Eliminating Listeria in your Facility…the musical

Listeria monocytogenes on oxford agar
L. monocytogenes on Oxford Agar. Source: wikipedia commons author Nathan Reading

So I know that all of you who subscribe to Fur, Farm, and Fork do so for the meticulously researched analysis of food safety and regulatory issues.

So… here’s a Rihanna song parody about eliminating Listeria from a food plant!

…it was fun. And this is my site so I can do what I want.

If you want to listen to someone  sing it, download the mp3 here.

Lyrics below, basically covering where Listeria can be found in the food plant enjoy!

 Listeria (Disturbia Parody)

Bum Bum bio bum bum bio-film

Bum Bum bio bum bum bio-film

Bum Bum bio bum bum bio-film

Bum Bum bio bum bum bio-film

 

[what did we find

I didn’t expect this

What are we gonna do now]

 

What do these results mean

(presumptive positive)

Near the wall, near the sink

(where there was standing water)

Right where we process cream

(and products ready-to-eat)

Get the QA team together

 

It’s a sneaky microbe

Riding on your shoes

It can grow in the cold

Where it eludes you

A poison in your food

And it can end you

It’s too close for comfort

 

Let’s tear this room apart

We need to swab every square foot

Then the spare parts

We can get to the cause root

Use those trending charts

Why didn’t we catch this last year

It’s not in the product, we swear

 

But we just found Listeria

All the product’s been retained

Listeria

Biofilms in our drains

Listeria

Might be from the supply chain

Listeria

Listeria

 

Bum Bum bio bum bum bio-film

Bum Bum bio bum bum bio-film

Bum Bum bio bum bum bio-film

Bum Bum bio bum bum bio-film

 

Condensate drips from the walls

(we can’t see from where it comes)

These concrete cracks aren’t that small

(The floors are twenty years old)

We need some new grout

Old equipment thrown out

It’s too close for comfort

 

It’s a sneaky microbe

Riding on your shoes

It can grow in the cold

Where it eludes you

A poison in your food

And it can end you

It could be anywhere

 

Let’s tear this room apart

We need to swab every square foot

Then the spare parts

We can get to the cause root

Use those trending charts

Why didn’t we catch this last year

It’s not in the product, we swear

 

But we just found Listeria

All the product’s been retained

Listeria

Biofilms in our drains

Listeria

Might be from the supply chain

Listeria

Listeria

 

Bum Bum bio bum bum bio-film

Bum Bum bio bum bum bio-film

Bum Bum bio bum bum bio-film

Bum Bum bio bum bum bio-film

 

Risk assessments are now change-in

Zero tolerance And we’re jumpin-in

We didn’t no, oh, oh

Grab your swabs and let’s go oh oh

 

Let’s tear this room apart

We need to swab every square foot

Then the spare parts

We can get to the cause root

Use those trending charts

Why didn’t we catch this last year

It’s not in the product, we swear

 

But we just found Listeria

All the product’s been retained

Listeria

Biofilms in our drains

Listeria

Might be from the supply chain

Listeria

Listeria

 

Bum Bum bio bum bum bio-film

Bum Bum bio bum bum bio-film

Bum Bum bio bum bum bio-film

Bum Bum bio bum bum bio-film

 


Inspired by various warning letters at companies associated with outbreaks of Listeria monocytogenes. Original song performed by Rihanna, music composed by Robert Allen, Chris Brown, Andre Darrell Merritt, and Brian Kennedy Seals. Instrumental background sourced from www.karaoke-version.com.

This media file may contain copyrighted material that qualifies as fair use under the Copyright act of 1976. 17 U.S.C. Section 107. See Campbell vs. Acuff-Rose Music (92-1292), 510 US 569

 

Not just “in bed with business”, 5 things FDA does for consumer advocacy and safety

At FF&F, I’m often harsh on FDA for lack of enforcement, ownership of their own role in preventive food safety, and failing to consistently stand by their guidance. However, you will still see me using FDA research and policy decisions as a primary source of credible primary source material. After all, it’s right there in the agency’s mission:

The Food and Drug Administration is responsible for protecting the public health by ensuring the safety, efficacy, and security of human and veterinary drugs, biological products, and medical devices; and by ensuring the safety of our nation’s food supply, cosmetics, and products that emit radiation.

