USDA-FSIS Quarterly Enforcement Report: Downloadable Raw Data and 10 Year Trends

data-graphicIn my mass of emails from the government each day, every quarter I get one from FSIS letting me know what they’ve released their quarterly enforcement report. These reports detail actions taken against specific establishments, as well as details on how many enforcement-type actions are taking place ongoing.

I have a problem with this report however. It’s presented as a pdf with no metrics or historical data to put the information in context. FDA has done a good job in the past few years at releasing metadata in formats that allow analysis (CFSAN adverse event reports, inspection database, etc.), but USDA takes the time to kick out this report without showing what the trends are.

Alright raw data nerds, here at FF&F we’ve got your back. For all your analysis needs, we’ve collected a few of the more “top level” reporting numbers from reports going back to 2007, and put them all in excel for you to strip apart and analyze to your hearts content. We’ll even keep updating this spreadsheet and re-uploading every quarter ongoing.

fsis enforcement reports data (.xlsx)

Because some of us like bringing home a growler on a Friday night and entering data to do basic trending on government statistics, here are some of the trends I found interesting that aren’t visible by looking at any one of the individual reports.

verification-procedures-performed

These are the number of individual verification procedures performed by FSIS inspectors each quarter. We can’t speak as to why there was such a change in 2010-2011, as these numbers could simply have started being calculated differently in the system. But NPR had some data to suggest that overall meat consumption started declining in 2010, which could lead to fewer establishments or approved inspection hours, and thus fewer verification events.

compliance-rate

Compliance rates have always remained above 98% (meaning that 98% of all verification activities end with an inspector going “okay, you’re doing the right thing here”). But like overall verification, compliance seems to have a slight downward trend as well. It’s hard to say this decline is significant since the standard deviation of these percentage data is only 0.0016, but the whole point of getting this data organized to demonstrate the trend is to keep tabs on things like this. It’s hard to never have a downward trend when you hover near 100%, but it will be interesting to see if there is any FSMA effect in the next few years on this trend in either direction.

percent-of-nr-appeals-that-were-granted

That 2% noncompliance rate is a count of Noncompliance Records (NR’s) that are issued. Per FSIS:

An NR is a written record that documents noncompliance with FSIS regulations. An NR notifies the establishment of the noncompliance and that it should take action to remedy the situation and prevent its recurrence. Noncompliance reported on NRs varies from non-food safety issues to serious breakdowns in food safety controls.

When an establishment fails a verification activity, it is issued an NR and has the option to appeal if they think an observation was out of context, the inspector was incorrect in his/her interpretation of the regulation, or some other circumstance led them to believe the finding was incorrect. The graph above shows that historically about 1/3 appeals are granted by regional offices/DC when establishments challenge an NR. But in recent years that number has dropped from around 35% to 30%. This could have also contributed to the increased number of noncompliances observed earlier, now that fewer appeals are being granted.

percent-livestock-carcasses-condemned-of-those-inspected

The poultry carcass inspection/condemn data didn’t have any interesting trends, it swung up and down without a lot of overall variation. The livestock carcass data was more interesting in that it seems to have a sustained downward trend.  This could be to better herd health in the last decade or more efficient slaughter practices that result in fewer condemned carcasses from injury or contamination. While the cause is uncertain, as long as it isn’t the result of poor or inconsistent enforcement, this is a great trend! Fewer condemned animals is better for the animals and the environment.percent-meat-and-poultry-refused-on-inspection

I’m not sure this paints a completely accurate picture, but the data points were real, they actually wrote zeroes in the older reports. While the number of products imported has increased overall, this % refused trend shows that even though imports are increasing, we’re also rejecting more meat at the border than ever before. You can check out this FSIS directive to learn more about inspection of imported meat and poultry and what refusal criteria might be.

If you’re more intense than I am and want to do advanced statistics that excel can’t handle, you can see what’s out there in terms of software and let me know if you discover any new insights from this data! The spreadsheet and all graphs were created from source data in the FSIS quarterly enforcement reports.

 

ResearchBlogging.org

USDA/FSIS (2017). Quarterly Enforcement Report for Quarter 1, Fiscal Year 2017 United States Department of Agriculture

FDA Warning Letters this week 2/14/17

I’m back! Check out the About page for more information on the new direction of the blog. Today’s post will be a recurring one. Each week I’ll go through the FDA warning letters recently posted, read through the ones related to food, and offer a summary of any interesting findings and/or findings that we as consumers should or shouldn’t be paying attention to.

warning-letters

First, because this blog is about education and communication, let’s help out those who don’t know what an FDA warning letter is. Per FDA:

When FDA finds that a manufacturer has significantly violated FDA regulations, FDA notifies the manufacturer. This notification is often in the form of a Warning Letter.

The Warning Letter identifies the violation, such as poor manufacturing practices, problems with claims for what a product can do, or incorrect directions for use. The letter also makes clear that the company must correct the problem and provides directions and a timeframe for the company to inform FDA of its plans for correction. FDA then checks to ensure that the company’s corrections are adequate.

This is a good description of what a warning letter is, but when does FDA hand them out?

FDA sees warning letters as a method for encouraging voluntary action to correct problems they found in investigations, after-market product testing and label review, plant inspections, and to increase the pressure on companies that aren’t responding to form 483 findings (inspection violations).

In FDA-speak this means that they’re avoiding forced action that would be supported by a judge or federal officer, such as injunctions or seizing products and facilities. However as far as any reputable food company is concerned, it’s really being voluntold. After all, companies that do not respond to warning letters are almost guaranteed to subsequently receive actual enforcement actions, and because warning letters are public, if a company is in the public space in any large way (e.g. a recognizable brand) getting your warning letter closed is an additional public step to regaining consumer trust.

