“In recent years, several assays have been designed to meet the need of providing testing results in near real-time (same day), but by and large, they still require some cultural enrichment for pathogen detection, even though enrichment may be abbreviated,” Dr. Jaykus relates.
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To get true real-time (in a matter of minutes) pathogen detection will require methods that are completely culture-independent, she says.
“Such pathogen detection will also require pre-analytical sample processing methods, also called ‘sample prep,’ to concentrate the organisms from the sample matrix, and remove matrix-associated inhibitory compounds,” she elaborates. “While some novel sample prep technologies have been launched in the past several years, no silver bullet has been found yet.”
Many groups, be they academic, industry, or government, are actively developing biosensor technologies, Dr. Jaykus points out. “Many of these technologies are novel and ‘sexy’ but still do not have the low detection limits necessary for pathogen detection in foods,” she says. “In addition, the sample matrix can be a significant impediment to analytical sensitivity. Another reason for sample prep, and a personal caution, is that without one (sample prep) we cannot have success in the other (biosensors).”
Dr. Jaykus believes that as detection become less dependent upon culture and more dependent upon nucleic acid sequence, the issue of bacterial cell or virus viability becomes more important. “Just because we can detect DNA does not mean that the organism is alive,” she notes. “This issue is of importance in making decisions about prevention and control in food safety, as well as management of recalls and outbreaks. It has not yet been resolved.”
Metagenomics, a term that reportedly first appeared in peer reviewed literature in 1998 (Handelsman et al), basically the study of genetic material recovered directly from environmental samples, promises to impact laboratory analysis with ever increasing significance. In 2005 Chen and Pactor defined metagenomics as “the application of modern genomics technique without the need for isolation and lab cultivation of individual species.”
What some scientists call the metagenomic revolution has resulted in a lot of DNA sequence data for various foodborne pathogens, Dr. Jaykus says, while emphasizing that, “relative to the volume of data available, we currently do not have the critical mass of scientists necessary to interpret it. We are also not entirely certain as to the practical use of those data in food safety management. This will become clearer in years to come, but the field is currently in its infancy stage.”
“Like genomics itself, metagenomics is both a set of research techniques, comprising many related approaches and methods, and a research field. In Greek, meta means ‘transcendent.’”
So says the U.S. National Research Council (NRC) Committee on Metagenomics in its 2007 publication The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet.
“In its approaches and methods, metagenomics circumvents the unculturability and genomic diversity of most microbes, the biggest roadblocks to advances in clinical and environmental microbiology,” the NRC relates.
“Meta in the first context recognizes the need to develop computational methods that maximize understanding of the genetic composition and activities of communities so complex that they can only be sampled, never completely characterized,” the NRC continues. “In the second sense, that of a research field, meta means that this new science seeks to understand biology at the aggregate level, transcending the individual organism to focus on the genes in the community and how genes might influence each other’s activities in serving collective functions.
“Individual organisms remain the units of community activities, of course, and we anticipate that metagenomics will complement and stimulate research on individuals and their genomes,” the NRC predicts. “In the next decades, we expect that the top-down approach of metagenomics, the bottom-up approach of classical microbiology, and organism-level genomics will merge.”—L.L.L.