This is a huge endeavor, and for all my criticism, threading the line between public health, consumer advocacy, and some portion of business advocacy is an incredibly hard task that they do what they can with.

Unfortunately, because tackling this mission requires individuals with knowledge of food as an industry, and because the agency is part of the federal government, many people do not recognize any scientific information provided by FDA either because they believe they’re part of a grand conspiracy (which is a group I don’t expect to be reached by this post), or because so many senior members are inevitably connected to conflicts of interest from the business side of food.

However, of FDA’s 14,000+ employees, many of them are doctors, scientists, and public servants who believe in the mission and perhaps even more compelling, there are many others who just have a “steady job” who don’t have a stake in the results. These folks produce great work that helps make our food supply safer. Work that is rigorous, effective, and from a market standpoint, impartial.

So I’ve generated this list to identify a few things to counter the “FDA isn’t an advocate for consumers” argument. To make it onto this list the items need to meet three criteria. First, that the actions taken are intended to protect the public or provide transparency; second, that the action taken doesn’t provide some obvious benefit or perk to industry; and third, that the action is transparent and verifiable (unlike an outbreak response or inspection/approval activities).

1. Interstate Milk and Shellfish Shipper Certification and List

These two lists are published monthly to the public. The list of milk shippers not only provides the names of approved shippers, but also approved manufacturers of packaging for milk in accordance with the Pasteurized Milk Ordinance. Even moreso, FDA publishes the current scores they received on their last sanitation audit so that consumers can hold companies accountable and make decisions based on food safety, or ask their favorite dairy product brands who they use. Public scores not only help consumers evaluate companies who otherwise wouldn’t share them, but they actively benefit consumers by incentivizing companies into trying for higher scores even though they technically “passed”.

2. Public posting of Warning Letters

We discuss warning letters often at FF&F because they offer great insight into events where FDA has actually moved forward with enforcement for violations of the law. For the public though, it’s a rare opportunity where FDA has taken the worst-of-the-worst offenders and laid their failures out for all to see, and even more so, note their lack of response when given a first opportunity to correct them.

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).

Warning letters are all public for companies big and small, and outline the specifics of the violations along with how they relate to the written law. They also remain posted online forever, even after the problems have been corrected, giving the public a direct look at who in the industry has been most negligent in adhering to the law.

3. Retail Surveillance for Foodborne Pathogens

FDA does a ton of microbiological surveillance activities to get data on the prevalence of foodborne pathogens at the retail level. Whether to evaluate the safety of a specific commodity or to check domestic vs. imported items, this data is not only valuable to consumers and industry alike, but also results in enforcement actions taken against those companies that have their products turn up positive (though unfortunately without some detective work it’s difficult to to see that follow up). Here are some examples of recent retail surveillance activities turned into reports for the public:

National Antimicrobial Resistance Monitoring System: ongoing evaluation of antibiotic resistance in retail meats and other commodities

Microbiological Surveillance Sampling: FY16 Cucumbers and Hot Peppers

Microbiological Surveillance Sampling: FY14-16 Raw Milk Cheese Aged 60 Days

Microbiological Surveillance Sampling: FY14-16 Sprouts

4. Pesticide Residue Monitoring Program

Each year, FDA samples thousands of produce samples both domestic and imported and tests them for hundreds of different pesticides to see what commodities coming from where are in violation of established limits or even detectable. They conduct targeted checks of commodities of concern and take enforcement action against violators.

Once the tests are complete, every year FDA produces a report to show what the current rates of violation and detected levels are. This allows consumers who are concerned about pesticides to either choose imported vs. domestic produce, or avoid certain fruits and vegetables that may be known for more violations. Consumers who are also buying Organic can check out pesticide levels/usage in conventional foods to make sure that their chosen commodity is worth the extra certification for their pesticide concerns.

5. Posting of Recalls, Withdrawals, and Safety Alerts

One that most people know about, but we often take for granted. Think about what a recall is: a company identifies (or has FDA identify for them) an issue with a product that makes it either illegal to sell or potentially unsafe to sell to the public, so the company pulls it from the market. Who needs to be made aware that this happened?

