|January 17, 2013
Misleading statements from: “Food poisoning test breakthrough could pose risk to public safety measures”
The article written by Jalonick and Neergaard, “Food poisoning test breakthrough could pose risk to public safety measures,” encompasses a handful of false truths which when taken together, adds up to misleading the public regarding sequencing techniques and their applications. Let’s take a brief moment to go through the article and identify some misleading or false statements.
“These new tests [NGS] can’t detect crucial differences between different subtypes of bacteria, as today’s tests [PFGE] can.”
This statement is misleading. NGS and PFGE test for different things. PFGE provides a subtype based on sequences of select housekeeping genes in a bacterium’s genome where NGS sequences the entire genome. NGS provides more data, that is accurate, which is ultimately better for pathogen surveillance as was highlighted in Allard et al., 2012, High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach. The article demonstrates how PFGE wasn’t able to distinguish between S. montevideo isolates. Allard et al., 2012. High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach. BMC Genomics 13: 32
“It all comes down to what’s called a bacterial culture — whether labs grow a sample of a patient’s bacteria in an old-fashioned petri dish, or skip that step because the new tests don’t require it.”
Pathogen identification through culture is an ancient technique that isn’t accurate and misses the majority of pathogens in a sample. How do you account for pathogens that aren’t able to grow on the selected medium the laboratory is using? NGS can give you a better representation of which species is present in the population. For evidence that modern sequencing techniques are more accurate than classical identification, read about how newer sequencing techniques have shed light on the microbial community in cystic fibrosis airways:
Rabin HR and Surette MG. 2012. The cystic fibrosis airway. Curr Opin Pulm Med. 18(6): 622-7.
“Tracking an outbreak of E. coli back to this peanut butter and nut processing plant in eastern New Mexico, for example, would become next to impossible if new food poisoning tests are adopted on a wide scale.”
False. Read up on how the University of California Davis is developing a database (free of course) of all sequencing information that would allow for proper surveillance of food pathogens and at a much faster rate: click here for the full story.