Tracking Antimicrobial Resistance: Down on the farm

Tracking Antimicrobial Resistance: Down on the farm

In the summer of 2016, Pipestone set forth the challenge to be global leaders in antimicrobial stewardship. As swine veterinarians, we feel a responsibility to lead the industry with science-driven decisions on how to manage the use of antimicrobials, track resistance, and make proactive changes to practices if increased resistance was shown. With that in mind, we crafted  PART (Pipestone Antimicrobial Resistance Tracker), a tool to measure antibiotic use on farm, as well as to track antimicrobial resistance (AMR) across veterinary pathogens, over time.

My role in this effort is a bit “out-of-the box”, as I tried to develop a means of how to measure pathogens of food safety and human health at the level of the farm. I got my inspiration from a group called NARMS, the National Antimicrobial Resistance Monitoring Service. NARMS is a federal organization, which measures the level of 4 specific bacteria, known to cause food-borne illness in people: E coli, Salmonella, Enterococcus, and Campylobacter. NARMS is composed of the CDC, which measures cases of food-borne illness in people, the FDA, which monitors the presence of select food-borne pathogens at the level of the meat case and the USDA, who measures these pathogens at the level of the harvest facility.

A few things became very clear to me as I contemplated my approach:

  1. No one in NARMS was measuring at the farm.
  2. I needed to use NARMS-standards on the farm as they were already accepted by the government and the national medical community.
  3. Unlike tracking AMR at the veterinary level, where you post 1-2 sick pigs out of 2400 and send a few samples to a lab, I wanted a more comprehensive, representative sample of the population and its environment.

To help answer, we collaborated with the Veterinary and Biomedical Sciences Department and Food Safety Microbiology Laboratory at South Dakota State University to craft a protocol to sample both live animals prior to marketing and their environments. In addition, we mimicked the exact antimicrobial susceptibility panel used by NARMS, so we could start to track resistance patterns across the 4 bacteria. Now that we had a set of nationally-accepted standards and a validated sampling protocol we could go to work. I can’t thank everyone at SDSU enough for all their expertise and help with this important project!

To make a long story short, our methods have proved to be accurate and repeatable, not only in swine environments but across alternative environments, such as human waste water treatment plants, playground dirt and companion animal facilities. We can routinely detect our 4 NARMS bacteria and determine their level of AMR. For third-party validation, we have also worked with Drs. Jonathan Frye and Charlene Jackson from the USDA-ARS lab in Athens, GA (who helped set up the original NARMS standards) to determine whether a report of resistance from the SDSU VDL is indicative of the presence of a resistance gene. In other words, if the lab says bacteria are “susceptible” or “resistant” to a specific antibiotic, is it true? Short answer= Yes!

Whew…I realize this is a lot of information BUT I wanted to try to explain the degree of detail we put into the process of sampling swine environments and the collaboration we had with nationally recognized agencies.  As we collect more information, I will keep you posted on what we are learning! Thanks for your support.

PART Webinar: Tracking Antibiotic Resistance

PART Webinar: Tracking Antibiotic Resistance

We are all concerned about antimicrobial resistance (AMR.)  But how does use of antibiotics in livestock contribute to resistance in humans and what steps are being taken to know for sure?

Listen in to Dr. Joel Nerem and Dr. Scott Dee as they review a 15-year history of AMR data, along with ongoing Pipestone research trials.

PART Webinar: One Year Review of Antibiotic Resistance and Use Data (Series 1)

PART Webinar: One Year Review of Antibiotic Resistance and Use Data (Series 1)

Pipestone continues to make strides tracking antibiotic resistance and use.  Since launched in January 2017, PART (Pipestone Antibiotic Resistance Tracker) has provided swine producers a tool for further Responsible Antibiotic use.  Join Dr. Joel Nerem and Dr. Scott Dee as they detail what we’ve learned in the past twelve months.

My “Pioneer Woman” Experience

My “Pioneer Woman” Experience

I recently had the opportunity to host a group of food bloggers at a farm that I am the veterinarian for in South Dakota.  Prior to this event, I didn’t have a good understanding of what food blogging entailed aside from a couple quick visits to The Pioneer Woman’s blog!  But let me tell you… I learned a lot about food blogging.

The nine bloggers who visited our farm were amazing people who had worked with companies like Kraft food, Bushes Baked Beans, Taste of Home, and even Captain Morgan!  Some of them have written cookbooks and all of them demonstrated an AMAZING PASSION FOR FOOD!  In return, I shared my passion for pig farming and our desire to give the best care to our animals.

The bloggers brought a unique perspective to our farm visit which inevitably led to some candid conversations about antibiotics, health and care of the animals.  I thought our readers may be wondering about these questions too:

“Do all pigs get antibiotics here at the farm?”

First stop on our tour was in the area that is like the “medicine cabinet” and supply room.  One of the bloggers asked if all the pigs on the farm get antibiotics.  I clarified that we do not give all pigs on the farm antibiotics.  As a veterinarian, I took an oath to protect animal health and prevent and relieve animal suffering – so using antibiotics to treat sick pigs or to prevent significant diseases spreading through a group of animals is of the utmost importance to me.  We do use antibiotics because they are an important tool for caring for our animals, when necessary. We also talked about ways that we prevent disease and measures we take to keep the animals healthy – for example, the vaccinations that we give, having our animals inside to keep their environment comfortable, and working with nutritionists to provide the best nutrition.

 “How are the mom pigs taken care of while they are at the farm?”

Sow (mom pig) comfort is a top priority on the farm.  We had the opportunity to walk through the area where the pregnant sows are located.  Our visitors noticed that there was “mood music” playing in the background – they enjoyed this surprising find!  We also talked about special nutritional needs that change throughout pregnancy and how we are able to adjust to meet these needs and keep the sows healthy.

“What happens when mom pigs give birth?”

As we walked through the part of the farm where piglets were being born (aka farrowing rooms), we discussed how a specially trained individual is checking on the moms every 20 minutes to make sure they are progressing with farrowing. They also are drying piglets off as they are born and putting them under the special heat lamps to make sure piglets warm up quickly.  This sounds similar to the steps taken when my children were just born!  Some of the bloggers tried their hand at helping deliver piglets – those who did seemed to glow with pride and excitement when the new piglet was delivered into their arms!

The bloggers enjoyed seeing first hand all the actions that we take to care for the sows and pigs. Farmers and Veterinarians work together to keep them healthy and reduce our need to treat animals with antibiotics.  Sharing this message as well as demonstrating our passion for pigs helped resonate with the bloggers – it was great to share that we are raising animals to provide that SAFE WHOLESOME DELICIOUS FOOD THEY LOVE & BLOG ABOUT!!

The Truth of the Matter

The Truth of the Matter

scott-deeRecent stories in some well-read media publications make it very difficult for consumers to weed out the difference between the truth about antimicrobial resistance (AMR) versus assumptions.

Media suggests that the livestock industry is not properly managing the antibiotic issue.  Assumptions like this have led to action, such as the recent San Francisco law requiring grocery stores and meat producers to label the average time and quantity of drugs given to livestock.

Let’s talk about the truths of AMR, before assumptions.


Truth #1:  There is no direct evidence that links antibiotic use in livestock to clinical failure of therapy in humans.

Truth #2: Livestock producers must follow federal withdrawal times to make sure the antibiotic has left the treated animals body by time of harvest.

To ensure farmers follow withdrawal dates and our meat supply is safe and nutritious, the USDA monitors and tests the meat supply for antibiotic residues in the meat.

Truth #3: Withholding treatment to sick animals is inhumane.

Veterinarians take an oath to protect animal health and prevent and relieve animal suffering, conserve animal resources, promote public health, and advance medical knowledge.  What does this have to do with antibiotics?  When an animal is sick, treatment with antibiotics is the ethical thing to do to relieve the animal from suffering.

Data from a recent Pipestone Applied Research scientifically validated study indicate that the inability to use antibiotics in a judicious, responsible manner to treat sick animals can result in unacceptably high mortality levels.  As a veterinarian and animal care-taker, it’s at my core to use every approved tool I can to save animal lives while being judiciously responsible for my family, community and environment.

Truth #4: Antibiotic Resistance has been happening in bacteria for millions of years, long before the discovery and development of antibiotics.

  1. Antibiotic resistant bacteria have been identified in the stomach contents of mummified humans.
  2. Antibiotic resistant bacteria have been identified in 4-million-year-old caves in which humans have never set foot.
  3. Samples of bacteria collected from pens of pigs indicate resistance to antibiotics that have never been used on the farm.

Truth #5: The environment is the real driver of resistance.

Often overlooked is the effect of environmental bacteria on the development and spread of resistance, specifically,

  1. Bacteria & molds have been in our environment for millions of years.
  2. In order to compete and to survive, they have developed metabolites which are the precursors to antibiotics.
  3. The genetic code for these metabolites are easily exchanged from one bacteria to another
  4. The widespread exchange of genetic material results in the development of bacteria that are resistant to the metabolite (antibiotic).
  5. Because of this phenomenon, bacteria can develop resistance to antibiotics, even if they are never used in the population or on the farm.

Truth #6: More research is needed to understand AMR.

Antimicrobial Resistance is extremely complicated, and with research so new on this topic it is too easy for people to jump to conclusions.  Pipestone takes AMR and our responsibility of antibiotic use very seriously, which is why we have dedicated time and resources to developing programs such as PART (Pipestone Antibiotic Resistance Tracker).  PART provides Pipestone veterinarians and livestock producers the tools for Responsible Antibiotic Use with ability to track antibiotic use.  Pipestone is also undergoing research trials in regard to AMR so we can better understand how we can combat antibiotic resistance.


We applaud others who are taking steps to better understand the truths of AMR, and ask others to join us before making assumptions.


What’s New in the World of Antibiotics?

What’s New in the World of Antibiotics?

scott-deeBy: Dr. Scott Dee

Greetings from Pipestone! I am sorry I haven’t written for a while, but I am busy learning how viruses travel the globe in contaminated feed (really) and how we can try to prevent our pigs from getting sick in the first place!…Anyway, I had a chance to do a little reading on the topic of antibiotic use/antimicrobial resistance in food animals and found a few articles that were both interesting and concerning. Here is what I learned:

1.  Maryland has become the second state (after California) to ban routine use of antibiotics in livestock. “Routine use” can be defined as use in animals that are not sick, in other words, for the prevention of disease. An example of routine use is administration of antibiotics shortly after birth, when new piglets are stressed and most vulnerable to infection.

2.  European pig farmers continue to push to limit per pig antibiotic use to a predetermined amount. In other words, there will be regulations limiting the amount of medicine that would be available to treat sick animals. As a veterinarian who took an oath to care for animals when sick, his is worrisome, for several reasons:

a. Many of the European pig farmers raise pigs outside. Since it is impossible to “clean the dirt”, the bacterial challenge (and the subsequent need for antibiotics) to pigs raised in this type of environment would be much greater than pigs raised in barns that are cleaned and disinfected on a regular basis; like ours.

b. I am not sure where the predetermined number for approved antibiotic use will be derived from. I am concerned about the potential for not treating an illness well enough to completely eliminate, which would actually promote antimicrobial resistance; much like my medical doctor scolding me for not having my daughter finish the ENTIRE bottle of medicine for an ear infection.

c. As a veterinarian, I prefer to focus and practice “responsible use” instead of focusing only on “reduced use”. This involves obtaining a proper diagnosis, selecting an appropriate antibiotic to treat the infection, administering the correct dose for the correct period of time and following the stated withdrawal period. We believe this is the most responsible and judicious way to use antibiotics in food animals, not trying to compete on “how low can we go”.

3.  A new antibiotic may be in the works! Scientists from Rutgers University have discovered a new antibiotic called “pseudouridimycin” that comes from a bacteria in soil. This new drug works on bacteria differently than current products, thereby reducing the development of resistance. Very exciting! While this won’t happen overnight, I am encouraged by the search and advancement for better tools to treat infections, and allow us to provide the best care to the animal while continue to ensure responsible use for our families and communities.

I can’t wait to see what’s next!  Thanks for reading!  See you soon.

Antibiotic Resistance Myth Busters

Antibiotic Resistance Myth Busters

fact or mythBy: Dr. Carissa Odland

Often we are so overwhelmed with information being shared – through main stream news, social media, and conversations with friends or co-workers.  It can be challenging to decipher what is true versus a myth.  As a veterinarian and mother of two young children, I recognize the importance of getting the facts about the food we feed our families – so here are a couple myths that I wanted to debunk:

Myth #1: Antibiotic Residue and Antibiotic Resistance are the same thing

Antibiotic Residue = molecules that remain in the meat from animals that have been treated with antibiotics.  When an animal is treated with an antibiotic, the drug moves through the animals body to treat the infection for a period of time while it is being metabolized or broken down.  Eventually the antibiotic will leave the animals body, however this can take a varying amount of time depending on the drug.  When drugs are approved for use in food-producing animals, the FDA establishes the amount of time from when an animal is treated until the antibiotic is out of the animal’s body or at a low enough level that it is safe for human’s to consume.  This period of time is called the “withdrawal period”.  Farmers work with their veterinarian to make sure they follow the withdrawal period between when an animal is treated with an antibiotic and when they can be harvested.
Additionally, random testing and inspections occur when animals are harvested for food to ensure that the food supply is safe.

Antibiotic Resistance = when a bacteria develops the capacity to inactivate or exclude antibiotics or develop a mechanism to block the killing effects of antibiotics.  This process of antibiotics developing resistance occurs naturally regardless of how antibiotics are used – this is part of the “survival of the fittest” as bacteria evolve to survive.  However we can impact antibiotic resistance.  Responsible antibiotic use by human health & veterinary health sectors is an important aspect of preserving antibiotics as an important tool to stay healthy.

