Antibiotic Misuse and Resistance: How it Affects Your Family

A handful of colorful pills on a silver tray

Antibiotics play an important role in our society. They treat bacterial infections, and ensure they don’t spread or cause further complications. Antibiotics like penicillin, amoxicillin, doxycycline and more are life saving, but can also cause more harm than good when not used correctly.

What is Antibiotic Misuse?

Antibiotic misuse refers to the incorrect use of antibiotics–whether that be overuse, unnecessary use, or use as a result of a misdiagnosis. Antibiotic misuse can cause antibiotic resistance, adverse side effects and it can destroy your microbiome.

What are the Consequences of Antibiotic Misuse?

Antibiotic Resistance

According to the Centers for Disease Control and Prevention, at least 2 million people per year get an antibiotic-resistant infection, resulting in at least 23,000 deaths [1]. The CDC calls antibiotic resistance “one of the biggest public health challenges of our time.”

Antibiotic resistance evolves through natural selection as bacteria randomly mutate in the microbiome. The resistant bacteria can then transfer these genes to each other horizontally by plasmid exchange. The overuse of antibiotics speeds up this process, as bacteria mutate to resist the antibiotics after they’ve been repeatedly exposed. The bacteria that are resistant will then outlive the bacteria that aren’t, and will go on to reproduce, thus giving those genes to their offspring [2].

This problem is exacerbated by the fact that the creation of new antibiotics has declined rapidly over the past thirty years. Therefore, when bacteria become antibiotic-resistant, there’s no alternative antibiotic to help treat the illness. This decline can largely be attributed to pharmaceutical companies. The return on investment for developing new antibiotics is less than developing drugs for chronic conditions, because antibiotics are relatively cheap and curative. For those companies who do develop new antibiotics, getting through regulatory barriers can be a challenge [3].

Antibiotic Side Effects

Although antibiotics cure an infection, they can cause adverse side effects such as “allergic reactions, end-organ toxic effects, subsequent infection with antibiotic-resistant organisms, and Clostridium difficile infections (CDIs)” [4]. One study showed that out of 1,488 patients who were prescribed antibiotics after a hospital visit, 20% had adverse side effects. Furthermore, for every ten days of continual antibiotic use, the risk for experiencing a side effect increased by 3%.

Adverse side effects cause nearly 70,000 emergency room visits for children each year. Most cases were due to an allergic reaction and children age two and younger were most likely to experience side effects [5]. Being cognizant about the risks antibiotics can have for children, and questioning whether an antibiotic is necessary may reduce the number of cases each year.

Antibiotics Disrupt the Gut Microbiome

An understanding of the gut microbiome (a complex community of microorganisms) has increased dramatically in the past decade, since the NIH Human Microbiome Project was founded in 2009. The gut microbiome plays a crucial role in digestion and getting nutrients into your body. Since then, the effect of antibiotics on the gut microbiome has been studied, identifying important links between antibiotics and the gut microbiome. [6]. One study showed that even a short course of antibiotics can disrupt the gut microbiome for up to four years [7].

When the microbiome comes in contact with antibiotics, they attack the good and bad bacteria, leaving your microbiome defenseless and unable to do its job properly. The devastation is increased with broad-spectrum antibiotics, or antibiotics that are discharged through bile or the gut [6]. This can cause a host of adverse effects, like the depletion of vitamin-producing bacteria, changes in the proportion of metabolic functions, and an increase in inappropriate immune functions, to name a few [8]. Furthermore, in recent years, research has found there’s an undeniable link between gut and brain function, called the gut-brain axis. When the gut microbiota is off, the communication with the brain is off, thus causing memory problems, anxiety, depression and other brain-related problems [9].

Antibiotics’ effect on the gut is detrimental for healthy individuals, but life-threatening for severely ill patients. When the gut is worn down by antibiotics, gut permeability is high, allowing microorganisms and bacteria to travel through the bloodstream and cross the gut barrier easily. Once the gut is defenseless, colonization of resistant bacteria and microorganisms becomes rapid [6].