This is just a brief overview, for more information on FDA decision-making in regards to why a warning letter might be issued you can read their procedures. It also contains a lot of information about “prior notice” and other legal requirements the warning letter satisfies.

FDA warning letters this week

Now let’s get to the goods! In these posts I’ll be using the warning letter numbers to identify specific letters and avoid typing company names simply for the sake of making it about the information in the letter and not the addressee. If you’re curious about which companies received the letters, you can check them out yourself or google the warning letter number, that should get you there.

I picked a doozy of a week to start doing this, there are some extensive and complex letters here, I’ll keep my comments “brief”, but check out the letters for yourself to read the full scope of violations.

WL# 14-17

Subject: Seafood HACCP/CGMP for Foods/Adulterated/Insanitary Conditions

Seafood shows up a lot in warning letters for HACCP violations. Companies and produce Juice and Seafood have specific critical control points and HACCP plans spelled out in the regulations. Oftentimes small companies or importers who have never been inspected, or were never aware of what their requirements were, violate or do not put these programs in place. Because this is considered an imminent threat to food safety, FDA almost always issues a warning letter. Most of what you see are companies that just straight up don’t have the programs in place, rather than specific violations. This warning letter is actually a follow up to a previous one, where FDA reviewed the corrective actions of the company and determined that they weren’t enough.

We received your written response dated January 10, 2017 which included Product Specifications and Importer Written Verification Procedures…However, your product specifications failed to identify the hazards that are specific to the product.

Off the top of my head, I would guess that the person who wrote the specifications in response to the letter has not had formal HACCP training and didn’t understand how to carry out an actual hazard analysis, or where the information could be found in the CFR. Ultimately this warning letter represents a failure of a company both to follow prescribed regulations and understand the value of HACCP and Preventative Food Safety.

If you are interested in HACCP, I’ll probably cover many basic principles throughout this blog, but there are many people much smarter and experienced than me who have written solid books on the subject that can be very helpful for the studious. Otherwise there are a ton of classes and free online materials out there, go find what works for you!

WL# 2017-NOL-03

Subject: CGMP/Food/Prepared, Packed or Held Under Insanitary Conditions/Adulterated

I love seeing this subject on warning letters, because it usually means we get some insight into how FDA enforces current good manufacturing practices (cGMP or GMP). Other times, we just get to hear about gross conditions within a plant. It’s really a mixed bag of findings, but they’re usually interesting in one way or another.

The first set of findings for this letter concerned inspectors finding flies, bugs, and rodent excreta pellets (REP’s, and one of my favorite acronyms ever) in the bakery. Thankfully, the REP’s were found underneath a mop sink in the corner, and not somewhere closer to food (some warning letters are much more nauseating with respect to where they find these things). The flies were found throughout the facility, both on products and equipment as flies in your home would. Not a good start. I imagine this facility has either no pest control program or doesn’t use a professional. Either way the presence of the flies indicates that their presence was “normal” and that this facility needs culture change. Further demonstrated by FDA noting that they found pests in inspections for two previous years (clearly no lesson was learned).

Next time you are in a fast food restaurant, look around and see if you can spot an insect light trap (ILT). Often they’re decorative like the one in the link, and they work super well at immediately attracting bugs that make it through the door (or other openings). Facilities with preventative pest control will have these in areas where they will be most effective, attracting pests away from sensitive areas.

The second set of findings concerned handwashing practices. These weren’t the worst ones you see. The ones that are immediately concerning are when FDA notes things like employees using the restroom or dirty surfaces like pest traps and mop buckets, then going back to touching products. In this plant the inspector took note every time an employee left the area or touched non-food surfaces and returned to food without stopping to wash their hands. This is wrong, and the company again has a culture issue, but remember that doctors only follow proper handwashing 40% percent of the time as well. So while it’s the wrong behavior for handling food, it’s far from abnormal and a constant struggle in all settings.

Additional findings concerned sanitation and handling of food contact surfaces. And…well, these some things that directly inoculate your products with bacteria.

packaging material…was observed in direct contact with the floor soiled with food debris

The baking sheet pans came into direct contact with a trash can during scraping.  The sheet pans were not cleaned or sanitized after contact with the trash can before unbaked 9” pie shells were placed onto the sheet pans.

observations [of accumulated food debris on equipment] were noted after the previous day’s production run and prior to production start-up on each of the aforementioned dates.  Production commenced without removal of the observed food debris.

The rest of the findings show pretty severe deficiencies with the way the company conducts itself, handles products and materials in the facilities (including storing secondary packaging in the employee bathroom…) and in general fails to maintain a sanitary facility for food production. Honestly this warning letter is so chock full of obvious contamination issues it’s frustrating that FDA hasn’t taken action sooner. After all, more than half of the observations are followed by the note:

This is a repeat observation from the 9/20/2010 FDA inspection.

This is where I get frustrated as a member of the industry, a taxpayer, and a consumer. According to FDA’s database of inspections, they’ve visited this facility on the following dates: 4/14/09, 9/23/10, and 6/10/11. According to the database, that’s the last time they’ve been there until the inspection noted in this warning letter (10/18/16). They were also never issued a warning letter for those inspections in 2011. Either they decided the State of TN was in charge of following up at the state level, they contracted FDA inspections through the state of TN in the intervening 5 years, or no one inspected this facility for 5 years after finding all these problems in 2011.

We won’t ever know, but regardless of what happened in the intervening 5 years, we should be grateful FDA is taking action now, and found the facilities response to a 483 issued at the inspection:

…[we] have determined your response is inadequate.  You have not provided evidence such as photographs, receipts, and/or training documentation to show you have corrected any of the violations observed.

