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Abbott's PCR/ESI-MS System Detects Rare Anaerobic Bacterium; Next-Gen Platform Under Development

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NEW YORK (GenomeWeb) — A recent case study has shown the utility of combined PCR/electrospray ionization mass spectrometry (PCR/ESI-MS) for detecting a rare pathogen in a case of meningitis.

The PCR/ESI-MS technology is currently used by Abbott in its Plex-ID platform, and is being incorporated into a next-generation platform called Iridica, the company said recently.

Published in late June in The Journal of Clinical Microbiology, the case study describes a 33-year-old man with culture-negative meningitis and cerebral abscesses. Using PCR/ESI-MS, clinical researchers determined occult Fusobacterium nucleatum — a strictly anaerobic, non-spore forming gram-negative bacillus —to be the infectious agent. Identification of the bacterium ultimately led to more effective treatment, and may have helped save the patient's life.

"I thought this was a threshold case, I really did," Robert Bonomo, corresponding author on the study and chief of the medical service at the Louis Stokes Cleveland Department of Veteran Affairs Medical Center, told PCR Insider this week.

"Being able to identify an anaerobic pathogen in this serious brain infection was a really step forward for us," he said.

According to the case study, F. nucleatum is associated with important infectious disease syndromes, but the true spectrum of disease may be underappreciated by clinicians due to inability to identify the bacterium by traditional culture techniques.

PCR/ESI-MS may be particularly useful to clinicians in suspected anaerobic infection, even when cultures are obtained following the initiation of antimicrobial treatment, the study said.

The case echoes another report, recently described in PCR Insider, in which PCR/ESI-MS was used to find the fungus that caused brain abscesses in a female patient.

In that case, however, the analysis was only attempted after the patient had died. The authors argued that universally adopting PCR/ESI-MS for fungal pathogen identification might save lives in the future.

Bonomo, who is also a professor of medicine, pharmacology, molecular biology, and microbiology at Case Western Reserve University, said he first learned about PCR/ESI-MS when a study led by David Ecker to diagnose strep infection in military recruits grabbed his attention. Ecker was then at the Ibis division of Isis Pharmaceuticals.

The initial developer of the PCR/ESI-MS technology, Ibis was acquired by Abbott in 2009 for $215 million. Ecker is now divisional vice president and general manager for Abbott's Ibis Biosciences.

"It was simply an accident," Bonomo said. "I was responsible for the literature review for the Interscience Conference on Antimicrobial Agents and Chemotherapy meeting. When I saw this, I said 'Whoa, this is going to change things.'"

In the ensuing years, Bonomo said he has kept in touch with Ecker. He has no financial interest in Abbott, but said he does send samples for testing on occasion, and has collaborated with the company on writing National Institutes of Health grants.

He also lobbied the Cleveland VA Medical Center to purchase a PCR/ESI-MS platform a few years ago.

So, when the first author on the recent case study, Sudha Nagalingam of University Hospitals Case Medical Center, presented the mystery meningitis at a local meeting, Bonomo thought PCR/ESI-MS might help.

"This was a fresh case, and it was perplexing. A patient with abscesses, and they were not able to recover a pathogen by direct examination of the pus in the clinical microbiology laboratory," Bonomo said.

The team tried PCR/ESI-MS, and also sent samples from the brain abscesses to the US Centers for Disease Control and Prevention. Both analyses detected the same rare bacterium. This led to a change in treatment.

"That was thrilling to me, because this is one of those cases where you don't know what is causing a disease syndrome," he said. "Physicians are handcuffed by the limitations of culture sensitivity and specificity, by the time limitations of these tests ... and limited in what they can offer patients if they don't have full information."

The Abbott platform automates sample preparation, broad PCR amplification, and electrospray ionization mass spec of DNA amplicons to identify base composition as determined by molecular weight, comparing results to a curated database to identify pathogens such as protozoa and fungi. "I've worked in the bacterial space a lot, and it's really robust," Bonomo said.

He also noted the current version of the platform is an improvement over the previous version, and suggested that more updates are imminent.

"The previous version of this instrument, the T-5000, was huge, too many moving parts exposed to air," he said. "The Plex-ID became a lot more comfortable, easy to work, and all contained, but it was big."

The $500,000 price tag of the Plex-ID was also a bit steep for some clinical labs, but the company has previously disclosed that it is developing a next-generation version of the platform that will be easier to use and possibly less expensive.

In May at the European Congress on Clinical Microbiology and Infectious Diseases in Barcelona, Spain, Abbott presented preliminary results of European clinical trials using the new platform, which it calls Iridica.

In a study called Rapid Diagnosis of Infections in the Critically Ill (RADICAL), samples from more than 180 patients with suspected severe infections were retrospectively analyzed to compare the results of Abbott's technology to culture.

Analysis of the data found the sensitivity of Iridica for bloodstream infection and pneumonia assays was 88 percent and 91 percent, respectively, when compared to culture. The technology was able to detect pathogens that the initial culture missed in many patients, and Abbott noted that physicians on an adjudication panel would have changed their treatment plans in more than half of the cases had they had the Iridica data available.

The company also noted that Iridica is being designed to produce results in approximately eight hours.

The RADICAL study is expected to be completed in late 2014, and Iridica is expected to be available as a CE-marked in vitro diagnostic device in European countries within the next 12 months. The platform is currently designated for research use only in the US, and Abbott has not disclosed its plans to pursue US regulatory clearance.

Bonomo said he believes this method may ultimately supplant matrix-assisted laser desorption/ionization in clinical labs. "MALDI right now requires a colony, it's a protein-sensitive method. Nucleic acid sensitivity far outstrips protein sensitivity, because you need less — you can amplify it, and once you amplify it, you can study it," he said.

For the time being, there is still a need to rely on traditional methods. "Right now I don't think we can get away from standard culture and sensitivity methods, we are not ready to go on to that. This is still in the early stages. The platforms ... still need to be developed more," he said.

However, he added, "I can't think of anything better that's coming down the pike."

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