Why would eating the meat of cows fed with antibiotics trigger an immune response to the antibiotics?

Why would eating the meat of cows fed with antibiotics trigger an immune response to the antibiotics?

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The document "Antibiotics and Antibiotic resistance" contains the following paragraph:

The indiscriminate use of antibiotics in feed stuffs means that humans may receive unwanted doses of antibiotics in meats, eggs and milk. This exposure may cause the development of an immune or inflammatory response to the antibiotic so that the human cannot be treated with the drug at a later date. The practice has also resulted in the development of antibiotic-resistant strains of bacteria.

Here are my two questions that test general biology principles:

  1. How can there be an immune response to an antibiotic?
  2. I think that the answer to the first question will answer this one anyways, but for the sake of completeness: why would the immune response to an antibiotic prevent the antibiotic from being used again? (I may know how to answer this once I actually know what an immune response to an antibiotic looks like.)

It's difficult to know how to answer this question because it is unclear why you think that this might not happen.

As skymningen has said in comments, any foreign molecule is capable of acting as an antigen, in principle. We know that people develop allergic reactions to penicillin. And if you do a Google search for immunoassay [insert name of antibiotic] you will probably find results indicating that there are commercially-available kits for assaying the antibiotic based upon antibodies directed against it.

It is however worth noting that these anti-antibiotic antibodies were certainly not raised directly by feeding, or even injecting, the antibiotic. This is because the immune system doesn't really respond to small molecules. If you want to make antibodies directed against a small molecule you have to tag it on to a protein - this is called haptenisation. Then some of the antibodies that develop against the modified protein will recognise the hapten (the small molecule). Another example of this is the development of immunoassay for steroid hormones.

So we have to imagine that a fed antibiotic enters the bloodstream and then reacts chemically with a blood protein - essentially the antibiotic has haptenised itself. I seem to recall reading that β-lactam antibiotics are fairly reactive against lysine residues. The propensity of different antibiotics to provoke an immune response may be simply a function of their reactivity.

Overactive food quality control system triggers food allergies, Yale scientists say

Food allergies have been increasing dramatically across the developed world for more than 30 years. For instance, as many as 8% of children in the U.S. now experience potentially lethal immune system responses to such foods as milk, tree nuts, fish and shellfish. But scientists have struggled to explain why that is. A prevailing theory has been that food allergies arise because of an absence of natural pathogens such as parasites in the modern environment, which in turn makes the part of the immune system that evolved to deal with such natural threats hypersensitive to certain foods.

In a paper published Jan. 14 in the journal Cell, four Yale immunobiologists propose an expanded explanation for the rise of food allergies -- the exaggerated activation of our food quality control system, a complex and highly evolved program designed to protect us against eating harmful foods. The presence of unnatural substances, including processed food, or environmental chemicals, such as dishwashing detergent, in the modern environment, as well as the absence of natural microbial exposure, play a role in disrupting this food quality control program, they argue.

The theory can lay the groundwork for future treatment or prevention of food allergies, the scientists suggest.

"We can't devise ways to prevent or treat food allergies until we fully understand underlying biology," said co-author Ruslan Medzhitov, Sterling Professor of Immunobiology and investigator for the Howard Hughes Medical Institute. "You can't be a good car mechanic if you don't know how a normal car works."

The quality food control program present in the biology of all animals includes sensory guardians -- if something smells or tastes bad, we don't eat it. And there are sentinels in the gut -- if we consume toxins, they are detected and expelled. In the latter case, a part of the immune system as well as parasympathetic arm of the nervous system also mobilize to help neutralize the threat.

This type of immune system response triggers allergies, including food allergies, a fact that gave rise to the so-called "hygiene hypothesis" of food allergies. The lack of natural threats such as parasites made this portion of the immune system hypersensitive and more likely to respond to generally innocuous proteins found in certain food groups, the theory holds. This helped explain why people living in rural areas of the world are much less likely to develop food allergies than those living in more urban areas.

However, food allergies have continued to rise dramatically long after elimination of parasites in the developed world, Medzhitov noted. So the Yale team now theorizes that other environmental factors influenced activity within the natural food quality control system and contributed to immune system hypersensitivity to certain food allergens.

"One factor is increased use of hygiene products and overuse of antibiotics and, secondly, a change in diet and the increased consumption of processed food with reduced exposure to naturally grown food and changed composition of the gut microbiome," Medzhitov said. "Finally, the introduction of food preservatives and environmental chemicals such as dishwashing detergents introduced novel elements for immune system to monitor." Collectively, these changes in the environment effectively trigger food quality control responses making the immune system react to food proteins the way it would react to toxic substances, the team argues.

"It's guilt by association," Medzhitov said.

Food allergies are no different than many other diseases, which are caused by abnormal versions of normal biological responses, he said. Understanding the underlying biology of normal processes such as food quality control system should help researchers identify potential culprits not only in food allergies, but other diseases as well, the authors argue.

Yale co-authors are Esther Florsheim, a former postdoctoral research associate, Zuri Sullivan, a postdoctoral associate, and William Khoury-Hanold, a postdoctoral fellow, of the Yale Department of Immunology.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

Foods That Cause Inflammation

Sugar gets a bad rap because all sugars are often lumped together. It is the processed or refined sugars and the large amounts of additive natural sugar that triggers the inflammation process.

