Deadly Dish – How Our Food System Is Creating The Next Superbug

Most US meat comes from Confined Animal Feeding Operations (CAFOs) (photo courtesy of


We live in a new world, pathogenically speaking. Every year we see a whole host of new, serious diseases afflicting humans worldwide. Some of these “emerging” infectious diseases are bacteria pathogenic to humans that have evolved to resist many (or all) modern anti-microbial therapies.  These “superbugs” are of tremendous concern to scientists and the public alike. While many factors contribute to the rise of superbugs, the manner in which we raise food animals in the U.S. drives the emergence and dissemination of these drug-resistant bacteria in our environment and in our communities.

Concentrated animal feeding operations (CAFOs) keep thousands (sometimes hundreds of thousands) of animals in highly confined spaces. These animals live shoulder-to-shoulder with each other and with (literally) tons of animal waste.  To promote faster growth to market weight, and to reduce disease outbreaks, CAFO animals are fed sub-therapeutic (read: low) doses of antimicrobial drugs with every meal they eat for the vast majority of their lives.

CAFOs are dirty, crowded, and saturated in antimicrobial drugs and active drug residues. These factors create a perfect niche environment for superbugs to gain an evolutionary foothold.

How does the emergence of superbugs actually happen?

First, antimicrobial drugs, and their pharmacologically-active residues, are abundant on CAFOs. These circumstances create an environment that selects for the survival of multi-drug resistant pathogens over their more drug-susceptible counterparts. The low-dose antibiotics kill off susceptible microorganisms and leave room for the drug-resistant bacteria to multiply and colonize the local environment (the CAFO) with less competition for space and resources. Though mutations to the bacterial genome that confer different types of drug-resistance do occur naturally, recent evidence suggests that sub-therapeutic levels of antimicrobial drugs increase the incidence of reactive oxygen species in the microbiological environment, which in turn increases the incidence of resistance-conferring mutations in the bacterial genome (reactive oxygen species actually react with DNA base pairs to cause spontaneous mutations!). In other words, low levels of antibiotics in the environment increase the likelihood that spontaneous mutations to the bacterial genome (mutations that can cause the bacteria to acquire drug-resistance traits) will occur.

So what happens next?  If CAFO environments foster the emergence and growth of drug-resistant superbugs, how has drug-resistance spread so widely, and between so many species of pathogenic bacteria?

A phenomenon known as “horizontal gene transfer” helps explain the spread and emergence of these diseases.  Horizontal gene transfer describes the process whereby bacteria “share” pieces of their genome between different individual organisms and between entirely different bacterial species. Within a microbiological ecosystem (say, a CAFO, or even  the gut of an individual chicken), two bacteria from different species can release small pieces of their DNA into the local environment. These pieces of bacterial DNA can then be picked up and incorporated into the genome of other nearby bacteria. Where the acquired genes confer a trait favorable for survival (such as drug-resistance), the mutant bacteria multiply and spread, outcompeting their less-fit relatives. Resistance genes are disseminated in this manner between bacterial species co-existing in a single environment.

Once established at an animal production site, superbugs (and their genes) have many different pathways into the broader environment, where they can colonize and infect susceptible human populations. Workers at animal production and processing facilities, along with families of those workers, and members of communities near production and processing operations are all at higher risk of exposure to and infection with animal-associated strains of drug-resistant bacteria and other livestock-associated pathogens. Humans are also exposed to resistant bacterial pathogens through contact with contaminated meat and produce – meaning you can become infected with these diseases without ever setting foot near a CAFO.

Your midnight snack could be harboring the next superbug.

A 2010 study (Price et al.) of grocery store retail meat found staphylococcus aureus (the kind of bacteria that cause staph infections in humans) on about half of all beef and chicken sampled. About half of the staph found in the study was resistant to multiple classes of antibiotics, meaning about 25% of all retail meat sampled was positive for contamination with multi-drug resistant staph aureus!

Non-meat, agricultural crops may also be contaminated with resistant and non-resistant bacterial pathogens when CAFO manure is used as a crop fertilizer—an acceptable practice under current standards for organic crop production.

Resistant bacteria can also spread from the CAFO into the ecological environment through the water, air and soils. This “ecological drift” occurs when resistant bacteria or their intact genes are transferred to local waterways in crop runoff or accidental releases or spillage from manure storage sheds and lagoons on CAFOs. Live bacteria are also released into the air in and around CAFOs as aerosols (especially when liquid CAFO manure is sprayed through high-pressure hoses and sprinklers for direct application to cropland as fertilizer) and attached to airborne dust or particulate matter. Transfer to non-farm environments may also occur through transfer of contaminated agricultural soils.


