Scientists from Abbott and collaborating academic institutions have recently published a pair of studies demonstrating the ability of Abbott's Plex-ID platform to detect and identify in human samples a wide array of clinically relevant infectious organisms not picked up using more established methods, further underscoring the clinical diagnostic potential of the technology.
In addition, PCR Insider has learned that Abbott is discontinuing the current version of the Plex-ID system as it prepares for market a next-generation system intended to be smaller and easier to use, and thus more conducive to a clinical diagnostics setting.
Abbott's Plex-ID system is based on technology that the company acquired along with Ibis Biosciences in 2009. The platform combines automated sample preparation, broad PCR amplification, and electrospray ionization mass spectrometry of DNA amplicons to identify base composition based on molecular weight. The company generally refers to the core underlying technology as PCR/ESI-MS.
In general, the system can be used to screen and identify bacteria, viruses, fungi, and protozoa by comparing assay results to a library of more than 750,000 entries; perform high-resolution subtyping; identify known virulence markers and antibiotic resistance genes; and identify mixtures of microbes direct from a single sample.
According to the company's website, Plex-ID can analyze as many as 250 samples per day and can produce results within 8 hours, from sample preparation to identification.
Both Ibis and Abbott had early success selling the platform into applied markets, such as biodefense, but in recent months the company and its collaborators have published multiple peer-reviewed studies and presented at scientific conferences on the clinical diagnostic potential of Plex-ID.
For instance, in April at Cambridge Healthtech Institute's "Innovative Sample Prep & Target Enrichment in Clinical Diagnostics" in Newport Beach, Calif., Mark Eshoo, director of new technology development at Abbott, disclosed that the company was working on a Plex-ID assay to detect and genotype Borrelia burgdorferi, the bacterium responsible for causing Lyme disease in humans (PCR Insider, 4/19/2012).
And in August, researchers from Johns Hopkins University reported that their high-resolution melting assay and a Plex-ID assay performed similarly in identifying pathogens from a cohort of positive blood culture samples — with the Plex-ID scoring particularly high marks in terms of throughput, automation, and sensitivity (PCR Insider, 8/16/2012).
In addition, in March Abbott and Dallas-based Genetics Laboratory said they were co-developing a molecular test designed to rapidly detect microorganisms that cause orthopedic infections (PCR Insider, 3/8/2012).
Bacterial Meningitis
More recently, at the Association for Molecular Pathology meeting held last month in Long Beach, Calif., scientists from Abbott subsidiary Ibis and the Instituto Adolfo Lutz, a Brazilian national reference laboratory, presented a poster describing the detection and identification of bacterial pathogens in cerebrospinal fluid and sera from meningitis patients using the Plex-ID BAC Detection assays. According to Abbott's website, the assay is designed to be able to identify more than 3,400 species of bacteria, and more than 40 species of Candida, based upon the identification of a single species, a small cluster of indistinguishable species, or the closest known species in the company's database.
The study examined 77 CSF and 94 sera specimens from suspected meningitis patients. The researchers performed culture, real-time PCR, countercurrent immunoelectrophoresis, fragment analysis, and PCR/ESI-MS using the Plex-ID on the specimens.
Of the 77 CSF specimens, 43 were positive by real-time PCR and only 19 were culture positive. In comparison, PCR/ESI-MS identified bacteria in 61 specimens, including all 43 found by real-time PCR. Meantime, of the 94 plasma specimens, 33 were real-time PCR positive and five were culture positive. In contrast, 45 specimens were PCR/ESI-MS positive, including 29 of the 33 the samples that were real-time PCR positive.
In other words, the Plex-ID analysis yielded a 53 percent reduction in negative CSF samples and a 20 percent reduction in negative sera samples compared to real-time PCR.
The Abbott scientist who presented the poster at AMP declined to discuss the findings in greater detail; however, the researchers noted in their poster that "PCR/ESI-MS using a broad bacterial detection assay is a potentially attractive solution to screening for bacterial pathogens in meningitis patients," and that "the clinical relevance of the significantly increased pathogen detection rates by PCR/ESI-MS merits further investigation."
Fungal ID
In another study published online ahead of print last month in the Journal of Clinical Microbiology, a group including clinical researchers from Abbott's Ibis business and Vanderbilt University Medical Center explored the use of Plex-ID to detect and identify fungal organisms in bronchoalveolar lavage specimens.