Obviously anyone selling the product needs to know to pull it from the shelf, and they need to let their customers know that they should throw it away or bring it back to the store. But does the entire country need to know that the local supermarket is recalling their muffins because they forgot to label the walnuts?

Not only does FDA make sure that the entire country knows when a company has a recall, but why they had the recall. They then keep a permanent public record that anyone who ever wants to buy a product or do any business with that company can look up with a simple google search.

In addition to publicizing these events, FDA uses this same forum to call out companies who don’t recall things voluntarily by issuing safety alerts and advisories. In the face of defiant companies who aren’t willing to “voluntarily” recall, FDA uses the forum to make sure the public knows both of the potential danger, and that the company isn’t allowed to keep the issue a secret.

———–

There are a thousand other ways that FDA helps protect the public through policy-making, data collection, or enforcement, but these 5 are unique in that they’re immediately verifiable by anyone with access to a search engine, and that “big industry” doesn’t benefit by them unless they’re also advocating for the public. If anyone has anything else they think should be added to this list, please comment and I’d be happy to review and add it in!

Presence of fecal coliforms does not mean “there’s poop here”, but for aspiring poop-hunters is there an alternative?

Image created by Austin Bouck. Dear god let there be no egregious mistakes…

Recently a podcast I often listen to has discussed several articles with a similar note in their conclusions.

Nearly half of the 90 beverages from soda fountain machines in one area in Virginia tested positive for coliform bacteria — which could indicate possible fecal contamination

The study, conducted over six months at six licensed day-care centers in California, found high levels of coliform contamination, particularly in kitchen areas and on the hands of day-care workers. Coliform bacteria are transmitted through feces.

But recent reports reveal that the coffee or tea you’re sipping  – and even the cash you used to pay for it –  also carry bacteria found in feces.

Seven out of 10 samples of Costa ice were found to be contaminated with bacteria found in faeces.

40 percent of office coffee mugs contain coliform bacteria, which can be found in feces.

I don’t need to rehash arguments that have already been made here. Fecal coliform is a group of organisms historically used to identify whether drinking water could be contaminated with sewage or fecal material. Because it’s still a valid test to determine if water has been contaminated (they don’t survive forever in clean water, so if they’re present it’s because there’s a likely a failure in the system), the CDC and tons of state regulations still falsely state that these organisms are only found in fecal material.

Part of the issue is that coliforms as an indicator in general were extrapolated to environmental samples and food. NACMCF summarized the most recent scientific conclusion:

…whether coliforms, fecal coliforms, Enterobacteriaceae or E. coli. Kornacki and others (Kornacki et al., 2013) provide an historical evaluation of these criteria for foods and their utility based on current knowledge. None of these criteria accurately and consistently reflect fecal contamination of raw and processed foods nor are they useful or reliable as index organisms predicting the presence of pathogens.

The Kornacki reference is from the Compendium of methods for the Microbiological Examination of foods, which while expensive is an excellent reference for any food micro lab:

The debunking of the coliform=feces absolute conclusion was well covered by Doyle and Erickson in 2006, and more recently some thoughts were posted by barfblog.

But I’m writing this post today because I have a follow up question,

How exactly would someone actually test for fecal material?

Apparently, this is actually a problem in forensics, as an article published as recently as 2013 stated”no sensitive and simple fecal identification method using molecular biological techniques has been reported.” (Nakanishi et al., 2013). Here were the methods I was able to find with a cursory review of the literature.

1. Direct (macro) observation

A.k.a, the stain on the tighty-whities. Feces can be identified from it’s characteristic green-brown color from bile digestion and characteristic odor…this detection method isn’t really worth going into and I apologize for the mental image/odor.

2. Microscopy

Now we’re getting sciencey. Fecal material is a hodgepodge of various microscopic indicators. An experienced eye would be able to find bacteria (the bulk of the dry weight), but also undigested food particles and cellulose cell walls from plant material. Some epithelial and mucousal cells from the GI tract would also be visible. Interestingly, one way to determine if the fecal material was from a person or animal would be to look for excess hair in the sample, either from digesting prey or from grooming. The hair has to go somewhere, and I’m really curious if you would see a difference in hair mass between bearded and clean shaven men…

3. Chemical Indicators

Urobilinogen is a byproduct of bilirubin metabolism, and will be found in animals which consume meat and/or are otherwise digesting blood.  This appears to be a fairly classic test to discriminate fecal material from other bodily fluids like sweat or saliva and can be performed on site using a fluorescence indicator solution. Unfortunately, urobilinogen can also be found in urine since it is also returned to the kidneys for excretion.

