NEW YORK (GenomeWeb) – A multiplex panel assay that tests for pathogens responsible for meningitis and encephalitis has been evaluated in a large prospective study and found to have the potential to improve patient care.
The FilmArray ME Panel from BioMérieux subsidiary BioFire Diagnostics is a one-hour, sample-to-answer test for 14 different pathogens associated with infectious meningitis or encephalitis, including common bacteria, viruses, and yeasts. It is meant for close-to-patient testing of cerebrospinal fluid specimens that are collected by a lumbar puncture from patients who are acutely ill and suspected of neurological infection, and requires only 200 microliters of CSF.
The evaluation, published in the Journal of Clinical Microbiology last week, is the result of a study of the ME Panel that was performed on 1,560 patient samples collected at 11 sites in the US over a period of eight months in 2014. It was the largest clinical trial of a commercial in vitro diagnostic test for detection of multiple agents of meningitis and encephalitis in CSF specimens, according to the study.
The work was part of the clinical trials for the panel, which was cleared by the US Food and Drug Administration earlier this year.
However, "The publication attempts to go into more depth about the clinical trial than presented in the manufacturer's package insert," Amy Leber, director of the clinical microbiology and immunoserology laboratory at Nationwide Children's Hospital and the corresponding author on the JCM study, told GenomeWeb in an email.
"A simple, rapid, and accurate diagnostic test for diagnosis of meningitis and encephalitis has the potential to impact morbidity and mortality in a wide range of patients," Leber said. Infections that involve CSF can be deadly and "delays in diagnosis and proper treatment can have serious adverse consequences," she said.
The gold standard for suspected bacterial infections is culture. Some larger hospitals run lab-developed tests for viruses, but most send samples to references labs. Both of these strategies have days-long turn-around times.
The clinical trial was designed and supported by BioFire. Based on FDA guidance, the firm also designed the comparator PCR and sequencing assays, determined the number of specimens to be enrolled, and established how comparator testing would take place, Leber said.
The study reported the results of the FilmArray test versus comparator tests of bacterial cultures and Gram stains performed at the study sites, or viral and yeast PCRs and sequencing performed at BioFire labs. The most common organisms detected were enterovirus, human herpesvirus type 6, S. pneumoniae, herpes simplex virus type 2, and human parechovirus, accounting for 113 of the 136 cases detected, with co-infections observed in five cases.
Overall, the test had high positive and negative percent agreement for the various targets, with the exception of two that were undetected in this study. However, there were 43 presumed false positive results in which the comparator test did not detect any pathogen.
Using additional laboratory and clinical data, some of the false positives were determined to be true positives, Leber said. But 22 tests were not resolved this way. The reasons why are not clear, "but may be due to contamination during the processing of the sample, or some other aspect of the testing, assay chemistry, or process," she said. Additionally, for the viral targets, some of the tests called false positives relative to the comparator tests showed cycle thresholds by viral PCR that were indicative of very low levels of analyte.
One target reported in the paper was subsequently dropped from the panel before it was submitted to the FDA. The Epstein Barr virus was detected by the panel in 41 cases, but "the vast majority did not have other clinical data indicative of ME disease," Leber said. Detection of EBV in these subjects was likely explained by the presence of latent viral nucleic acid, for example from B cells, or re-activation in response to other medical conditions, and the detection of EBV was incidental yet could have led a clinician to an incorrect diagnosis, she added.
The JCM study also highlighted particular patient cases in which the panel could have resulted in timelier information to make therapeutic decisions, including more targeted antimicrobial therapy.
BioFire has three other tests cleared by the FDA. All have identical workflows, and have also been cleared to run on the firm's higher-throughput platform, the FilmArray Torch. But this is the first using CSF, Kevin Bourzac, director of clinical affairs at BioFire, told GenomeWeb in an interview.
The test was a de novo submission and was the first of its kind cleared by the FDA, he said. "There are currently FDA cleared tests that are singleplex assays — Focus has a herpes simplex virus test, and Cepheid has a test for enterovirus – but this was the first test for bacteria, viruses, and yeast from a CSF sample," Bourzac said.
Andrew Hemmert, associate director of biochemistry at BioFire, said the development process was similar to that for other FilmArray panels, but compared to nasopharyngeal swabs, blood culture, or stool, CSF is a "very clean, simple matrix to work with." Indeed, the biggest challenge was the fact that lumbar puncture can only draw small sample amounts.
"For other matrices you generally have much larger volumes — if you think of a blood culture bottle you have a lot of volume to play with — but for this panel we needed to do a lot with a little," Hemmert said.
Bourzac noted that the panel development "leveraged all of the experience and technology" that the firm has gained in previous tests. The study was also the first of its kind looking at so many patients with a broad panel examining the etiology of meningitis and encephalitis.
However, the ME test was made to be "extremely sensitive" to cope with the low levels of pathogen in small volumes. "That posed some challenges ... you have to be careful during development and manufacturing, and labs have to be careful when the run it, because some of the things that are detected by the test are found in healthy persons," Bourzac said.
The FilmArray is a closed system, and that can limit potential for contamination. It also has a very low failure rate, with a nearly 99 percent success rate on the first run, according to the study.
The market size is admittedly small for meningitis and encephalitis. Although the infections are associated with significant morbidity, there are only about 4,100 cases of bacterial meningitis per year in the US and about 20,000 encephalitis-related hospitalizations that are often caused by viruses but for which up to 70 percent of cases have unknown etiology.
On the other hand, in the JCM study only 136 of the 1,560 tested specimens were positive for at least one pathogen using the ME panel, suggesting there is a lot of testing for suspected cases.
"Although we're the first commercial test on the market like this ... meningitis and viral encephalitis testing was one of the big things that brought PCR into hospitals to begin with [in the form of lab-developed tests], so there definitely is a recognized need," said Hemmert.
Like other FilmArray panels, the test will be marketed to moderate- or high-complexity CLIA-certified hospital labs. And unlike the firm's respiratory, blood culture, and gastrointestinal panels, there are no competing multiplex panels for ME at this point. "It's really getting us noticed by labs that we haven't penetrated yet," Lou Banks, senior global brand manager of commercial products at BioFire, said. The firm's parent company, BioMeriuex has not released specific sales figures, but Banks said "it has been categorized as one of our best product launches [and] we're well ahead of our forecast at this point," in the US.
The firm also obtained CE marking for the assay in January of this year, and in the subsequent months has seen "tremendous success internationally as well," Banks added.
BioFire next plans to start regulatory studies this summer on a lower respiratory panel, Bourzac said.
The FilmArray ME Panel will be used in conjunction with conventional testing such as bacterial culture and Gram stain, Leber emphasized. It does not target all possible bacteria causing infection nor does it allow susceptibility testing. "Therefore, culture is still needed." For viral targets, however, it could conceivably be used as a standalone test, and this could be "incredibly useful for many hospitals that are currently limited in the molecular testing available to diagnose ME," she said.