Prescribed collateral damage


I want to start this post by saying that I would not want to live in a world without effective antibiotics. Countless lives have been saved because of these miraculous drugs and modern medicine as we know it couldn’t function without them. Most surgeries that we take for granted couldn’t be performed without them either.

So please don’t take this post as an excuse to avoid antibiotic treatment if you need it. When you weigh having potentially disturbed gut flora due to antibiotic use or extinction from not treating a deadly infection, I think you would agree that the former outcome is preferable to the latter.

There’s no doubt that antibiotics have been over prescribed and still are. As a kid growing up in the 60’s, it wasn’t unusual to get a penicillin shot for most visits to the doctor, whether you needed it or not. The belief then was what harm could come of it? Because of this, a whole generation was raised believing that if you visited your doctor and didn’t leave with a prescription for an antibiotic there was something wrong with your doctor or your acting skills.

Today’s doctor knows that there are real disadvantages to over prescribing antibiotics. This particular realization, however, has escaped many in the public who harangue their physician for an antibiotic prescription even if medically unnecessary.

That said, I’m still not convinced that everyone in the medical community fully understands the ramifications of prescribing antibiotics. Yes, many have been taught that rampant antibiotic use leads to resistant strains and it’s this reason that likely prevents them from writing out that prescription. But many doctors remain ignorant of the potentially long-term impacts on their patient’s health via the mechanism of disturbed gut flora. For many in the medical community, this was considered part of an “alternative medicine” viewpoint and rejected out of hand as so much “woo”. (1)

In this post I want to concentrate on is what effect antibiotics have on our commensal or friendly gut flora. Therefore, I won’t be covering the direct toxic effects of various antibiotics, possible allergic reactions or their interaction with other drugs and food. While those issues are important, they are best discussed with your physician or pharmacist when prescribed a course of antibiotics.

As those who have read my post The many vital functions of healthy gut flora know, our beneficial gut flora are involved in a whole host of physiological processes—nutrition, gut barrier function, vitamin production, immune system regulation, protection against pathogenic organisms, etc. Accordingly, any disturbance of this microbiota has the potential of negatively impacting these functions.

With recent advances in bacterial DNA sequencing, we now have a better understanding of how antibiotics impact commensal gut flora. So what does the research show?

In early infancy, antibiotic use has been associated with decreased populations of colonic Bifidobacterium and Bacteroides and significant increases in pathogenic Enterobacteriaceae. (2) (3). Enterobacteriaceae is a large family of gram-negative bacteria that includes the well-known pathogens Salmonella, E.coli, Yersinia, Klebsiella and Shigella.

A recent study found that children who had been exposed to antibiotics before five years of age tended to weigh more as they grew older than children who had no antibiotic treatment. While this study only showed an association (remember, an association is never proof of causation) it’s intriguing given the correlation seen in adults between disordered gut flora and obesity.

In adults, a course of ciprofloxacin (Cipro) had marked effects on host gut flora within three days of ciprofloxacin initiation, but the good news is that commensal gut flora communities were pretty resilient after the antibiotic course ended. (4) However, after two five-day courses of oral ciprofloxacin over a ten-month period, an altered gut flora population was established that was different from what existed prior to treatment. (5)

A study that tracked the effects of a short course of metronidazole (Flagyl) and clarithromycin (Biaxin) found disturbed effects in both commensal oral and gut communities for up to four years after treatment. (6)

These effects can have serious consequences for immune-compromised hospital patients. Bloodstream infections by resistant Enterococcus was shown to have been preceded by colonization of the digestive tract with this pathogen as a result of earlier antibiotic treatment. (7) Likewise Clostridium infection is closely related to disturbed gut flora caused by antibiotic usage. (8) (9)

Apart from disturbing gut flora populations, antibiotic use is also implicated in the promotion of antibiotic-resistant pathogenic organisms within patients thus complicating any future treatment. (10)

One study showed MRSA infections were 1.8 times higher in people with recent antibiotic exposure. (11) In Taiwanese children, rates of nasal MRSA were higher in children who had taken antibiotics within the last 12 months. (12).

