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Antibiotic resistant bacteria at the meat counter
May 2013, updated June 2014, updated July 2016, updated June 2017

packaged meat
The pork chops you buy in the supermarket neatly packaged in plastic and styrofoam may look completely sterile, but are, in fact, likely to be contaminated with disease-causing bacteria — and not with just any old bugs, but with hard-to-treat, antibiotic resistant strains. In a recently published study, researchers with the National Antimicrobial Resistance Monitoring System bought meat from a wide sampling of chain grocery stores across the country and analyzed the bacteria on the meat. Resistant microbes were found in 81% of ground turkey samples, 69% of pork chops, 55% of ground beef samples, and 39% of chicken parts. Of course, thoroughly cooking the meat will kill the germs, but if the meat is undercooked or contaminates other food with its bacteria — perhaps via a shared cutting board — the result could be an infection that can't be cured with common medications. Such infections are a serious health concern — a strain of antibiotic resistant staph was recently estimated to cause nearly 20,000 deaths per year in the U.S. — and the problem seems to be getting worse. An evolutionary perspective helps us understand how antibiotic resistance arises in the first place and why the prevalence of resistant bugs in livestock has health professionals and scientists worried.

Where's the evolution?
It should be no surprise that antibiotic resistant bacteria are the products of evolution via natural selection: as bacteria reproduce, small, random errors (i.e., mutations) occur as their DNA is copied. Just by chance, some of those mutations may help their bearers survive and reproduce better and so will increase in frequency in the bacterial population. Other mutations may be detrimental and will be weeded out of the population. Still others may have no impact at all to the bacterium's fitness (i.e., neutral mutations) and will change in frequency through genetic drift. When antibiotics flood the environment of the bacteria, individuals that happen to carry random mutations that allow them to survive and reproduce despite the drug will be favored. Eventually, the entire lineage of bacteria may carry genes that confer antibiotic resistance.

This process seems to be inevitable. If a bacterial lineage is consistently exposed to a particular antibiotic, it will eventually evolve resistance to that drug, and this will occur in the soil, in livestock, in the human body — wherever bacteria are exposed to antibiotics. This same basic process is responsible for the evolution of advantageous traits in familiar organisms, like a hawk's keen eyesight or a polar bear's insulating fur. However, bacteria have a leg up on birds and bears when it comes to evolution. Most species rely on mutations somewhere in their historical lineage for their genetic variation — that is, an improved ability to spot prey will evolve in a lineage of hawks only if mutations conferring keener sight occurred somewhere in the hawk lineage and were then passed down to the generation of hawks experiencing natural selection. Bacteria, on the other hand, get their genetic variation both from their ancestral lineage and through a process known as horizontal transfer.

In horizontal transfer, organisms share genetic material with one another directly, as opposed to passing genetic material only to their offspring. In this way, genes from distantly related lineages of bacteria can wind up in the same individual. A gene version that first arose in Escherichia coli could easily be passed on to Salmonella.

Horizontal transfer represents a special danger when it comes to the evolution of resistance because, through gene sharing, antibiotic resistance genes that evolve and become common in one lineage of bacteria that is exposed to a particular antibiotic can be passed to distantly related bacterial lineages. In other words, a bacterial lineage can evolve resistance to a particular antibiotic even if its ancestors never carried a mutation that conferred resistance to that drug. With all this genetic variation being shared, antibiotic resistant bacterial strains can evolve quickly. Furthermore, different antibiotics often have similar modes of action (e.g., amoxicillin and methicillin both work by preventing bacteria from forming cell walls), so resistance to one drug often means partial resistance to a host of other medications. To make matters even worse, bacteria often transfer multiple genes for resistance to different antibiotics on the same piece of DNA. Since the genes are physically attached to one another, selecting for one of those resistance genes lets the others hitchhike to high frequency. So exposing a bacterial population to say, streptomycin, may also unintentionally favor the evolution of a strain that resists many other antibiotics as well — making for a particularly hard-to-cure infection.

