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Bruker Releases Results From CDC Microbiology Collaboration

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NEW YORK (GenomeWeb) – Bruker announced at last week's American Society for Microbiology annual meeting in Boston results from its ongoing collaboration with the US Centers for Disease Control and Prevention to develop an expanded microorganism reference library for its MALDI Biotyper platform.

The reference library currently contains MALDI spectra for more than 800 rare and emerging microbes and is now available for public use, George Goedesky, Bruker's vice president for microbiology, told GenomeWeb. The library is part of the CDC's MicrobeNet website, a resource offering public health researchers information on more than 2,400 bacteria and fungi that they can use for purposes like tracking and containing outbreaks.

"MicrobeNet is a tool for microbiologists with a lot of different functions," Goedesky said, noting that the database contains information like colony morphology and biochemical data used in traditional identification methods as well as newer molecular information like genomic sequence and proteomic data.

The resource's MALDI data provides researchers with additional spectra beyond what is available in Bruker's commercially available libraries.

"Say somebody in the Pennsylvania Department of Health gets an isolate and they test it on the Bruker system and it doesn't come up with a match," Goedesky said. "They can then go to the MicrobeNet website and look to see if the spectra they generated matches anything in the MicrobeNet library."

Bruker and CDC launched the collaboration at the 2012 ASM annual meeting. At that time, the company said the project was slated to last one year, during which time the CDC would compare the performance of the Biotyper to traditional phenotypic and genetic tests to determine the value of including it as part of the organization's rare bacteria identification workflow.

Goedesky said this week that the project is ongoing and that the CDC would continue to add new MALDI spectra to the MicrobeNet site. While MicrobeNet currently contains only spectra from the Bruker system, Goedesky said CDC plans in the future to add spectra from BioMérieux's competing Vitek MS MALDI-based microbiology platform.

CDC has also developed a MALDI-based assay for Botulinum toxin, the neurotoxic protein produced by Clostridium botulinum. Currently, he said, the organization uses mouse-based methods to test for this toxin, but they plan to replace these with the MALDI approach. "Public health organizations that have [Botulinum toxin testing] as part of their charter are investigating that method, as well," he said.

The MicrobeNet MALDI library is intended for use by public health labs, and so does not require the same US Food and Drug Administration clearances that Bruker's clinical Biotyper platform and libraries do, Goedesky said. "A public health laboratory is not treating these [infections]. It is not diagnosing. It is using it for surveillance and following outbreaks."

Bruker considers public health laboratories an important market for the Biotyper, Goedesky said. Several recent studies suggest that the company could face competition in this space from LC-MS/MS-based systems particularly for applications where higher sensitivity and resolution is required.

For instance, in April, researchers at the at the National Institutes of Health published a paper in Clinical Chemistry describing a tandem mass spec approach to strain typing Acinetobacter baumannii isolates. That paper followed recent similar work by researchers at the Public Health Agency of Canada's National Microbiology Laboratory who used LC-MS/MS for H-typing of Escherichia coli.

Both studies also looked at MALDI-based methods, but found the LC-MS/MS approaches to be capable of making more identifications.

"There are a variety of approaches that are being used, each of which has its merits and domain of application," John Dekker, an NIH scientist and author on the A. baumannii paper, told GenomeWeb upon its release. "One thing that has become apparent is that fragmentation-based methods [like conventional LC-MS/MS] may have more power to identify strain-specific signatures than intact protein profiling methods [like MALDI]."

Because it does not require protein digestion or LC separation, MALDI offers advantages in terms of throughput and ease of use, however. Bruker also released at ASM versions of its MBT Pilot and Galaxy tools, which are aimed at extending those advantages.

Pilot is a light-guided system intended to help researchers pick colonies and place them on a MALDI target. Galaxy is an automated reagent addition system. Both, Goedesky said, are aimed at helping high-volume labs automate and streamline their Biotyper workflows.

Bruker also continues to work on developing MALDI Biotyper workflows for detecting antibiotic resistance, a major area of interest within clinical microbiology. At the European Congress of Clinical Microbiology and Infectious Diseases annual meeting this April in Amsterdam, the company released a pair of research-use-only modules for resistance detection.

The MBT Subtyping Module is intended for detection of carbapenem-resistance strains of Bateroides fragilis and Staphylococcus aureus via detection of the presence of, respectively, the cfiA gene and the mecA cassette expressing the protein PSM.

This latter method is similar to an approach published last year by NIH researchers that used the Biotyper to identify carbapenem-resistant Enterobacteriaceae. In that work, the NIH team used the protein pKpQIL_p019 as a proxy for resistance mediated by the blaKPC gene, which encodes the Klebsiella pneumoniae carbapenemase (KPC) protein, which hydrolyzes carbapenems.

The protein pKpQIL_p019 is encoded by a gene found on some blaKPC-containing plasmids. It can be identified in spectra collected by the MALDI Biotyper during routine identification assays, and its presence can be used to then infer the presence of the blaKPC gene.

Bruker also released at ECCMID its MBT STAR-BL assay, which detects antibiotic resistance in Gram-negative bacteria by looking for products generated when these antibiotics are degraded by carbapenemases. The assay looks for mass shifts produced by degradation of betalactam antibiotics like penicillins, cephalosporins, and carbapenems.

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