In a French study tracing 3,507 children ages 6-24 months most seeing the doctor for ear infections, the use of antibiotics within the last three months was associated with resistant Pneumococci. (13)

The message here is that while antibiotics are life-saving drugs, they should only be used when absolutely necessary. If your doctor tells you that what you suffer from is viral or fungal in origin, don’t pester him or her for an antibiotic. Apart from any placebo effect you may experience, it’s not going to cure what you have (cold, flu) and will harm your gut flora and you.

Even in cases where there is a bacterial infection, if your doctor suggests waiting to see if it clears up on its own, please follow their advice.

This holds true for many parents who are quick to ask for an antibiotic for their kids. Kids are particularly susceptible to the long-term health consequences of disordered gut flora, especially when exposed before the age of 5. Think twice about asking your doctor to prescribe antibiotics for your child if the condition does not warrant it.

If you are taking antibiotics, I strongly recommend you take both a probiotic and prebiotic during your course. Just remember to take them at least an hour after or before your scheduled antibiotic dose and continue taking them after your prescription has ended.

Antibiotics are powerful and life-saving drugs, but they should not be taken without assessing the potential risks to your microbiome. Weigh the pros and cons of any antibiotic treatment with your doctor to make an informed decision that’s right for you.


  1. Stewardson A. J. Huttner B., Harbarth S., et al., 2011.  At least it won’t hurt: the personal risks of antibiotic exposure. Current Opinion in Pharmacology, 11:446-452.
  2. Penders J., Thijs C., Vink C., et al., 2006. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118:511-521.
  3. Hussey S., Wall R., Gruffman E., et al., 2011. Parenteral antibiotics reduce Bifidobacteria colonization and diversity in neonates. International Journal of Microbiology doi: 10.1155/2011/130574.
  4. Dethlefsen L., Huse S., Sogin M.L., Relman D.A., 2008. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6:e280.
  5. Dethlefsen L., Relman D.A., 2011. Incomplete recovery and
 individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proceedings of the National Academy of Sciences U S A 108(Suppl. 1):4554-4561.
  6. Jakobsson H.E., Jernberg C., Andersson A.F., et al., 2010. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One 2010, 5:e9836.
  7. Ubeda C., Taur Y., Jenq R.R., et al., 2010. Vancomycin-resistant enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. Journal of Clinical Investigation 120:4332-4341.
  8. Manges A.R., Labbe A., Loo V.G., et al., 2010. Comparative metagenomic study of alterations to the intestinal microbiota and risk of nosocomial Clostridium difficile-associated disease. Journal of Infectious Disease  202:1877-1884.
  9. Rousseau C., Levenez F., Fouqueray C., et al., 2011. Clostridium difficile colonization in early infancy is accompanied by changes in intestinal microbiota composition. Journal of Clinical Microbiology 49:858-865.
  10. Costelloe C., Metcalfe C., Lovering A., Mant D., Hay A.D., 2010. Effect of antibiotic prescribing in primary care on antimicrobial resistance in individual patients: systematic review and meta-analysis. British Medical Journal 340:c2096.
  11. Tacconelli E., De Angelis G., Cataldo M.A., Pozzi E., Cauda R., 2008. Does antibiotic exposure increase the risk of methicillin-resistant Staphylococcus aureus (MRSA) isolation? A systematic review and meta-analysis. Journal of Antimicrobial Chemotherapy 61:26-38.
  12. Miller M.B., Weber D.J., Goodrich J.S., et al., 2011. Prevalence and risk factor analysis for methicillin-resistant Staphylococcus aureus nasal colonization in children attending child care centers. Journal of Clinical Microbiology 49:1041- 1047.
  13. Cohen R., Levy C., Bonnet E., et al., 2011. Risk factors for serotype 19A carriage after introduction of 7-valent pneumococcal vaccination. BMC Infectious Diseases 11:95.


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