4. Microbiological Profile

Well, crap. Here we come full circle. The most recent research on this subject seems to be using newer sequencing techniques to identify the unique organisms in the microbiome of feces. The goal is to find specific organisms or genes that would allow forensic scientists to discriminate between fecal material and other bodily fluids.

Here’s the thing though, none of the research identifies coliforms as a group of interest. It’s too broad and unhelpful! Rather than traditional “fecal bacteria”, the Bacteriodes genus has been identified as the predominant organism group in feces. Specific organisms identified were B. uniformis, B. vulgatus, and B. thetaiotaomicron. However, the state of California has specifically identified these organisms thriving in marshlands, yet still attribute them directly to feces. It would seem that again we can infer that fecal material is likely to contain these organisms, but it seems improper to assume that the presence of the organisms means that fecal material was the source.

I’d love to hear from some forensic scientists on what I got right and wrong here. From what I can tell from the literature it seems like there isn’t as much forensic interest in fecal material. The authors referenced how it is hard to isolate DNA due to interference from bile enzymes and microorganisms, which would reduce its value as evidence.

It seems like at this time a definitive test for “there is poop on this plate/ice/food/hand” doesn’t exist.

Much to the chagrin of PCRM, who would like us to declare the invisible feces on our meat.

Maybe we can just stop making the correlation between feces and food hygiene and instead focus on pathogen detection/prevention/pervasiveness as a means to evaluate foods on the market. While we talk about the fecal-oral route a lot, we’ve known for a long time that pathogens can be found almost anywhere if you start looking, so let’s look for them instead of fecal coliform clickbait (which this post totally is).

 

 

Resources for fecal identification forensics:

Drexler, Judith Z., et al. “Marsh Soils as Potential Sinks for Bacteroides Fecal Indicator Bacteria, Waccamaw National Wildlife Refuge, Georgetown, SC, USA.” Water, Air, & Soil Pollution 225.2 (2014): 1861.

Forensic Resources.Serology – Blood and other Bodily Fluids. http://www.ncids.com/forensic/serology/serology.shtml

James, Stuart H., Jon J. Nordby, and Suzanne Bell, eds. Forensic science: an introduction to scientific and investigative techniques. CRC press, 2002.

Li, Richard. Forensic biology. CRC Press, 2015.

Nakanishi, Hiroaki, et al. “Identification of feces by detection of Bacteroides genes.” Forensic Science International: Genetics7.1 (2013): 176-179.

Virkler, Kelly, and Igor K. Lednev. “Analysis of body fluids for forensic purposes: from laboratory testing to non-destructive rapid confirmatory identification at a crime scene.” Forensic Science International 188.1 (2009): 1-17.

Zou, Kai-Nan, et al. “Identification of vaginal fluid, saliva, and feces using microbial signatures in a Han Chinese population.” Journal of forensic and legal medicine 43 (2016): 126-131.

New FDA 483: Euthanasia drug found in canned dog food, misc. facility findings, and questions for FDA

fda-483-footerI would be remiss in the goal of this blog if I didn’t do some digging into the form 483 that was just released by FDA this week following a recall for canned dog food containing Pentobarbital. For information on the products recalled and company involved check out the FDA recalls page and search for the issue. As usual I’ll refrain from writing company and product names on this blog when there isn’t any pending civil or criminal action associated with an event. But that information is readily available for anyone by clicking through the links or performing a simple search.

The 483 is short, just two pages. What the goal of this post will be is to go over each of the observations and try to provide additional information that isn’t included in the document to hopefully provide a complete picture.

All FDA observations began with the heading clarifying which portion of the law (FDCA) the firm violated:

The following observations were found to be adulterated [sic] under the Federal Food, Drug, and Cosmetic Act: A food shall be deemed to be adulterated if it bears or contains any added poisonous or added deleterious substance that is unsafe within the meaning of section 402.

