ST398 carriage and infections in farmers, United States

I’ve been working on livestock-associated Staphylococcus aureus and farming now for almost a decade. In that time, work from my lab has shown that, first, the “livestock-associated” strain of methicillin-resistant S. aureus (MRSA) that was found originally in Europe and then in Canada, ST398, is in the United States in pigs and farmers; that it’s present here in raw meat products; that “LA” S. aureus can be found not only in the agriculture-intensive Midwest, but also in tiny pig states like Connecticut. With collaborators, we’ve also shown that ST398 can be found in unexpected places, like Manhattan, and that the ST398 strain appears to have originated as a “human” type of S. aureus which subsequently was transmitted to and evolved in pigs, obtaining additional antibiotic-resistance genes while losing some genes that help the bacterium adapt to its human host. We also found a “human” type of S. aureus, ST5, way more commonly than expected in pigs originating in central Iowa, suggesting that the evolution of S. aureus in livestock is ongoing, and is more complicated than just ST398 = “livestock” Staph.

However, with all of this research, there’s been a big missing link that I repeatedly get asked about: what about actual, symptomatic infections in people? How often do S. aureus that farmers might encounter on the farm make them ill? We tried to address this in a retrospective survey we published previously, but that research suffered from all the problems that retrospective surveys do–recall bias, low response rate, and the possibility that those who responded did so *because* they had more experience with S. aureus infections, thus making the question more important to them. Plus, because it was asking about the past, we had no way to know that, even if they did report a prior infection, if it was due to ST398 or another type of S. aureus.

So, in 2011, we started a prospective study that was just published in Clinical Infectious Diseases, enrolling over 1,300 rural Iowans (mostly farmers of some type, though we did include individuals with no farming exposures as well, and spouses and children of farmers) and testing them at enrollment for S. aureus colonization in the nose or throat. Like previous studies done by our group and others in the US, we found that pig farmers were more likely to be carrying S. aureus that were resistant to multiple antibiotics, and especially to tetracycline–a common antibiotic used while raising pigs. Surprisingly, we didn’t find any difference in MRSA colonization among groups, but that’s likely because we enrolled relatively small-scale farmers, rather than workers in concentrated animal feeding operations (CAFOs) like we had examined in prior research, who are exposed to many more animals living in more crowded conditions (and possibly receiving more antibiotics).

What was unique about this study, besides its large size, was that we then followed participants for 18 months to examine development of S. aureus infections. Participants sent us a monthly questionnaire telling us that they had a possible Staph infection or not; describing the infection if there was one, including physician diagnosis and treatment; and when possible, sending us a sample of the infected area for bacterial isolation and typing. Over the course of the study, which followed people for over 15,ooo “person-months” in epi-speak, 67 of our participants reported developing over 100 skin and soft tissue infections. Some of them were “possibly” S. aureus–sometimes they didn’t go to the doctor, but they had a skin infection that matched the handout we had given them that gave pictures of what Staph infections commonly look like. Other times they were cellulitis, which often can’t be definitively confirmed as caused by S. aureus without more invasive tests. Forty-two of the infections were confirmed by a physician, or at the lab as S. aureus due to a swab sent by the patient.

Of the swabs we received that were positive, 3/10 were found to be ST398 strains–and all of those were in individuals who had contact with livestock. A fourth individual who also had contact with pigs and cows had an ST15 infection. Individuals lacking livestock contact had infections with more typical “human” strains, such as ST8 and ST5 (usually described as “community-associated” and “hospital-associated” types of Staph). So yes, ST398 is causing infections in farmers in the US–and very likely, these are flying under the radar, because 1) farmers really, really don’t like to go to the doctor unless they’re practically on their deathbed, and 2) even if they do, and even if the physician diagnoses and cultures S. aureus (which is not incredibly common–many diagnoses are made on appearance alone), there are very limited programs in rural areas to routinely type S. aureus. Even in Iowa, where invasive S. aureus infections were previously state-reportable, we know that fewer than half of the samples even from these infections ever made it to the State lab for testing–and for skin infections? Not even evaluated.