The emergence of drug-resistant human pathogens and their spread into the human environment is a serious threat to public health. Mounting evidence suggests a crucial link from this issue to the use of sub-therapeutic doses of feed antibiotics in food animal production. There is a pressing need for meaningful regulations to guard against the misuse of drugs important for human and veterinary medicine. The FDA recently passed a law restricting the use of many species of cephalosporins (a class of antibiotic drugs considered crucial for human medicine) in cattle, swine, and poultry production in the U.S. While this is certainly a step in the right direction, the agency failed to address many potential loopholes in the law, or to pass similar legislation regarding other important drugs (such as penicillins) that operate using the same antimicrobial mechanisms as cephalosporins. A good analysis of the FDA decision can be found here.*

Reforming the current model of food animal production over time to a more sustainable model that addresses the issues of these emerging infectious diseases will require systemic change of our food system. The current industrial models of animal production need to amend their practices to ensure judicious use of drugs that are critically important to human and veterinary medicine. Alternative models of animal production must be explored for their potential to provide a sustainable solution to raising food animals without introducing dangerous drug-resistant pathogens into the food system and the human environment.


*Shameless plug alert: I am a Fellow at the center responsible for maintaining and publishing this blog, and the author of the linked post is my colleague.

– Featured photo provided by the author, courtesy of The Center for a Livable Future, John Hopkins Bloomberg School of Public Health.

Patrick Baron

Patrick Baron, MSPH, is a PhD student in the Environmental Health Science Department at the Johns Hopkins Bloomberg School of Public Health, and a Doctoral Fellow at the Center for a Livable Future.

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  1. How can we help this atrocity? just being a vegan doesn’t do much. and i actually have trouble doing that, but i want to help and the only orgs i know who are trying are peta and hsus.

    • Patrick Baron says:

      Dear Ann,

      Thanks for your interest! In my opinion, there are lots of things we can do on a personal, community and global level to try and address these issues.

      First, being a vegan/vegetarian certainly helps to keep your dollars from directly supporting an industry with deeply troubling practices, which is good. However, I (as an ex-vegetarian for similar reasons) believe that supporting alternative models for food animal production goes an important step further towards creating a more healthful and sustainable food system. Small-scale animal producers who do not use antimicrobial feed inputs and who do not send their animals to be processed in enormous centralized processing facilities are (in my opinion) the safest options for the consumer. These farmers are generally priced out by their industry-scale competitors, and they need your support! The most direct way to foster and help mainstream a better model for food animal production is to “vote with your dollars”. I cook almost all of the meat I eat, and I get all my meat from Maryland farmers who market directly through farmer’s markets and who use animal-rearing practices I am comfortable with (no prophylactic antimicrobials, no hormones, no steroids).

      Disclaimer: The smaller, drug-free supply chain does NOT GUARANTEE a safe product. These pathogens and these genes can persist and migrate through the air, water and soil, creating MANY possible secondary routes of food contamination. Fully cook your meat and use good kitchen hygiene practices, always.

      Second, there are a lot of groups doing some very interesting work on this topic. Often, the important policy work is happening locally. Here in Baltimore, the city has recently created the Office of Sustainability within city hall, which has (amongst other initiatives) pushed forward plans for urban agriculture, increased food access by fostering the expansion of farmer’s markets and co-ops in the city, and has allowed citizens on food stamps to use their benefits at farmer’s markets (with bonus incentives for buying extra fruits and vegetables). Those are just a couple of examples, but those changes are very recent and have come as a response to increased demand from citizens and advocates for food system reform and for better access to more healthful local food. So, wherever you are, find out what groups are advocating for the local changes you would like to see enacted, and join them!

      In terms of nationwide groups, there are local chapters of Slow Food USA all over the country:

      Other nationwide groups actively involved in this issue include: the Union of Concerned Scientists (UCS), the Coaltion to Keep Antibiotics Working (KAW), and many others…

      Also, there is pending legislation in Congress currently that you can pressure your local representatives to support: the “Local Farms, Food, and Jobs Act” is designed to support local farmers and food markets and is sponsored by Sen. Sherrod Brown (D-OH) and Rep. Chellie Pingree (D-ME).

      Hopefully there are a few things in there to get you started! Again, this is a global movement where most of the important action happens locally–find out what’s going on in your area! Thanks again for your interest.

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