Ever since the Danish bacteriologist Hans Christian Gram developed his eponymous test (the Gram stain) in 1882 to differentiate between types of bacteria, diagnostic tests have been integral to both public and individual health. The ability to rapidly and accurately detect microbes is becoming increasingly important given the emergence of diverse drug resistant strains, such as Methicillin-resistant Staphylococcus aureus (MRSA; Gram positive bacteria resembling purple grapes), as well as the length of time it currently takes to diagnose and treat certain infections (e.g. Mycobacterium tuberculosis, which cannot be detected via Gram stain but rather an acid-fast stain, has an incredibly slow doubling time which is why it can take weeks to accurately diagnose tuberculosis). In recent years genomic technologies have fortunately opened the doors for faster and more accurate detection of microbes than petri dish cultures and chemical staining can provide. Medgadget had the opportunity to interview two partner companies – PathoGenetix and Sagentia – that are developing a state-of-the-art Genome Sequence Scanning (GSS) technology, which promises to bring rapid microbial detection to the fields of microbial genomics research, food and product safety, and clinical infectious disease testing.
Shiv Gaglani, Medgadget: How many micro-organisms can be detected through the partnership technology?
PathoGenetix: Unlike PCR or antibody-based tests, Genome Sequence Scanning (GSS) does NOT use a specific reagent set to detect a specific microorganism. Instead, GSS uses a universal reagent set to create barcodes on all microbial DNA in a sample. Detection of specific microorganisms is based on reading the barcodes in a sample and performing a lookup in a database (similar to a bar code scanner at a supermarket). In this way, GSS can detect thousands of different microbial organisms in a sample, using a single reagent set.
PathoGenetix’s proprietary GSS technology combines automated sample preparation and single molecule detection making it possible to detect and characterize microbes from complex biological samples in as little as three hours. Specifically, the technology extracts genomic barcodes from microbial DNA as it flows through a microfluidic chip at 150 million base pairs per second. A universal reagent set decorates the DNA enabling specific pathogens to be identified by comparing their unique DNA ‘barcode’ with PathoGenetix’s own library of templates. With this approach, it is possible to identify thousands of different microbial strains through a single test, days faster and at far lower cost than current techniques.
Medgadget: Since the test relies on DNA, which can be detected even after a cell dies, how will your technology distinguish between living and dead micro-organisms?
PathoGenetix: The barcodes used for detection in GSS are based on very long DNA fragments – typically 80,000 – 350,000 base-pairs. These long DNA fragments provide the specificity required for accurate detection. As part of the death cycle of cells, an organized process for DNA degradation occurs (apoptosis). Because of this, dead cells do not yield a sufficient quantity of the long DNA required by GSS for analysis, and are not detected.
Medgadget: Along the same lines, do you have initial sensitivity and specificity data?
PathoGenetix: GSS is a single molecule detection technology, meaning that during the detection process, individual DNA molecules pass through the detector and have barcodes read. Detection of a specific microorganism can be determined from as few as ten molecules. GSS is exceptionally specific and it routinely differentiates strains of closely related species. PathoGenetix has published data that indicates that GSS is at least as specific as PFGE in its ability to differentiate strains. However, GSS can perform such differentiation directly from a complex sample and does not require a cultured isolate.
Medgadget: What are the key success factors for making a technology like this into a commercially successful instrument?
Sagentia: Success factors include understanding the users and market requirements; ease of use; engineering reliability and robustness; complex integration of multiple high-tech subsystems in a technologically empathetic way that is economically viable, user friendly, and highly functional; and a deep understanding of the technology throughout the product development.
Medgadget: When will this technology be available at the “bench” and/or “bedside,” or – as the press release suggests – at other venues such as food processing factories?
PathoGenetix: The first systems will be available for field trials in late 2012. PathoGenetix initial focus is on markets for food safety and genomics research. PathoGenetix plans to enter clinical trials in the second half of 2013 for infectious disease diagnostics.
Special thanks to Medgadget editor Jan Sinnige for his expertise in the production of this story.