Animal & Veterinary
by Dr. Tom Chiller
DR. CHILLER: Thanks, Linda. It is great to be here to summarize a little bit about what we are doing at CDC. For those of you who don’t me, I am Tom Chiller, and I run the epidemiology side of the human arm of NARMS at the CDC.
I’m an M.D. I don’t think there are any other M.D.s in the room, which is a first for me I have to admit, because usually at these kinds of things there are lots of M.D.s. This is not about getting on soap boxes and preaching. This is about reviewing the entire NARMS system.
My only soap box issue that I do want to say is that we are here because of human health, and that is what I do. I deal with sick people, sick kids, sick adults, and so, we always need to be thinking about that in public health and why we are doing surveillance, and I think that has been brought up a few times here.
I have only been with the NARMS system now for two years, and as you have all heard, NARMS has been in existence for quite some time. In the two years that I have been here my sole goal in NARMS has been to integrate the surveillance reporting, which has not been done in 11 years. We have separate reports. We have separate systems. We don’t look at the data together.
That has been very frustrating to me, and that has really been my primary goal for the last two years; is trying to integrate and trying to understand. I think that is the only way we are going to be able to get something out of this surveillance system, is when we have some sort of integrated reporting.
So, now I am off of my soap box. What I am going to do is I am just going to tell you a little bit about the human arm. The review questions and the discussion focus more on the animal retail stuff as I looked through them. We conducted an external review. Two of you were on the panel, Lyle and Scott. So I am going to sort of review that.
As I mentioned, I handed that out to you; what the reviewers said about what we did, and also, some of our internal responses to some of the external review’s comments. So, I will rush through the background about the human arm. I am not going to spend a lot of time, and I am not going to talk about data at all.
I am just more going to give you a little bit about what we sample, what we sample and then highlight a few of the external review issues, and then turn it over to Tim Barrett, who is here and who is the leader of our NARMS lab to talk about more laboratory based molecular characterization issues that we deal with.
So, NARMS is located within the Foodborne and Diarrheal Diseases Branch, and we have some overriding missions in our branch. Obviously, to reduce the burden of foodborne diseases is one, and that includes diseases caused by resistant bacteria.
We do through surveillance, epidemiological investigations and applied research, and I will talk to you a little bit about all of those. And we have numerous partnerships, but our major partners in all of our activities are our state public health departments. Both from the lab and from the epidemiology side.
Just to see where we are organized, and I have to admit that CDC organization seems to changing daily, but for now, just within our branch, this is sort of how we are organized within the overall structure. You can see that there are -- in our branch there are three sections. Foodborne diseases, diarrheal diseases and a lab section, and within the foodborne diseases section there is an outbreak unit and a FoodNet/NARMS unit, and obviously within the FoodNet and NARMS unit there is NARMS and there is FoodNet.
As you have heard a little bit, and you will hear about it more tomorrow, Global Salm Survey within actually the NARMS group.
The lab though is within the laboratory section, and so we actually are -- NARMS is actually within two different sections, and we have managed to continue to work as one big NARMS group, despite the fact that sometimes it is difficult to involve epi and lab together.
Just to show you our group, this is the folks on the epi side. We have got a couple of veterinarians, a couple of M.D.s and a group of MPH epidemiologists, as well as data analysis. Terrell Miller, who was mentioned before.
Similarly, on the lab side we have a couple of veterinary microbiologists and then several microbiologists and technicians that do all of the hard work that you are hearing about.
So, public health surveillance. I like to define it as ongoing, systematic, collection analysis, interpretation and dissemination. We feel very strongly that surveillance is data for decision making, as was mentioned, or information for action. Something needs to come about as a result of surveillance.
I like to show this slide. Anyone who has ever seen me talk -- or probably anyone from the CDC talk, we always show this slide. We love this slide. This could be applied to a different diseases, but here I apply to the cycle of foodborne disease control and prevention.
Starting with surveillance and, as you can see, moving to epidemiologic investigations, applied research, both of which could lead to prevention measures, which you then to reevaluate your prevention measures by doing more surveillance.
So, let me talk about how NARMS fits into that cycle from the human side. As we mentioned, we do routine surveillance of susceptibility and resistance. We look at non-typhi Salmonella, O157, Shigella. We also look at some traditionally human-to-human transferred pathogens, like Typhi, Vibrio and then again, we have been intermittently looking at Listeria. And as I already mentioned we look at Campylobacter in sort of a separate setting in our FoodNet sites.
We also are involved, as has been mentioned, in the Retail Food Study, and we also have now an Enterococci resistance study, which has really been converted into surveillance.
When we look back at NARMS, at CDC back in 1996 when it began, we had 14 states that were submitting isolates to us with two different bacteria. Salmonella and E. coli 0157. There was one epidemiologist, one laboratory and we had no dedicated office or lab space and our budget was approximately $100,000 from FDA that year.
Here is what we looked like in 1996. You can see that some of these were FoodNet sites, and we also had other sites back then in the beginning.
And now, in 2005, we are nationwide. So we receive isolates from every state in the nation. We look at nine different bacteria. Campylobacter, Enterococci, E. coli. I have already said them. I won’t keep saying them. I didn’t mention Shigella, another traditionally human-to-human transmitted enteric pathogen.