This wouldn’t be FF&F if I didn’t pause here for some definitions. Adulterated is a condition of food by which it cannot be sold in commerce. It includes both reasons of safety as this case demonstrates, but it could also be forms of “economic adulteration”, where something claims to be what it isn’t or has otherwise been robbed of characteristics that the consumer would expect. Like if I were to sell you caviar but it was actually flavored gelatin balls or something.

Poisonous or added deleterious substance is a substance that when added to food “may render it injurious to health; but in case the substance is not an added substance such food shall not be considered adulterated under this clause if the quantity of such substance in such food does not ordinarily render it injurious to health.” (emphasis mine)

FDA says two things there. First, don’t add anything poisonous to food (Protip). Second, if the food happens to contain something poisonous naturally, you need to make sure it occurs at a level where it isn’t toxic. This is the often cited”dose makes poison” principal. An example would be that I can’t sell food into which I accidentally spilled some cyanide (whoops) no matter how much or little it was, but I can sell fruits that may have trace amounts of cyanide precursors in the seeds, because it’s not expected to cause an issue in both the actual dose of the seeds and the expectation that people will avoid them when eating. This clarification is actually pretty critical as we try to make sense of past FDA guidance in this case and why the food was adulterated.

So, how did these dog food products cause themselves to be adulterated?

Your low-acid canned dog food product…was found by chemical analysis to contain the barbiturate drug pentobarbital.

By Harbin (Own work) [Public domain], via Wikimedia Commons
By Harbin (Own work) [Public domain], via Wikimedia Commons
Pentobarbital is a sedative that in the form sodium pentobarbital is used as a euthanasia drug. This recall/483 event was initiated when 5 dogs became sick and one subsequently died. Several new updates have occurred since then and I encourage you to follow the story on a site like food safety news.

Here’s the thing about this finding, it’s annoying that the 483 made no mention of the dose that was recovered. This is important because FDA did a study on pentobarbital in dog food in 2002. In that study, the samples (not randomized/representative, convenience samples selected for likely positives) tested positive for the presence of pentobarbital in more or less than 50% of the samples. However, in the same study FDA made a determination of dose that caused adverse effects:

Based on the data from this study, CVM scientists were able to determine that the no-observable-effect level – which is the highest dose at which no effects of treatment were found – for pentobarbital was 50 micrograms of pentobarbital per day

Dogs would have to consume 5-10 micrograms of pentobarbitol per Kg body weight to hit that dose. The highest value FDA found in their samples was 32ppb (32 micrograms per Kg of food). This means that 7 Kg (15.4 lb) dog would need to eat between 35-70 micrograms to reach the minimum dose, which would have been a little over 1Kg of the highest testing food. Pet food isn’t very dense (canned pet food is denser but contains more water that dilutes other ingredients) and 2.2 lbs of it is a lot of food for a 7Kg dog. Therefore FDA concluded:

the results of the assessment led CVM to conclude that it is highly unlikely a dog consuming dry dog food will experience any adverse effects from exposures to the low levels of pentobarbital found in CVM’s dog food surveys

Which means that FDA concluded that the mere presence of pentobarbital does not make the product adulterated because “the quantity of such substance in such food does not ordinarily render it injurious to health” per the FDA study.

Now, because there is report of adverse events and an Oregon State College of Veterinary Medicine report out there showing that the levels in this food were high enough to cause an effect, this food is clearly adulterated. But it seems like FDA should have included a note about the concentration of the drug found in the food in this 483 to clarify why it was legally adulterated, given the past study.

Now for the findings not related to the chemistry analysis and recall:

Condensate dripped throughout your processing facility from the building…including condensate dripping directly into open cans of the in-process low-acid canned dog food product…and also into multiple open totes of raw meats including beef intended for your canned dog food product

steam-hood
Example: steam hood over my stove that I apparently need to clean…gross.

Condensate is found wherever foods are heated and cooled, and FDA has been addressing it more and more. Condensate was noted in the Blue Bell 483’s as well. The logic is that while steam or vapor may be clean, once it collects on a surface like the ceiling or whatever else, it can carry bacteria from these “non product contact” areas back onto your food. Think of it this way, would you lick the underside of the steam hood/vent above the stove if you hadn’t just cleaned it? Now imagine that the steam from your stroganoff was condensing on the underside of the hood and dripping back into it, carrying all that old grease and dust. Yum.