Sugar from plant life exists in a synergistic way with the plant’s other nutrients and fiber. The nutrients and fiber regulate how the sugar is released into the body. This balance is thrown off in processed foods containing refined or added natural sugars, and the sugar from those foods do not enter the bloodstream in a regulated manner and they become foods that trigger inflammation:

Arachidonic Acid

Arachidonic acid (AA) is often cited as a source of inflammation, and because AA is found primarily in eggs and meat, this concern could contribute to the view that red meat is inflammatory. AA is an essential omega-6 fatty acid that is a vital component of cell membranes and plays an important role in the inflammatory response. (8) It’s especially necessary during periods of bodily growth or repair, and is thus a natural and important component of breast milk. (9) AA is sometimes portrayed as something to be avoided entirely simply because it is ‘inflammatory,’ but as usual, that view drastically oversimplifies what actually happens in the body.

It’s true that AA plays a role in inflammation, but that’s a good thing! It ensures that our body responds properly to a physical insult or pathogen, and it also helps ensure that the inflammatory response is turned off when it’s no longer needed. AA interacts with other omega-3 and omega-6 fatty acids in intricate and subtle ways, and an imbalance in any of those fats has undesirable effects. For example, low doses of EPA tend to increase tissue levels of AA, while high doses decrease levels of AA, which probably explains why the benefits of fish oil supplementation are lost at higher doses. (10) In epidemiological studies, higher plasma levels of both AA and the long-chain omega-3 PUFA were associated with the lowest levels of inflammatory markers. (11, 12) And clinical studies have found that adding up to 1,200 mg of AA per day—which is 12 times higher than the average intake of AA in the U.S.— to the diet has no discernible effect on the production of inflammatory cytokines. (13, 14) What’s more, our Paleolithic ancestors (who were largely free of chronic, inflammatory disease) consumed at least twice the amount of AA that the average American does today. (15)

Finally, it’s important to note that red meat actually has a lower concentration of AA than other meats because of its lower overall PUFA content. (16)(17) Additionally, red meat has been shown to increase tissue concentrations of both AA and the long chain omega-3s DHA and EPA, preserving the all-important balance of omega-3 and omega-6. (18)

Nom, nom! These bacteria eat antibiotics for lunch

Some bacteria can use antibiotic drugs as fuel. Now, scientists have figured out how they do it.

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Bacteria have a lot of ways to avoid the drugs people use to kill them. Some pump the drugs away. Others shield their vulnerable parts with protective coatings. Some bacteria even chew up drugs. And if they’re chewing, why not also eat them? A new study shows how some microbes do just that: They turn the drugs meant to kill them into a bacterial buffet.

Scientists might one day harness these findings to help rid the environment of polluting drugs.

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Some of the first antibiotics — chemicals used to kill bacteria — were found in organisms living in soil. Bacteria, mold and other microbes constantly duke it out for space, food and other resources. Some have evolved chemicals to kill each other. People simply took those molecules and adapted them for medicine and other uses.

Explainer: Where antibiotics came from

But in this kill-or-be-killed world, one bacterium’s weapon can trigger another’s new defense. And some bacteria living in the soil indeed have learned not only to break down antibiotics, but also to eat them.

Such bugs can use parts of the germ-killing drug as fuel, explains Daria Van Tyne at Harvard University in Cambridge, Mass. As a microbiologist she studies microbes.

All of this “makes sense,” Van Tyne says, “given that a lot of antibiotics come from the soil.” Until now, she points out, scientists did not know “exactly how the eating worked.”

To catch a drug eater

Gautam Dantas is a microbiologist at Washington University in St. Louis, Mo. He and his colleagues set out to discover how bacteria could safely nosh on antibiotics. First, they had to find some germs that knew the trick. To do that, they needed dirt. “My father-in-law and mother-in-law live in Minnesota. They sent us some soil,” he says. “We [also] got some in Pennsylvania and went hiking in Massachusetts.”

The scientists set up their soil samples in petri dishes — shallow dishes used to grow bacteria. Then they gave the soil microbes nothing to eat but antibiotics, such as penicillin. Afterward, they waited to see if any bacteria grew. Some did. The researchers then separated these bugs out, gave them more penicillin and let them grow some more.

“It was a tedious process,” Dantas says.

Though some bacteria can grow on antibiotics, they don’t much like it. “It’s not their preferred food,” he says. Bacteria usually feed on sugars or amino acids (the building blocks of proteins). When fed only antibiotics, the microbes grow at only one-half to one-third the rate they would when fed their usual diet.

After working with many, many petri dishes of germs, Dantas and his group were left with four types of bacteria that could survive dining on antibiotics. They now looked at the genes — cellular instructions — within these bacteria. They also looked at what chemicals these microbes produced. The scientists were hunting for a shared set of instructions that would let a bacterium chop up and eat a penicillin molecule.

They didn’t know whether all four bacteria would use the same drug-digesting strategy. “But if they were all doing it the same way,” Dantas says, “the same pathway [should] come up.”

How to eat a lion … or an antibiotic

Penicillin belongs to a group of antibiotics called the beta-lactams. The name comes from a chemical structure in the middle of the molecule called a beta-lactam ring. This ring has three carbon atoms and one nitrogen atom. The rest of the antibiotic hangs off this ring in all directions. And bacteria need three major steps to snack on penicillin.

The beta-lactam ring is the most dangerous part of the antibiotic. This ring allows the antibiotic to pop into the cell wall of a bacterium. It then stops the wall from holding the cell together. Fluids now leak out of the bacterium causing the cell to die.

The first step in dismantling an antibiotic is smashing its beta-lactam ring. It does this with an enzyme, a molecule that speeds up a chemical process. This enzyme, called beta-lactamase, chews open the ring. Now the antibiotic can no longer do its job.

Now it’s time to eat. But even with its beta-lactam ring busted open, the antibiotic is too big for a bacterium to eat whole. The drug must be cut down to size.