We have around six epidemiologists, nine laboratorians, we have a new office and we have a nice new lab space that CDC has given us. We are budget ed at -- I put $1.7 million. I am confused about a lot of the numbers these days, but budgeted at approximately $1.7 million. That is from both FDA and CDC. That is minus the retail food money.
That is why it looks a little lower.
And then, of course, for those Republicans in the room don’t get excited, but this is actually to show that we are in all 50 states.
This shows our submission and sampling. You can see when we began. We began with Salmonella and 0157, and we asked state sites to submit every 10th. So as they went down, what they received give us every 10th Salmonella, every fifth E. coli and 0157, and we did that for a while.
But as you see, as we started layering in more criteria, of course the burden to the lab increased and we had to do then essentially dilute out that sampling to a certain extent in 2003 where we went to every 20th. When we went nationwide in 2003 as well.
That was simply because as we were adding sites we were not changing the sampling and we were getting more and more numbers, and so -- and we are also adding pathogens. So, as was mentioned earlier, there has been tremendous growth. There was growth in funds and we were able to handle that, but we had to back off on our absolute numbers to be able to handle just the numbers of organisms coming in.
Specifically, to point out in Campylobacter we collect Campylobacter just from the 10 FoodNet sites. Again, there are lots of issues, and I will go into that in a second, with Campylobacter, because that was covered in our external review.
But just in 2005, at the recommendations of the external review and our own internal evaluations, we have now switched to a slightly different sampling for Campylobacter. You can see that we do get all of some pathogens, like Typhi, Listeria and Vibrio, and that means all that state health departments can isolate they send us.
Important trends. We’ve seen increase in resistance to clinically important antimicrobial agents. Again, that is one of our primary concerns and what we look at. Fluoroquinolones. You have seen data on that from the animal side; Campylobacter and Salmonella. But also, including Salmonella Typhi and Shigella.
Third generation cephalosporins. We are seeing increased resistance mainly in Salmonella, but we also now see some in 0157.
And then specifically looking at increase in multi drug resistance, like the MDR-AmpC in Newport, which now -- we now have MDRMC in over 18 different Salmonella serotypes, because it is a plasmid mediated spread, as you all know.
I wanted to point out some good things. This is not NARMS, but FoodNet. You guys may or may not all be aware that FoodNet has reported some nice, important declines in major foodborne diseases for 2004 compared to ‘96 when they started. O157, Campylobacter, even a little bit in Salmonella have declined between eight to 42 percent, and this was reported recently in the MMWR.
This is just a graph. We have made some tremendous success in Campylobacter. It is a really good success story. E. coli and O1057 was worrying us, but is now going down. And unfortunately, the red line, Salmonella, is not decreasing, despite a lot of effort. If you sort of look at Salmonella and get an idea and break it down by serotype, you can see sort of where the issues are.
Typhimurium has declined dramatically. There have been no change in Enteritidis or Heidelberg and the new kid on the block, Newport, which is a multi drug resistant Newport is up very high in Javiana because this is FoodNet and has some southern states. Javiana has particularly gone off the roof in Georgia and in some of the other southern areas.
Again, not so concentrating on the numbers, this is older data, but I just wanted to highlight one of the things that we do and one of the things that I think we are able to do, because we have other surveillance systems at the CDC. It is overlay data, and here is where you are seeing a FoodNet data. Again, looking at Campylobacter going down, and then we look at Ciprofloxacin, resistant Campylobacter and NARMS. Again, from these same sites.
And then we are able to actually do modeled prevalence and incidents based on those two data points and those two surveillance systems. As you can see, although Campylobacter is going down, what is going down is susceptible Campylobacter, not resistant Campylobacter.
So, that is surveillance. Next is epidemiological investigations. We try to pay more of a role now in outbreak investigations. Specifically, I think we have played a major role in the MDRMC and Salmonella Newport story, which was really identified in human illness through NARMS because NARMS was testing for a wide variety of antibiotics.
We get involved also in case-control studies looking at sporadic infections. One was fluoroquinolone resistant Campylobacter that was recently published, and we are currently in the throngs of doing a clinical outcome study for multi drug resistant salmonella, looking at the fact that we know there is a lot of evidence now that multi resistance Salmonella has the worst clinical outcome.
I think clearly we contributed, as was already mentioned, to the risk assessment process and to the NOH that FDC/CVM did when they were looking at fluoroquinolone resistant Campy.
So now, to applied research. Tim will talk a little bit more about this in the molecular characterization part. I just wanted to mention that we are obviously involved in applied research in an attempt to contribute to our understanding of the epi and maybe assist in directing specific prevention measures.
We can do this because of the surveillance framework that we have, and we conduct it upon that surveillance framework.
And finally, to prevention. I think one of the ways that we try to do prevention or maybe I should say education is through communication, and we have a lot of partners within NARMS. Some of them are here, and we truly enjoyed the concept of an annual scientific meeting. I think as Paula mentioned.
Unfortunately, we haven’t been able to have one this year, but this does enhance communication and collaboration around certain issues. It gives us a chance to share information with stakeholders, and we enjoy that process.
We also participate in local and state public health laboratory communication efforts. We have actually quarterly conference calls, and we have quarterly conference calls with all 50 states, which no one does at the CDC. NARMS is the only group that does that.