In this study, the researchers used the Plex-ID Broad Fungal assay to examine a total of 691 bronchoalveolar lavage samples that had been collected at VUMC between 2005 and 2011 and tested for the presence of fungal organisms using standard culture-based methods. According to Abbott's website, the Plex-ID Broad Fungal assay is designed to detect and identify nearly 30 fungal agents, some at the species level and some at the genus level.
Yi-Wei Tang, corresponding author on the paper and currently chief of the Clinical Microbiology Service at Memorial Sloan-Kettering Cancer Center in New York, told PCR Insider that the group compared Plex-ID to culture-based methods because "culture was the test ordered by clinicians for their routine practice." He added that while some molecular methods based on real-time PCR have in recent years been developed, they are mainly used for identification, and not direct detection from patient samples.
Of the 691 total samples tested, 134, or 19.4 percent, were positive for fungi by both culture and PCR/ESI-MS. Of the dual-positive specimens, 125, or 93.3 percent, were Candida and Aspergillus species with concordances between culture and PCR/ESI-MS of 67.2 percent at the species level and 87.2 percent at the genus level.
In addition, 243, or 35.2 percent, and 30, or 4.3 percent, of specimens were positive only by PCR/ESI-MS or by culture, respectively. Among 53 specimens in which culture failed, PCR/ESI-MS identified at least one fungus was in 26 specimens, or 47.3 percent.
Thus, similar to the study presented at AMP, this study revealed that Plex-ID was able to identify a significantly greater number of infectious agents than culture-based methods.
The additional positives picked up by PCR/ESI-MS could be false, but for this study Tang and colleagues did not verify the Plex-ID positives using other molecular methods. However, Tang noted that his group has done this before in other experiments, and as such "knows that the positives we detected are real."
However, he also noted that "we do not know the details of why culture did not pick up these positives, but we know the general reasons." The first potential reason is that culture would not be positive for an organism that had died, while PCR/ESI-MS is likely to. The second and more likely reason is that in culture-based identification, normal bacterial flora often overtakes the fungal organism in the culture plate.
The researchers note in their paper that PCR/ESI-MS "possessed promising concordances with culture in specimens in which fungal organisms were detected by both methods;" and that the technique detected single and multiple fungal organisms at significantly higher frequencies in a given specimen than culture.
"Most importantly, PCR/ESI-MS detected potential fungal organisms in specimens in which cultures failed due to bacterial overgrowth … [and] provides an advanced tool for rapid and sensitive detection and identification of fungal organisms directly from [bronchoalveolar lavage] specimens." However, they also noted that the clinical relevance of their findings merits further investigation, a point that Tang expanded upon.
"Yes, we know that the bug is there," he said. "But what does that mean clinically? Is it causing disease or not? We don't know. It could be clinically irrelevant." For instance, as he previously alluded to, an organism could be dead but still picked up by the Plex-ID assay. In addition, he said that “Some fungal organisms such as Aspergillus species commonly exist in environment and can “colonize” in the respiratory track in low level without causing diseases”
Next-Gen System
Abbott in April received CE marking in the European Union to market its Plex-ID platform along with three assays: Plex-ID Viral IC Spectrum, Plex-ID BAC Spectrum BC, and Plex-ID Flu (PCR Insider, 4/5/2012).
And, in addition to the BAC Detection and Broad Fungal assays used in the aforementioned studies, Abbott offers a variety of Plex-ID assays for microbial identification for research use only, including tests for biothreats, Clostridium difficile, food-borne illnesses, methicillin-resistant Staphylococcus aureus, and multi-drug resistant tuberculosis.
During his presentation at the CHI conference in April, Abbott's Eshoo indicated that the company was at least looking into seeking approval from the US Food and Drug Administration for Plex-ID.
However, this week Abbott confirmed that it is planning to discontinue the current version of Plex-ID in favor of a next-generation system that would be more conducive to clinical implementation. The current Plex-ID platform has been reported by users to cost in the range of $750,000, and the instrument is about the size of a large refrigerator, making it ill-suited for use in most clinical diagnostic laboratories.
An Abbott spokesperson this week confirmed that the company was developing a next-generation version of Plex-ID, but did not elaborate. It is unclear whether Abbott will discontinue the current platform in both Europe and the US; or whether the company plans to seek FDA approval for a newer version of the system.