Here’s hoping some pretty good evidence was provided in 2011.

WL# 2017-NOL-05

Subject: Seafood HACCP/CGMP for Foods/Adulterated/Insanitary Conditions

This letter is for similar violations as the first one we discussed for failing to adhere to seafood HACCP regulations. However this producer actually has a properly constructed hazard analysis and HACCP plan, but failed to properly execute it.

The firm had a cook step for crab that included a time/temperature combination to ensure that any pathogens would be killed. By reviewing the companies records, FDA observed that 9 different times employees had ended the cooks too early but no notes or corrections were made. This is concerning because it means that product may have been released undercooked, and employees running the equipment didn’t have the training necessary to follow the cook instructions, or understand why ending it prematurely was unacceptable.

The letter indicates that the company and FDA have been working through this issue, FDA indicates that the response has been inadequate for lack of evidence. Protip: if you tell FDA “we modified our HACCP plan to your recommendations”, you have to send them the modified HACCP plan. It’s amazing how many follow-up letters have to tell companies this or similar.

This facility also had sanitation issues, not as severe as the bakery above, but running on dirty equipment undermines any HACCP plan or cooking step you do.

You are not monitoring the cleanliness of food contact surfaces as evidenced by previously cooked crab parts from operations on the previous day and after cleaning operations were observed on the metal conveyor were observed to come into direct contact with newly cooked crabs on the conveyor belt.

Protip: if there’s still pieces of the food from the last time you used it, it isn’t clean.

Among the sanitation violations however, FDA notes that the correction actions the company informed them of are acceptable enough that they will verify at next inspection, rather than simply reply that “response was not adequate”, which is a good sign that FDA has confidence the company will get it together and can be trusted to keep improving without direct supervision. From the letter I get the impression that the company had problems, but didn’t have the longstanding culture and facility issues we saw manifesting in the bakery discussed earlier. After all, they couldn’t demonstrate that the low concentration of chlorine in their sanitizing stations was such a pervasive problem without also noting that employees were actually using the sanitizer stations frequently.

WL# CMS Case # 516352

Subject: Acidified Foods/Prepared Packed or Held Under Insanitary Conditions

Acidified foods are foods in hermetically sealed (airtight) containers that could support the growth of microorganisms (high water activity), but are modified with acidic ingredients to bring their final pH to 4.6 or below. FDA strictly regulates these foods because they have the potential to support the growth of Clostridium botulinum which causes botulism, a truly terrifying disease.

Because of these strict regulations, we often see warning letters related to not following HACCP/regulatory requirements for acidified or low-acid foods, very similarly to those we see for juice and seafood. This producer had a lot of issues that come down to them not following these regulations and controlling the process of production, leading FDA to crack down because they present a risk of growing Clostridium species in their products. Check out the letter for those specifics.

In addition to the acidified foods violations, the firm had some interesting violations connected to glove use. Nitrile gloves are often associated with food safety, but they aren’t magic. A clean hand is better than a dirty glove, and this firm demonstrated this with a few well observed glove observations:

an employee…had a tear on the glove worn on his right hand. The tear extended from the palm to the backside on the hand across the area between the thumb and fore finger.

an employee…was observed picking up a lid which had fallen to the floor and placing it in a sink. The employee did not wash or sanitize his gloves before returning to capping the filled jars of product

The only food safety “magic” that gloves provide is that they can be changed. A glove change and sanitize can save time and provide convenience to employees who do things like pick up objects they dropped on the floor or open doors when they don’t have to walk away to a handwashing sink. Provided that the gloves themselves are also in a convenient nearby location.

And when it comes to enforcing food safety behaviors, convenience=compliance.

 

FDA officially refers consumers to Wikipedia for information on food pathogens

I was perusing the Bad Bug Book while doing some research on the recent Blue Bell outbreak and came across a hyperlink. After hearing “do you want to know more?” in my head, I clicked through on some non-L. mono species of Listeria and was…confused. I quickly doubled back, thinking that maybe I had been redirected, but there it was.

FDA Bad Bug Book linking directly to wikipedia
FDA Bad Bug Book linking directly to Wikipedia

FDA describes the reference as “current information about the major known agents that cause foodborne illness.” Descriptions also include a statement that it should not be used as a comprehensive or clinical reference. However, this isn’t an excuse for making a consumer and industry reference link to a completely uncontrolled document source. The Bad Bug Book (2nd ed.) is a wonderfully written resource, both for a lay and industry audience; but the fact that the authors of the Listeria page referred to Wikipedia as an ongoing resource, without knowing or being able to control the content presented to consumers, is irresponsible. A nefarious Wikipedia troll could at any moment have an article claiming that L. grayi is a GMO herbicide borne bacteria found in bananas that causes uncontrolled crying and hair growth, and have the full support of the FDA behind their article.

Please don’t write that article.

A  currently live example of why this was such a poor decision is that if you click through to some of the pages, they don’t exist (as of 7/27/15). I don’t know if the author intended to write them him/herself and never got around to it, or if they simply assumed the pages existed, and then didn’t bother to review the content. I’m not satisfied with either of those answers, and if alternatively the reference articles were removed at some point, that also highlights what a poor decision those links were.

Given the sheer number of PhD’s involved in the book’s creation, I think taxpayers should expect a resource with material actually reviewed and sanctioned by FDA. The poor editing here is unacceptable and a change should be made to the current edition of the book.

