The bug can usually be treated with a different type of antibiotic but it is sometimes referred to as a ‘superbug’ due to its resistance to treatment in some instances.
Nice said that clinical trials have shown that FMT treatment is significantly better than antibiotics alone at resolving a stubborn C.diff infection.
It said that it had been presented with evidence that the treatment could save the NHS thousands of pounds.
Meanwhile patients may need to take fewer antibiotics and have reported a better quality of life after treatment, it added.
FMT swallowed in a pill or it can be delivered through a tube inserted directly into the stomach through the nose, or alternatively be deposited directly into the colon through a tube.
Mark Chapman, interim director of Medical Technology at NICE, said: “There is currently a need for an effective treatment of C.diff in people who have had two or more rounds of antibiotics.
“Our committee’s recommendation of this innovative treatment will provide another tool for health professionals to use in the fight against this infection, while at the same time balancing the need to offer the best care with value for money.
“Use of this treatment will also help reduce the reliance on antibiotics and in turn reduce the chances of antimicrobial resistance, which supports NICE’s guidance on good antimicrobial stewardship.”
Nice said that it made its decision after reviewing evidence from five trials of 274 adults. The data showed that more C.diff infections were resolved with FMT than antibiotic treatment in four of the trials and there was no difference in the other. It said the data showed that the treatment can resolve up to 94% of infections.
FMT can be considerably cheaper than antibiotics if given as an oral capsule – saving more than £8,000; it can save hundreds of pounds if given as a colonoscopy but it is more expensive when given as an enema.
Nice has estimated that 450 to 500 people in England could be treated using FMT for multiple recurrences of C.diff infections each year.
It said that a strict donor screening programme should be in place and that treatments should be manufactured in accordance with human medicine regulations.