As warnings are sounded all over the world about the looming problem of antibiotic resistance, we need to rein in the denial of antibiotic resistance in the food/meat industry. Some positive steps are being made–just the other day, Tyson foods announced they plan to eliminate human-use antibiotics in their chicken, and places like McDonald’s and Chipotle are using antibiotic-free chicken and/or other meat products in response to consumer demand. However, pork and beef still remain more stubborn when it comes to antibiotic use on farms, despite a recent study showing that resistant bacteria generated on cattle feed yards can transmit via the air, and studies by my group and others demonstrating that people who live in proximity to CAFOs or areas where swine waste is deposited are more likely to have MRSA colonization and/or infections–even if it’s with the “human” types of S. aureus. The cat is already out of the bag, the genie is out of the bottle, whatever image or metaphor you prefer–we need to increase surveillance to detect and mitigate these issues, better integrate rural hospitals and clinics into our surveillance nets, and work on mitigation of resistance development and on new solutions for treatment cohesively and with all stakeholders at the table. I don’t think that’s too much to ask, given the stakes.

Reference: Wardyn SE, Forshey BM, Farina S, Kates AE, Nair R, Quick M, Wu J, Hanson BM, O’Malley S, Shows H, Heywood E, Beane-Freeman LE, Lynch CF, Carrel M, Smith TC. Swine farming is a risk factor for infection with and high prevalence of multi-drug resistant Staphylococcus aureus. Clinical Infectious Diseases, in press, 2015. Link to press release.

 

The human origins of “pig” Staph ST398

I recently gave a talk to a group here in Iowa City, emphasizing just how frequently we share microbes. It was a noontime talk over a nice lunch, and of course I discussed how basically we humans are hosts to all kinds of organisms, and analysis of our “extended microbiome” shows that we share not only with each other, but also with a large number of other species. We certainly do this with my particular organism of interest, Staphylococcus aureus. There are many reports in the literature showing where humans have apparently spread their strains of S. aureus to their pets (dogs, cats, hamsters)–and sometimes the pets have been nice enough to share it right back. My own research looks at S. aureus in pigs and the humans who care for them, and many studies have shown that a “pig” type of MRSA, dubbed sequence type 398 (ST398), can be transmitted from pig carriers to their human caretakers. The assumption has been that this is truly a “pig” strain, originating in swine, and has spread to humans (and other animals, including cattle, poultry, dogs and horses) from pig hosts, either directly or indirectly via contaminated meat products.

According to a new study (open access in mBio), it seems that there has been more sharing of ST398 than we’d realized. Led by Lance Price at TGEN (full disclosure–I’m a coauthor on the paper), his group analyzed 89 ST398 isolates from China, Europe, and North America, including isolates from humans and animals as well as both methicillin-susceptible and -resistant strains. Using whole genomic sequence typing, the evolutionary history of these isolates was reconstructed.

The findings throw the ST398 story a bit on its head. Instead of being a true pig strain, ST398 appears to have originated as a methicillin-susceptible human strain which was transferred into the pig population, picked up antibiotic resistance genes (including resistance to methicillin and tetracyclines), and then has been passed back to farmers as more resistant organisms. Some prophages were also gained or lost along the way, probably due to selection by host factors.

This also suggests that there is still likely a low level of “native human” ST398 circulating in people. There have been a few case reports of ST398 colonization and/or infection in people without any known livestock contact. Some of these have been resistant to methicillin and/or tetracycline, which are more frequently associated with livestock-adapted strains. Are these truly “human” strains which aren’t involved in livestock at all, or are these ST398 findings in people lacking livestock contact still due to some livestock exposure along the chain of transmission (farmer neighbors? Transmission via food?) We still don’t know, but carrying out more of this WGST will give us better targets in order to be able to differentiate true “human” ST398 strains from those that have been hanging out in animals, and then transmitted back to people.

Now, for long-time science blog readers, this story may sound a bit familiar. Indeed, it looks like ST398 has taken a very similar path to that of another animal-associated S. aureus strain, ST5. As Ed Yong described back in 2009, humans are also the ultimate origin of a “chicken” type of S. aureus ST5, which spread around the world in broiler chicken flocks. In Ed’s article, the first author of the chicken ST5 paper, Bethan Lowder, notes that the change in chicken farming from small farms to multinational corporations likely aided the spread of this organism–and the exact same thing has happened with pig farming.

One difference between the two is that ST5 causes disease in chickens, whereas ST398 seems to be a very rare cause of illness in pigs. This is likely one reason that ST398 in pigs went undetected until relatively recently–it’s simply not much of an economic issue for pig producers, whereas in chickens, S. aureus can cause several nasty diseases (such as bumblefoot and BCO) leading to animal loss (and thus, less money for the farmer).