Bacteria have many characteristics that allow them to evolve resistance to whatever antibiotics we throw their way — short generation times, high mutation rates, and horizontal transfer — and current agricultural practices (in particular, the heavy use of antibiotics in livestock) seem destined to speed this process even further. In the U.S., around 80% of antibiotics are destined for farm animals, not for treating human disease. The majority of those animal antibiotics are used preventatively and to promote faster growth and speed meat production, not to treat sick individuals. Unfortunately, this approach also encourages the evolution and proliferation of antibiotic resistant strains on factory farms. So, it should come as no surprise that a large percentage of supermarket meat carries antibiotic resistant bugs!

Clearly, the ubiquity of antibiotic resistant bacteria in livestock has implications far beyond highlighting the need to cook meat thoroughly. It suggests that, lurking in farm animals, is a vast pool of dangerous resistance genes that could easily make their way out of the bacteria in which they currently reside and into strains that would represent an even more significant human health threat. We have many lines of evidence suggesting that horizontal transfer of genes, including resistance genes, is commonplace among bacteria. What we have not had is a major outbreak of an antibiotic resistant infection that has been definitively linked to resistance from bacteria inhabiting livestock — yet. If the American Medical Association, the World Health Organization, and the National Academy of Sciences have their way, we may be able to avoid that fate, at least for certain antibiotics. These groups have all signed on to support new legislation that would prevent widespread use of certain antibiotics on livestock, helping to protect the effectiveness of these drugs in humans.


News update, June 2014

In December of 2013, the U.S. Food and Drug Administration announced a major step to curb the indiscriminate use of antibiotics on livestock and help rein in the evolution of antibiotic resistant bacteria strains. Over the next three years, the FDA will ask animal pharmaceutical companies to label antibiotics so that it is clear that the drugs should not be used to boost animal growth. In a further step, these drugs will no longer be available over the counter but will require the oversight of a veterinarian when they are used to prevent or treat disease. Twenty-five of 26 antibiotic manufacturers have signed on to the agreement. These measures are expected to reduce the prevalence of antibiotics in the environment and, hence, reduce the strength of natural selection favoring resistant bacterial strains.



News update, July 2016

The risk posed by using antibiotics in livestock is a global one, according to recent news. In May, researchers announced the first case of a patient in the United States infected with bacteria resistant to a so-called "treatment of last resort" — an antibiotic reserved for certain, unusually dangerous infections. The antibiotic, called colistin, is used sparingly in the U.S. and is only deployed to treat hospital-acquired infections that are already resistant to many other antibiotics. Doctors had hoped to slow the evolution of resistance to colistin by using it rarely. However, colistin is commonly used in pigs and poultry in China. There, resistance to the drug evolved and was discovered in 2015. Now, resistant strains have popped up in the U.S. as well. We don't know for sure how the colistin-resistant infection arose in the Pennsylvania woman it infected, but because bacteria readily transfer genes to one another — including genes for antibiotic resistance — once resistance to a particular antibiotic has evolved, it can spread quickly... without stopping at international borders!


News update, June 2017

Our last update reported that resistance to colistin, an antibiotic of last resort in the United States that was commonly used on livestock in China, had popped up in Pennsylvania. Since then, the threat of colistin-resistant infections has only increased. At least 12 additional cases have been identified in the U.S. and many more have been found in hospitals in China. So far, untreatable infections — those resistant to colistin as well as to other key antibiotics — are rare, but health workers and scientists worry that they will not remain so for long. In April of this year, China stopped using the drug in livestock feed and began focusing on human use — but it may be too late. As bacteria were exposed to colistin in livestock, the antibiotic resistance genes evolved and then spread to human bugs. Now, it's likely that, as colistin is deployed widely in hospitals in China, the existing resistant bacterial strains infecting humans will be favored by natural selection and spread even further.