Just to mention, NARMS is also the only surveillance system that actually receives isolates from all 50 state health labs on a regular basis. No other surveillance system at CDC does that.
So, we take advantage of that relationship. We have a wonderful relationship with the state and local public health labs, and we use these quarterly conference calls to share information, talk about issue and problems, and this is also the forum at which are now introducing the concept of pulsing all NARMS isolates.
And then, communicating with the general public is important. We have a website, as everyone does. We have an annual report and then we do individual requests, as necessary. Obviously we get FOIA-ed quite a bit by our friends and colleagues out there, but we also with a lot of individual requests from the public.
We also are now involved in educational activities on prudent use. We have a program that we are involved in called Get Smart, Know When Antibiotics Work on the Farm, which is part of a larger program called Get Smart, Know when Antibiotics Work, which has been in existence for about seven years at the CDC. It is very successful.
That deals with the human issues, which we are very aware is just as important, and now we are trying to partner with groups that are working in this area as well.
So, after eight years we are -- NARMS, on the human side, we are clearly more robust nationwide. We collect information. Some information now about travel and other epidemiological information. We found it to be an excellent platform for studies and we are obviously conducting further studies.
We have a very good established collaboration through the retail food with the FDA Office of Research, but there is clear gaps in our surveillance and they remain. It is a challenge. It is going to be a challenge to deal with those gaps as we face level funding or probably actually reductions, as we have all been talking about.
I heard a question earlier about how we want to think about applying this data or how it can be analyzed, and I think one of the things that would clearly help in how we look at this data is to understand the quantity of antimicrobial agents used in specific food animals. This was a high priority action item in the Antimicrobial Resistance Action Plan.
This will give us precision to interpret surveillance on all of the arms, and obviously my goal is to integrate the report so we can actually try to interpret some of this. But this use data would help us focus prevention efforts, and there is really no surveillance on that that we can get our hands on.
So then, let me briefly then talk about the summary of the external review. Again, this was conducted in August of 2004. You can see the participants, two of which are here.
We focused on some basic issues. The first was our sampling strategy for Campylobacter, and I will go into that in a second, reporting and dissemination of data on susceptibility testing, resistance in human commensal bacterial and then molecular characterization and how to move forward in that.
And just to go over sampling on the human side, obviously sampling in laboratory based surveillance -- you have to think of this surveillance pyramid, and you have probably all seen this, but I think it is important to highlight the fact that we are catching the tip of that pyramid at CDC because a person has to become sick and has to then want to go see the doctor. The doctor hast o then want to send the sample.
The specimen then has to reach the clinical laboratory, get tested, get confirmed and that clinical lab then has to forward that to the state health department and then the state health department has to record it and tell us about it. And so, whenever we think of laboratory based surveillance, we realize we are only picking the tip of that pyramid, and CDC works very hard to try to understand what is happening at the bottom of the pyramid. In other words, to estimate burden of illness.
So one of the things in Campylobacter that we wanted to do is to see if we couldn’t move toward a sampling system that helped us delineate burden.
It is important to know that for Campylobacter there are no routine submission of isolates to CDC. As I mentioned, everything we do is asking the state and public health labs to submit isolates to us, which has not been the norm for any CDC surveillance system.
When we looked at how we sampled Campylobacter before NARMS existed, there was a sentinel county survey done. In ‘89 and ‘90, 19 U.S. counties sent the first five sporadic Campylobacters per month.
CDC did testing, susceptibility, they did species confirmation and they found the lessons learned from that was that the sampling scheme worked very well and that the Campylobacter isolates are very fragile and some isolates didn’t survive the shipping process.
That is what sort of led to the system that has been place for the last eight years, because of these challenges; the survivability of these isolates, require special shipping and then just the availability.
There are few states in this country -- I think we are at 12 now -- that require clinical laboratories to send isolates to the state public health lab. So, a lot of Campy surveillance is voluntary from the human side, and so, there are actually very few isolates often at state public health labs.
So, if we were going to get a representative sample from New Mexico, they might only have five Campylobacter. Again, I exaggerate to make the point that you just don’t know how many they have, except for the states where this is some sort of active surveillance going on or where there is mandatory submission.
The sampling scheme started with Campylobacter in FoodNet sites. Here are the FoodNet sites. There are 10 sites across the United States, representing about 16 percent of the population.
The collection for Campylobacter began in 1997. Isolates came from five sites, because that is where FoodNet was. It expanded through the years to 10 sites in 2004 and sites -- five out of the 10 sends isolates from their state public health labs, and five out of the 10 actually send isolates from a sentinel clinical lab. The sampling scheme that was chosen was the first isolate isolated each week.
So, we asked the reviewers, given all that history, and I really threw it at you quickly and you can read about it in a little more detail in the review, should the sampling strategy for Campylobacter be changed, and if so, how? And these are some quotes and comments from the review.
Campylobacter susceptibility testing is a higher priority and needs to be maintained. However, the limitations of the current sample need to be examined/evaluated and they emphasized that changes should be made to increase completeness of submission and representativeness; e.g., taking into account sampling by population and incidence, as well as by time of year, improving percentage of isolates received per site per week, et cetera.