“Say you want to chop a lion in half,” Dantas says. If you cut it in the middle, between the front and back legs, you get two halves. “But they’re not equal halves,” he notes. “You’ve got the back end and the front end. It gives you two options: You can eat the head or the tail.”

For a bacterium trying to break down an antibiotic (instead of a lion), the second step is to use an enzyme called amidase. That breaks the molecule in two, leaving a front half and a back half.

The final step is to chew up the pieces. Dantas and his team pinpointed a group of 15 enzymes that other scientists had seen before. Those 15 enzymes did the trick. “They’re really good at eating the tail half of the ‘lion,’” he says. The enzymes reduce the “tail” of this drug to parts that the cell can use.

The scientists wanted to prove that the whole process was needed for bacteria to use antibiotics as food. So Dantas’ group took the genes for making the essential enzymes and stuck them in a different bacterium. This one belonged to a different species. They used E. coli, a germ that is popular in labs. E. coli normally die when faced with large amounts of antibiotics. But after being provided the new genes, the E. coli could eat up the drug.

Dantas and his colleagues published their findings April 30 in the journal Nature Chemical Biology.

Eating antibacterial trash

It might seem like bad news that soil microbes can eat the drugs designed to kill them. But Dantas actually sees it as an opportunity.

“A problem with antibiotics is that we tend to overuse them,” he notes. And the more people who are treated, the more wastes they excrete. Those excreted drugs leave toilets as part of the wastes flowing into sewers. They also may flow into streams from cows and other livestock that had been treated with drugs. Once in the environment, people need some way to break those drugs down, Dantas explains. And the newfound bacterial process might point to one possible solution.

“It’s interesting to think about using these bacteria to try and degrade the antibiotics that humans are putting into the environment,” says Van Tyne. But, she warns, scientists would have to be very careful. Bacteria love to swap genes with each other. Introducing a modified bacterium into the environment could end in disaster, she worries. How? Some dangerous neighboring microbe might pick up the genes needed to help it chew up the drugs meant to kill it.

What’s more, this bacterial pathway has evolved to tackle only one class of antibiotics in soil. It might be useless against related drugs made in a lab, Van Tyne says.

Dantas agrees that it’s important to be careful. It might be possible, however, to use the enzymes alone, he says, rather than putting them into some bacterium. Releasing something that could eat antibiotic pollution has a lot of potential. But there are risks to consider,” he says, such as “whether it should be done.”

Power Words

amidase A type of enzyme that can break down a part of a molecule containing nitrogen atoms.

antibiotic A germ-killing substance, usually prescribed as a medicine (or sometimes as a feed additive to promote the growth of livestock). It does not work against viruses.

atom The basic unit of a chemical element. Atoms are made up of a dense nucleus that contains positively charged protons and uncharged neutrons. The nucleus is orbited by a cloud of negatively charged electrons.

bacteria (singular: bacterium) Single-celled organisms. These dwell nearly everywhere on Earth, from the bottom of the sea to inside other living organisms (such as plants and animals).

bacterial Having to do with bacteria.

beta-lactam antibiotic A family of germ-killers that includes penicillin. Beta-lactam refers to a four-atom ring structure in the molecule. It helps the chemical burst bacterial cell walls.

biology The study of living things. The scientists who study them are known as biologists.

bug The slang term for an insect. Sometimes it&rsquos even used to refer to a germ.

carbon The chemical element having the atomic number 6. It is the physical basis of all life on Earth. Carbon exists freely as graphite and diamond. It is an important part of coal, limestone and petroleum, and is capable of self-bonding, chemically, to form an enormous number of chemically, biologically and commercially important molecules.

cell The smallest structural and functional unit of an organism. Typically too small to see with the unaided eye, it consists of a watery fluid surrounded by a membrane or wall. Depending on their size, animals are made of anywhere from thousands to trillions of cells. Most organisms, such as yeasts, molds, bacteria and some algae, are composed of only one cell.

chemical A substance formed from two or more atoms that unite (bond) in a fixed proportion and structure. For example, water is a chemical made when two hydrogen atoms bond to one oxygen atom. Its chemical formula is H2O. Chemical also can be an adjective to describe properties of materials that are the result of various reactions between different compounds.

colleague Someone who works with another a co-worker or team member.

defense (in biology) A natural protective action taken or chemical response that occurs when a species confront predators or agents that might harm it. (adj. defensive)

degrade To break down into smaller, simpler materials &mdash as when wood rots or as a flag that&rsquos left outdoors in the weather will fray, fade and fall apart. (in chemistry) To break down a compound into smaller components.

E. coli (short for Escherichia coli) A common bacterium that researchers often harness to study genetics. Some naturally occurring strains of this microbe cause disease, but many do not.

environment The sum of all of the things that exist around some organism or the process and the condition those things create. Environment may refer to the weather and ecosystem in which some animal lives, or, perhaps, the temperature and humidity (or even the placement of components in some electronics system or product).

enzymes Molecules made by living things to speed up chemical reactions.

gene (adj. genetic) A segment of DNA that codes, or holds instructions, for a cell&rsquos production of a protein. Offspring inherit genes from their parents. Genes influence how an organism looks and behaves.

germ Any one-celled microorganism, such as a bacterium or fungal species, or a virus particle. Some germs cause disease. Others can promote the health of more complex organisms, including birds and mammals. The health effects of most germs, however, remain unknown.

glucose A simple sugar that is an important energy source in living organisms. As an energy source moving through the bloodstream, it is known as &ldquoblood sugar.&rdquo It is half of the molecule that makes up table sugar (also known as sucrose).