Read more about it

Primary literature:

  • National Antimicrobial Resistance Monitoring System. (2013). Retail meat report 2011.
    read it

  • Smillie, C. S., Smith, M. B., Friedman, J., Cordera, J. X., David, L. A., and Alm, E. J. (2011). Ecology drives a global network of gene exchange connecting the human microbiome. Nature. 480: 241-244.
    read it

News articles:

Understanding Evolution resources:

Discussion and extension questions

  1. Explain how mutation and horizontal transfer affect the genetic variation in a bacterial population.

  2. Review the process of natural selection. Explain why genetic variation is so important to this process.

  3. Would you expect reducing antibiotic use in livestock to decrease the prevalence of antibiotic resistant infections in humans? Explain why or why not.

  4. Advanced: If a particular antibiotic is reserved exclusively for treating human illness, would you expect this to eliminate the possibility of bacteria evolving resistance to the antibiotic? Explain why or why not.

  5. Advanced: Imagine that a physician treats a serious case of salmonellosis (food poisoning caused by the Salmonella bacterium) with the antibiotic ampicillin. At first, it seems that the antibiotic is working, but eventually it becomes clear that the bacterial strain that has become established in the patient is resistant to ampicillin. The physician then tries treating the patient with ciprofloxacin instead. This time, the antibiotic doesn't work for even a short amount of time. Explain what has likely occurred in evolutionary terms, beginning with the ampicillin treatment and referencing the frequency of different gene versions in the Salmonella population.

Related lessons and teaching resources


  • Aubrey, A, and Barclay, E. (2013). Antibiotic-resistant bugs turn up again in turkey meat. The Salt: What's on your Plate. NPR. Retrieved May 2, 2013 from NPR
  • Centers for Disease Control and Prevention. (2017, Apr 27).  Tracking mcr-1. Retrieved May 25, 2017 from Centers for Disease Control and Prevention (https://www.cdc.gov/drugresistance/tracking-mcr1.html).

  • Dall, C. (2017, Jan 27). Studies show spread of MCR-1 gene in China. Center for Infectious Disease Research and Policy. Retrieved May 25, 2017 from University of Minnesota (http://www.cidrap.umn.edu/news-perspective/2017/01/studies-show-spread-mcr-1-gene-china).

  • Environmental Working Group. (2013). Superbugs invade American supermarkets. Retrieved May 2, 2013 from EWG
  • FDA. (2013, Dec 11). FDA takes significant steps to address antimicrobial resistance. Retrieved May 27, 2014 from the U.S. Food and Drug Administration
  • FDA. (2014, March 26). FDA update on animal pharmaceutical industry response to Guidance #213. Retrieved May 27, 2014 from the U.S. Food and Drug Administration
  • Huang, E. (2017, Apr 4). China is about to change the way it uses a last-resort antibiotic for the better—but it’s too late. Quartz. Retrieved May 25, 2017 from Quartz (https://qz.com/940080/china-is-about-to-change-the-way-it-uses-a-last-resort-antibiotic-for-the-better-but-its-too-late/).

  • National Antimicrobial Resistance Monitoring System. (2013). Retail meat report 2011. Retrieved May 2, 2013 from FDA
  • Slaughter introduces preservation of antibiotics for medical treatment act. Congresswoman Louis M. Slaughter. Retrieved May 2, 2013 from Congresswoman Louis M. Slaughter
  • Smillie, C. S., Smith, M. B., Friedman, J., Cordera, J. X., David, L. A., and Alm, E. J. (2011). Ecology drives a global network of gene exchange connecting the human microbiome. Nature. 480: 241-244.
  • Standing up to antimicrobial resistance. (2010). Nature Reviews Microbiology. 8: 836
  • Strom, S. (2013). Report on U.S. meat sounds alarm on resistant bacteria. New York Times. Retrieved May 2, 2013 from The New York Times
  • Tavernise, S., and Grady, D. (2016). Infection raises specter of superbugs resistant to all antibiotics. Retrieved June 24, 2016 from The New York Times

Meat photo from fda.gov

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