And so, what we have done is in January of this year we started a new sampling scheme, which no longer gets this one isolate per week. Sites submit a proportion now of the total isolates their lab receives; so that now we have a proportional relationship to the number, and hopefully, that will help us them estimate burdens because now again we have a representative sample that deals with a proportion.
We are hoping to expand this now to more sites in 2006. Specifically, the second phase would be sites that mandatorily require Campylobacter submission at their state public health lab, a natural place to go. Of course, that means more testing, more isolates, more money, and again, as we are discussing today, that is one of the reasons we are sort of reevaluating everything we are doing to understand how priorities lie and where that money can be spent.
Again, the development and the hard work by CVM to do that broth microdilution plate is clearly helping us a lot. We normally got around 500 isolates of Campy. This year we are getting closer to 1,000, but we are able to crank them out in a minimal amount of time compared to what we were doing when we were doing E-tests. So, that is going to help. It is helping us become better efficient, but still, if we then expand to another 12 states, that is a whole bunch more isolates and we are going to have to consider the ramifications of that.
The other question we asked was about reporting and dissemination of data on susceptibility testing, and we said what are the advantages and disadvantages of reporting data as percent resistant versus percent non-susceptible. This is a big issue in clinical medicine. In clinical medicine I don’t care if something is resistant. I care if it is susceptible because I am treating with drug and I need to know whether my drug will work.
We wondered in reporting this surveillance data should we be changing the way we report it. Of course, then that would have to change the name from NARMS to NARSTS or something, because we would be reporting the National Antimicrobial Susceptibility Testing Service.
We asked the panel what they thought. We also asked the panel how could we improve our NARMS annual report.
And again, just to highlight a few of the comments, looking at percent resistance versus percent non-susceptible, a couple of the quotes: "From a clinical and molecular perspective, presenting results primarily in terms of
non-susceptible compared with susceptible is the most useful."
"However, we advocate continuing to present the basic data in tables and figures in a variety of formats."
"We recognize that this change will present challenges in terms of comparison of future reports with earlier ones."
What we have done as a result of these recommendations and thoughts is for the 2003 annual report which, hopefully, will be out in the next month or so -- or the next couple of months. By the summer. We will present both resistant and intermediate data, and we will have it all as resistant RIS. Essentially, SIR. So we can show that and we can see what people think and what comments are made.
We are in the process of reviewing how our international peers present their data and present their findings for enteric bacteria, because we didn’t feel comfortable to just switching to susceptible -- resistant to susceptible and non-susceptible reporting, and although the panel recommended that, they did say that we should look at a variety of formats. And so, that is what we are doing now. We really want to evaluate that change before we do it.
Finally, we asked that other question about how should we improve the annual report. They commented on timeliness. You already heard Lyle talk about timeliness a little bit. They talked about a summary report like DANMAP or CIPARS does a nice summary report.
Again, this is an integrated summary. But they said for each arm, if you had a summary report that was a little more streamlined, that would be very helpful.
They recommended more statistical consultation and trend analysis and to develop a web based way to query the data for those interested parties and, eventually, the general public.
Our actions to date. We have actually really made a tremendous amount of progress in our testing. If you saw my old isolate submission slide, we got really bogged down in 2002 and 2003 because we suddenly add a lot of pathogens, added all these states. Everything sort of happened at the same time, and it sort of -- we had to recover from that.
We also, in the middle of that, changed our database format, which has been a painful effort, but we are reaping huge rewards from that, including better collaboration with USDA because we are collaborating on less political issues. We are collaborating on data and how data is organized, and actually, that is a really good way to collaborate with people to begin to build a nice foundation for, hopefully, further integrative reporting and things like this.
We will, hopefully, have our annual reports out for both 2003 and 2004 this year and then we want to release our report every June. So, it will be a six month delay. That is our goal. That is clearly feasible for us now that our database is almost done. We also are going to change the format, as I mentioned. That format change you will see in the 2003 report this summer.
We will probably have a summary report that will be much more streamlined and much thinner than our traditional report. We found a way to collapse a lot of the data. And then, we will have a more extensive web based version that will have a lot more of the graphs and tables.
Again, as I mentioned, future reporting for us and for, I think, all of NARMS is that we need an integrated report. We need something integrated. As Paula mentioned, we are starting by actually just formatting our reports the same, but I want to go a step further and say can we actually put something together where we are actually looking at all the data, all the three different arms together in the same graph or the same table.
And we have all agreed that that would be a great
-- that is the appropriate step. That is why the surveillance system was established. We are going to work toward doing that in a summary -- a small summary report for the MMWR next year. We are hoping that will happen, and again, we are working toward that.
As Paula mentioned, we are making tremendous strides in the database integration, in the sense that we are designing our databases -- they are almost identical and that is huge when it comes to cranking out reports that are similar. Then our goal is to make our data web based and accessible by the year 2006, although I don’t know if that is really going to be feasible. So I put ‘06/’07.
There are a lot of hoops to jump through to make data accessible in this day and age of security. When you have a server housed within the firewall, it changes things a lot. You are going to have people accessing that server. So we have to work on a lot of issues like that, but it is going to be feasible and we are working hard toward doing that.