journal (in science) A publication in which scientists share their research findings with experts (and sometimes even the public). Some journals publish papers from all fields of science, technology, engineering and math, while others are specific to a single subject. The best journals are peer-reviewed: They send all submitted articles to outside experts to be read and critiqued. The goal, here, is to prevent the publication of mistakes, fraud or sloppy work.

livestock Animals raised for meat or dairy products, including cattle, sheep, goats, pigs, chickens and geese.

microbe Short for microorganism. A living thing that is too small to see with the unaided eye, including bacteria, some fungi and many other organisms such as amoebas. Most consist of a single cell.

microbiology The study of microorganisms, principally bacteria, fungi and viruses. Scientists who study microbes and the infections they can cause or ways that they can interact with their environment are known as microbiologists.

molecule An electrically neutral group of atoms that represents the smallest possible amount of a chemical compound. Molecules can be made of single types of atoms or of different types. For example, the oxygen in the air is made of two oxygen atoms (O2), but water is made of two hydrogen atoms and one oxygen atom (H2O).

nitrogen A colorless, odorless and nonreactive gaseous element that forms about 78 percent of Earth's atmosphere. Its scientific symbol is N. Nitrogen is released in the form of nitrogen oxides as fossil fuels burn.

organism Any living thing, from elephants and plants to bacteria and other types of single-celled life.

penicillin The first antibiotic (although not the first one used on people), it&rsquos a natural product that comes from a mold. In 1928, Alexander Fleming, a British scientist, discovered that it could kill certain bacteria. He would later share the 1945 Nobel Prize in Medicine for it.

pollutant A substance that taints something &mdash such as the air, water, our bodies or products. Some pollutants are chemicals, such as pesticides. Others may be radiation, including excess heat or light. Even weeds and other invasive species can be considered a type of biological pollution.

tedious (n. tedium) An adjective for something that is disturbingly slow, boring, monotonous and/or repetitive.


Journal:​ ​​T.S. Crofts et al. Shared strategies for b-lactam catabolism in the soil microbiome. Nature Chemical Biology. Published online April 30, 2018. doi: 10.1038/s41589-018-0052-1.

About Bethany Brookshire

Bethany Brookshire was a longtime staff writer at Science News for Students. She has a Ph.D. in physiology and pharmacology and likes to write about neuroscience, biology, climate and more. She thinks Porgs are an invasive species.

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Unhealthy conditions for farm animals are—no surprise—bad for humans, too

Last spring a man was admitted to Mt. Sinai Hospital in Brooklyn for surgery. A blood test revealed he was positive for the deadly antibiotic-resistant fungus, C. auris, and he was quickly quarantined. After three months of intensive treatment, he died. In order to eradicate traces of the germ from his room, the hospital had to acquire special cleaning equipment, rip out parts of the ceiling and floor, and get rid of some treatment tools. “Everything in the room was positive,” Dr. Scott Lorin, the hospital’s president, told The New York Times. The germ, deemed an “urgent threat” by the Centers for Disease Control and Prevention, has so far been found in two more states, New Jersey and Illinois.

Experts warn it’s only going to get worse. In 2014, the Review on Antimicrobial Resistance, commissioned by the UK Government and Wellcome Trust, estimated that 700,000 people around the world die each year due to drug-resistant infections. Without action, that number could grow to 10 million per year by 2050. A leading cause of antibiotic resistance? The misuse and overuse of antibiotics on factory farms.

Flourishing antibiotic resistance is just one of the many public health crises produced by factory farming. Other problems include food borne illness, flu epidemics, the fall out from poor air and water quality, and chronic disease. All of it can be traced to the current industrial approach to raising animals, which values “high stocking density” over safe working conditions and farm animal welfare. Oversight for the way factory farms operate and manage waste is minimal at best. No federal agency collects consistent and reliable information on the number, size, and location of large-scale agricultural operations, nor the pollution they’re emitting. There are also no federal laws governing the conditions in which farm animals are raised, and most state anti-cruelty laws do not apply to farm animals.

For example, Texas, Iowa and Nebraska have excluded livestock from their animal cruelty statute and instead created specific legislation aimed at farm animal abuse that makes accepted or customary husbandry practices the animal welfare standard. After New Jersey created similar legislation, the New Jersey Society for the Prevention of Cruelty to Animals (NJSPCA) sued the New Jersey Department of Agriculture (NJDA), claiming that “routine husbandry practices” was too vague. NJSPCA won, and as a result, the NJDA has created more specific regulations: tail docking of cattle is only allowed when performed “by a veterinarian for individual animals,” and debeaking of birds is only allowed if performed by a knowledgeable individual and in compliance with the United Egg Producers Animal Husbandry Guidelines for U.S. Egg Laying Flocks. In North Carolina, any person or organization can file a lawsuit if they suspect animal cruelty, even if that person does not have “possessory or ownership rights in an animal.” In this way, the state has “a civil remedy” for farm animal cruelty.

The general lack of governmental oversight results in cramped and filthy conditions, stressed out animals and workers, and an ideal set up for the rampant spread of disease among animals, between animals and workers, and into the surrounding environment through animal waste.


The problem: In 2017, nearly 11 million kilograms of antibiotics––including 5.6 million kilograms of medically important antibiotics––were sold in the US for food animals. Factory farms use antibiotics to make livestock grow faster and control the spread of disease in cramped and unhealthy living conditions. While antibiotics do kill some bacteria in animals, resistant bacteria can, and often do, survive and multiply, contaminating meat and animal products during slaughter and processing.

What it means for you: People can be exposed to antibiotic-resistant bacteria by handling or eating contaminated animal products, coming into contact with contaminated water, or touching or caring for farm animals, which of course makes a farmworker’s job especially dangerous. Even if you don’t eat much meat or dairy, you’re vulnerable resistant pathogens can enter water streams through animal manure and contaminate irrigated produce.

