AREAS COVERED

In the current article, the main parameters playing a role for a successful etiological diagnosis of acute CNS infections are analysed and the syndromic approach based on clinical and demographic data combined with surrogated indicators is discussed. For the development of a relevant test panel, knowledge on the microbes causing CNS infections in a particular geographic region is essential. The modern screening strategies covering a large panel of potential causative agents are described. Examples of the successful application of next generation sequencing in the identification of etiological agents, including novel and emerging viruses, are given. Expert commentary: Knowledge on epidemiology of the viruses, expertise on syndromic grouping of the etiological agents and advances in technology enable the laboratory diagnosis of acute CNS infections, and the rapid identification, containment and mitigation of probable outbreaks.

Deep sequencing approach for investigating infectious agents causing fever

Acute undifferentiated fever (AUF) poses a diagnostic challenge due to the variety of possible aetiologies. While the majority of AUFs resolve spontaneously, some cases become prolonged and cause significant morbidity and mortality, necessitating improved diagnostic methods. This study evaluated the utility of deep sequencing in fever investigation. DNA and RNA were isolated from plasma/sera of AUF cases being investigated at Cairns Hospital in northern Australia, including eight control samples from patients with a confirmed diagnosis. Following isolation, DNA and RNA were bulk amplified and RNA was reverse transcribed to cDNA. The resulting DNA and cDNA amplicons were subjected to deep sequencing on an Illumina HiSeq 2000 platform. Bioinformatics analysis was performed using the program Kraken and the CLC assembly-alignment pipeline. The results were compared with the outcomes of clinical tests. We generated between 4 and 20 million reads per sample. The results of Kraken and CLC analyses concurred with diagnoses obtained by other means in 87.5 % (7/8) and 25 % (2/8) of control samples, respectively. Some plausible causes of fever were identified in ten patients who remained undiagnosed following routine hospital investigations, including Escherichia coli bacteraemia and scrub typhus that eluded conventional tests. Achromobacter xylosoxidans, Alteromonas macleodii and Enterobacteria phage were prevalent in all samples. A deep sequencing approach of patient plasma/serum samples led to the identification of aetiological agents putatively implicated in AUFs and enabled the study of microbial diversity in human blood. The application of this approach in hospital practice is currently limited by sequencing input requirements and complicated data analysis.

The UK joint specialist societies guideline on the diagnosis and management of acute meningitis and meningococcal sepsis in immunocompetent adults

Bacterial meningitis and meningococcal sepsis are rare conditions with high case fatality rates. Early recognition and prompt treatment saves lives. In 1999 the British Infection Society produced a consensus statement for the management of immunocompetent adults with meningitis and meningococcal sepsis. Since 1999 there have been many changes. We therefore set out to produce revised guidelines which provide a standardised evidence-based approach to the management of acute community acquired meningitis and meningococcal sepsis in adults. A working party consisting of infectious diseases physicians, neurologists, acute physicians, intensivists, microbiologists, public health experts and patient group representatives was formed. Key questions were identified and the literature reviewed. All recommendations were graded and agreed upon by the working party. The guidelines, which for the first time include viral meningitis, are written in accordance with the AGREE 2 tool and recommendations graded according to the GRADE system. Main changes from the original statement include the indications for pre-hospital antibiotics, timing of the lumbar puncture and the indications for neuroimaging. The list of investigations has been updated and more emphasis is placed on molecular diagnosis. Approaches to both antibiotic and steroid therapy have been revised. Several recommendations have been given regarding the follow-up of patients.

A tale of two approaches: how metagenomics and proteomics are shaping the future of encephalitis diagnostics

PURPOSE OF REVIEW

We highlight how metagenomics and proteomics-based approaches are being applied to the problem of diagnosis in idiopathic encephalitis.

RECENT FINDINGS

Low cost, high-throughput next-generation sequencing platforms have enabled unbiased sequencing of biological samples. Rapid sequence-based computational algorithms then determine the source of all the nonhost (e.g., pathogen-derived) nucleic acids in a sample. This approach recently identified a case of neuroleptospirosis, resulting in a patient's dramatic clinical improvement with intravenous penicillin. Metagenomics also enabled the discovery of a neuroinvasive astrovirus in several patients. With regard to autoimmune encephalitis, advances in high throughput and efficient phage display of human peptides resulted in the discovery of autoantibodies against tripartite motif family members in a patient with paraneoplastic encephalitis. A complementary assay using ribosomes to display full-length human proteins identified additional autoantibody targets.

SUMMARY

Metagenomics and proteomics represent promising avenues of research to improve upon the diagnostic yield of current assays for infectious and autoimmune encephalitis, respectively.