Source: MEATINGPLACE, 12/27/11

Dr. Martin Wiedmann and colleagues at Cornell University recently reported on their development of a new method of genome sequencing that enable government agencies and food companies to pinpoint the nature and origin of foodborne bacteria with much greater accuracy than allowed by current methods including pulsed-field gel electrophoresis (PFGE).  

Wiedmann took time to discuss his findings with Meatingplace:

How is this method going to change the investigation of foodborne illness outbreaks?
Full genome sequencing is changing how outbreaks that are caused by common PFGE types are investigated. Some PFGE types can be very common and found in unrelated foods and human cases. With a common PFGE type, the fact that the same PFGE type was isolated from two patients does not necessarily mean both patients are part of the outbreak. Similarly, isolation of a matching (common) PFGE type from a food or another potential sources does not necessarily mean this food represents the outbreak’s sources. In these cases, full genome sequencing can be used to provide better evidence whether a human case is part of an outbreak or a food is a possible source of an outbreak.

Importantly though, even with full genome sequencing, epidemiological data are still necessary to define the scope of an outbreak and to identify outbreak sources.

How specific will the method be in terms of tying cases of foodborne illness to a particular food source?
While full genome sequencing based approaches will improve our ability to accurately tie foodborne disease cases to an outbreak source, epidemiological evidence will remain critically important for linkage between a food source and a disease case or outbreak. Genome sequencing will though reduce the risk of an incorrect linkage as it will provide increased discriminatory power over currently used approaches such as PFGE.

Suppose you have a few samples from people apparently involved in an outbreak.  How long will it take to do the sequencing so you tie their cases to a particular food source?
The actual DNA sequencing from receipt of a bacterial isolate to completion of the actual DNA sequencing can now be achieved in approx 2 days or less. In some cases more in-depth genome comparisons may be necessary; these types of follow up bioinformatics analyses may take from days to weeks.

What will this approach allow investigators to do that they can’t do now?
This approach will allow for improved detection of outbreaks and identification of outbreak sources in cases where common PFGE types are responsible for an outbreak.  In addition, these approaches will allow investigators to clarify situations where outbreaks appear to be caused by two or more closely related PFGE types. In these situations, full genome sequencing will help clarify whether two closely related PFGE types are so similar that they may have originated from the same source within a time frame that is consistent with a causal relationship or not.

For example, sequencing of human isolates and isolates from an epidemiologically linked food that had a PFGE type that differs by a single band from the human isolates can clarify whether the differences between the human and food isolates are such that they could occur over short time period (e.g., during isolation from a food or during passage through a human).

You’ve published the results of an experimental investigation using genome sequencing. Do you think this will become the standard method of outbreak investigation, or will be it used only in special cases?
I believe that within the next year genome sequencing will become standard procedure in outbreak investigations where PFGE provides data that can be difficult to interpret or ambiguous. FDA CFSAN is already starting to routinely use full genome sequencing for these applications. Health Canada, the Canadian CDC equivalent, is also staring to use genome sequencing for these applications. I expect the U.S. CDC to have its full genome sequencing capabilities up and running soon.  I do not think it is out of the picture that full genome sequencing will fully replace PFGE within the next 5 to7 years.

What should members of the meat industry think about this approach?  Should they be worried that investigators and plaintiffs’ attorneys will more easily target them?
I think industry should be excited about these tools as they have the potential to provide better data than PFGE. There will be some challenges as to how to deal with full genome sequencing data in the short run, but this will sort itself out very quickly.

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