With research on antibiotics’ effect on the microbiome, scientists are discovering better ways to protect your gut microbiome and heal disease and infection. Some tactics include restoring the microbiota, the use of probiotics, and fecal microbiota transplants [8].

Where We Come in Contact With Antibiotics


A recent study of 19.2 million Americans found that almost one-fourth of antibiotic prescriptions were inappropriate [10]. The study also discovered that most of these unnecessary antibiotics are prescribed for viral conditions, like the common cold, bronchitis and sinus infections, which don’t react to antibiotics. Furthermore, 50% of antibiotic prescribing to adults and 75% of antibiotic prescribing to children are for viral acute respiratory infections other than pneumonia, despite the fact that evidence shows antibiotics don’t work for these types of infections [11].

Medical practitioners prescribe unnecessary antibiotics for many reasons, such as [12]:

Pressure from the patient

Patients may expect a prescription for an antibiotic to cure their ailment, or the doctor might think they are expecting one.

Time constraints

Appointments are only so long, and some may not be long enough to correctly diagnose a patient.

Decision fatigue

Doctors are seeing patients all day, every day. This fatigue can lead to poor decision making and more antibiotic prescriptions [13].

Uncertain diagnoses

The symptoms of viral infections such as the common cold, non-bacterial sore throat and high fever can be similar to those of bacterial infections. Doctors will prescribe antibiotics in this situation just to cover their bases.

Assuming other doctors are responsible

Even if doctors are over prescribing antibiotics, they don’t believe that they’re the problem, and often attribute it to other doctors or specialties [14].

Defensive Measures

The medical malpractice system holds doctors accountable, but it also causes “defensive medicine,” in which doctors will prescribe too many health measures, including antibiotics to avoid getting sued. [15]


Antibiotic resistant genes (ARGs) are able to travel from bacteria to bacteria and sometimes bacteria to the environment. A recent study focusing on 30 ARG sub-types resistant to seven classes of antibiotics showed that ARGs can in fact be airborne. The study focused on 19 urban cities, including Beijing, San Francisco and Paris, and the diversity and levels of ARGs varied, but overall, the study found that they were present in the air, and humans can breathe in the antibiotic resistant genes [16].


According to a study by the Center for Science in the Public Interest, 55 antibiotic-resistant foodborne outbreaks were recorded from 1973 to 2011 [17]. A majority (31 of 55) of these outbreaks were traced back to dairy products, poultry and ground beef and the same amount of outbreaks were caused by pathogens that were resistant to five or more antibiotics. The repeated and overuse of antibiotics cause livestock to become immune to antibiotics, natural selection has claimed the “superbug” gene, thus passing the antibiotic-resistant gene to offspring, through animal byproducts, its meat, and feces [18].

Over the course of the study, antibiotics were used for growth promotion, to treat clinical disease and to prevent and control common disease [19]. Since then, the FDA has created and implemented new outlines on use of antibiotics in livestock [19]. In 2017, they implemented a ban on antibiotics used for growth promotion and did an audit of drug applications. It’s now required for farms to get veterinary prescriptions to use antibiotics on livestock. However, some feedlot veterinarians support giving antibiotics in feed and will write the prescriptions without question [20]. While antibiotic sales have decreased dramatically since the growth promotion ban went into effect, there’s still a long way to go. {21}

Seafood is also affected by antibiotics. Farmed fish are given antibiotics to fight infections, and can be introduced to them through fish meal (fish food made of fish) [22,23]. One study of shrimp, salmon, catfish, trout, tilapia, and swai from 11 different countries found five of the 47 antibiotics tested [24]. Another study of Norwegian salmon has shown a 95% decrease in antibiotic use in the last 20 years [25].The use of fishmeal is being replaced with cheaper alternative protein sources, such as soybean meal [25]. All of these improvements are steps in the right direction, but it’s still important to be cognizant of where your seafood is sourced.