I won’t really go into resistance on human. I have talked probably too long already. Again, the review--and you can read it more extensively in the document--said it was important to continue to monitor resistance in commensals to determine the role of these bacteria as reservoirs of resistance determinants for human pathogens.
And to this end, it is important, where possible, to integrate monitoring and epidemiological data; e.g., antimicrobial use from animals, food and the environment, as well as humans.
NARMS should focus on the important commensals, like Enterococci and E. coli, and use susceptibility panels that, at a minimum, include those drugs important to human health, especially if members of the same class are used in animals.
And now, I will turn it over to Tim, and please, hold your comments or questions until Tim is done. Tim will go into a little bit of the molecular characterization issues.
DR. BARRETT: I just have a few slides. I am going to summarize the sorts of things that we were doing at the time of our review and are continuing to do now, and some of the things that we have changed as a result of our external review back in August.
As far as molecular characterization, we really are involved in three types of characterization, and I will mention something about each of them. Strain characterization. That would be subtyping, like PFGE. Identified of specific resistance determinants and the characterization of the resistance-mediating elements, being plasmids, transposons, et cetera.
For strain characterization, for Salmonella, as I mentioned to Lyle’s question about Typhimurium, we don’t serotype all of our Salmonella isolates. We assume that the state serotyping is correct by and large. But when something is important that we want to know that we are reporting a particular isolate serotype correctly, then we will confirm that serotype at our reference laboratory.
We do PFGE typing for special studies. That would be there in our laboratory. And we phage type Enteritidis and Typhimurium isolates for outbreaks and for special studies. For Campylobacter we are PFGE typing. We will, hopefully, finish soon the 2003 collection.
We can compare our isolates with Dave White’s retail food isolates, and after we have had a chance to see what we think that information tells us, then we will decide whether we need to do any different methods or additional methods. And again, we do PFGE on Campylobacter for special collections.
For Enterococcus the only strain characterization we do is to confirm the resistance. A lot of our isolates come from selective media. So we presume that they are resistant, but we confirm that. And, we do speciation.
For identifying specific resistance determinants one of the things we have been interested in, primarily because of the Salmonella Newport emergence, is Salmonella with decreased susceptibility to cephalosporins. We have done isoelectric focusing for beta lactamases. We routinely do PCR for the blaCMY2.
As you probably already heard or probably already know, most all of them have the blaCMY2 gene. We are also beginning to do some PCR and sequencing for other type of beta lactamases, which I will mention more about.
As far as resistance determinants for Salmonella with decreased susceptibility to ciprofloxacin, again we confirm the phenotypic results. We did a good bit of PCR sequencing for gyrA and parC, and we haven’t seen anything remarkable to this point. It is probably not something that we want to continue to do routinely.
We are currently collaborating with David Hooper on potential plasmid-mediated ciprofloxacin resistance, and I will mention more about that also.
For Campylobacter we are not routinely characterizing any genes in Campylobacter right now. At one time we sequenced a collection of QRDR genes from fluoroquinolone resistant isolates. All of the mutations that we saw had already been reported and it didn’t like anything worth continuing to do for a long time.
Likewise, we identified macrolide resistance mechanisms in a subset. They were all 23S mutations, as have already been reported, and we screened the subset with a multiplex PCR for TET determinants. They were all tet-o, as has already been reported. So we have decided that we probably don’t want to do any of these things on a continuing basis.
A couple of years ago it looked like we might be seeing an emergence of E. coli 0157 with ACSSuT phenotype. Fortunately, that hasn’t happened, but we characterized the specific genes involved there by PCR. And for Enterococcus we are identifying mechanisms of resistance for quinupristin/dalfoprostin and, as Dave mentioned, we are seeing the same thing that -- probably most of our isolates don’t have one of the already described mechanisms for vancomycin and for high level gentamicin.
As far as characterizing the resistance mediating elements, this is something that we felt was largely outside of our area of expertise. So, we have been collaborating with others to characterize plasmids from cephalosporin resistant Salmonella and from the E. coli O157.
The questions that we asked our reviewers, which included Dr. Vogel and Dr. McEwen, was whether we should continue to focus on problems that would be things that we perceive to be important, such as the Salmonella Newport and on unusual isolates. Or, should we be more surveillance oriented? Should we try to find out something about everything as opposed to details about a few things?
And if that was the case, then what should we say survey. And finally, should we emphasize special collections that we have, such as FoodNet studies, for example, or outbreaks and is that what we should focus our efforts for extensive characterization?
Well, their response was generally that, yeah, we should continue to focus on the problems and we should continue to look for unusual isolates or unusual mechanisms. Although we may not be in a position to really define those ourselves, we are in a good position to recognize them.
So, one f the things that we have done is we have started using the SWIN Software that operates the Sensititre. It has the capability of flagging interesting isolates, and so, we have set up a number of things to get flagged so that we see this right away and don’t wait until we are looking at the data several months later.
One of those things is isolates that have reduced susceptibility to both extended spectrum cephalosporins and quinolones, and we are flagging those and -- I don’t remember who is doing it from Tom’s group, but is following up and trying to get some clinical information; travel. That sort of thing on anyone with that kind of an isolate.
We are also interested in isolates that have reduced susceptibility to ceftriaxone or ceftiofur that doesn’t look like -- phenotypically doesn’t look like it is mediated by CMY-2. That would be isolates that are not resistant to cefoxitin or to amoxicillin and clavulanic acid, and we have had a few of those.