The floors throughout your processing facility are pitted, cracked, and otherwise damaged causing pooled water in areas where food is exposed including where open cans of…dog food are staged

pitted-concrete
Source: my patio.

Uncleanable floors = environmental pathogens. While they didn’t go on a “swab-a-thon” in this facility (yet), uncleanable floors are essentially considered harborage points for things like Listeria and Salmonella. In any other business than food, pitted floors aren’t normally an issue, which makes it a common finding in plants holding themselves to a manufacturing efficiency standard rather than a “food grade” standard.

Additional sanitary conditions observed…include peeling paint and mold on walls throughout the processing facility including in areas where food is exposed, a live fly-like insect in the …hand-packing area during processing, and an open sanitary sewer within approximately 25 feet of two food storage trailers and one food processing trailer at the rear exterior of the facility.

Really just shows a lack of preventative maintenance and facility investement when there wasn’t a clear ROI. This particular company has been in business for a long time in the same location, so it’s possible they themselves put that old coat of paint in years ago to spiff it up and make it look nice and be good for food. These kinds of things are expensive preventative maintenance tasks (mold removal, repainting) because it causes downtime as well as the expense of the repair. Typically FDA will show discretion depending on risk to product (e.g. if you only have closed containers in a room with old paint), but the inspectors here probably determined that this was facility neglect and should be noted. Same thing happens in restaurants and retail establishments where facilities have aged but there’s been no spiffing up.

You lack operating refrigerated storage facilities or other means of controlling the temperature exposure of raw meats during thawing, storage, and processing.

Ding, ding, ding! We have a winner, here’s where we demonstrate the true lack of food safety commitment/appreciation at this facility. The last findings all relate to proper temperature control:

…raw beef and other meats in various stages of thawing were stored in ambient temperature inside your processing facility and also at abmient temperature inside three trailers…the exterior ambient temperatures were below freezing…there was frozen ice containing a blood-like substance across the floors of the three trailers and also on the ground…

Open cans of beef were staged on a pallet at ambient temperature during the hand packing process [from the start of operations until 2:00 PM]

So here’s what the deal is with food safety here. This product is going to be retorted, which means that as a low-acid product, it’s going to be cooked until it’s commercially sterile.

So, in theory, it doesn’t matter if your raw meat doesn’t stay refrigerated, since you’ll kill anything that might grow on it! Heck, you can pack it in a dirty facility with dirty tools if you wanted to…

That was sarcasm.

Processors who think like this fail to understand how cooking and kill steps work, and don’t have respect for your food at all stages of production.

FDA expects the thermal process for low-acid foods to provide a minimum of a 5 or 7-log reduction for spores and pertinent pathogens. What this means is that the process should destroy a minimum 99.999% of spores/bacteria in the product, or alternatively, it would sterilize meat that contained 10,000 spores/gram (bacteria are easier to kill than spores, and would have a much higher log reduction with the same process).

This would work for most “raw” products used in this process. However, if you don’t refrigerate or otherwise control raw meat to keep it out of the danger zone of 40-140ºF, bacteria will start to grow. And with the average piece of beef trim having anywhere from 100 to 100,000 bacteria/gram, if these bacteria are allowed to multiply to the ten-millions from lack of refrigeration suddenly that 5-log reduction doesn’t work anymore!

99.999% of 10,000,000=100

While 100 un-killed spores may not seem like much, one of them could be C. botulinum, and with a shelf life of years in a can of dog food, it only has time to grow.

Take this home: every cook or “kill” step in food processing has a log-reduction value. So while you can technically cook spoiled meat until all the bacteria are dead, you have no way of knowing (without testing) that your standard procedure of cook until 165ºf will work if the number of bacteria are 100 fold higher than what the cook was intended for.

If you still think you can throw away your refrigerator and just cook everything through, I recommend purchasing an autoclave to really sock-it-to-em. Don’t think what comes out will be very tasty though. Oh, and general autoclave parameters will give you a 12-log reduction. Happy cooking.

