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Proteomics Technologies Making Their Way into Pathogen Detection


By Adam Bonislawski

While biochemical- and PCR-based techniques have traditionally dominated the pathogen detection market, proteomics is becoming an increasingly popular tool for identifying agents of infectious disease.

This week, Quanterix became the latest firm to stake a claim in this space, announcing that it plans to develop its Single Molecule Array technology to enable the direct and non-amplified detection of pathogens.

Efforts to apply the SiMoA platform to this purpose are still in the early stages, "but it is extremely promising work. It's a new field of inquiry that we started this year," Martin Madaus, executive chairman and acting CEO of the company, told ProteoMonitor. "It's very early, but we have data that it works."

The aim is to use the high sensitivity of the SiMoA system, which the company says is able to detect proteins at sub-femtomolar levels, to enhance protein-based pathogen detection and identification.

"If you can get the right level of sensitivity, you have a very highly simplified and very elegant way to check for pathogens at very low sensitivity levels," Madaus said, noting that the platform would represent an alternative to PCR-based methods.

Quanterix disclosed its plans to move into pathogen detection in a recent announcement that it had signed an agreement with the German instrument manufacturer Stratec to co-develop and manufacture SiMoA instruments for both the research and in vitro diagnostic markets.

The company said it expects to launch the research-only version of the device in 2013 and a US Food and Drug Administration-approved version in 2014.

The company decided to divulge its early-stage pathogen-detection work "to show that the platform is a broad life science and diagnostic platform that can be applied across many different fields," Madaus said.

Currently, Bruker is the biggest player in the protein-based pathogen-detection space. Its MALDI Biotyper instrument is a MALDI-TOF mass spec-based platform designed to identify bacteria and yeast by matching their protein fingerprints against fingerprints in a proprietary database. According to the company, the platform can perform 30 to 60 identifications per hour.

Available in both research-only and clinical versions, the platform debuted in Europe in 2006 and has since installed more than 250 of the instruments worldwide. In April, the company received Health Canada approval to offer it to all clinical microbiology sites in the country (PM 04/08/2011). Bruker is currently preparing it for an FDA submission for clearance, and is planning a submission to Australian regulators.

In June, it announced a trio of deals regarding the device: A collaboration with the Institute of Medical Microbiology at the University of Zurich focusing on research into coryneform bacteria, actinomycetes, fastidious gram negative bacteria, and molds that could expand the platform's reference library; an extension of Bruker's agreement with Swiss diagnostic laboratory Viollier for use of the platform; and a distribution agreement with Francisco Soria Melguizo that added Portugal to the companies' pre-existing deal for distribution of the instrument in Spain.

The primary advantage of proteome-profiling approaches like that employed by the Biotyper is lower costs due to minimal reagent needs compared to conventional biochemical tests and PCR, said Sasha Sauer, a Max Planck Institute researcher who specializes in using mass spec to type bacteria.

"The advantage is really the cost," he told ProteoMonitor. "If you calculate after one to two years of steady use it is much more cost efficient, because what contributes to the cost is really only the mass spec itself and maybe the software package for analyzing the data."

Systems like the Biotyper, however, are relatively low-resolution compared to techniques like PCR, Sauer noted.

"If you have, for example, different strains of a sub-species, it will become very difficult to distinguish the strains by using the proteome profiles," he said. "It really depends on the application. If you first want to identify bacteria species and sub-species, proteome profiling is good. If you are in need of higher resolution, you have to switch to genetic methods."

As Madaus noted, Quanterix hopes that the SiMoA platform's high sensitivity will overcome this issue, allowing it to replace PCR-based techniques.

Proteomics software firm Sage-N Research is also trying to up the resolution of proteomics-based pathogen detection. The company signed an exclusive license agreement in June with the US Army Edgewood Chemical Biological Center allowing it to integrate the ECBC's Agents of Biological Organs Identification, or ABOID, system — which can identify 4,500 different bacteria, viruses, and fungi — into Sage-N's Sorcerer proteomics informatics platform (PM 06/03/2011).

Sage-N CEO David Chiang told ProteoMonitor that he envisioned the system as a "next-generation Biotyper" that will use the increased sensitivity afforded by Sage-N's and the ECBC's informatics platforms to "take the technology places it hasn't been before."

The system is capable of identifying pathogens down to the strain level. Its increased sensitivity can also identify pathogens without having to culture them first, Chiang said, "which is huge because culturing can take a lot of time and there are a lot of [pathogens] that don't culture well."

The ABOID system has run into some controversy recently, however, as several scientists have called into question data generated on the platform for a study of honeybee colony collapse (PM 07/15/2011).

Last October, a team of scientists from the University of Montana and the ECBC published a study in the journal PLoS One that used it to identify co-infection by the fungus Nosema and invertebrate iridescent virus as a possible cause of honeybee colony death. Since then, several outside scientists have raised questions about the group's findings, with some focusing in particular on the accuracy of their proteomic results.

Fundamentally, though, the questions have revolved not around the ABOID system itself, so much as the appropriateness of the peptide database the researchers used with it. As University of British Columbia researcher Leonard Foster — one of the critics of the study — told ProteoMonitor last month, "I don't think there's a fundamental problem with [the ABOID platform]. It's just how it's been applied in this case."

Have topics you'd like to see covered in ProteoMonitor? Contact the editor at abonislawski [at] genomeweb [.] com.