So, where do we go from here? Clearly studies like this show the utility of using WGST to examine the evolution and spread of these strains. If you look at how spa types are distributed throughout the tree, you can see that those alone don’t tell you much about where the strain came from, or if it’s fully “human” or a pig-adapted lineage. Ideally, a set of simple markers could be found to distinguish ancestral human strains from livestock strains (as methicillin-sensitive ST398 can also be found in pigs, so methicillin resistance alone isn’t enough of an indicator that it’s a “pig” strain). We’ll be working on this in ST398 and other strains we see being shared between animals and humans, in order to better understand this generous sharing we’re doing amongst species.

Reference:

Lance B. Price, Marc Stegger, Henrik Hasman, Maliha Aziz, Jesper Larsen, Paal Skytt Andersen, Talima Pearson, Andrew E. Waters, Jeffrey T. Foster, James Schupp, John Gillece, Elizabeth Driebe, Cindy M. Liua, Burkhard Springer, Irena Zdovc, Antonio Battisti, Alessia Franco, Jacek Żmudzki, Stefan Schwarz, Patrick Butayej, Eric Jouy, Constanca Pomba, M. Concepción Porrero, Raymond Ruimy, Tara C. Smith, D. Ashley Robinson, J. Scott Weese, Carmen Sofia Arriola, Fangyou Yu, Frederic Laurent, Paul Keima,, Robert Skov, & Frank M. Aarestrup (2012). Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock mBio, 3 (1), 305-311 : 10.1128/mBio.00305-11

MRSA in pork products: does the “antibiotic-free” label make a difference?

Back in November, I blogged about one of our studies, examining methicillin-resistant Staphylococcus aureus (MRSA) in Iowa meat products. In that post, I mentioned that it was one of two studies we’d finished on the subject. Well, today the second study is out in PLoS ONE (freely available to all). In this study, we focused only on pork products, and included 395 samples from Iowa, Minnesota, and New Jersey. We also looked at not only conventional meats, but also “alternative” meat products. Most of the latter were products labeled “raised without antibiotics” or “raised without antibiotic growth promotants”–in the markets we tested, very few USDA-certified organic products were available unfrozen, and we were looking for fresh meat products.

In our previous paper, we found MRSA on 1.2% of 165 meat samples. In the current study, we found a higher prevalence–6.6% of 395 samples were contaminated with MRSA. (More about the differences in methods between our two studies later). Interestingly, we didn’t find a statistically significant difference in MRSA prevalence on conventional versus alternative pork products–a finding that surprised me, as it contradicts what we’ve found to date looking at the sources of this meat–conventional versus “alternative” pig farms. Other groups have also found differences on-farm versus on-meat: a 2011 study looking at feedlot cattle didn’t find any MRSA in animal samples, though the same group found MRSA in beef products. So, our disparate findings between farms and meat samples are not unheard-of. However, even though our sample size was larger than other U.S. studies to date, it was still fairly small overall–300 conventional and 95 alternative pork samples over a 4-week sampling period from 3 states, so larger multi-state studies are needed to further examine this angle.

It also suggests that we need processing plants and packing companies to work with us to determine where products are being contaminated–because while there may be arguments about the public health importance of MRSA on meats (or lack thereof), it’s very likely that if S. aureus are ending up on meat products, other pathogens are as well.

What does the molecular typing tell us, speaking of contamination source? We carried out analyses on all the MRSA and found that the most common type of MRSA was ST398, the “livestock” strain that we previously found on pig farms in the U.S. We also found two “human” types were common: USA300 (a “community-associated” strain) and USA100 (typically considered a “hospital-associated” strain). In the simplest analysis of these findings, these molecular types (a combination of “human” and “pig” strains) suggests that MRSA on raw pork products may be coming both from farms and from food handlers. However, in real life, it’s not quite so straightforward. USA100 types have also been found in live pigs. So has USA300. As such, the source of contamination and relative contributions of live pigs versus human meat handlers currently isn’t certain.

Within the MRSA strains, we found high levels of antibiotic resistance, similar to what was reported in the recent Waters et al. study. In ours, 76.9% were resistant to two or more antibiotics and 38.5% were resistant to three or more antibiotics tested. (I’ll note that we only had funding to test the MRSA–we weren’t able to do these tests on all the methiciin-susceptible strains).

Did MRSA prevalence increase in the period between our first study (spring 2009) and this one (late summer/fall 2010)? I doubt it. For this paper, we used a different sampling method, adding the samples to a sterile stomacher bag so that the entire sample was immersed in the culture medium; for the first paper we used external swabbing and so likely didn’t capture as many bacteria. This current study more likely represents the “true” MRSA prevalence. But–all isolates were only called as positive/negative, and we didn’t measure the number of bacteria on each piece of meat. So, there theoretically could have been just a few colonies of MRSA on the entire piece of meat, and that would have been called a positive sample, while another meat product covered with hundreds of MRSA would have been put in the same category. Therefore, more subtle differences may exist that we didn’t pick up in this study, but we will examine in other ongoing studies.