Many pharmaceutical companies have placed their manufacturing facilities in Bangladesh, China, India and Pakistan, due to the low cost of labor and land. Unfortunately, The wastewater in these areas contains antibiotics. For example, Patancheru, an industrial zone home to a number of pharmaceutical manufacturers, discharges 400,000 gallons of wastewater per day. Researchers have tested the nearby city, Hyderabad’s water, and found amounts of antibiotics, sometimes more potent than the amount in patient’s blood [26].

In New Mexico, a study tested samples of wastewater from hospitals, residential facilities, and more, for 11 antibiotics. Fifty-eight percent of the samples showed a presence of one antibiotic, and 25% had three or more. Four out of five hospitals had at least one antibiotic present, and three had four or more. Antibiotics were found in retirement community and assisted living effluent (liquid waste or sewage discharged into a body of water), but not in college dormitory effluent [27]. Even though discharge gets treated in wastewater treatment plants before it’s flushed into a body of water, it’s been proven that it doesn’t get rid of the ARGs [28]. According to the EPA, treated wastewater “is released into local waterways where it’s used again for any number of purposes, such as supplying drinking water, irrigating crops, and sustaining aquatic life” [29].

These ARGs and ARBs can end up in your drinking water, studies show. One found small amounts of antibiotic-resistant genes and bacteria in drinking water from several cities in Michigan and Ohio [30]. Just one ARB can enter your system and multiply, creating more [31].


Feces contain a significant amount of bacteria, which can be transferred in many different ways. Manure from animals can spread antibiotics and antibiotic-resistant genes. Fifty-eight percent of veterinary antibiotics are excreted, and more than half end up in our soil. Manure applications change the soil resistome and horizontal gene transfer spreads the ARGs in the soil [32,33].

There’s a high risk of spreading ARBs through feces in hospitals, especially in the ICU, and long-term care facilities [6]. Bacteria can be found in high concentrations in the rectum, and can be spread through the hands. Poor hand hygiene and lax infection control methods can help spread the bacteria. Overall, it’s important to practice good hygiene, even outside of hospital environments.

How You Can Protect Your Family

Focus on Prevention

Boost your immune system by eating healthy foods, taking appropriate supplements, and getting enough water. Make a habit of washing your hands often, including after you go to the bathroom, as well as after touching items that other people have touched. You don’t know where others’ hands have been!

Eat Safe, Sustainably-Sourced Meat

When buying meat, be cognizant about where it’s sourced and how it’s treated. Look for words like “American Grassfed Certified,” “Certified Organic” and “Certified Humane.” Some companies use buzzwords like “Cage Free,” “Kosher” and “Natural” on their packaging to trick consumers into thinking they’re safe, but those labels are meaningless. For more information, read this guide by the Animal Welfare Institute.

For seafood, different regions have different safe options, because of the distance they are to the source. Seafood Watch has state-specific guides to which seafood choices are: “Best Choices,” “Good Alternatives” and ones you should “Avoid.”

If it sounds like a lot of work to study your options, there are programs out there that will do the work for you! Butcher Box is a subscription service that sends you high-quality meat that checks all the boxes. You can also find sustainably-sourced seafood and meat boxes on Thrive Market. Also, consider looking for a local organic or beyond-organic farmer in your area who uses optimal farming practices. You can buy a quarter or half of a cow and have a great stock of frozen organic, antibiotic and herbicide/pesticide free meat. If you’re in a pinch and need to pick up something quick, your local health foods store should carry sustainably-sourced options and the employee behind the meat counter is there to help!

Also, handle and cook meat according to the FDA’s guidelines. Mishandling or undercooking meat can allow bacteria into your system by accident.

Get a water filter

Water filters can remove a number of harmful contaminants from your water, including pharmaceuticals, viruses and microorganisms. We recommend high quality carbon block water filters like Berkey, or high quality reverse osmosis filters (if using RO water, make sure to add trace minerals back into the water by using drops like Concentrace).  Check out’s water filter buying guide to help you choose a water filter that is best for you.

