NTR: food (kill step)

[KaylaPenn]

NTR: food (kill step)

Parent Term/Class:

food product by process:FOODON_00002645

Definition:

food which has undergone a processing step that is expected to be lethal to pathogens

Definition Source:

https://www.fda.gov/regulatory-information/search-fda-guidance-documents/guidance-industry-guide-minimize-microbial-food-safety-hazards-fresh-cut-fruits-and-vegetables

Synonym(s):

Exact Synonym(s):

food (lethal step)

Additional Comments (not an annotation):

Non-government blog post explaining "kill step": https://www.fdareader.com/blog/2017/07/25/on-the-kill-step-and-leftovers brief definition from FDA:

[maweber-bia]

Hi there!

Thank you for your valuable FDA resource; I am aware that the killing step (or lethal step) are operations of a process aimed at destroying a certain amount of bacteria present in a food but this process can have different forms, as explained in the FDA website:

• Cooking

• Use of chemicals: For example, using anti-microbial produce wash reduces bacteria counts in vegetables that will be served raw.

• Pasteurization: heating something up without meaningfully changing it's composition to kill bacteria

• Freezing: The majority of fish intended for raw consumption is frozen for a period of 7 days to kill harmful parasites. Note that freezing isn’t effective as a kill step against bacteria.

So I wonder if we can also create a "lethal type" process in the process hierarchy ?? This could be a parent class for cooking, use of chemicals, pasteurization, freezing (or even other techniques that are lethal for bacteria, for instance high pressure treatment, etc..) However, the lethality is depending on factors such as time, temperature and the kind of bacteria... @ddooley can we deal with such constraints ?

[KaylaPenn]

Having a lethal type process sounds even better to me

As for different factors, maybe make keep it general for now? If there's use for it later, then add separate qualifiers. I hope this makes sense as a visual example:

General process map

   food processing
     ^          ^
     |        temperature type
  lethal           ^ 
   type  <-- food (boiling)

Qualifier map

processing factor  <-- microbe targeted <-- Salmonella enterica
   ^        ^                     ^
  time      |               Escherichia coli
       temperature    
        ^     ^
      high   low

[KaylaPenn]

As an update, we're working with others to determine if the term 'food (kill step)' could be better phrased, preferably changed to something in current use by the US FDA.

[ddooley]

I was just working on a related problem, defining the gradations of cooking. Here's the diagram:

So I'm wondering about the possible cross-over terminology from food-safety or food science, to biomedical realm. I was looking up difference between disinfection and sterilization. https://www.sciencedirect.com/topics/chemistry/sterilization-and-disinfection

Tarini and I have been working on the distinction between referencing food processes by objective, vs by mechanism. Mechanism = pasturization, freezing, application of chemicals; objective = cleaning, disinfection, sterilization. Whether application of a mechanism achieves a process objective is dependent on the amount of time the mechanism is applied, or other variables. Mechanisms are a means to an end.

Now I read that disinfection achieves a partial reduction of pathogens, while sterilization achieves elimination of pathogens. So I suspect that like the food cooking process, a "kill step" leads to either disinfection or sterilization, and we should have a class hierarchy that reflects this.

So: food (cleaned) food (disinfected): a food which is the immediate output of a pathogen reduction process. food (sterilized): a food which has no pathogen organisms.

and possibly: food (disinfected or sterilized)

and lethal food process draft definition: a food process which reduces (disinfects) or eliminates (sterilizes) the quantity of pathogen organisms in some food.

Then the lethal food process can perhaps logically have (preferably by inference) the "full cooking process" as subclass - but to be nit-picky, can something be called fully cooked, and yet still have pathogens, like giardia which I recall takes at least 3 minutes in boiling water to get rid of? If so, then only some instances of full cooking process will be equivalent to lethal food process.

But does this fit/align with existing food-inspection etc. vocabularies?

[maweber-bia]

Hi ! Sorry to disappoint you but things are not so simple! In fact sterilization is also a thermal process which involves the use of kill curves, which display a logarithmic relationship between the “dose” of sterilizing agent applied (in this case, temperature) and the percentage of the initial number of organism present

I think that disinfection refers to use of chemicals (desinfectants)

see the reference to medical /surface cleaning :

Disinfection can be achieved at varying levels as defined by the CDC:

•

High-level disinfectants are chemical sterilants that may be used for a shorter exposure period than would be required for sterilization to kill all microorganisms with the exception of high numbers of [bacterial spores](https://www.sciencedirect.com/topics/engineering/bacterial-spore).

•

Intermediate-level disinfectants will kill mycobacteria (causes of tuberculosis and leprosy), vegetative bacteria, most viruses (such as poliovirus), and most fungi but do not kill all bacterial spores.

•

Low-level disinfectants kill most vegetative bacteria, some fungi, and some viruses such as Staphylococcus species, Pseudomonas species, Salmonella species, HIV virus, herpes simplex virus, hepatitis B, hepatitis C, and many common cold viruses.

In food, you may not found chemical residues and you have to rinse with clean water any surface after a chemical disinfection process so it is strange to have food 'disinfected'

In the case of milk, you may have sterilized milk (UHT milk) or pasteurized milk but I don't think you will say that milk has been "desinfected" (and same for cooking, even if it is full cooking : you don't say your meat has bean "disinfected" or "sterilized" but that you have killed or strongly reduced the number of bacteria or microorganism ...

so to me it is more appropriate to have a lethal food process defined without reference to disinfection or sterilization:

lethal food process draft definition: a food process which reduces or eliminates the quantity of pathogen organisms in some food.