Many of the other pages in the book name multiple related species, but either included links to NIH or CDC or included no link at all, both of which are acceptable alternatives. I won’t name the authors and editors of the book here, anyone who wants to know can find them at the front of the document. If you’re interested in bringing this to FDA’s attention in your own way, they’re on twitter as @US_FDA and additional points of contact are available at www.fda.gov.
ResearchBlogging.org

Food and Drug Administration (2012). Listeria Monocytogenes Bad Bug Book, Foodborne pathogenic microorganisms and natural toxins. Second Edition, 99-100

Misinformation and selective coverage change perception of outbreaks, but can be corrected by presenting the facts

While it’s not an animal product, the Listeriosis outbreak recently traced to apples is just as relevant to the food industry as a whole as any other food-borne illness outbreak. While I was looking for more information on the outbreak, I came across this gem* of an article posted on cnn.com.

*When this post was originally written, the text on the website read: “At least seven people have died after eating caramel apples that may have been infected with Listeria monocytogenes. Followed immediately by a quote from CDC which stated ‘Thirty-one ill people have been hospitalized and six deaths have been reported. Listeriosis contributed to three of these deaths, and it is unclear whether it contributed to an additional two deaths. The sixth death was unrelated to listeriosis.'” CNN has since removed the CDC quote, but kept their original ‘7 deaths’ statement.”

I found this disturbing on two levels. First, the fact that they reported that at least six people had died after eating contaminated apples, when listeriosis was only confirmed as cause of death for 3 of the cases and ruled out for the 6th.

“Hey Jen, what’s the body count up to on that outbreak article?”

“Looks like 3 for sure, could be 3-5”

“Thats it?”

“Don’t worry, we’ll round up to 6+, if you use a Log scale, they’re practically the same number.”

Second, they used the direct quote from CDC’s 12/31 update to directly contradict themselves in the following sentence. Who wrote this article? (update, clearly they wizened up and removed the quote on Jan 15, I wonder if they saw the reddit post. This is also a rhetorical question, their name is on the article, but we also need to assign blame to their editor.).

So what sort of impact could this statement have? Young, Norman, and Humphries reviewed the impact of media coverage on how dangerous we think they are. They found that indeed, those conditions/diseases that receive more media coverage are perceived by medical students as a “worse” condition. This can actually be a very good thing for infectious disease outbreaks, as rapid media coverage of the danger encourages people to avoid contact with others, leading to exponentially fewer cases the earlier you do it. This is less good however, when non-infectious diseases or inaccurate correlations are blown out of proportion (e.g. people avoiding pork to avoid H1N1).

The literature review included in the beginning of the article shows that this isn’t necessarily new information. However, the authors also examined the effect or including additional “objective” information about the conditions when asking students to rank their risk. The result was that, as seen in the chart below, when provided additional information the study participants then changed their views of the diseases. The large separation between what they had seen in media and what they had not seen shrank and they assigned more risk to those threats that aren’t often talked about, and became less nervous of the high coverage items in comparison.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003552As a science blogger, this is my soapbox, as this study highlighted the responsibility for those who know more than the headline to speak up and share their knowledge, because people can and will be receptive to it as long as it’s available.

Unfortunately, the study was inherently biased as medical students are more likely to be receptive to new data (especially related to disease) as opposed to other groups with stronger existing bias’ (e.g. CAM users, anti-vaccination proponents, specialist doctors, or epidemiologists who may be swayed by previous outbreak coverage). The authors specifically did not survey students on their current media usage or biases, and therefore could not demonstrate the power of providing additional information on subjects they may have already formed strong opinions on.

I’d like to see the study repeated with an older group, as student’s opinions are more likely to be malleable as they are less likely to know as much about these illnesses or had personal experiences with them. A repeated study with participants of at least 40-years-old would be more telling and help us understand what effect providing additional objective information can have.

After all, as nice as it is to know students can be taught, they’re not the ones in public office. Are they also willing to change their minds when new information is made available?
Young ME, Norman GR, & Humphreys KR (2008). Medicine in the popular press: the influence of the media on perceptions of disease. PloS one, 3 (10) PMID: 18958167

Mummert A, & Weiss H (2013). Get the news out loudly and quickly: the influence of the media on limiting emerging infectious disease outbreaks. PloS one, 8 (8) PMID: 23990974ResearchBlogging.org

Anatomy of a “Serving”

NFPIs it how much you’re expected to eat? How much you should eat? Pardon me, but if I want to eat an entire bag of potato chips, that’s exactly what I’m going to do.

I say this as the guy who helps create nutrition facts panels for food products for a living. I have read, reread, proof read, and colored red hundreds of these little tables in my time, and believe it or not, people aren’t lining up at parties to hear my thrilling stories.

I know!

Right now you’re thinking, “But Austin, I remember back in 2008 the FDA called 2,584 adults from the US to ask them questions about their diet. And 24% of the respondents said they had no idea if serving sizes were determined by government rules or by manufacturers.”

Your oddly specific observation would be correct, and I should have at least ¼ of the room hovering around me in rapt attention, waiting for me to clarify this confusing point. Time has shown however that everyone is clearly too intimidated to approach and ask the simple questions, even when I’m subtly firing off labeling trivia from the empty cracker box carelessly left by the cheese platter, or establishing my mastery of the dance floor.

Fact: Every party has a dance floor, here’s the label. dance floor Well let’s clear this up right now while I’ve got you at home/work/somewhere, on your computer/phone/tablet (scary that I know where you are, isn’t it?). Who determines serving sizes, manufacturers or the government?

Answer: The government!…ish.

Well that was unsatisfying, but it’s the most accurate answer I can give. Essentially what happens is that our government, via the FDA and FSIS (Food Safety Inspection Service), determine how serving sizes are to be calculated and presented, but also leave manufacturers options in specific situations.

So how are serving sizes determined?

