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Understand  –  Why should I care?


One reason to avoid taking unnecessary antibiotics is that antibiotic treatment puts you at risk for additional infections - so called superinfections.

Such infections are unrelated to the first infection for which the antibiotic was originally taken. Instead it is the antibiotic treatment that makes the second infection possible because it disturbs the normal microbiome in the body. Imbalance in the microbiome, dysbiosis, can last for several months, even up to several years following treatment (reviewed in).

When the microbiome is reduced, it provides an opportunity for pathogenic microbes to grow and potentially cause a new infection. The microbes can come from a person’s own microbiome or from the outside environment. The risk for superinfections is higher when using broad-spectrum antibiotics, as compared to narrow-spectrum antibiotics affecting a smaller number of bacteria. Further, long duration of antibiotic treatment, immunosuppression and poor health status of the patient increase the risk. Superinfections range from mild infections that do not need further treatment to very severe infections that can lead to death

Diseases associated with antibiotic use, examples:

  • Clostridioides difficile can cause severe, even deadly, diarrhea. As an example, it is one of the most common hospital acquired infections in the US, where around 250,000 patients get infected every year, and 14,000 patients die. C. difficile infection is strongly associated with antibiotic treatment, especially antibiotics that kills many different types of bacteria (for example fluoroquinolones and extended-spectrum cephalosporins). Also, C. difficile can be resistant to antibiotics commonly used in health care settings. This allows the bacteria to thrive in health care facilities where antibiotic usage is high.
  • A common complication following antibiotic treatment is a fungal infection, for example, oral or vaginal thrush caused by different types of the fungal yeast Candida. Yeast can often be found in small numbers in and on the body, but antibiotic treatment disturbs the balance between different microbes and paves the way for the yeast to increase in numbers. In some cases, fungal infections can spread to the blood and be very severe.
  • Several studies have found a link between antibiotic use and increased risk of urinary tract infections. For example, women treated with antibiotics were 2 to 5 times more likely to contract a urinary tract infection than untreated women.
  • Preliminary studies of the effects of antibiotics on the human microbiome link several severe diseases/conditions to antibiotic exposure at different stages in life, including obesity.

Selected Resources

Resource Description
The human microbiome and what we do to it Video that describes the role of the bacteria normally living in our bodies and the negative consequences antibiotic treatment can have (5 min).
Rapid risk assessment: Candida auris in healthcare settings – Europe Document. Example of a risk assessment: The yeast Candida auris was first described in 2009 and has since then been associated with invasive infections and outbreaks in healthcare settings across the world. Patients who developed infection had frequently been treated with broad-spectrum antibiotics.
Why Would Anyone Get a Fecal Transplant? Watch a Brother and Sister Explain Video and article that describe the case of a young woman who became ill from Clostridium difficile after being treated with antibiotics for a dangerous antibiotic-resistant MRSA infection. It further describes what is at stake when getting C. difficile and the use of an experimental new method to treat it: Fecal transplants. (Video 12.5 min)
Clostridium difficile Infection Information for Patients Fact sheet. The majority of the cases of C. difficile infection develop in patients taking antibiotics. Learn more about C. difficile infections in this material developed by the Centers for Disease Control and Prevention (CDC).
Centers for Disease Control and Prevention - CDC. Antibiotic resistance threats in the United States, 2013 [Internet]. CDC; 2013 [cited 2015 Jan 9]. Available from:
European Centre for Disease Prevention and Control. Rapid risk assessment: Candida auris in healthcare settings – Europe [Internet]. 2018 [cited 2018 Dec 8]. Available from:
Mayer FL, Wilson D, Hube B. Candida albicans pathogenicity mechanisms. Virulence [Internet]. 2013 Feb 15;4(2):119–28. Available from:
Takahashi S, Uehara T, Shima M, Takasugi S, Hashimoto K, Itoh N. Septic pulmonary embolism caused by Candida albicans after treatment for urinary multidrug-resistant Pseudomonas aeruginosa. J Infect Chemother [Internet]. 2008 Dec;14(6):436–8. Available from:
Modi SR, Collins JJ, Relman DA. Antibiotics and the gut microbiota. J Clin Invest [Internet]. 2014 Oct;124(10):4212–8. Available from:
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Centers for Disease Control and Prevention - CDC. Clostridium difficile Infection Information for Patients [Internet]. [cited 2015 Aug 24]. Available from:
Phenomena: Germination, McKenna M. Why Would Anyone Get a Fecal Transplant? Watch a Brother and Sister Explain [Internet]. 2015 [cited 2015 Aug 19]. Available from:
Smith HS, Hughes JP, Hooton TM, Roberts P, Scholes D, Stergachis A, et al. Antecedent antimicrobial use increases the risk of uncomplicated cystitis in young women. Clin Infect Dis [Internet]. 1997 Jul;25(1):63–8. Available from:
Bonfrate L, Tack J, Grattagliano I, Cuomo R, Portincasa P. Microbiota in health and irritable bowel syndrome: current knowledge, perspectives and therapeutic options. Scandinavian Journal of Gastroenterology [Internet]. 2013 [cited 2014 Nov 11];48(9):995–1009. Available from:
The human microbiome and what we do to it [Internet]. 2012 [cited 2014 Nov 21]. Available from:
Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet [Internet]. 2012 Apr;13(4):260–70. Available from: