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U.S. Department of Health and Human Services

Animal & Veterinary

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Antimicrobial Resistance Activities at ARS by Mary E. Torrence, DVM, Ph.D.

DR. TORRENCE: Thanks, Pat. I’m going to try and just give a brief overview of some of the antimicrobial resistance activities in USDA, specifically ARS. But I also don’t want to leave out the fact that other USDA agencies are integral to our antimicrobial resistant activities.
NIFA, which is now the National Institute For Food and Agriculture, which was the old Cooperative State Research Education and Extension Service, for the first time in their integrating program listed antimicrobial resistance as a special emphasis grant.

So, this was the first time that I saw the antimicrobial resistance being a focus, at least with the integrated program, which funds research, education and extension activities around a certain issue. Certainly antimicrobial resistance has been a part of some of the other grant programs within NIFA.

APHIS and FSIS play an important part in the animal ARMS sampling program. APHIS through their national antimicrobial health monitoring system programs collects samples nationally representative of food animals throughout the United States in different years. They collect information on antibiotic use, management practices and various other factors.

FSIS has given of slaughter isolets for the animal ARMS sampling through this entire process. And as well they also are responsible for the testing and evaluation of residues, which include pesticides and chemicals and have kind of an ancillary role in antimicrobial resistance.

Again, you’ll hear much more detail of the presentations on the animals ARMS part of NARMS, so I’m not going to go into too much detail on that.


As far as ARS, you can kind of look at our focus of areas really in two-prongs, really. But in both surveillance and monitoring which all of you know about NARMS and VetNet.

And then we have a fair amount of research. And it’s based around method development, enhancing methods, some prevention and control strategies and looking at alternatives, specifically to growth promoters and to antibiotics.

So, I’ll talk a little bit about each of these.


Again, Doctor Cray is going to talk about the animal ARMS of NARMS, so I’m not going to into great detail. Basically to talk about the fact that there are four major organisms that they collect which is Salmonella, Campylobacter, Enterococci and E. coli. These have been going on since 1998. With the different organisms. And as you can see some of the methods have been changed over the years to try to become much more sensitive and standardized among NARMS.


USDA-ARS specifically at the Athens research unit, also in conjunction with NARMS is very much into method development. And re-looking at methods and how do we get more sensitive specific data and how do we get more detailed data. So this includes multiplex CPR, height, throughput, sequencing, microarrays, DNA chips, you’ll hear more about that. But I think that’s the advantage of the NARMS sampling program in that it allows us to try to dig a little further for some of the detailed information and the genomic information.


USDA VetNet, which was started in Athens, is a complementary FGE fingerprint database. And really to compliment CDC and I think it shows a great collaboration between ARS and CDC. So it’s really to determine the PFGE patterns of Salmonella and Campylobacter that are submitted to NARMS so they can be compared to CDC’s PulseNet to help in foodborne illness outbreaks, to provide comparative data and also within USDA to help look at farm level animal illness outbreaks. Paula really has established that. And also has training programs to make them PulseNet certified. So, this really shows a great collaboration between USDA and CDC.


Our research is really based around kind of two tenants, and that’s trying to look at our systems approach or population biology approach, more of a metagenomics, and really trying to look at interventions along the entire food chain. And so I’m just going to discuss a couple of the research projects.

The research projects are scattered within USDA, ARS, among our different centers. Certainly if you have any questions about the specific presentations please see the individual scientists and if you don’t know them, contact me and I’d be happy to send you on the way to some of the scientific research that we’re doing.


Thad Stanton at the National Animal Disease Center in Ames, Iowa, is really looking at the Swine microbiota. And the two objectives of his research which he’s ongoing and will continue in the next few years, is what is the role of the commensals in the ecology of antimicrobial resistance. We talk about it. But have we really looked at it very specifically. So he’s trying to really get a handle on the role of commensals. And then what are the effects of antibiotics on the intestinal microbiota. What does it do to either the commensals or potentially foodborne pathogens.


These are just a little bit of the results and you can see that there is change among the Swine flora, at least after two weeks. But the question is, is the diet selecting for specific resistant bacteria or is it really selecting for a bacteria that likes the gut flora. So we have a ways to go on that.

But this is a really exciting start. NADC is really trying to build their metagenomic program. And really get a handle on different diets that are fed to swines specifically but also cattle and what it does to the microbiota.


Another research program within NADC, this is Shawn Beardson’s work, she does a lot of work with Salmonella virulent, but she’s also looking at Rumen microbiota, but this is really interesting because we found that protozoa in Rumens kind of hide the Salmonella. Kind of protect it so it maintains itself in the Rumen. And we’re wondering if it plays two roles. One that it makes Salmonella more hyper invasive, and two, whether it’s really an exchange site for antibiotic resistance genes.

So, I think you know the protozoa works really interesting. We’re going to look at it in different animals species and then is it just protozoa or is it other parasites. So we’re going to follow this line a little bit more because it’s just a really interesting fact that we really hadn’t thought about in the area of antibiotic resistance.


The role of plasmids, David mentioned that, and antimicrobial resistance. We’ve got various projects going on that really to look at the transfer of resistance. Can we look at plasmids and develop better methods to understand what plasmids are doing. Determining if the number of plasmids effects the growth rate in different strains. And then we have project in College Station looking at the Darkling Beetle, which is a common poultry insect in poultry houses that helps spread foodborne pathogens, but has also been used as a research model to study to plasmid transfer. And they can actually infect this Darkling Beetle with several different foodborne pathogens and watch the gene transfer.
So that’s another really interesting thing in looking at plasmid transfer.


Alternative to antimicrobials, this includes a lot of different types of products. And this kind of our idea at the pre-harvest level for foodborne pathogens. Can we use alternatives to decrease foodborne pathogens and at the same time can they be alternatives to growth promoters or antibiotics.

And this covers a range of food animals, cattle, poultry, even turkeys, swine and a range of products as you can see, even some natural products and herbs. Of course if we find one that works then we’re going to have to do a little more collaboration with FDA to see if we can get them through. But very interesting research. And this is done in several parts of the United States, College Station, Fayetteville, Athens, and NADC.


On the post harvest kind of side of interventions we’re looking really at the product rinses, specifically the carcass rinses on cattle, the poultry rinses and whether they are effective, first off, on the foodborne pathogens, and what they might do as far as resistance. Do they get rid of resistant organisms better than regular foodborne pathogens, do they cause resistance, and can we look at alternatives. And I think this is important not only for the research in antimicrobial resistance but also for trade issues, particularly in poultry rinses, and the fact that we can’t export poultry to Europe.

So, we’re trying different poultry rinses. And organics, lactic acids, alternatives to chlorine as well. And these are being done at Clay Center and Athens.


The future, I just listed a few things. Some of it’s being done right now, but it is hopeful areas of research that we can look at it, to go along with CDC and the NARMS’ mission as far as looking at standardization enhancing methods, to looking at our sampling plan and how do we make it more representative like the retail ARM and the human ARM.

Alternatives again to antimicrobial and growth promoters, and there are some other potential risk factors, biofilms, we have several people looking at biofilms, both on farm and in the processing plant, and what role do the biofilms play in the foodborne pathogens. But also on resistance genes and organisms.

For instance we have some work in biofilms in dairy farms in the milk liners. And they do exist. And biofilms in the processing plants.
Distiller-grains is a big movement in feeding animals. Distiller-grains, there have been papers on the effect of the distiller-grains on E. coli and foodborne pathogens, but what is the potential there for resistance. Either increasing antimicrobial resistance organisms or resistant genes. Carcass rinses, again, for foodborne pathogens and what role do they play in resistance.

Disinfectants on farm or a processing plant, and this goes kind of Stuart Levy’s talk about antimicrobial in everything. And I don’t know if this even plays a role and do we even want to get into this, but it’s certainly an area that we can think about.

And then the last one is kind of water, soil and produce. I was at a produce food safety meeting a couple of weeks ago talking about what’s been done in produce research. And while the emphasis was on foodborne pathogens, there are also foodborne pathogens that have some resistance. And what is the role of water and soil in foodborne pathogens in produce and in resistance.

And I’ll just close with the fact that we will continue to collaborate with everybody. And I think we’re really looking at opportunities, what research that we do internationally. ARS has a lot of international research opportunities, and what can we fill in as far as research gaps for specifically FDA that may not have the infrastructure and what can we bring to the table.

Thank you very much.