Myth #2: Only if you use antibiotics incorrectly will it lead to antibiotic resistance

The first modern day “antibiotics” were developed in the 1920’s.  However scientists recently discovered evidence of antibiotic resistance found in 1000-year-old mummies.  They found genetic material within bacteria in the mummy GI tract that has the potential to resist modern-day antibiotics.  So despite the fact that antibiotics were not even developed yet, we can infer from this example that in an effort to survive, bacteria will transform / modify to resist the effects of antibiotics that might kill them.

Myth #3: Meat is less safe today than it was in the past

When we talk about safe food, this can mean different criteria for different people.

To you this may mean it will not cause a food-borne illness; it may mean it does not contain harmful chemicals or have antibiotics in it; it may mean it is wholesome & nutritious… When I am feeding my family, I want all of these criteria to be met so here are some of the facts that I found regarding meat safety:

  • Bacteria counts are down compared to 10-15 years ago
  • Food-borne illness counts are down according to CDC
  • Increased technology at time of harvest to eliminate or reduce the bacterial load from meat
  • According to USDA data in 2014, less than 1% of all carcasses tested & inspected had a violative residue (chemical or antibiotic)
  • Increased awareness about proper food preparation & handling of raw meat

We still need to work on making food safer – 1 out of 6 Americans get sick from a foodborne disease and 3,000 will die each year.  Precautionary measures such as washing hands while preparing & handling food or simply cooking all meat to proper temperatures will kill the bacteria and eliminate the risk of a significant percent of foodborne illnesses.  So this is a team effort that starts at the farm and needs to continue all the way to your kitchen & table.

GOOD NEWS: Antibiotics still work in pigs!

GOOD NEWS: Antibiotics still work in pigs!

scott-deeBy: Dr. Scott Dee

I recently read an interesting article in the Journal of Swine Health and Production (May-June 2017) entitled “Antimicrobial susceptibility of Actinobacillus pleuropneumoniae, Pasteurella multocida, Streptococcus suis and Bordetella bronchiseptica in the United States and Canada, 2011-2015”. The article was written by Michael Sweeney and others and featured teams from Zoetis and Microbial Research Inc.

Once I finished the title (and had a chance to catch my breath), the article proved to be very interesting reading. Basically, the team compared susceptibility data from 4 different bacteria across 10 different antimicrobials. Novel features of the article included:

  1. The study involved a total of 2940 bacterial isolates collected across 7 provinces in Canada and 35 US states over an extended period of time.
  2. All labs in the study used a consistent method of determining susceptibility.
  3. It focused on antimicrobial susceptibility versus antimicrobial resistance, which I found refreshing (for a change).
  4. Overall, the isolates surveyed indicated a high degree of susceptibility to the majority of the antibiotics tested and this is very good news.

Regarding the strengths of the study, this report demonstrated over a large sample size and period of time that many of the antibiotics we use to treat respiratory disease in pigs are still very effective.

Bottom line: This is a clear signal that the swine industry is practicing responsible use of antibiotics on farm, which is a very good thing to see.

However, as it pertained to limitations, some degree of antimicrobial resistance was observed with tetracyclines, indicating that we still have to be careful when managing this important medication. At Pipestone, we track use and resistance patterns of this important antimicrobial, as directed by PART. Furthermore, no data were available regarding intestinal pathogens. Finally, as the bacteria included in the study are not of food safety origin, the results cannot be extrapolated across pathogens related to human health.

Bottom line: We still have work to do.

In closing, I applaud the authors for this nice piece of work. It will clearly shows that the swine industry understands the meaning of “responsible use”.

Managing Antimicrobial Resistance: What Do We Know and What Do We Do?

Managing Antimicrobial Resistance: What Do We Know and What Do We Do?

fact checkBy: Dr. Scott Dee

The topic of antimicrobial resistance (AMR) is both confusing and controversial. It seems that a day doesn’t go by without the opportunity to read a new article, blog and/or a social media posting. Unfortunately, most of these publications attempt to scare us rather than educate us. In addition, many of these communications focus on the topic of overuse of antimicrobials in livestock populations and how this is promoting AMR. However, based on what I have read, the discussions I have had with experts in the field, as well as the results of internal studies we have conducted in Pipestone, I don’t think it’s quite that simple and here are a few examples:

  1. AMR occurs in the absence of antimicrobial use.

Fact: Peer-reviewed publications have reported the identification of resistance genes from a 4-million year old cave (Nature Communications) and the colon and feces of an 11th-century human mummy (PlosOne), long before antibiotics had been discovered.