While this is a significant finding, it isn’t related to the issue causing the current recall (and subsequent enforcement). The issue with the product had to do with pentobarbital in the food, which is a supplier sourcing issue (pentobarbital didn’t make it’s way in at the plant unless it was a malicious act). This plant has had a poor history with supplier approval (sourcing duck that wasn’t actually duck for example), and also has a history of being ignored by the FDA based on inspection history.

What this warning letter serves to do is show that FDA is doing it’s job (or backtracking to do so) enforcing all the regs at this plant regardless of the specifics of the current problem. But I have a lingering problem with this timeline:

12/31/17: Dogs become sick after eating the implicated food.

1/3/17: Oregon State University receives the samples for autopsy and analysis, report indicates FDA was informed.

1/10/17: FDA shows up at the plant to perform inspection that led to the facility 483 findings

1/17/17: Michigan State University confirms Pentobarbital contamination

2/1-2/2/17: FDA continues inspection according to the 483, no new findings noted from the later dates

2/3/17: Recall initiated, presumably this was a result of the meeting with FDA from the previous two days where they informed them of the results and helped identify the scope of the recall and “recommended” a “voluntary” recall.

2/8/17: FDA continues inspection according to the 483, no new findings noted from later dates.

2/17/17: FDA releases their own independent press release through CVM updates

This facility had multiple problems in 2011 and 2012 that led to FDA action, and FDA had last interacted with them (according to the inspections database, which does not include contracted inspections through the state) on 2/28/13.

Did FDA inspect a facility, find problems, and then decide not to go back for 4 years? And from this timeline above, did they only go back to this facility because they had a potential poisoning related to it on file?

Thorough and rapid response to a crisis FDA, good job! But shouldn’t you have been inspecting a known problem facility to prevent problems like this from happening?

After all, in 2011, you said this:

The FDA Food Safety Modernization Act (FSMA), signed into law by President Obama on Jan. 4, enables FDA to better protect public health by strengthening the food safety system. It enables FDA to focus more on preventing food safety problems rather than relying primarily on reacting to problems after they occur.

We can’t say whether increased visits from FDA (which should have been every 3 years at minimum) would have prevented this from happening. But it certainly couldn’t have hurt.

FDA’s Bad Bug Book refers consumers to Wikipedia for information on Listeria

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

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

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

Staphylococcus aureus diversity and subclinical mastitis

This is the first study I’ve found that was interested in cataloging bacterial diversity among subclinical (or asymptomatic) infections. While they may be less threatening to the animal’s overall health, these infections have great significance in the world of animal agriculture, where they restrict growth (or in this case, milk production), and encourage the use of medicated feeds which in turn motivate people to purchase organic products. Identifying the risk factors and causes of these infections could therefore impact both the management of food animals, and any legislation defining how and when medications can be used. With that in mind, let’s jump back into mastitis, and everyone’s favorite gram-positive, S. aureus.

It’s because of my plasmids, people can’t help but stare.
Image from http://cellimagelibrary.org/

S. aureus is one of many bacteria that cause mastitis, however it is of additional importance as it often causes chronic or recurring cases of mastitis that result in unusable milk and discomfort of the animal. In this study, the authors investigated 11 dairy farms where they expected to find S. aureus, based on previous culture findings at each farm. They defined cows that they took milk samples from as having new or chronic infections based on somatic cell counts (SCC) in the milk. If values were >200,000 cells/mL for the month of collection the infections were considered new, whereas if cell counts were  >200,000 cells/mL for more than 2 months, those infections were considered chronic. They took a single milk sample from each teat of the infected cows, for a total of 1,354 mammary glands from 350 cows.

Pulse field electrophoresis was used to identify the different subspecies/serotypes/pulsotypes (pick your word), and to identify the genes coding for enterotoxin production that had been amplified by PCR. An ELISA test was used last to detect the presence of several enterotoxins.

