Gut Ruminococcaceae Levels are Associated with Risk of Antibiotic-associated Diarrhea

Antibiotic-associated diarrhea (AAD) occurs in up to one-third of patients, leading to premature antibiotic discontinuation and sub-optimal treatment of infection. However, it remains unclear why only a subset of patients develop AAD and if specific antibiotic-induced gut microbiome changes may increase risk. To address this knowledge gap, we administered a 3-day course of oral amoxicillin-clavulanate to 30 healthy adult volunteers. Stool samples were collected at baseline and up to 4-weeks post-antibiotic administration. Based on Bristol Stool Scale scoring, individuals were classified into AAD and non-AAD groups. Stool microbiome compositions were analysed using 16S rRNA gene sequencing. 13 out of 30 individuals developed AAD. There was a greater decrease in microbial diversity on days 1-3 in the AAD group compared to the non-AAD group, with recovery to near-baseline diversity by day 7. Interestingly, significantly lower levels of Ruminococcaceae were observed in the AAD group, consistently from baseline to day 14. Ruminococcaceae levels could be simply recapitulated with levels of Faecalibacterium prausnitzii derived from qPCR. Our results show that lower baseline Ruminococcaceae levels are associated with a higher risk of AAD. Quantification of F. prausnitzii in stool prior to antibiotic administration may help risk-stratify patients, and aid clinicians in devising individualised treatment regimens to minimise adverse effects.