[KaylaPenn]

Great discussion, and the draft looks fitting, too. I'll take it back to my colleagues to get their thoughts.

[ddooley]

@maweber-bia good stuff and we'll need to accommodate those categories! I think we're now debating the use of these terms in different fields - which is of course necessary to achieve an interdisciplinary vocabulary. What about sterilization by radiation? https://www.rpi.edu/dept/chem-eng/Biotech-Environ/Projects00/sterilize/radiation.html . And disinfection by pasteurization? https://www.cdc.gov/infectioncontrol/guidelines/disinfection/introduction.html#:~:text=Disinfection%20describes%20a%20process%20that,liquid%20chemicals%20or%20wet%20pasteurization.

d.

[ddooley]

I think then perhaps if sterilization can (across disciplines) mean full or partial removal of pathogens, then we could just create a vocabulary oriented to those states, and attach disinfection as a synonym where appropriate?

e.g. food (fully sterilized) food (partially sterilized)

similar to the food (cooked) structure?

[maweber-bia]

@ddooley

sterilization by radiation : agreed "decontamination" by pasteurization would better fit to my view

but I fully understand the need to have cross-disciplinary terms... sterilization and aseptie have specific meanings in the biomedical sectors so I do not think it is easy to change these meanings (I don't know if partially or fully sterilized would be accepted)

I suggest fully decontaminated or partially decontaminated instead ?

[ddooley]

@KaylaPenn It would be great to get feedback on term name viability. @maweber-bia I like your notion of turning to "decontamination" as a catch-all for both disinfection and sterilization, as long as it doesn't imply some contamination has necessarily occurred over and above what is "naturally" in the food? This document supports your use of decontamination I think.

decontamination process
   food-safe decontamination process
       food-safe partial decontamination process
       food-safe full decontamination process
   biomedical decontamination process
        ...

Then the nouns to back that up:

food (decontaminated)
   food (fully decontaminated)
   food (partially decontaminated)

Thoughts?

[maweber-bia]

Great!

we should then define what a "contamination" and a "contamination process" are :

contamination is the outcome of a contamination process which can occur at any time in the food life (from contaminants originally present in the raw materials to the end of life (consumption) of the food product)

contaminants can be either from biological or chemical nature

@ddooley what is the meaning of your "food-safe" decontamination process ?

[KaylaPenn]

I was on leave yesterday, but the feedback from the term 'lethal food process' and draft definition was positive with no suggested changes. To quote one person:

I also had impression that different processes are intended to meet different thresholds and can get a bit
involved. From the metadata collection perspective maybe just that one or more of these lethal food
processing steps was used is good information to collect

Having exact definitions is a great objective. For our metadata collectors, they may be satisfied with more general and surface-level parent terms

[ddooley]

I guess I can say "food decontamination process" rather than "food-safe ... " I'd put the "safe" word in there to suggest the level of tolerance of pathogen removal, i.e. decontaminating to a food-safe level, as opposed to decontaminating to a completely sterile level. Thoughts? Shall I keep it simpler and use "food" rather than "food-safe"?

[maweber-bia]

I would simply keep "food decontamination process" and the children "food partial decontamination process" and "food full decontamination process"

[ddooley]

I see this needs resolution. I've tried to list all the revised new terms here, with definitions for final comment. One note, APOLLO has contamination and contaminated thing ; as APOLLO states this is preferred term "biological contamination" but doesn't allow it to apply to organisms, which rules out many food items by and large! I have opened https://github.com/ApolloDev/apollo-sv/issues/234 for clarification. We are allowing wider sense of contamination here to include toxins etc. on or in food material.

MATERIAL ENTITIES food (cleaned): Food which is the output of a cleaning process. (DONE) --> output of some food cleaning process

This is something like ChEBI's environmental contamination but would be a material entity bearing that role when on or within another material entity. contaminant: Any minor or unwanted substance introduced into or on a material entity that can have undesired effects.

food (contaminated): Food which has one or more contaminants in or on it. axiom: output of some food contamination process.

food (decontaminated): Food which is an output of a food decontamination process. ...food (disinfected): Food which is an output of a pathogen reduction process. ......food (fully sterilized): Food which has no pathogen organisms. ......food (partially sterilized): Food which has some quantity of pathogen organisms.

PROCESSES

food contamination process: A process occurring within a food product's rearing or assembly or distribution, up to the point of consumption, in which contaminants are introduced on or within the product. comment: The food contaminant(s) involved can be chemical or biological. There is also the case where a contaminant is created in a material as a result of other introduced chemicals or pathogens.

decontamination process: A process which removes contaminants from a material entity.

food decontamination process: A decontamination process applied to food. food partial decontamination process: A food decontamination process applied to food which yields the partial removal of one or more contaminants. food full decontamination process: A food decontamination process applied to food which yields the complete removal of one or more contaminants.

biomedical decontamination process: (can be defined elsewhere)

food detoxification process: A process which removes toxins from food material. comment: This makes no commitment to whether a toxin was introduced to the food or naturally occurs in the food, such as cyanide in raw casava. We would say the cooking process involves detoxification, but not decontamination per se. since the cyanide was not introduced or created as a result of other contaminants.

[hoganwr]

It is a misconception that Apollo-SV's "contamination" does not apply to organisms. I reproduce the definition here:

"The process of existence without reproduction of a pathogen of a particular biological taxon in or on some material entity"

It says material entity not organism. I believe organism is a subclass of material entity, so organisms may be contaminated.