Antibiotic Could Disrupt Gut Flora for Up to a Year


The side effects of some antimicrobials may last far longer than originally thought.

Last month, I wrote about some of the challenges that fall under the polypharmacy umbrella. One challenge I want to highlight here is the fact that so many patients are struggling with the unwanted side effects of antimicrobials.

Many antimicrobials are associated with gastrointestinal side effects. They’re usually considered to be relatively benign consequences that patients must live with in order to ensure they don’t die from a more serious bacterial infection, but are they really benign?

Just this past month, I cared for half a dozen patients with Clostridium difficile-associated diarrhea (CDAD), all of whom had recent antimicrobial exposure. The Infectious Disease Society of America highlights recent antimicrobial use as the single most important modifiable risk factor for developing CDAD, an infection that can be fatal.1

One of the challenges health care providers face regarding the side effects of antimicrobials is quantifying the negative impact of their use and weighing it against their potential benefits.

One recent study2 compared the impact of 4 different antimicrobials from different classes (ciprofloxacin, clindamycin, amoxicillin, and minocycline) on the salivary and fecal microbiomes over a period of time. The objective was to observe the degree of disruption in the microbiome and the length of time it persisted.

The research showed that the antimicrobial impact on the salivary microbiome is relatively insignificant and very short-lived. The clinical implications of this impact is considered negligible.

On the other hand, 2 of the tested antimicrobials had a significant impact on the diversity of healthy volunteers’ gastrointestinal flora for months after a single exposure. For clindamycin, specifically, the fecal flora diversity was reduced for up to 4 months, which likely explains why it is commonly associated with the development of CDAD.

Surprisingly, the study also found that ciprofloxacin use reduced microbiome diversity for 12 months. Neither amoxicillin nor minocycline had a significant or lasting effect on fecal microbiomes.

While the clinical significance of reduced biodiversity wasn’t proven in this study, it’s still fascinating to consider that the effects of some antimicrobials may last much longer than we originally thought, and far beyond the duration of therapy.

Additional high-quality research is certainly warranted to correlate the clinical relevance of an altered microbiome and potentially determine strategies to minimize antimicrobials’ negative side effects.

It’s my hope that health care providers will be able to use this information to successfully argue against the inappropriate prescribing of antimicrobials for patients they suspect to have a viral illness, asymptomatic bacteriuria, or any other indication for which antimicrobials aren’t warranted, especially in light of this recent article that suggests many antibiotics are inappropriate in the first place.


1. Cohen SH, Gerding DN, Johnson S, et al; Society for Healthcare Epidemiology of America; Infectious Diseases Society of America. Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the society for healthcare epidemiology of America (SHEA) and the infectious diseases society of America (IDSA). Infect Control Hosp Epidemiol. 2010 May;31(5):431-455.

2. Zaura E, Brandt BW, Teixeira de Mattos MJ. Same exposure but two radically different responses to antibiotics: resilience of the salivary microbiome versus long-term Microbial shifts in feces. mBio. 2015 Nov-Dec; 6(6): e01693-e01615.

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