When we see these situations, we screen for the sort of usual suspects of mechanisms by PCR, and if we don’t find them to be among our usual suspects, then we look for other people; for collaboration.
A good example of this is we have three isolates that apparently have a qnr, a plasmid mediated quinolone resistance gene, and we have three Salmonella. They are an ogana, abobis*, morbificans* and mendoca*. David Hooper’s lab has been doing most of this work, and we hope we are getting near publishing that information.
We are collaborating with Alesandro Carratoli in Rome to have a PCR based plasmid typing system all of the internet laboratories. Many of them are participating in a study that we are also participating in, and we hope this will prove to be a useful method for plasmid tying.
And we have worked with Dr. Fred Tinover’s lab for characterizing the bla-tem and the bla-shv genes, which I will mention in a moment here.
One of the things that I had in mind when I asked the question about whether we should be doing surveillance -- this is a good example. This is one that I think we needed to do.
It occurred to us that Salmonella that had the
blaCMY2 mechanism may have other beta lactamases and we wouldn’t be able to tell from the phenotype that we see, because the cmy-2 expression will mask any SBL of the phenotype. So we took all of the Salmonella -- well, in fact, all of the shigella that had reduced susceptibility to extended spectrum cephalosporins, and we did IEF and did some PCR, and we found, not surprisingly, that most of them did have the blaCMY2.
But there were 10 Salmonella that, in addition to the cmy-2, had a bla-tem gene. This is by PCR, and it is just a generic bla-tem. We didn’t identify which one. Two had only a bla-tem, one had only a bla-shv, and interestingly, that was the Mendoca isolate that had the qnr.
It looked like the presence of the bla-tem or shv was distributed among a number of serotypes that didn’t have any particular geographic relevance or anything that struck us as being -- you know, telling us a lot of information that it was worth the effort to go through to get. So we decided we probably don’t need to continue doing this.
It was worth finding out and maybe we will do it again in a few years, but we don’t need to do this every year.
As far as special collections, just to give you a couple of examples of what we are involved in, we are currently receiving isolates from every Salmonella outbreak in FoodNet sites, and we are receiving isolates from the study that Tom mentioned on the burden of multi drug resistant illness compared with people who have infections with susceptible strains.
And as far as PFGE, we are encouraging the states to do PFGE on all of their NARMS isolates. We have made this request several times. Most states actually do their Salmonella isolates anyway and many of them have agreed that they will do their NARMS isolates, if they are not already doing them.
As it turns out, most have already been done and they are submitted to PulseNet, but a lot of the time the states don’t use the same numbers for PulseNet and for NARMS. And so, we have this data already and we don’t know it. So we are making a big effort to get people to use the same number so that we don’t have to reinvent the wheel and repeat tests.
We are making further efforts to link PulseNet, FoodNet and NARMS data. I think that is all. Yes.
DR. SAHM: Yes. I guess first, Tom, I take your point early on about doing this kind of surveillance work on human isolates because these are the ones, we already know, have made it all the way to infecting the human population and what those strain characterizations are.
But in terms of part of the NARMS goal of integration that needs to happen, you showed some very interesting data about over-trending what has happened with Campylobacter and Salmonella and how Salmonella still remains relatively constant. And then amongst the Salmonella in 2004, how it was mostly -- I can’t remember the -- Javiana?
DR. CHILLER: Yes. Javiana.
DR. SAHM: Javiana. Well, back when I went to school there was only two species. But anyway, can Paula look at her data or look at any of the other two arms to see, well, geez, you know what? That is the strain or species that is most common in the retail products and is this reflective of what is happening in the animal arms of NARMS? Or is that integration just not there yet to even ask that question?
DR. CHILLER: That is a good question. When I was referring -- the majority of my referring to integration was from an annual report. So I was thinking of when we actually submit this or we present an annual report, that we present that in a yearly basis in an integrated reporting fashion.
What you are talking about is actually sort of more the detective work that we do when we see something interesting, and I think that that kind of detective work and that kind of collaboration we have definitely been doing for years. We will call Paula and we will say, have you seen this increase? She will look at her data and she will say, yeah, actually I have seen this.
I think the classic example is with Salmonella Newport when it was emerging in the late ‘90s. She was seeing it in animals. We didn’t have much of a retail food study at the time. There was just the pilot studies in D.C.
And so that kind of collaboration? Absolutely. That kind of integration we do. What I was really referring to is the kind of integration that I would like to see; is actually in a surveillance standpoint where there is ongoing reporting of these three arms looking at the data side by side in some sort of systematic fashion, and that we don’t do.
So, we will look at our data. We will see something interesting. For example, the javiana issue. Javiana we don’t think is coming from food animals. I don’t think you see it much in food animals, and we certainly don’t isolate it from any retail meats.
Well, I can give you my estimation of where we think it is coming from, but we don’t think it is coming from food animals; reptiles and things like this. It is a southern oriented issue. You don’t see it in New York for example.
So yes. We definitely call each other and ask those questions, and certainly NARMS has been a fruitful way to dig deeper into specific issues that come up.
