Impact-2

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Bacteriophage, Multi-Drug Resistant Escherichia coli and MicroRNA dynamics in the gut microbiome of critically ill patients

Aim

We plan to use faeces obtained from ICU patients to track the E. coli strains and bacteriophages that colonise the intestinal tract during ICU stays. We will record previous exposures to antimicrobials prior to the ICU admission to determine the impact this has on the colonisation process. We will perform longitudinal studies on the faeces of patients who are treated in the ICU for 3 days or more (the stage at which becoming ESBL positive would be considered a hospital acquired event).

We will also collect salivary samples at the same time of stool sampling to analyse whether changes in the gut microbiome are reflected in the salivary miRNA profile.

Background/method

Faced with the aftermath of end-stage organ failure, burns, trauma, organ transplant or chemotherapy, long-stay patients on the adult intensive care unit (ICU) are among the sickest and most vulnerable in the hospital. Once in the ICU, they are subjected to numerous physiological and pharmacological assaults including: intubation, immobility and prone position, enteral feeding, gastrointestinal reflux, suppression of gastric acidity and administration of inotropes, opioids and antibiotics.

In health, the human gut is home to a rich and stable collection of microbes and their associated genes and genomes, the human microbiome. However, in the long-stay ICU patient, the above assaults trigger dysbiosis – a disruption in microbial communities from the mouth to the anus, with effects on the abundance, diversity and transfer of organisms and genes associated with antibiotic resistance. Dysbiosis in the critically ill patient often results in a vulnerable, radically simplified, ultra-low-diversity gut microbiome, dominated by one, or just a few, usually drug-resistant microorganisms. For example, researchers in the US have shown that, in patients undergoing stem cell transplants, domination of the gut microbiome by pathogens such as enterococci and the Enterobacteriaceae (E. coli and its derivatives) drastically increases the risk of bloodstream infection and death. Similarly, a study from the University of Chicago found ultra-low-diversity gut microbial communities (just one to four taxa) in around a third of patients on their ICU.

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