Critically ill lose microbial gut diversity as pathogens dominate, study finds

By Will Chu

- Last updated on GMT

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©iStock/

Related tags: ICU, Hospital, Pathogen

Long-term hospital patients receiving intensive care lose gut microbial diversity as researchers observe how potentially harmful microbes overwhelm the healthy gut microbiota.

Research led by the Quadram Institute in the UK pave the way for a rethink into how hospital care is administered with precise patient-specific interventions that protect the gut microbiota mentioned.

These measures include enhanced infection control, tailored use of microbiota-sparing antibiotics, oral administration of antibiotic-absorbing charcoal or of a beta-lactamase.

According to the study, 16 of the 24 patients enrolled showed a marked reduction in microbial diversity at some stage during their stay in the Intensive Care Unit (ICU).

 “The gut microbiome performs many important and diverse roles and many of these roles can be lost if microbial diversity is lost,”​ says lead researcher, professor Mark Pallen from the Quadram Institute.

“This is likely to impact on nutrition, gut motility and inflammation in the bowel.”

Research suggests life-saving measures used in ICU patients may negatively impact on the gut microbiota.

These approaches include assisted ventilation, enteric feeds and a range of medications, including broad-spectrum antibiotics, proton pump inhibitors, inotropes and opioids.

In recent years, interest has grown in protecting or restoring the integrity of the gut microbiome in ICU patients, using ecological approaches such as probiotics or faecal microbiota transplants.

Shotgun sequencing

Along with the Quadram Institute, researchers from the Queen Elizabeth Hospital in Birmingham began taking faecal samples from the 24 ICU patients.

These samples underwent DNA analysis using shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses to determine which microbes were present.

Two-thirds of the patients experienced a marked drop in gut microbial diversity at some stage of their ICU stay. This was often accompanied by the absence or loss of potentially beneficial bacteria.

“We saw Enterococcus faecium most commonly and this is of concern as this is an important and common pathogen among hospitalised patients,”​ professor Pallen says.

“More worrying still, we detected evidence of spread of a single strain between three patients.”

E. faecium​ can cause severe infections, particularly at sites where medical devices – such as intravenous cannulas – have been used.

If these bacteria get into the bloodstream, they can cause fatal infection. Enterococcal ​infections are particularly difficult to treat as many species have developed resistance to multiple antibiotics.

Further findings reveal that intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity,

However, administration of other antibiotics, including piperacillin/tazobactam, failed to trigger statistically detectable changes in microbial diversity.

Patent concerns

According to professor Pallen, domination of the gut by a single potential pathogen can put other hospital patients at risk.

“When a single potentially pathogenic microbe increases substantially in biomass in this particular niche, it is then more likely to spill over into other compartments of the body, for example, the blood or the lungs, where it can cause life-threatening disease,”​ he adds.

“What’s more, it is then likely to spread to other patients, facilitating the dissemination of multi-drug resistant pathogens throughout the hospital.”

The study acknowledges some limitations, namely the sensitivity of metagenomics as a diagnostic, which the team say remains uncertain

“Is unlikely to compete with culture – in terms of costs or sensitivity – in the detection and characterisation of culturable pathogens present in low abundance,”​ the team conclude.

“In addition, in its simplest form, the ability of shotgun metagenomics to link mobile elements to the chromosomes from their host cells is poor, although proximity linkage approaches might overcome this limitation.”

Source: Microbial Genomics

Published online: doi: 10.1099/mgen.0.000293

“Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients.”

Authors: Anuradha Ravi et al

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