So–what’s the take-home here? Don’t assume that any meat product is contamination-free, and always use good food handling/cooking practices when dealing with raw meats. As far as the titular question, well, we’re still hashing that one out.

References

Hanson et al. Prevalence of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA) on retail meat in Iowa.

Waters et al. Multidrug-Resistant Staphylococcus aureus in US Meat and Poultry.

O’Brien et al. MRSA in conventional and alternative retail pork products.

Lin et al. Evidence of multiple virulence subtypes in nosocomial and community-associated MRSA genotypes in companion animals from the upper midwestern and northeastern United States.

Weese et al. The Prevalence of Methicillin-Resistant Staphylococcus aureus Colonization in Feedlot Cattle.

Weese et al. Detection and quantification of methicillin-resistant Staphylococcus aureus (MRSA) clones in retail meat products.

MRSA found in Iowa meat

I’ve blogged previously on a few U.S. studies which investigated methicillin-resistant Staphylococcus aureus in raw meat products (including chicken, beef, turkey, and pork). This isn’t just a casual observation as one who eats food–I follow this area closely as we also have done our own pair of food sampling investigations here in Iowa, and will be doing a much larger, USDA-funded investigation of the issue over the next 5 years.

Let me sum up where the field currently stands. There have been a number of studies looking at S. aureus on raw meat products, carried out both here in North American and in Europe. In a study from the Netherlands, a large percentage of samples were found to harbor MRSA (11.9% overall, but it varied by meat type–35.3% of turkey samples were positive, for example). Most of there were a type called ST398, the “livestock” strain. This was also found in one Canadian study (5.5% MRSA prevalence, and 32% of those were ST398), but no ST398 were found in a second study by the same group.

Here in the US, prevalence has found to be lower than in that Dutch study (from no MRSA found, up to 5% of samples positive). Furthermore, in the previously-published studies, no MRSA ST398 was found in samples of US meat, though this paper did find plenty of methicillin-sensitive S. aureus (MSSA) ST398 strains. Instead, most of the MRSA isolates have been seemingly “human” MRSA types, like USA100 (a common hospital-associated strain) and USA300 (a leading community-acquired strain).

Why am I rehashing all of this? We have a new paper out examining S. aureus in Iowa meats–and did find for the first time MRSA ST398, as well as MRSA USA300 and MSSA strains including both presumptive “human” and “animal” types. This was just a pilot study and numbers are still fairly small, but enough to say that yes, this is here in the heart of flyover country as well as in the other areas already examined.

As I mentioned, this is one of two studies we’ve completed examining MRSA on meat; the other is still under review and much more controversial, but I will share that as soon as I’m able. And with the USDA grant, we’ll be working on better understanding the role that contaminated meats play in the epidemiology and transmission of S. aureus for the next several years, so expect to see more posts on this topic…

References

Hanson et al. Prevalence of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA) on retail meat in Iowa. J Infect Public Health. 2011 Sep;4(4):169-74. Link.

Waters et al. Multidrug-Resistant Staphylococcus aureus in US Meat and Poultry . Clin Infect Dis. 2011 May;52(10):1227-30. Link.

Weese et al. Methicillin-resistant Staphylococcus aureus (MRSA) contamination of retail pork. Can Vet J. 2010 July; 51(7): 749-752. Link.

De Boer et al. Prevalence of methicillin-resistant Staphylococcus aureus in meat. Int J Food Microbiol. 2009 Aug 31;134(1-2):52-6. Link.

Pu et al. Isolation and characterization of methicillin-resistant Staphylococcus aureus strains from Louisiana retail meats. Appl Environ Microbiol. 2009 Jan;75(1):265-7. Link.

Bhargava et al. Methicillin-resistant Staphylococcus aureus in retail meat, Detroit, Michigan, USA. Emerg Infect Dis. 2011 Jun;17(6):1135-7. Link.

In the lab–the year in review

Ah, classes are finally over. The last two summers I’ve taught a short, intense course in Applied Infectious Disease Epidemiology, condensing a semester’s worth of work into a week. It’s a fun course to teach, but exhausting–after teaching, I head back home or to the office to finish last-minute preparation for the next day’s talks and assignments, and by the time that’s done, the nightly student homework is rolling into my email inbox for me to grade and comment on for the next morning. By Friday, I feel like a zombie who hasn’t seen my family in a week.