The CDC breaks down how routine antibiotic use on factory farms can lead to antibiotic resistance harming human health. Image source

Developments: The European Union has been much more aggressive than the US in regulating antibiotic use on factory farms, banning the use of all antibiotics for growth promotion in 2006. But the US is making some progress, too. Under the FDA’s new rules, which went into effect January 2017, antibiotics that are important for human medicine can no longer be used for growth promotion or feed efficiency in cows, pigs, chickens, turkeys, and other food animals. In addition, 95 percent of medically important antibiotics used in animal water and feed for therapeutic purposes were reclassified so they could not be bought over the counter, and a veterinarian would have to sign off on its use in animals. As a result, domestic sales and distribution of medically important antimicrobials approved for use in food-producing animals decreased by 43 percent from 2015 (the year of peak sales) through 2017, reports the FDA.

However, the FDA still allows routine antibiotic use in factory farms for disease prevention in crowded and stressed animals, so these new rules aren’t nearly enough, says Matthew Wellington, antibiotics program director for the US Public Interest Research Group Education Fund. "The FDA should implement ambitious reduction targets for antibiotic use in the meat industry, and ensure that these medicines are used to treat sick animals or control a verified disease outbreak, not for routine disease prevention," Wellington said in a statement to the Center for Infectious Disease Research and Policy.

National Resources Defense Council senior attorney Avinash Kar agrees. “We are seeing real progress, but the American meat industry continues to have a drug problem and the clock is ticking to solve it," she says. "Far more antibiotics important to humans still go to cows and pigs—usually when they're not sick—than to people, putting the health of every single one of us in jeopardy."


The problem: Livestock in this country produce between 3 and 20 times more waste than people in the US produce, according to a 2005 EPA report, or as much as 1.2–1.37 billion tons of manure a year. Some estimates are even higher. Manure can contain “pathogens such as E. coli, growth hormones, antibiotics, chemicals used as additives to the manure or to clean equipment, animal blood, silage leachate from corn feed, or copper sulfate used in footbaths for cows,” reports a 2010 report by the National Association of Local Boards of Health. Though sewage treatment plants are required for human waste, no such treatment facility exists for livestock waste.

Since this amount far exceeds what can be used as fertilizer, animal waste from factory farms typically enters massive, open-air waste lagoons, which spread airborne pathogens to people who live near by. If animal waste is applied as fertilizer and exceeds the soil’s capacity for absorption, or if there is a leak or break in the manure storage or containment unit, the animal waste runs off into oceans, lakes, rivers, and streams, and groundwater. Extreme weather increases the possibility of such breaks Hurricane Florence, for example, flooded at least 50 hog lagoons when it struck the Carolinas last year, and satellite photos captured the damage. Eight years ago, the EPA reported that 29 states identify animal feeding operations as contributing to water pollution. To offer some idea of what that looks like, the EPA reported in 1998 that factory farm runoff polluted 35,000 miles of river in 22 states.

Whether or not the manure is contained or spread as fertilizer, it can release 400 different types of harmful gases, including ammonia and hydrogen sulfide, as well as particulate matter comprised of fecal matter, feed materials, pollen, bacteria, fungi, skin cells, and silicates into the air. Manure is also an abundant source of nitrate, which seeps into groundwater and can be toxic at elevated levels.

Factory farms contain animal waste in massive open-air lagoons that run the risk of leaking and breaking, contaminating surrounding air and water. Image source

What it means for you: Pathogens can cause diarrhea and severe illness or even death for those with weakened immune systems, and gases like ammonia and hydrogen sulfide can cause dizziness, eye irritation, respiratory illness, nausea, sore throats, seizures, comas, and death. Particulate matter in the air can lead to chronic bronchitis, chronic respiratory symptoms, declines in lung function, and organic dust toxic syndrome. The CDC has reported that children raised in communities near factory farms are more likely to develop asthma or bronchitis, and that people who live near factory farms may experience mental health deterioration and increased sensitization to smells. Nitrates in drinking water have been connected to birth defects, miscarriages, poor general health. For infants it can mean blue baby syndrome and even death.

Developments: It is difficult to hold factory farms accountable for polluting surrounding air and water, largely for political reasons. The GOP-controlled Congress and the Trump administration recently excused big livestock farms from reporting air emissions, for instance, following a decade-long push for special treatment by the livestock industry. The exemption indicates “further denial of the impact that these [emissions] are having, whether it’s on climate or whether it’s on public health,” says Carrie Apfel, an attorney for Earthjustice. In a 2017 report from the EPA’s Office of the Inspector General, the agency admitted it has not found a good way to track emissions from animal farms and know whether the farms are complyimg with the Clean Air Act.

No federal agency even has reliable information on the number and locations of factory farms, which of course makes accountability even harder to establish. Two Stanford scholars are hoping to change that. Professor Daniel Ho and doctoral candidate Cassandra Handan-Nader published a paper in Nature Sustainability last month demonstrating how a new map-reading algorithm could help regulators identify CAFOs more efficiently. They retrained an existing image-recognition model to recognize large-scale animal facilities from publicly available satellite images. The researchers estimate that their algorithm can capture 95 percent of existing large-scale facilities using less than 10 percent of the resources required for a manual census.

Food & Water Watch has compiled data from the USDA Census of Agriculture to estimate the number and density of livestock operations in the United States. Factory farms don’t always need permits to operate, which makes it hard to know where they are located and how many there are. Image source


The problem: The United States has “shockingly high” levels of food borne illness, according to the Bureau of Investigative Journalism and The Guardian, and unsanitary conditions at factory farms are a leading contributor.