Step 1, what are you eating?

he first step companies need to take when determining serving size is to determine what type of product they are selling. Back in 1993 when they had to decide all of this stuff, FDA determined that they could use data collected in the NHANES dietary surveys conducted in 1978 and 1988 to set these standards. These were nationwide surveys that collected all sorts of data, including nutritional intake and food frequency data. With this information, FDA created “Reference Amounts Customarily Consumed,” or RACC, for different categories of food.

The first step is easy, find the category that a food falls into, and look up the RACC used to determine the serving size in 21 CFR 101.12 (for non-meat items). For example, if I was making mashed potatoes, my category would be “Potatoes and Sweet Potatoes/Yams: Mashed, candied, stuffed, or with sauce” and my RACC would be 140 grams.

Step 2, how can someone measure it out?

Here’s where the variation begins! You might just want to use that 140 grams we saw above; however, not everyone has a scale in their kitchen, and let’s see you try to guess how much mashed potato makes up 140 grams. Can you think of the last time you weighed your food, much less with metric weights (provided you live in the U.S.)?

So at this juncture, the government instructs manufacturers to determine what the closest “common household measurement” to one RACC of your product is. So if we take 140g of our potatoes and see that that’s about 2/3 of a cup, our serving size becomes 2/3 of a cup!

>THIS IS IMPORTANT<

Imagine we made a new, super fluffy mashed potato with more butter, and 140 grams of these potatoes actually wind up closer to ¾ of a cup. This means that even though both potato products were based on a RACC of 140g, they might have two completely different serving sizes, and the manufacturer arrived at each using the same government reference amount!

So there you have it, two serving sizes created based on a government standard, but completely different once observed on the store shelf. How could there be even more variation?

Single Serving

Ah, right. For many products, if the entire container contains less or near 200% of the RACC amount, then there are different rules to play by. In most cases, the product will be considered a single serving, but in others, manufacturers have the choice to label them as one or two servings. This is why you see different types of labeling in small containers such as ice cream, muffins, soda, and other “single serving” containers that appear significantly larger than the usual RACC amount.

As eaten, not as sold

Ah, and this is critical. When you ask someone how much cake they eat, they typically don’t respond with, “about 1/3 of a box of cake mix”. RACC values are based on products as they are consumed. However, serving sizes are based on products as they are sold. The reasoning? Because it would be bizarre to buy a bag of flour and see “two slices of bread” for a serving size. This makes more sense for some products than others, but ultimately serving sizes for products that require further preparation are the amount of packaged product it takes to make about 1 RACC of product as eaten. And remember, this must be rounded off at a common household measure!

Final thoughts

As we realize that our beloved nutrition facts panel is now old enough to drink (enforcement began in ’94), we look back and start to wonder if that data from the 70’s and 80’s used to determine RACC values still holds water. I can’t think of anyone who eats ½ cup of ice cream in a sitting, nor leaves the potato chip bag untouched after their first 10-20 chips.

But how about we think about RACC values in a different way. These values were never intended to be an expectation, but simply a way to bring nutrition information into context using consumer data. The thousands of calories in a 20 lb. bag of rice don’t have a lot of context when I eat it one bowl at a time, but that’s also not to say that I’ll never eat an obscene amount of rice in one sitting just because I’m starving.

Instead think of it this way, if these values are simply references to what we customarily consume at a time, we’ve got a great tool on our hands. I wouldn’t expect you to eat only ½ cup of ice cream, but have you noticed that many ice cream scoops happen to portion about ½ cup of ice cream at a time? And while I’ve been known to turn a bag of kettle fried chips into a meal, I still eat them one handful at a time, which just so happens to contain approximately 10-15 chips.

If only some sort of reference was available so that I could tell about how many calories I ate with each handful…

To learn more about how serving sizes are determined for all food products, check out the labeling and nutrition documents on the FDA website, this PowerPoint provided by the FSIS, or the Guide to Federal Food Labeling Requirements for Meat, Poultry, and Egg Products. Check out what consumer opinions of labels are looking like since 2008 in the FDA’s consumer research.

Choinière C. & Lando A. (2008). 2008 Health and Diet Survey, DOI:

ResearchBlogging.org

Conrad J. Choinière, & Amy Lando (2008). 2008 Health and Diet Survey FDA Consumer Behavior Research Foos Safety Surveys (FSS)

Microscopic observation of cell function in live tissue, awesome! But don’t ignore the methods, and the animals they required

It has been far too long since I wrote a blog post. Look out internet, I have a blogging itch that needs scratching, and it’ll probably cause a rash!

…I apologize for that mental image.

The NIH sent me an email this week (via the various government listservs I’m enrolled in) that was proudly declaring that the mysteries of the cell were being solved right now, so I took the clickbait. In it was a cool study where we were able to actively watch mitochondria oscillate inside a living animal.

Fig from the article
http://dx.doi.org/10.1016/j.celrep.2014.09.022

There are two rabbit holes to enter with this article. The first is the observation of interest, which was mitochondrial oscillation. While these slinky moves have been observed in cell cultures, the authors wanted to see if there were any differences in cells that were part of a living, breathing animal.

Movement isn’t a surprising thing. If you’ve ever drawn the ATP synthase lollipop (totally relatable experience for everyone, right?), you already know that some of the main membrane proteins in mitochondria are constantly rolling around attaching phosphates to create ATP. The cool thing though, is that since they’re synching up with each other, that means there could be cellular communication mechanisms that are helping coordinate mitochondrial efforts to produce energy as needed. Which makes sense if you’re generating ATP in response to a stress event on a cellular level.

