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 drug-resistant bacteria mutations will occur, even before antibiotic resistant bacteria have formed.

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.

You can become infected with these diseases without ever setting foot near a CAFO

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 lawrestricting 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.*

Alternative models of animal production must be explored

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.