In a study of 47 meat plants across the U.S., investigators found that hygiene incidents occur at rates experts described as “deeply worrying.” One dataset covered 13 large red meat and poultry plants between 2015 and 2017 and found an average of more than 150 violations a week, or 15,000 violations over the entire period. Violations included unsanitary factory conditions and meat contaminated with blood, septicemic disease, and feces.

“The rates at which outbreaks of infectious food poisoning occur in the U.S. are significantly higher than in the UK, or the EU,” said Erik Milstone, a food safety expert at Sussex University interviewed by The Guardian. “Poor hygiene in the meat supply chain is a leading cause of food poisoning in the U.S.”

Poor sanitary practices allow bacteria like E. coli and Salmonella, which live in the intestinal tracts of infected livestock, to contaminate meat or animal products during slaughter or processing. Contamination occurs at higher rates on factory farms because crowded and unclean living conditions increase the likelihood of transmission between animals. It also stress out animals, which suppresses their immune response making them more susceptible to disease. The grain-based diets used to fatten cattle can also quickly increase the risk of E. coli infection. In poultry, the practice of processing dead hens into “spent hen meal” to be fed to live hens has increased the spread of Salmonella.

What it means for you: According to the CDC, roughly 48 million people in the US suffer from food borne illnesses annually, with 128,000 hospitalizations and 3,000 deaths each year. Salmonella accounts for approximately 11 percent of infections, and kills more people every year than any other food borne illness.

Developments: In January of 2011, President Obama signed The Food Safety Modernization Act (FSMA), the first major piece of federal legislation addressing food safety since 1938. FSMA grants the FDA new authority to regulate the way food is grown, harvested, and processed, and new powers such as mandatory recall authority. The FSMA “basically codified this principle that everybody responsible for producing food should be doing what the best science says is appropriate to prevent hazards and reduce the risk of illness," according to Mike Taylor, co-chairman of Stop Foodborne Illness and a former deputy commissioner for foods and veterinary medicine at the FDA. "So we're moving in the right direction." However, almost ten years later, the FSMA is still being phased in, due to a shortage of trained food-inspectors and a lack of funding. "Congress has gotten about halfway to what it said was needed to successfully implement" the act, Taylor said.

In 2011, President Obama signed The Food Safety Modernization Act (FSMA), the first major piece of federal legislation addressing food safety since 1938. Image source

The problem: Both the number and density of animals on factory farms increases the risk of new virulent pathogens, according to the US Council for Agriculture, Science and Technology. In addition, transporting animals over long distances to processing facilities brings different influenza strains into contact with each other so they combine and spread quickly. Pigs are susceptible to both avian and human flu viruses so they can serve as ground zero for all sorts of new strains. Because of intensive pig farming practices,“the North American swine flu virus has jumped onto an evolutionary fast track, churning out variants every year,” according to a report published in Science magazine.

What it means for you: These viruses can become pandemics. In fact, viral geneticists link the genetic lineage of H1N1 to a strain that emerged in 1998 in US factory pig farms. The CDC has estimated that between 151,700 and 575,400 people worldwide died from the 2009 H1N1 virus infection during the first year the virus circulated.


The problem: Factory farms in the US use hormones to stimulate growth in two-thirds of beef cattle. On dairy farms, 54 percent of cows are injected with recombinant bovine growth hormone (rBGH), a growth hormone that increases milk production.

What it means for you: The health effects of consuming animal products treated with these growth hormones is an ongoing international debate. Some studies have linked growth hormone residues in meat to reproductive issues and breast, prostate, and colon cancer, and IGF-1 has been linked to colon and breast cancer. However, the FDA, the National Institute of Health and the World Health Organization have independently found that dairy products and meat from rBGH-treated cows are safe for human consumption. Because risk assessments vary, the EU, Australia, New Zealand, Japan, Israel, and Argentina have banned the use of rBGH as a precautionary measure. The EU has also banned the use of six hormones in cattle and imported beef.

Developments: USDA guidelines allow beef products to be labeled with “no hormones administered” and dairy products to be labeled “from cows not treated with rBST/rBGH” if the producer provides sufficient documentation that this is true. Consumers can use this information to make their own decisions about the risks associated with hormone-treated animal products.

While the health risks of consuming animal products from livestock treated with hormones are up for debate, USDA guidelines allow beef and dairy products to be labeled as hormone-free, if it can be proven. Image source


You can vote for local initiatives that establish health and welfare regulations for factory farms, but only a tiny number of states, including California and Massachusetts, are even putting relevant propositions on the ballot. Another option is to support any of the nonprofits that are, in lieu of effective government action, taking these factory farms to task. The Environmental Working Group, Earthjustice, and Animal Legal Defense Fund are among those working hard to check the worst practices of these CAFOs. Another good organization is the Socially Responsible Agriculture Project (SRAP), which works with local residents to fight the development of factory farms in their own backyards.

Dr. Mark Post of Mosa Meats holds a ‘clean meat’ hamburger grown from cell culture. Clean meat is produced without the use of antibiotics and hormones and eradicates animal waste management and thus air and water pollution problems. Image source: The Good Food Institute

Buying humanely raised animal products from farms, and farmers, you trust is another way to push back against factory farming. Sadly, products from these smaller farms make up only a fraction of the total. In the US roughly 99 percent of chicken, turkeys, eggs, and pork, and 70 percent of cows, are raised on factory farms.

You can support “clean” burgers, chicken, and pork, by buying it once it becomes widely available. Made from animal cells, the process completely spares the animal and eliminates the factory farm. “The resulting product is 100 percent real meat, but without the antibiotics, E. coli, Salmonella, or waste contamination,” writes the Good Food Institute, a resource for many clean meat start-ups, which currently number 27. Says Paul Shapiro, CEO of The Better Meat Co., “this promising field will only continue to get bigger.”