DR. SAHM: I think the interest to the public and the scientific and medical community would be when is there and when is there not a correlation between what is being seen in food animals and what is being seen in human health to help clarify, because the other thing that points at it, interestingly, is it has to do with the question I asked Paula.
One of the recommendations from our external review is to continue, by all means, doing surveillance with commensals, such as Enterococci. But in human health the VRE rate is high and regular and there has been on the animal side. So, having that kind of information at their fingertips might give them a better perspective on what should and shouldn’t be done and going forward.
DR. CHILLER: I think you bring up a great point. I think one of the reasons we are here today to ask this question about integration. But I think, as Sue brought up earlier, you see different objectives because, honestly, we have some different objectives besides some common objectives.
With Enterococci we are finding VRE now from community isolated stools, and do we think that VRE is coming from analog use in animals? No, it is not. It is banned here. I mean, we don’t think that it is coming. But the fact that we are documenting that it is in the community and there may be now sort of a community reservoir of this within humans is important to know, but it may not necessarily be important to test for in animals, where it is important to maybe test for vancomycin in humans.
So there are some specific issues that sort of fold off of NARMS in each of arms that are specific to us. So you bring up a good point, but I think part of what we are doing here today is understanding how is the integration and how is the surveillance in these three arms to be linked together to actually inform us about food and the food supply and how resistance is moving back and forth through that system.
DR. SAHM: And I think that that is what I am a little bit fixated on today, is how the information coming from the three branches could address not only what is going on in foodborne diseases, but in terms of association. I mean, what is going on in the ecology of animal and humans.
One last question then for Tim. With all of those things that you are doing, which is a pretty impressive menu of characterizations that you are doing, is there any effort to connect with Paula and other arms so that you would have the same line listings of characteristics for strains across all three arms so that she could see whether or not there is qnr, plasmid qnr in the Salmonella that she is seeing so you could cross compare strain characteristics?
DR. BARRETT: To some extent we have different purposes. For example, the ‘tem’ and ‘shv’ issue. We looked at that. We don’t think there is really anything there. I mean, I might ask Paula have you done -- do you happen to have this information? But I wouldn’t go ask her to go and do a bunch of work when we don’t really think there is much of interest there.
Now, as far as things that we do think are of interest, like Salmonella Heidelberg, for example, we have talked with Dave and Paula about what we have seen in Heidelberg and how we could do the same things and do just what you say to try to put those together.
DR. FEDORKA-CRAY: Actually, we have a study ongoing with Jean Richard with Salmonella Heidelberg, and she has characterized --- and we are finishing the characterization of the animal one. We are going to link the two together and put out a joint publication.
DR. SAHM: I think that would be something that is very valuable. If you know these are the molecular and phenotypic characteristics of the Salmonella that you are seeing in your system or the retail food arm, versus what do the Heidelbergs look like from the CDC arm, I think it would be very valuable in terms of differentiation and molecular characterization. Thanks.
DR. KOTARSKI: Just a follow up question on that point. Are you looking for similarities between the isolates that you see in the human versus the animal isolates? And also, when you see dissimilarities between the two, are you reporting those?
I think, in all likelihood, when you find a similarity, you are going to bring it to the attention of the world. When you see a dissimilarity, how does that get a prioritization?
DR. BARRETT: That is a good question.
DR. FEDORKA-CRAY: I think I would answer that to say it doesn’t ---
DR. CHILLER: Again, one of the issues is that we may -- we on the human side may decide that this is an incredibly important resistant phenotype and we really need to look into it, and we may stomp the pavement and call our colleagues and say can you guys look into it. And it may not be a priority for Paula or Dave. It may come 10th on their list.
And so, part of that is we may think it is number one and we need to know about it now. Paula might say, yeah, it is interesting, but I have got 10 other things that I am looking at within my system now.
And so, that has led to us really focusing on probably the similarities, because for us to get to the differences then that goes way down the priority list and it becomes even more of a challenge. But I agree that both of those concepts need to be talked about.
I think that in this whole integration scheme we need to figure out some way that if we have something that is a high priority or she has something that is a high priority, each of us tries to make that a high priority for each other. I think that is what we need to figure out exactly how to do.
DR. KOTARSKI: And if that is a future goal for the integration of three arms, can you -- I think back to the population base that are being sampled. So, for example, for the animal isolates that are collected, some of those animal isolates are coming from the HACCP Program, and I think we are going to hear more about that and that sampling strategy.
In fact, in terms of what is coming from healthy animals, we are getting isolates every four years from a particular species. So, if that is the case, in terms of what is in the healthy animals that, presumably, are going into the food chain, if we are only getting isolates every four years and you start making comparisons to what is similar, then are you making similarities to what is actually on the farm or are you making similarities to something that is closer to the consumer, which might be the slaughter plant? And how do you trigger that information then?
And I am not necessarily asking for a question, because that is future based. But in terms of thinking about integration, I guess I would ask, as you make plans, is how representative are your samplings for the on-farm, for the slaughter plant and then for humans and in between?
DR. CHILLER: I think it is a great question, and hopefully, you guys will continue to battle that question after the next presentation of Neena, because it is a question that we have too. Anyone else?