But what if you’re an animal? A slice of muscle tissue is made up of many muscle fibers, all of which contain mitochondria. It seems like there would be a need to coordinate increased energy production if you were planning to use all those fibers in sync to move. When looking at the cellular tissue inside a living rat’s salivary gland epithelium (the covering layer of the gland), the authors observed that mitochondria oscillated in sync not only within individual cells, but in sync with other cells in the tissue. The authors describe it in their press release wonderfully:

“You look through the microscope, and it almost looks like a synchronized dance”

It’s always more fun looking at living cells and tissue, it reminds you that all of that stuff we can’t see is always buzzing around without our notice and crawling all over our skin and gut.

Hypochondriacs I apologize for that second image.

So since we like looking at living things, let’s get to the second cool part that the press release seems to gloss over, how the hell were we observing cell structures in a living animal!

The principal author, Roberto Weigert, was the first one to publish this technique, so I went to that article to better understand what’s going on. I don’t want to dig into the microscopy so much, as the technical information is a little overwhelming. I’ll just say that there are really cool microscopes that can use near-infrared light to penetrate deep into different tissues (segregated visually by the injection of fluorescent dyes). The article has some amazing images of mouse vasculature that are both easy to observe and understand. But that technology isn’t what this blog is about. What I want to know is, what did this study entail for the animals used?

For this procedure, the research rats were anesthetized and had their salivary glands “externalized”, meaning that they gained access to them presumably by opening/removing the skin, fat, and muscle layers and segregating the gland as far as they could for the procedure (you’d be surprised how far you can pull things out while they’re still attached). Then, they bathed/saturated the glands with various dyes and chemical/hormone baths depending on what they were observing in that particular instance.

Once the images were taken, presumably these brave rats were euthanized, I couldn’t find a reference in the procedure but ultimately it had no bearing on the ability to replicate the experiment and was not included.

Now imagining these experiments in vivo (in living animals) brings up nasty words like vivisection. However it’s always important that the authors of the study aren’t left to singly decide if the research is necessary or not, it’s up to the Animal Care and Use Committee to allow the use of animal subjects for research at the NIH.

In order to use and ultimately euthanize these animals, the authors had to prove that: the information learned from the study will benefit humans and/or animals, there is a rationale for using animals including why a surrogate (e.g. cell culture) would not work (the authors make a great statement in their press release by describing the observations as if you’re looking at a tree vs. the forest), and a description of how the authors have actively attempted to minimize pain and discomfort for the animals used.

Ultimately I chose to write about this article because the methods were cool, but also to acknowledge the animal use inherent, but understated, in this type of research. It’s important to remember that often new information comes at the cost of continuing to support animal research when justified, and to not hide the facts from ourselves.

In order to responsibly care for all of our domestic species, we need to remember that before they were beef, eggs, milk, nuggets, or a data point, they needed to be cared for and euthanized humanely.

ResearchBlogging.org

Natalie Porat-Shliom, Yun Chen, Muhibullah Tora, Akiko Shitara, Andrius Masedunskas, & Roberto Weigertemail (2014). In Vivo Tissue-wide Synchronization of Mitochondrial Metabolic Oscillations Cell Reports : http://dx.doi.org/10.1016/j.celrep.2014.09.022

Weigert R, Porat-Shliom N, & Amornphimoltham P (2013). Imaging cell biology in live animals: ready for prime time. The Journal of cell biology, 201 (7), 969-79 PMID: 23798727

Why isn’t the USDA declaring the invisible feces in our meat?

No, that wasn’t a typo. Today I came across this petition for rulemaking to FSIS from the Physicians Committee for Responsible Medicine.

First off: PCRM has some great programs that promote research, animal welfare, and better medicine. The overall merit of their organization cannot be judged by a single program or campaign they have in place.

Now let’s tear this petition apart, because I actually had to check their website to make sure it was real, and not an over-the-top satire from The Onion.

The concern the committee wishes to correct via this petition is thus:

“Inconsistent with its statutory mandate, USDA regularly passes at inspection meat and poultry that is  contaminated with feces. Although USDA implements a “zero tolerance” policy for fecal contamination, this policy applies to visible fecal contamination only. The result is that fecally contaminated meat and poultry products pass inspection as long as the feces on them are not “visible” to the naked eye.

This inspection policy conveys a misleading promise of “wholesomeness.” Feces may contain round worms, hair worms, tape worms, and leftover bits of whatever the animal excreting the feces may have eaten, not to mention the usual fecal components of digestive juices and various chemicals that the animal was in the process of excreting. Americans deserve fair notice that food products deemed “wholesome” by USDA would be deemed disgusting by the average consumer and adulterated under any reasonable reading of federal law.”

Not to quote without context, the petition goes on to list the ways in which non-obvious feces may be introduced to meat product, the most valid being shared scald/chill tanks in processing operations.

Ultimately, the corrections the committee is seeking are removal of the “wholesome” description from USDA inspected meats, begin treating feces as an adulterant, and:

“USDA should amend sections 317.2(l)(2) and 381.125(b)(2)(i) of the Code of Federal Regulations to exclude from the current mandatory label the sentence that reads, “This product was prepared from inspected and passed meat
and/or poultry.” USDA should amend sections 317.2(l)(2), 381.125(b)(2)(i), and 381.125(b)(2)(ii) of Title 9 to include in the mandatory label the following as the second-to-last sentence: “This product may be permeated with feces, which cooking does not remove.”

That’s some pretty heavy language, perfectly stated to play on the fears and squeamishness of your average consumer. However, I see nothing written there about food safety, so the intention of the change is obvious: prevent people from eating meat.

While the about page for PCRM mentions nothing about being proponents of animal rights, the amount of articles devoted to encouraging a purely vegan diet clearly shows that they have an anti-meat agenda. While they correctly advertize the health benefits of vegan foods, a quick search of their website saturates any visitor with the message “meat is bad, and animal agriculture is always cruel”.