In the meantime, you can register your objection to factory farming by doing your bit to reduce demand for their products. In short, eat less meat and dairy, and more plant-based proteins. Fortunately, the days when that meant forking in soy dogs and potato burgers are long gone. More than $13B were invested in plant-based meat, egg, and dairy companies in 2017 and 2018 alone, according to the Good Food Institute, and Beyond Meat’s IPO debut last week marked the most successful one since the year 2000. Lest you think that what you do on your own can’t possibly make a difference, consider one of the major drivers behind all this new investment: consumers are demanding change. Says Bruce Friedrich, executive director of Good Food Institute: “Shifting consumer values have created a favorable market for alternatives to animal-based foods, and we have already seen fast-paced growth in this space across retail and foodservice markets.”

Tia Schwab is a Stone Pier Press News Fellow and a senior at Stanford University, where she studies human biology with a concentration in food systems and public health.

Clinical Manifestations of S Aureus

S aureus is notorious for causing boils, furuncles, styes, impetigo and other superficial skin infections in humans (Figure 12-1). It may also cause more serious infections, particularly in persons debilitated by chronic illness, traumatic injury, burns or immunosuppression. These infections include pneumonia, deep abscesses, osteomyelitis, endocarditis, phlebitis, mastitis and meningitis, and are often associated with hospitalized patients rather than healthy individuals in the community. S aureus and S epidermidis are common causes of infections associated with indwelling devices such as joint prostheses, cardiovascular devices and artificial heart valves (Fig. 12-2).

Figure 12-1

Pathogenesis of staphylococcal infections.

Figure 12-2

Infections associated with indwelling devices.

Why You Should Consider a Gluten and Dairy Free Diet

In my clinical experience with patients, dairy is one of the biggest problems contributing to persistent symptoms of disease. The study above identifies the protein, casein, as the biggest culprit. 50% of the study participants had an inflammatory reaction when exposed to dairy.

There are many research findings and clinical observations as to why this can happen:

  1. Processing of dairy alters the casein protein creating a molecule that resembles gluten, thus creating an inflammatory response.
  2. Eating dairy processed with the enzyme, microbial transglutaminase (AKA meat glue), can increase inflammation and cause an immune reaction in people with gluten sensitivity.
  3. Cows are supposed to eat grass, hay, etc. They are not designed to process the huge quantities of corn and grain based foods that they are fed. Some would speculate that these grain based proteins might make their way into the milk, thus creating an inflammatory reaction.
  4. Leaky gut – gluten can cause intestinal permeability. When this happens, people often times become allergic to the staple foods in their diet. As milk is a major staple used by those on a gluten free diet, many develop an allergic response to dairy. deficiencies – those with gluten induced intestinal damage of long standing nature tend to lack the capacity to be able to break down the sugars and proteins in dairy (AKA – dairy intolerance). This type of problem can cause tremendous GI distress, gas, distention, bloating, and pain. The undigested dairy materials can putrefy (become rotten) while in the gut. This in turn can create secondary inflammatory reactions. This can also lead to disruption in the healthy bacterial counts of the gut. As these bacteria are largely responsible for regulating immune response and inflammation, disrupting their numbers is a common cause of GI disturbance.

There are a number of problems with mass produced modern dairy products.

  • The food for the cows are GMO (primarily corn and other grains)
  • Recombinant bovine growth hormone
  • Cows kept in tight quarters, little exercise, and exposed to massive quantities of antibiotics and hormones
  • Ultra pasteurization of the dairy denatures and destroys much of the protein and nutritional value.
  • For a more comprehensive breakdown on the topic click here ->> Is Dairy Safe On a Gluten Free Diet

50 comments on &ldquoAntibiotic Resistance: A Question or Two&rdquo

Linked in my handle is a JAMA paper that makes a statistical association between farm workers and MRSA infections.
That said, I’m not statistically savvy enough to tell if it means something or not I sense that if there was a direct connection (“this pig had strain Z, this person also had strain Z”) it would have been written that way.

Isn’t the concern more based on that widespread antibiotic use in livestock (or hand santizers for that matter) leads to increased populations of MRSA bacteria in general that we humans can then come in contact with? Not necessarily that someone is infected by direct transmission from an animal?

Would the resistance be developing in the animals themselves, though? I would think the problem would be contamination of the ground & waterways and resistance developing there (which would be much harder to pin on farm use).

More than half of antibiotics produced are used for live stocks for prevention of bacterial infections. Broiler chickens are often infected with C. perfringens which causes diarrhea and death. Antibiotics used for these animal are structurally similar to those used to treat human. The problem is that these antibiotics get metabolized by animal to produce metabolites (whose structures share the same framework of antibiotics for human), which go to environment where most of bacterial pathogens live. These exposure would certainly create bacteria “inherently” resistant to certain types of antibiotics that are to be used human.

It’s really all of the above. Direct and indirect zoonotic transmission, and environmental exposure to eliminated antibiotics and metabolites all lead to the same effect. Interestingly, Tyson seems to have figured out that using human approved antibiotics in their chicken feed is not a good idea: This article seems to suggest they plan to change their practices.

I worked on some small parts of the PCAST AMR report and although this wasn’t my part, and I don’t speak for anyone else associated with the report, there was some discussion about how the right thing was to call for more study on this using modern genomic tools (p. 50-52). As you note it’s something that hasn’t been extensively reported even though it’s a logical possibility, there just isn’t that much evidence of it yet. That, of course, made some people mad because they wanted an immediate ban of antibiotic use in farm animals, but there just isn’t that much data showing development of resistance in farm animals that then passes to other microbes (which is why we said to study it more!)

