Researchers Characterize Impact of Microbial Interactions on C diff Susceptibility to Antibiotics


Using a diverse human gut community, researchers investigated how gut microbiota interspecies interactions affected the response of Clostridioides difficile to vancomycin and metronidazole.

Findings from a new study shed light on patterns of response of a major gut pathogen to antibiotics.

Using a diverse human gut community, researchers investigated how gut microbiota interspecies interactions affected the response of Clostridioides difficile to vancomycin and metronidazole, relevant antibiotics in the treatment of the pathogen and with differences in activity spectra. Their findings, say the group in PLoS Biology, underscore the need for considering these biotic interactions in future approaches for treatment against pathogens.

“A fundamental question is uncovering the role of biotic interactions in shaping antibiotic susceptibility in microbiomes. In particular, understanding how microbial interactions alter the antibiotic susceptibility of major human pathogens such as C diff could enable tailored antibiotic treatments informed by ecological context,” explained the researchers. “This understanding could inform new microbiome interventions that selectively eradicate human pathogens while minimizing disruption of healthy gut microbiota and minimize the acquisition of antibiotic resistance.”

The researchers identified 2 sets of interactions that resulted in increased C diff growth in the presence of antibiotics. These interactions included an infrequent effect of the gut microbiome on C diff’s minimum inhibitory concentration (MIC) and a common impact on C diff’s response to subinhibitory concentrations of the antibiotics.

The group used a broth dilution method, finding that the MIC of C diff remained consistent in 15 pairwise communities and had a moderate increase in 5 pairwise communities vs monospecies. Notably, they found a more than 4-fold increase in the MIC of C diff in coculture with Desulfovibrio piger, with the metronidazole MIC increasing from 6 mcg/mL to at least 24 mcg/mL.

“The observed increase in C diff metronidazole MIC in the presence of specific gut may contribute to the ineffectiveness of metronidazole in treating C diff infections in the human colon,” detailed the researchers. “Due to the low achieved metronidazole concentration in the human colon, even modest increases in C diff metronidazole MIC could allow the pathogen to survive. Based on our results, future testing of C diff antibiotic susceptibility could include conditions of C diff cultured with physiologically relevant microbial communities.”

Meanwhile, increases in C diff at subinhibitory concentrations were observed in 52% of communities.

Among pairwise communities, the abundance of C diff tended to be similar or decreased in the subminimum inhibitory concentration (subMIC) range vs no antibiotic presence. However, in the presence of Bacteroides thetaiotaomicron, C diff abundance was significantly higher in the presence of 0.75-mcg/mL metronidazole than with no antibiotic present. When determining the subMIC fold change at each subMIC, the group found that increase in C diff was enhanced in at least 1 subMIC in 1 pairwise community for vancomycin treatment and in 11 pairwise communities for metronidazole treatment. The increased enhancement of C diff for metronidazole treatment was significantly greater than that observed for C diff monoculture for metronidazole across 7 of the pairwise communities.

The presence of subinhibitory concentrations of antibiotics may occur in several scenarios, explained the researchers, including if the pathogen gains resistance to the antibiotic or when starting and ending dosing regimens.

The researchers also performed metal supplementation experiments, which showed that the 5 metals resulted in a significant drop of C diff MIC. However, the addition of a single metal, including iron, did not yield the same effect. Based on the finding, the researchers hypothesized that several metal cofactors are needed in order for enzymatic activities that lead to metronidazole reduction.


Hromada S, Venturelli O. Gut microbiota interspecies interactions shape the response of Clostridioides difficile to clinically relevant antibiotics. PLoS Biol. Published online May 11, 2023. doi:10.1371/journal.pbio.3002100

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