Antibiotic-resistant bacterial infections often occur in patients with chronic inflammatory intestinal conditions such as inflammatory bowel disease and in patients who have taken antibiotics for a long time. Gram-negative bacteria such as Enterobacteriaceae are a common cause of these infections and have few treatment options. Fecal microbiota transplants have shown promise to curb some of these infections but their composition varies between batches and they aren’t always successful. 

The findings which appear today in Nature could lead to the development of a microbial transplant for patients that manages antibiotic-resistant bacteria in a more targeted way and with fewer side effects than current treatments.

Part of the challenge is that each person’s microbiome is unique. This collaborative effort allowed us to functionally characterize the different mechanisms of action these bacteria use to reduce pathogen load and gut inflammation

Microbiome studies can often consist of analyzing collections of genetic sequences without understanding what each gene does or why certain microbes are beneficial said Ramnik Xavier co-senior author on the study and a core institute member at Broad. Trying to uncover that function is the next frontier and this is a nice first step towards figuring out how microbial metabolites influence health and inflammation.

Antibiotic-resistant Enterobacteriaceae such as E. coli and Klebsiella bacteria are common in hospitals where they can proliferate in the gut of patients and cause dangerous systemic infections that are difficult to treat. Some research suggests that Enterobacteriaceae also perpetuates inflammation in the intestine and infection by other microbes. Honda Xavier and their colleagues wanted to understand which specific bacteria in fecal microbiota transplants could help protect the intestinal microbiome against Enterobacteriaceae. 

Although more work will be needed to shed light on the precise mechanisms underlying how different bacteria compete with each other the findings suggest that microbial therapeutics could be used to tweak the ecology of the gut and suppress harmful bacterial infections with fewer negative side effects than typical antibiotic treatments. 

In the meantime the team aims to uncover the identity and function of unknown metabolites that contribute to gut health and inflammation.

Source: https://www.broadinstitute.org/news/scientists-identify-unique-combination-bacterial-strains-could-treat-antibiotic-resistant-gut