But, it’s now wrapped up for another year, which gives me a small block of time to navel-gaze and reflect on the past year before diving back into more research (and starting prep for fall’s course, Introduction to Molecular Epidemiology).

First, this has been a Really Good Year. For those interested, we just put out a newsletter detailing all the events in the lab in 2010–3 federal grants received (the most recent one from USDA described here, and others from NIOSH and AHRQ), 3 PhD students graduated, 3 MS students graduated, 13 papers published and 15 conference presentations given. You can probably see why my blogging took a dip. However, all 3 PhD students have jobs, as does one MS student (the other 2 are continuing on to a PhD), so the graduates have also been successful–now just to wrap up all their papers…

This year marks the beginning of the new studies, meaning we’ll be enrolling and testing roughly 3,000 people this year around the state of Iowa, as well as carrying out molecular analysis of another couple thousand S. aureus isolates from the state’s diagnostic labs, and still carrying out some additional sampling on farms. It’s already an exciting (and busy) summer, with more to come in fall. We’re embarking on these studies with some new collaborators, and have some pilot projects coming to an end with a ton of manuscripts currently under review or in draft, so 2011 should hopefully be equally productive. Everything isn’t quite a well-oiled machine yet, but it’s definitely much closer this year than it was a year or two ago.

Epidemiological studies–why don’t people participate?

Maryn McKenna was awesome enough to take some time out of her vacation to blog about our recent ST398 paper, finding “livestock-associated” S. aureus in a daycare worker. She raised one question I didn’t really address previously, regarding our participation by kids and workers at the facility (eight kids out of 168, and 24 out of 60 staff members).

(Staph screening is very non-invasive, by the way; it effectively involves twirling a long-handled Q-tip inside the front of your nostrils. Kinda makes you wonder why families would not have wanted to participate. On the other hand, since Iowa is the pig-growing capital of the U.S., they may have been motivated not to want to know.)

I thought I’d chat a bit about enrollment for this project, since getting people to participate is one of the most difficult parts of these types of studies. First, there really wasn’t any mention of MRSA and swine for this particular study, so I doubt protecting the pig industry was high on anyone’s list for reasons not to participate. However, anytime we do these type of studies, we’re relying on the generosity of individuals in the community–particularly when we didn’t really have participation incentives, as was the case in this project, which was done on a shoestring budget. (We passed out mini hand sanitizer bottles for adults, and had some little toys for the children).

We ran into several challenges for the research which limited our ability to enroll children. Along with a swab, we also had a questionnaire for parents and employees to fill out (as well as a third questionnaire for the director of the facility). For parents and employees, we asked about exposures: did they spend time in hospitals, around animals, at the gym? Had they recently had an infection? etc. For the directors, we asked about cleaning routines at the facility, as well as facility size (number of children and employees). So it wasn’t only the swabs, but also a decent amount of paperwork to fill out when you include the informed consent forms. We also had to do all of this at the facility; because of the way we were sampling, parents didn’t have a chance to take the questionnaire home to fill it out and then return it. So only parents (and employees) who had some spare time during either child drop-off or pick-up really had the chance to participate.

This particular study also started in roughly March 2009–right around the same time as the emergence of novel H1N1. There was a lot of news about the swabs that were taken to test for flu, which are more invasive than regular Staph swabs, so perhaps many potential participants had the mistaken assumption that the swab collection would be more uncomfortable than it really is. (When we were able to swab the child participants, most of them giggled and said that the swab tickled).

Finally, I should note that this facility was one of the larger ones we sampled, and to do this, my grad student returned several times during the day to try and catch parents during common drop-off/pick-up times (and employees who worked different shifts). However, even with this, we certainly missed a number of children and employees, such as those who were part-time and simply didn’t attend or work the day that we were there. We did have higher participation rates at some of the other facilities.

So, I think timing and misinformation–rather than any kind of fear of finding out things they might not want to know–led to our lower participation rate at this facility.

Quick updates

The University of Iowa press office did a nice story on our recent article showing “livestock-associated” S. aureus in a daycare worker in Iowa. LabSpaces covers it here.

I started a new Facebook page for our research center, the University of Iowa Center for Emerging Infectious Diseases. Join up for research updates! We’ll have a lot coming up this summer.

And on that note, soon we’ll have a new Research Assistant starting at the Center: Megan Quick, who was featured today on in the “Photo of the Month” on the Association for Schools of Public Health website.

Have a few blog posts percolating but real life has been getting in the way; more next week!