Protect and serve: innovations in food pathogen detection

Take a moment to digest the figures. In the US, the food sector represents almost 50% of the total industrial microbiology testing market. It is more than double the size of any other industrial segment, including pharmaceuticals. In Europe, meanwhile, the food safety testing market is predicted to top $1bn in five years.

Statistics such as these from Strategic Consulting, a leading resource for business strategy and market intelligence in industrial diagnostics, confirm that protecting the public from food-borne diseases such as salmonella, E. coli, listeria, campylobacter and norovirus is big business.

"The global food safety diagnostics market continues annual expansion in double-digit figures," confirmed Crispin Philpott, strategic account manager at Roka Bioscience and a leading authority in food safety technology.

"It draws the increasing attention of both the investment community and method developers currently outside the space."

This injection of public and private capital is more than matched by intellectual investment on the part of regulators, industry and academia. In short, the brightest and the best in the food safety industry have come together in response to a series of high-profile food contamination cases on both sides of the Atlantic.

A painful reminder of the need for constant vigilance came in 2010 when a large outbreak of Salmonella Bareilly across the UK left one person dead and a further 241 infected. The outbreak was subsequently traced back to contaminated bean sprouts. Worse was to come the following year, when E. coli contamination in Germany killed more than 40 people before rapidly spreading across Europe, the US and Canada. This time, fenugreek seeds imported from Egypt were to blame.

Speaking from his Roka Bioscience office in Pennsylvania, Philpott said the shockwaves from the former E. coli outbreak are still being felt throughout the industry and wider society.

"Clearly, the STEC outbreak in Germany has created significant public health concern worldwide, indicating continuing vulnerability to unmonitored and unregulated organisms of significant pathogenicity," he said.

"Non-O157 STECs are also becoming a USDA-driven priority among beef grinders, for example. The Food Safety Modernization Act (FSMA) now requires FDA-regulated food processors to establish a Hazard Analysis and Critical Control Point (HACCP)-like process control programme, in addition to regularly testing the processing environment. USDA has also provided significant funding to a number of research centres to study norovirus."

Clearly, making food safe for public consumption is a collaborative effort, with private companies and research organisations working with government bodies to develop cutting-edge detection and prevention technology. Here we profile some of these next-generation techniques.

Molecular biology: the rise of DNA sequencing

DNA sequencing is the process of determining the nucleotide order of DNA fragments. Its application in the pathogen detection industry has transformed the science of food safety.

DNA sequencing is especially useful in the source-tracking of specific strains, as well as assay development. PCR (polymerase chain reaction)-based techniques, for example, allow scientists to target the genetics of microorganisms, rather than their phenotypic characteristics.

California-based Roka Bioscience is currently commercialising rRNA-based detection technology, financed in part by $47.5m of Series D financing. The ATLAS system is a fully automated molecular instrument for the detection of food pathogens in food and environmental samples and is capable of processing more than 300 samples in eight hours.

The initial menu for the ATLAS system will be the Roka Listeria and Salmonella Detection Assays. The Listeria assay has already received AOAC Performance Tested Method(SM) certification (Method 011201) from the AOAC Research Institute (AOAC-RI).

Another US biotech company, 3M, recently announced it has developed new pathogen testing technology incorporating isothermal DNA amplification and bioluminescence detection. The 3M molecular detection system delivers highly sensitive results by targeting and amplifying nucleic acid in enriched samples.

The automated technology has been evaluated with a variety of food types, including produce, meats, processed foods and food processing-related environmental samples.

"Pathogen testing has now been made simple and affordable," said Niki Montgomery, 3M Food Safety global marketing development manager. "Numerous organisms can be tested in a single run and it was designed to help our customers perform fewer repeat tests and make critical decisions faster."

As part of the 3M molecular detection system platform, individual pathogen-specific assays, or procedural tests, will be sold as test kits. Each assay test kit uses the same software interface and same DNA extraction protocol for testing between one and 96 samples on each run. Assays for salmonella, E. coli O157 (including H7) and listeria are already available. A test for listeria monocytogenes is expected in early 2012.

First defence: portable pathogen devices

In the wake of increased homeland security threats, the US military industrial complex has invested heavily in new state-of-the-art technology, a significant amount of which is being adapted by scientists working in the sphere of food pathogen detection and DNA analysis.

Idaho Technology has developed the R.A.P.I.D. LT, a real-time PCR instrument capable of analysing samples for the presence of targeted nucleic acid sequences.

Combining rapid air thermocycling and a real-time fluorimeter, it can reliably identify test samples in less than 35 minutes. Included with the instrument is a laptop computer pre-loaded with analysis software.

The revolution in portable pathogen detection devices is gaining momentum. Advances in nanobiotechnology have allowed for miniaturisation of devices, with experts in the fields of engineering, nanotechnology and food science joining forces to introduce lab-on-a-chip technologies, leading to the development of portable, hand-held biosensors.

Brain food: the role of academia

Research is by no means limited to private firms. Government and academic bodies both have a major role to play. In the US, the Food and Drug Administration (FDA) has requested funding of $4.3bn from President Obama’s 2012 budget.

This is an increase of around a third from the organisation’s 2010 budget, $324m of which would be spent on overhauling food safety and nutrition programmes to enforce the new food safety modernization act (FSMA).

Across the Atlantic, the UK Food Standard Agency (FSA) has identified priority pathogens whose control and reduction would deliver the greatest public health gains. These are campylobacter, which causes the most cases each year; listeria monocytogenes, which causes the greatest mortality, and norovirus.

The FSA has funded a research project by the University of Aberdeen, which used multilocus sequence typing (MLST) to compare Scottish campylobacter isolates from human infections with those from food and environmental sources. The research identified retail chicken as the single largest source of campylobacter infection in Scotland.

A further important finding from this project was that MLST profiles of campylobacter isolated from cattle and sheep faeces sampled during the study matched those isolated from human infections. This suggests that farm ruminants could also be a significant risk factor for campylobacter infection.

The future of food pathogen detection

Until recently, pathogen reduction efforts focused on the pre-release screening of the finished product, while doing little to prevent processing failure or improve production efficiency.

Today, food safety efforts strive to eliminate pathogens by focusing on the entire processing chain – from pre-process raw-material screening to process control and, finally, to limited finished-product screening.

The FSA’s chief scientist Andrew Wadge recently published a blog, in which he outlined his support for food pathogen detection innovation in general, and DNA sequencing in particular.

"It won’t be long before every lab has a sequencer," he said. "Imagine if the doctors and scientists investigating the German outbreak of E. coli could have compared the molecular sequence of the particular type of E. coli with international databases from previous outbreaks. We knew people were getting sick from food, but no one knew the source.

"As databases containing the molecular sequencing of foodborne pathogens become available, our task in identifying the source of foodborne outbreaks will become easier and quicker. It will also help prevent the wrong food source being implicated, with all the economic and political fallout that follows."