As the majority of exposure to enterotoxins produced my S. aureus is through milk and dairy products, subclinical infections of S. aureus are very important as a food safety control point. Unlike cows with clinical cases that are removed from production, cows with subclinical infections continue to contribute milk that makes it to the consumer, provided that the SSC is <750,000 cells/mL. The authors were unable to detect a large amount of enterotoxin in their samples, but many of the pulsotypes contained the genes coding for their production. Other studies cited by the author report the common presence of these genes in S. aureus  samples, but expression rates are inconclusive or unexplored. This means that theoretically, subclinical cows could be introducing these bacterial toxins into consumer milk in small amounts.

It’s difficult to tell how significant these amounts might be. Toxic doses of one of the enterotoxins, “Toxic Shock Syndrome Toxin 1”, has been found to be as low as 100 micrograms/Kg in miniature pigs. The concentrations that may be introduced through contaminated milk, and the bioavailability when ingested, should be explored. Takeuchi et al. (1998) were able to detect the presence of TSST- 1 in bulk milk tanks, but no one has yet to quantify the amounts of TSST- 1 potentially present in pasteurized milk.

All that being said, what good is this new information? It can be argued that because these infections are chronic and/or subclinical that these strains of S. aureus aren’t very pathogenic, but they’re still causing inflammation. By identifying common serotypes and factors leading to the subclinical infection of a herd, perhaps there are simple management changes that can prevent infection. Milking is an almost sterile procedure, with sanitation of the teats both prior and following milking, wearing gloves, and forestripping; but there could be other tricks that would target risk factors related to the spread of subclinical pathogens, especially those that are specific to a location.

 

ResearchBlogging.org

Bulanda M, Zaleska M, Mandel L, Talafantova M, Travnicek J, Kunstmann G, Mauff G, Pulverer G, & Heczko PB (1989). Toxicity of staphylococcal toxic shock syndrome toxin 1 for germ-free and conventional piglets. Reviews of infectious diseases, 11 Suppl 1 PMID: 2928643

Oliveira L, Rodrigues AC, Hulland C, & Ruegg PL (2011). Enterotoxin production, enterotoxin gene distribution, and genetic diversity of Staphylococcus aureus recovered from milk of cows with subclinical mastitis. American journal of veterinary research, 72 (10), 1361-8 PMID: 21962279

Takeuchi, S., Ishiguro, K., Ikegami, M., Kaidoh, T., & Hayakawa, Y. (1998). Production of toxic shock syndrome toxin by Staphylococcus aureus isolated from mastitic cow’s milk and farm bulk milk Veterinary Microbiology, 59 (4), 251-258 DOI: 10.1016/S0378-1135(96)01253-9

Article Review: Leptospira and Leptospirosis

In my latest ScienceDirect purge, I came across this article covering Leptospirosis. I had no idea it would be such a dense read, figuring it would be a simple review of the disease with emphasis on new discoveries. I ended up using a lot of immunology references and Google searches. This article isn’t just an entry from the Merck manual.

The article does a very good job of covering Lepto microbiology, but I was especially impressed with the point they made to identify everything we don’t know. Indeed that was the emphasis of the article, that lepto contains so many pathways unique to it as a bacterium that we don’t know nearly as much about it as we do something like E. Coli. Additionally, Lepto is extremely hard to culture, as you end up with non-virulent colonies. They identify and isolate the virulent daughters by inoculating lab animals.

You might assume that immunity to Lepto is a simple thing, given how prevalent Lepto vaccination is due to the zoonotic risk. However the article makes the point multiple times that immunity to one Lepto serovar does not grant immunity to others, though occasionally it can help grant passive immunity or resistance across different species. While the exchange of genetic material between parent and daughter lepto colonies is not well understood, it appears to be slow mutating, which is interesting given how unique the antigens between serovars seem to be.

There’s a lot of complicated immunology discussed in the article that I don’t feel qualified to comment on, but it’s very interesting, and I recommend glancing through. The more microbiology I learn the more I understand that 99% of the workings of the cell happen on membranes (a statement that probably produces a loud “duh” from any student, biologist, or doctor). For a more clinical discussion of Lepto, a simpler reference like Merck or Blackwells will help, as well as several peer-reviewed sources that the article itself recommends for information on clinical presentations.

Adler, B., & de la Peña Moctezuma, A. (2010). Leptospira and leptospirosis Veterinary Microbiology, 140 (3-4), 287-296 DOI: 10.1016/j.vetmic.2009.03.012