The petition shines a light on a group that is ready to intentionally scare and mislead consumers into changing their lifestyle. As part of their justification that feces is everywhere, they cite one of their own studies, “Fecal Contamination in Retail Chicken Products“. In this study, the committee proved that invisible fecal contamination is everywhere by “testing for the presence of feces.”

No such test exists.

What they actually did was test for generic E. coli, which can act as an indicator organism for fecal contamination.  HACCP programs in slaughter facilities use on-line enumeration of E. coli and other coliforms to validate critical control points for just that purpose. But in this case, rather than setting limits and using a statistical rationale to make a conclusion about the level of contamination, it appears that any evidence of the presence of E. coli  led to the determination that the sample was contaminated with feces. Because there are no methods declared, this evidence could be as mundane as RNA fragments from a non-pathogenic strain recovered in an enriched sample.

The study is absolutely meaningless. There is no available data to review in terms of the levels of contamination, no methods listed for how the E. coli was enumerated, and finally no legitimate publication, suggesting that the construction of the study and its conclusions would not have passed peer review.

As part of the rule change, PCRM would like feces to be declared as an adulterant. Generally, USDA inspectors cannot allow adulterated products to enter commerce, adding to the ludicrosity of this proposal. By the PCRM’s definition, all meat products are covered in invisible feces, and the presence of invisible feces should prevent any product from entering commerce. In one swift move, PCRM will ensure that only clean, wholesome meats will be sold, i.e. none.
But have things changed over the years to make eating meat less safe? The PCRM thinks so. I have no data to argue whether or not Americans are cooking less (PCRM also neglected to provide data), and eating more RTE products, but I did think it was funny that when I read this:
“Americans today consume far more meat and poultry than ever before, thereby increasing their potential exposure to fecal contamination in these products”
When the first link I read on their website contained this graph…
http://www.pcrm.org/media/blog/nov2013/youre-in-good-company-with-a-vegan-thanksgiving
http://www.pcrm.org/media/blog/nov2013/youre-in-good-company-with-a-vegan-thanksgiving
Which is it PCRM? Whichever is more convenient for the ad campaign at the time?
(side note: if people indeed are eating out more in restaurants, that would mean they are eating at inspected restaurants where county health inspectors ensure adequate cooking temperatures, rather than at home where people rarely if ever have proper process control)
Finally, the idea that the USDA needs to declare the presence of invisible feces on every product that passes inspection makes no logical sense,  and does nothing but mislead the consumer, not only by implying that the product isn’t safe in general, but that fully cooking the product makes no difference. If it wasn’t obvious by now that this proposed rule change isn’t solely to earn points with vegans, look closely the wording. In order to turn consumers off meat, PCRM would risk undoing years of public education and trust in proper cooking temperatures.
Clearly I took this proposal too literally, but because FSIS will actually have to review the proposal, and PCRM wants to brag about how these changes might occur, I offer one last piece of evidence to support my view that this proposal belongs on a tabloid.
Proposed legends
…one of their proposed inspection marks literally contains a DO NOT EAT symbol.

ResearchBlogging.org

Physicians Committee for Responsible Medicine (2013). Re: Fecal Contamination of Poultry and Meat USDA Petition for Rulemaking

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New name and URL

Animal Science Review is now Fur, Farm, & Fork! Because I graduated from OSU, I have had to move the hosting for this blog to a wordpress URL.

I will continue to generate new content, with a completely unpredictable schedule as usual, at the new location. So if you’re someone who actually likes to read my stuff, be sure to change your bookmarks and RSS over to furfarmandfork.wordpress.com, as I will no longer update at blogs.oregonstate.edu/abouck.

 

Cheers,

-Austin

The poultry microbiome, culture-based ecology continues to mislead us all

Shigella penetrating the intestinal wall. Source: cellimagelibrary.org

If the world was enriched and homogenized, we would actually have a very good idea of what the microbiological community within looks like. Fortunately, the world is much more complex than the miniature environments we culture in the lab, and high throughput sequencing (HTS) is allowing us to fully appreciate micro-biodiversity. As new information becomes available, many of our models for microbial communities continue to be challenged by the actual composition of species in natural environments.

In the world of food safety, we rely on these models to set policy on a regulatory level, and to set critical limits down at the production level. Which tests we run on what products depend directly on what organisms (that cause food borne illness or spoilage) are supposed to be found on that type of food. The authors of this study that came out in PLOS ONE this February examined the microbiome associated with poultry products from farm to fork (meaning from clucking chicken to packaged poultry product) using HTS rather than culture/enrichment methods. The results indicate that there is an unappreciated amount of diversity between different stages of the poultry production process, and that we may not acknowledge the presence of some organisms as much as we should.

In the study, samples were taken from multiple steps in the poultry production process: wet and dry litter, fecal samples, fluid from carcasses collected during the cooling process following slaughter, and fluid from raw retail poultry products (legs, wings, and breasts). Other than the retail portion, all of the samples collected were from the same batch of birds from start to finish. The available RNA from viable cells in each sample was amplified and identified as belonging to specific species using a combination of Illumina sequencing and database referencing (blastn and usearch).

From this pile of data, lists of organisms were compiled to compare the ecosystem profile for each point in production.

The numbers refer the the number of unique taxa found in each group

The authors were very surprised by the amount of diversity between the two litter samples (wet and dry) and the fecal sample. They expected to see very similar profiles, as all of the predicted microbes in those groups would be inoculated from contact with fecal material (young chicks have no inherited microflora, and are coprophagous); however, all of the groups’ microbial communities had very little in common. As shown above, of the hundreds of unique species identified, only 52 were actually found at every stage from farm to fork.

