132 Chapter 6 Abstract The gut microbiome is now considered an organ unto itself, essential in priming the immune system. The commensal organisms responsible for the framework of the gut microbiome are valuable in the protection against disease and various physiological tasks. Critical illness and the associated interventions have a detrimental impact on the microbiome. While antimicrobials are one of the fundamental and often life-saving modalities in septic patients, they can also pave the way for subsequent harm because of the resulting damage to the gut microbiome. Attributable to many of the nonspecific signs and symptoms of sepsis, the balance between the overuse of antimicrobials and the clinical need in these situations is often difficult to delineate. Given the potency of antimicrobials utilized to treat septic patients, the effects on the gut microbiome are often rapid and long-lasting, where a full recovery is never observed in some cases. The overgrowth of opportunistic pathogens is of significant concern as they can lead to infections that become increasingly difficult to treat. Continued research to understand the disturbances within the gut microbiome of critically ill patients and their outcomes is essential to potentially help develop future therapies to circumvent or restore the microbiome. In this review, we discuss the effect of sepsis and the antimicrobials used as empiric treatment on the gut microbiota.
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