This is kind of interesting. I thought I had heard that certain farm animals can’t take kanamycin because there are multiple ubiquitous bacteria that are now resistant, but when I look in the literature I really only came across this.
The way I remember hearing this anecdotally at least was this was a widespread problem….great question.

As far as I can tell, the association between antibiotic use in livestock and emergence of resistant strains has a very strong smell of speculation about it. The idea that resistant strains develop in animals’ gut flora and then are released in the environment makes intuitive sense, but the link between agricultural soil and waterways and a human population that is now mostly urban and rarely has contact with such an environment seems rather tenuous. I suppose that bacterial contamination of meat with animal flora at slaughter, and then contact of food preparers with raw meat could also contribute. But frankly, it seems to me that a random human is several orders of magnitude more likely to be directly exposed to other antibiotic-treated humans, rather than livestock. And as someone trained as a veterinarian, I am quite familiar with the facile tendency of MDs to want to blame everything on animals…

I fear the original question betrays a certain lack of understanding of the underlying problem. Antibiotic resistance genes rarely exist in isolation. Any given mobile genetic element (eg plasmid, ‘phage, etc) will most likely have half a dozen or more such resistance genes. While industrial farmers may not be using antibiotics used in humans they may well be unwittingly propagating genes coding for resistance to clinically relevant drugs.
While I’m sure there are some examples of direct transmission from farm animals to humans this isn’t really the main concern. Having said that, the documentary “Resistance” documents one case of a woman working in an industrial pork facility who’s husband will require life-long care due a nasty MRSA strain she brought home from work.
As most meat is cooked prior to consumption by humans, most bacterial contamination won’t pose much of a public health risk. I’m not aware of many bacteria that are capable of penetrating muscle to a significant extent in the time frame that is relevant to meat sales. This means that even a rare steak that has been at least seared should be fine.
What is of greater concern is what is done with the animal waste from such facilities. I don’t think that anybody would try and argue that such waste is abiotic and as such nearly all bacteria present will be resistant to the antibiotics used (and more than likely carrying other resistance genes along with them). I personally remember a talk at a mobile genetic element conference describing the transmission of such antibiotic resistance between bacterial species within the soil of a field over a period of 2 years. If such a field were used to grow produce that is not normally cooked (anybody remember Listeria in melons?) then it doesn’t take much imagination to see that adding antibiotic resistance to the mix would be A Very Bad Thing (TM).
I’m not trying to have a go at anybody here. After all, I’m reading (and loving) this blog as a microbiologist who is trying to learn more about the medicinal chemistry involved in generating new antibiotics. My hope is I might be able to give back just a little bit.

I fear the original question betrays a certain lack of understanding of the underlying problem. Antibiotic resistance genes rarely exist in isolation. Any given mobile genetic element (eg plasmid, ‘phage, etc) will most likely have half a dozen or more such resistance genes. While industrial farmers may not be using antibiotics used in humans they may well be unwittingly propagating genes coding for resistance to clinically relevant drugs.
While I’m sure there are some examples of direct transmission from farm animals to humans this isn’t really the main concern. Having said that, the documentary “Resistance” documents one case of a woman working in an industrial pork facility who’s husband will require life-long care due a nasty MRSA strain she brought home from work.
As most meat is cooked prior to consumption by humans, most bacterial contamination won’t pose much of a public health risk. I’m not aware of many bacteria that are capable of penetrating muscle to a significant extent in the time frame that is relevant to meat sales. This means that even a rare steak that has been at least seared should be fine.
What is of greater concern is what is done with the animal waste from such facilities. I don’t think that anybody would try and argue that such waste is abiotic and as such nearly all bacteria present will be resistant to the antibiotics used (and more than likely carrying other resistance genes along with them). I personally remember a talk at a mobile genetic element conference describing the transmission of such antibiotic resistance between bacterial species within the soil of a field over a period of 2 years. If such a field were used to grow produce that is not normally cooked (anybody remember Listeria in melons?) then it doesn’t take much imagination to see that adding antibiotic resistance to the mix would be A Very Bad Thing (TM).
I’m not trying to have a go at anybody here. After all, I’m reading (and loving) this blog as a microbiologist who is trying to learn more about the medicinal chemistry involved in generating new antibiotics. My hope is I might be able to give back just a little bit.

Oooops. Sorry about the double post. Must have hit the post button twice or something.

Making Healthy Swaps to Anti-Inflammatory Foods

Yikes. It sounds like every food you’ve ever enjoyed is out to get you. But that is not the case.

Choosing food products over real foods has never been a good idea .

Right now, there are healthier alternatives to choose from when you go shopping.

Don’t worry if you feel you could never give up cookies or sodas. Getting rid of the cravings for these inflammatory foods will take time because they’re designed to make you addicted.

However, as you eat more real food and less processed foods, those cravings will subside and you’ll begin to crave the flavor of real, healthy foods.

Choose healthy, keto-friendly nuts over chips and crackers. Make delicious Macadamia Nut Fat Bombs to satisfy your sweet tooth. Choose unsweetened coffee, tea, and water over soda, sports drinks, and cocktails.

Add more leafy greens, fatty fish, and other healthy foods to your diet to help fight inflammation.

The major key to success here is to bring healthy foods into your home and focus on making a healthy choice with every meal and snack. Thinking of it one meal at a time instead of a giant lifestyle change will make you more likely to succeed while decreasing your likelihood of developing several serious inflammatory diseases.


  1. Vudot

    Author, are you by any chance from Moscow?

  2. Daegal

    gut! I often invent something like this myself ...

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