Take probiotics

The Word Health Organization defines probiotics as, “live microorganisms which when administered in adequate amounts confer a health benefit on the host.” There are different types of probiotics, which include certain yeasts, bacilli and microorganisms [6]. Probiotics can help the gastrointestinal system maintain bacterial balance, which provides a host of benefits, including the treatment or prevention of diarrhea, irritable bowel syndrome, and more [34]. Probiotics can also prevent antibiotic-associated diarrhea, in the event that antibiotics are needed [35]. We recommend taking a probiotic every day, but talk to your functional healthcare provider about which probiotic they recommend for you.

Make sure antibiotics are necessary

If you end up getting an infection, antibiotics may be necessary. Do some research and talk to your doctor about the pros and cons of going on antibiotics and if it’s an option to opt out. If you have a viral infection, such as the common cold, acute bronchitis, or the flu, don’t take antibiotics, as they won’t have an effect. Your best bet is to just drink a lot of fluids and wait for your immune system to get rid of the infection, which could take 7-10 days.

Being cognizant of the effects of antibiotics and where you can come in contact with them is the only way to stay vigilant. While totally ridding your family of antibiotic exposure is probably not possible, reducing the exposure will help your immune system and gut remain strong enough to fight off infections that come your way. And when antibiotics are necessary, they’ll have a greater effect on your body.


  1. Biggest Threats and Data
  2. Antibiotic Resistance
  3. The Antibiotic Resistance Crisis
  4. Association with Adverse Events
  5. Association of Adverse Events With Antibiotic Use in Hospitalized Patients
  6. Gut is the epicentre of antibiotic resistance
  7. Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiome
  8. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation
  9. The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems
  10. Appropriateness of outpatient antibiotic prescribing among privately insured US patients: ICD-10-CM based cross sectional study
  11. Antibiotics for Acute Respiratory Infections: Shrinking Benefit, Increasing Risk, and the Irrelevance of Antimicrobial Resistance
  12. Why Doctors Prescribe Antibiotics—Even When They Shouldn’t
  13. Time of Day and the Decision to Prescribe Antibiotics
  14. Prescriber and dispenser perceptions about antibiotic use in acute uncomplicated childhood diarrhea and upper respiratory tract infection in New Delhi: Qualitative study
  15. Do Doctors Prescribe Antibiotics Out of Fear of Malpractice?
  16. Global Survey of Antibiotic Resistance Genes in Air
  17. Antibiotic Resistance in Foodborne Pathogens
  18. A Review of Antibiotic Use in Food Animals: Perspective, Policy, and Potential
  19. FDA Announces Implementation of GFI #213, Outlines Continuing Efforts to Address Antimicrobial Resistance
  20. At Hamburger Central, Antibiotics for Cattle That Aren’t Sick
  21. Antibiotics Sales for Farm Animals Dip Dramatically Following FDA Growth Promotion Ban
  22. Antibiotic resistance could spread through feed at fish farms
  23. Fishmeal Application Induces Antibiotic Resistance Gene Propagation in Mariculture Sediment
  24. Reconnaissance of 47 antibiotics and associated microbial risks in seafood sold in the United States
  25. Environmental Performance of Marine Net-Pen Aquaculture in the United States
  26. Who is Responsible for Antibiotic Resistance?
  27. Occurrence of antibiotics in hospital, residential, and dairy effluent, municipal wastewater, and the Rio Grande in New Mexico
  28. Prevalence of antibiotics and antibiotic resistance genes in a wastewater effluent-receiving river in the Netherlands
  29. Where does all the dirty water go?
  30. Prevalence of Antibiotic Resistance in Drinking Water Treatment and Distribution Systems
  31. Antibiotic Resistance Questions and Answers
  32. Antibiotics and antibiotic resistance from animal manures to soil: a review
  33. Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil
  34. Health benefits of taking probiotics
  35. Probiotics for the Prevention of Antibiotic-Associated Diarrhea in Outpatients—A Systematic Review and Meta-Analysis