Staph in Food: Reservoirs of Resistance and the Need to Embiggen Research

ScienceBlogling Tara Smith has a great summary of the recent paper reporting high frequencies of multi-drug resistant Staphylococcus aureus in uncooked meat products (S. aureus is the "SA" in MRSA--methicillin resistant S. aureus, so I won't go through the whole paper here (and Maryn McKenna, as usual, had the best early report). But there are two issues I want to raise, the first being that the agricultural system can serve as a 'reservoir' of antibiotic resistance genes and resistant organisms. That is, unlike Las Vegas, what happens on the farm doesn't always stay on the farm. Tara:

That also introduces a second issue with staph in meat--it's not only the "classic" problem of toxin-mediated staph food poisoning, but we also have to consider the potential for food-borne S. aureus to be transferred from the meat to the food handler. If they're not careful with their procedures, they could end up introducing staph into any wounds on their hands (thereby possibly causing an infection), or rubbing their nose/eye/skin and introducing the bacterium that way, potentially leading to long-term carriage. Really, in that manner it's no different from picking up S. aureus at your local gym, or school, or hospital--you touch something that's contaminated with the bacterium, and then unknowingly colonize yourself with the germ.

Whenever I read about drug resistance in bacteria isolated from agricultural habitats, what Tara describes is the far greater concern for me--you won't keel over and die from touching an uncooked piece of meat (JUST WASH YOUR DAMN HANDS! Haven't written that in a while...). But those bacteria could colonize you, and then use you to either colonize or infect (cause disease) other people or to spread resistance genes to previously sensitive bacteria (which then could cause hard to treat disease). Keep in mind that, in the U.S., most bacterial infections are caused by opportunistic commensals, organisms that usually don't cause disease unless given an opportunity (SO WASH YOUR DAMN HANDS!). This isn't idle speculation either--one of the common S. aureus clones observed was one often found in hospitals.

The ag lobby has argued that the study isn't large enough to draw definite conclusions. Which brings me to the issue of 'embiggening' science (yes, embiggen isn't a word, but, on my blog, it is).

First, kudos to the Pew Charitable Trust for funding this study. From their perspective, I'm sure this study was not cheap--it very well could have cost $200,000 once all of the costs are factored in. So it's a lot of money.

But it's not enough money to get the sample sizes we need. This project also highlights the need for larger, targeted grant awards:

So onto an antibiotic resistance example. A while ago, I wrote about some excellent work by ScienceBlogling Tara Smith, and that was written up in The NY Times by Nicholas Kristof. Basically, Tara established that a clone of MRSA, ST398, which spread throughout Europe's farming system, and is now entering Dutch hospitals, and has established itself as a commensal in the human population, is found at really high levels in two Iowa farm systems (covering ~20 facilities). Now, under our current system, the next step would be that Tara applies for a grant--and Tara's very smart so she would probably get it--to look at more farming systems over a longer period of time (An aside: Having been a weird hybrid of federally funded researcher/policy wonk, I have some experience in what typically gets funded in this field). This is about what an R01-like grant with several years of funding could accomplish. And if Tara does go down this route, I wish her best of luck--she certainly has earned it.

But that's not ideally how the question should be addressed (and I've actually testified in front of federal committees about this--I'm not just ranting). To address the question of the introgression of resistance genes and resistant organisms from the farm to the clinic, you would need to do work on a scale that simply can not be funded by the R01 mechanism. You would need to collect tens of thousands (if not more) of isolates from farms, abattoirs, retail meat, fecal lagoons, farm workers, human commensal isolates (both in farming communities and distant from pig farms), pigs, and clinical isolates. These isolates would need to be systematically stored, screened for resistance, and genotyped (including sequencing, plasmid profiling, virulence factor typing (PCR and hybridization). There should also be a genomic component for a subset of the strains, both gene array and genomic sequencing. Then, of course, you need the informatics to store all of these data. And this is a multi-year project, and probably should be expanded to a couple of other critical organisms.

I'm always picking on Tara.... Anyway, now that we have some compelling preliminary data, we need to embiggen this work--what I've called 'going Manhattan Project on its ass.' We should nail this down rigorously, with larger sample sizes, more sites, and more detailed genetic (and genomic) information to understand the fine scale evolution and spread of resistance, such that there's no wiggle room for sane people with a modicum of decency (the lobbyists will always come up with some sort of crapdoodle like 'statistically significant sampling'). Let's settle the issue and really fund this thing.

Anyway, it's a good piece of work, and one that's written in a way that is accessible to the general public. Go check it out.

Cited article: Waters, A., Contente-Cuomo, T., Buchhagen, J., Liu, C., Watson, L., Pearce, K., Foster, J., Bowers, J., Driebe, E., Engelthaler, D., Keim, P., & Price, L. (2011). Multidrug-Resistant Staphylococcus aureus in US Meat and Poultry Clinical Infectious Diseases DOI: 10.1093/cid/cir181