In evaluating food safety, several results are of concern. The first was that the authors found significant amounts of Shigella spp., which have traditionally not been associated with poultry products and may not be a part of many sanitation programs. The second is that in one of their dry litter samples, the authors found a large amount of C. jejuni. It’s presence was interesting as previous studies have found it difficult to cultivate C. jejuni onto dry litter, suggesting that it will not grow in that environment. This discovery further shows that our attempts to cultivate bacteria are not indicative of their behavior in “the wild”. There may be nutrient gradients or a symbiont in play that allows C. jejuni to grow; therefore the possible contamination of dry litter has to be acknowledged in that facility’s Campylobacter monitoring program.

The last point of interest I’ll discuss here is the large amount of unique species that were found in samples following slaughter. This suggests that these species did not come from the farm, but rather were introduced during slaughter and processing. Interestingly, among Campylobacter spp., there was little to no abundance of C. jejuni in the samples, but differing amounts of other Campylobacter spp. This is revealing, as we have been predisposed to expect C. jejuni to be present due to our use of selective media.

Let’s fully appreciate the amount of diversity found within the processing facility, the authors collected two post-processing samples labeled carcass rinse and carcass weep. The rinse was composed of fluid shaken off of the carcass following its removal from the chlorinated chill tanks, and the weep was the drippings from the same carcass 48 hours later. 2/3 of the unique species found the weep samples were not found in the rinse. The authors interpret this as being due to the fact that the sterilization of carcasses is not the goal of poultry processing, and provide the example that viable Salmonella can be recovered from carcasses even after they are sent through the standard antimicrobial processes. The goal is to reduce enumeration, not sterilization.

Finally, in examining the retail samples, we get what we expect. Similar organisms as the weep, with some new faces, presumably because they persisted through processing at undetectable levels, and slowly grew as the product was stored in refrigeration.

The authors conclude by examining some potential symbionts that would allow C. jejuni to persist, but ultimately say that due to the high number of environments C. jejuni can occupy, attempting to exclude it in a universal way will not be very effective.

So all in all, a thorough example of the misdirection we receive from culture bias, and a startling look at how, given enough incubation time, properly processed meat can still support a huge amount of microbial diversity, including many food borne pathogens.

Appreciate this diversity, and make sure you cook your chicken to temperature.

 

ResearchBlogging.org

Oakley BB, Morales CA, Line J, Berrang ME, Meinersmann RJ, Tillman GE, Wise MG, Siragusa GR, Hiett KL, & Seal BS (2013). The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations. PloS one, 8 (2) PMID: 23468931

Why rooster crowing isn’t that impressive, and chickens get jet lag like the rest of us.

Circadian rhythms and jet lag.  There, cyclic crowing behavior explained.

Quite a lot of people are discussing this study from Japan examining the effect of light on the crowing behavior of roosters. The authors observed several birds in experimental conditions where light intensity and duration were controlled, taking observations with audio recorders and cameras. The scenarios presented were a daylight cycle of 12 hours of light and dim light respectively, and constant dim light. Observations were recorded for a period of 14 days, producing this graph.

So many reporters on the study have run with this, making declarations about what great timekeepers roosters are, and how cool it is that they don’t need the sun to know when dawn is.

Well, approximately when dawn is.

“Under dimLL conditions, a free-running rhythm of crowing was observed with a period of 23.7 ± 0.1 h (n = 4), but this free-running rhythmicity gradually damped out”

Interesting, so the sun is unnecessary until it’s been gone for a while, then we start to get some variation. This dampening effect is even more obvious when you place testosterone implants in the roosters.

Testosterone implant roosters calling out “Bro, do you even lift?”

Don’t get me wrong, the fact that Roosters have this accurate of a circadian clock is impressive! It’s very interesting biologically, but it’s not some infallible atomic clock. While many news sites are toting that Roosters are independent of the sun, the opposite is true. Circadian rhythms are directly calibrated primarily by light cycling, with temperature being another important environmental cue. To confirm the roosters knew what time it was, the authors examined the effect of light or recorded crowing sounds at different times of day. They found that there were fewer crowing behaviors at random dawn times than at the “correct time” of day.

This doesn’t mean the roosters know it’s 5pm, but their circadian rhythm is telling them that it isn’t dawn. However, the sun still “came up” so we witness some halfhearted crowing. Anyone who has ever traveled out of their timezone knows exactly how this feels: these roosters have jet lag. While the sun may be coming up, their circadian clocks are telling them that it feels like a different time of day, so they crow in response to the light, but with reluctance and confusion, much in the same way you sleepily get up on vacation when the Louvre opens, even though it feels like 5PM to you.

“But Austin,” you tell me, “aren’t you anthropomorphizing?” While I admit roosters may not empathize with trans-Atlantic vacations, we know that chickens are dependent on daylight to calibrate their biological rhythms because we do it all the time. We increase egg production by simulating summer lighting year round, and alter feed intake in broilers by changing their daylight cycle. We also use this trick to bring mares into heat.

The loss of rhythm observed in 24 hour dim light is likely to become more and more sporadic, and even more so if the roosters were housed singly (as there is some group consensus due to competitive crowing). I would propose that if you could keep the roosters on a light cycle that progressively moved forward an hour a day until dawn was at 2pm, the roosters would crow with the same strict rhythm independent of the actual sun. If the authors of the study choose to pursue this hypothesis, an easy test would be to simply progress their artificial sun’s rise and fall over time.

Alternatively, we could fly several roosters with us to Paris, and see if they wake us up before the Louvre opens.

ResearchBlogging.org

Shimmura, T., & Yoshimura, T. (2013). Circadian clock determines the timing of rooster crowing Current Biology, 23 (6) DOI: 10.1016/j.cub.2013.02.015