Precision Modulation of Gut Microbiome Enteropathogen Colonization in Critical Illness (MicroMod)

Enteropathogen colonization of the gut microbiome in critically ill patients is associated with adverse outcomes. Observational studies have consistently reported that gut colonization with enteropathogens including Enterobacterales (e.g. Klebsiella spp., E. coli, Enterobacter spp., and others) and Enterococcus spp. (e.g. E. faecium) is associated with increased risks of hospital-acquired infections, death, organ dysfunction severity, prolongation of life support, and hospitalization. Mechanistically, gut enteropathogen colonization has been shown to contribute to adverse outcomes like hospital-acquired infections (HAI) through the gut's ability to serve as both a reservoir of HAI pathogens, as well as through pathological microbiome-immune interactions that suppress immune defences against HAI. Consequently, therapeutic strategies to reduce gut enteropathogen colonization have been identified as potentially impactful interventions to reduce hospital-acquired infections and adverse outcomes in patients with critical illness.

Prior clinical trials have employed diverse strategies to modulate the gut microbiome with the objective of reducing adverse outcomes, including large randomized controlled trials of probiotics, or opposing strategies such as digestive decontamination. However, outcomes have been heterogeneous owing to a number of crucial methodological limitations of both the interventions as well as study designs. First, despite proposed mechanisms involving microbiome modulation, none of the important trials have actually analyzed the microbiome to confirm whether their intervention favourably modified the microbiome (i.e. lack of confirmation of biological plausibility). Next, investigations of probiotics have suffered from a lack of rationalized designed for their intended mechanism. For example, the large RCT of probiotics in critically ill patients utilized Lactobacillus rhamnosus GG, yet the choice of this particular probiotic was not based on any prior mechanistic data demonstrating that this species could engraft in the ICU microbiome, nor whether it has the potential to displace enteropathogens from the gut. In fact, very few probiotic trials have ever even determined whether the probiotic strain could engraft into the ICU gut microbiome, nor have any trials determined whether interventions successfully decolonized enteropathogens.

To address these limitations, we will conduct a randomized controlled trial to assess both the safety and biological efficacy (microbiome engraftment and enteropathogen decolonization) of the synbiotic medical nutrition product in critically ill patients. In this phase 1b randomized controlled trial, 64 critically ill patients requiring mechanical ventilation will be randomly assigned to a 21-day course of enteral synbiotic or control (open label). Primary outcome will be safety and biological efficacy of synbiotic engraftment in the gut, with secondary outcome of gut enteropathogen colonization.