  1. The level of antibiotic usage does not influence the level of antibiotic resistance.

Fact: The percentage of resistant bacteria recovered from livestock populations treated with high levels of antibiotics is no different than what is found in those treated with low levels. In other words, it appears that level of use (high dose versus low dose) doesn’t matter.

  1. The key to AMR is gene acquisition.

Fact: The development of AMR is due to the transfer of resistance genes between bacteria via mobile genetic elements such as plasmids. These DNA fragments can carry resistance genes to multiple antibiotics. Since many of the antibiotics that are used in humans and animals are derived from a small number of bacteria and molds, there is a lot of conserved genes that can be passed around and resistance to a human antibiotic can be observed, even if it’s never been used in an animal.

  1. The source of resistant genes is not the animal, it’s the environment.

Fact: Evidence of AMR to certain types of antibiotics can be found in livestock environments, despite never using these medicines on the farm and in the animals.

So what do we do? Quit using antibiotics and let sick animals suffer? I strongly disagree with this approach and in particular disagree with the “No Antibiotics Ever” approach to raising livestock. This is simply a marketing ploy that cares more about return on investment than animal well-being. While antibiotic use always needs to be practiced responsibly, for the sake of reducing animal suffering, we need to treat those individuals afflicted with bacterial diseases. In addition, we need to:

  1. Become educated: Rather than rely on the Internet and social media for your information, talk to reliable sources, such as Dr. Mike Apley of Kansas State University, or Drs. Peter Davies and Randy Singer from the University of Minnesota. These people are highly qualified and are great sources of non-biased information.
  2. Record antibiotic use: Keep accurate records of how much medicine you use to treat sick animals. Use VFD and prescription information to measure actual usage.
  3. Track AMR: Use food safety-based protocols employing NARMS standards to measure the level of resistance in your herds. Remember that sampling the environment and/or healthy animals is more representative than tissue samples from a couple of dead pigs. Your veterinarian and the state diagnostic laboratory faculty are great resources for setting this up.
  4. Manage the environment: Utilize proven health technologies and effective sanitation programs to reduce pathogen load and subsequent challenge in the animal environment. A clean, well-ventilated facility, i.e., the proverbial “an ounce of prevention”, goes a long way to reducing the need for antibiotics, aka, “the pound of cure”.

Clearly AMR is a very challenging topic; however, my confidence is rising that we can not only understand it but also do our part to manage it properly and meet the needs of our consumer groups. We know what to do, we just have to get to work!

Have You Heard the News?

Have You Heard the News?

scott-deeBy: Dr. Scott Dee

What an interesting morning! I spent a few hours catching up on all the articles recently published in various periodicals on antimicrobial resistance (AMR). This was no easy task due to the vast amount of coverage that this topic is receiving, be it in scientific publications, trade magazines, blogs, websites, social media and the popular press. While I totally agree that AMR is a very important topic and needs to be taken very seriously (as Pipestone is doing with PART), I think it’s important to keep a few things in mind as we process and communicate this information:

  1. The world is full of expert microbiologists who love to make comment and take credit; however, if you search the internet for their credentials (such as where they went to school and the number of scientific papers they have published) they disappear.
  2. Many of these publications use confusing language to make their point such, such as “at least partly resistant” and “commonly resistant”…???..whatever this means!
  3. Some sites provide a “SIGN NOW” approach for readers to respond to the FDA regarding the use of antibiotics in livestock through pre-written text. No thinking or writing is required; all you need to do is type your name and hit send!
  4. Scare tactics are a common approach using Star Wars-like language that is easy to understand, such as “doomsday scenario”, “the attack of the superbugs”, and “last-resort antibiotics”. These tactics are great for increasing their readership, but not realistic of the scenario.
  5. Many studies quoted involve one patient which are then described in mysterious terms that send chills down your spine such as “The Nevada Case”.
  6. Others forget to tell you (unless you actually read the entire article) that the widespread, fulminating MRSA infections described in personnel working in pig farms was actually only diagnosed by a MD in one of the 45 people involved.
  7. In addition, good news, such as the 80% reduction in cases of Clostridium difficile infections (a bacteria that causes intestinal issues in people and pigs) secondary to basic sanitation (hand-washing) and responsible antibiotic use in English healthcare facilities is downplayed.

I apologize for my rant; however, we need to be very careful as we manage the very important message of AMR with our consumers. Critical evaluation of the literature is the first step as there is a great deal of misinformation that is very readily accessible, easy to read and cleverly marketed.

I need some Excedrin!