DR. ALTEKRUSE: Picking up on that, some of the isolates that we -- Paula mentioned there is a lot of heterogeneity in the slaughter isolates. It is the most, perhaps, heterogeneous group of isolates and some of them really kind of fall by the wayside in terms of concern, but some other isolates are of tremendous concern to us.
A very good example is the reduced susceptibility to beta lactam Salmonella Heidelberg isolates. I think that there has been an interest in that at FSIS, and it would be helpful to have more timely feedback on that, on the status of those investigations; what are being found.
Right now most of our information relates to what we have heard from CDC, but that is just some feedback about the HACCP isolates that are going into the NARMS system. It would be tremendously useful in terms of charting agency policy direction to have a heads up on the status of that very early, and really, frequently in terms of updates, not just to wait for a publication.
DR. MILLER: Thank you for the presentations. It is obvious a lot of excellent work has gone on in the year since I have been involved with NARMS. I just wanted to highlight a couple of points that I really agree with just to kind of go on the record.
I think that, Tom, you were able to really demonstrate the surveillance to the epi investigation, to the applied research and then back through prevention, and that is what I think would be ideal to be able to show for all the arms of NARMS; so that there is clear outcome use of the data; thinking and questioning that leads to other kinds of public health interventions. So, that was really nicely stated.
Obviously I agree with the integrative reporting and some of the questions that have been raised I think are good to be thinking about in terms of how to do that. Timely reporting obviously, and it sounds like you are moving towards a six-month turnaround, which would be excellent.
The other item is kind of a pet issue for me going back to working on the interagency antimicrobial resistance working group. Trying to get drug use information on the farms to link with the healthy animal data and to be able to interpret, in light of the other surveillance information.
I know it is a huge hurdle and some countries do it very elegantly, and I don’t know if anyone is really actively working on that. AVMA or not.
But that is an important piece and that will really help to make that full circle to be able to talk about outcomes and then impact use and ultimately resistance.
DR. CHILLER: Absolutely. Thanks.
DR. BARRETT: I would like to mention one more thing in terms of timeliness. Tom already alluded to this. The laboratory being behind in generating the data has been the major factor in our being behind in reports.
We got terribly behind in 2002 when we increased the number of sites without decreasing the frequency. So we got a lot more organisms, a lot more bugs in and we had problems with Sensititre. A whole lot of things went wrong that year.
As of now we are up to date now. We are up to date for 2005. So hopefully, we will stay there and we will be able to get this done faster.
DR. CHILLER: What Tim is saying basically now is that it is my fault that we are late. And that is fine. I will take the blame for that.
DR. VOGEL: This may be an unfair question, but I did send this article to you. There was a perspectives or opinion article published in Nature’s Review on microbiology in December of 2004. The title was, "Epidemiological Interpretation of Antibiotic Resistant Studies. What are we Missing?"
The abstract says that "surveillance programs examine changes in the proportion of isolates that are resistant. Although proportions are helpful for the clinician prescribing empirical therapy, proportion based analysis can be misleading to the public health professional, as they can yield biased estimates. Proportions do not adequately reflect the burden of resistance, a measure often of interest in public health."
"A more appropriate measure of this burden is the rate of isolation of resistant organisms. That is, the absolute number of resistant isolates in a population over time."
Have you had a chance to look at that article, and what is your interpretation? Could our surveillance system be changed to give us --
DR. CHILLER: Thanks. I definitely looked at that article after you sent it to us. Without going into a lot of detail, I think one of the -- for example, one of the changes that we made in Campylobacter I think will help us. I mean, we did it specifically to be able to address rates and burdens.
Clearly, when you are looking at proportions, which is what we do, because we simply can’t test every bug that comes in, we then put that in and look statistically about how that relates to a specific absolute number. And so, although we are collecting a certain number of isolates and we are reporting that as percent resistant, we are trying to determine whether we can put that into a model that allows us to determine rates.
I think that part of the issue with NARMS’ nationwide surveillance, for example, for Salmonella, is that it is difficult to put a denominator under that right now, and I think part of the advantage -- as Tim mentioned and others, of taking advantage of an active surveillance system like FoodNet where they actually go out and they count every single case in the community. I mean, they know. They know every single case that has been laboratory confirmed; to be able to put our surveillance on top of that framework.
And I think we are going to be able to get it at absolute numbers and we are going to be able to make better rate estimations. And after our external review with you guys, that is one of the things we said. You know, let’s try this now here on a platform where we think we can realistically do that.
And so, we have been involved with statistical folks at CDC now for the last six months hammering out how we might go about it. So yes. We are working on that, and I appreciate you bringing that up.
DR. ALTEKRUSE: I saw an example of that artifact. The isolates have been for --- they are really not representative of the population at large.
DR. CHILLER: FoodNet weeds that out and NARMS does now too. We are now asking about travel history because of that exact reason. But you are right. FoodNet takes that data right out of there, and we can then exclude that and we can focus on national data or we can look at just travel populations too, which is really important, because we know a lot of resistance comes in from overseas. No question about it.
DR. YOUNGMAN: Thank you very much. We need to keep pressing ahead, because we are kind of behind schedule right now. What I would like to propose is we have another talk and then, Terry, if it is okay with you, we will have a break before your talk.
I would like to introduce Dr. Neena Anandaraman, who is going to be talking about the animal isolate sampling for NARMS.