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Objective was to analyse bacterial composition and abundance of  Clostridioides difficile  in gut microbiome of patients with  C. difficile  infection (CDI) in association with clinical characteristics. Whole metagenome sequencing of gut microbiome of 26 CDI patients was performed, and the relative abundance of  C. difficile  and its toxin genes was measured. Clinical characteristics of the patients were obtained through medical records. A strong correlation between the abundance of  C. difficile  and  tcdB  genes in CDI patients was found. The relative abundance of  C. difficile  in the gut microbiome ranged from undetectable to 2.8% (median 0.089) .  Patients with fever exhibited low abundance of  C. difficile  in their gut, and patients with fewer  C. difficile  organisms required long-term anti-CDI treatment. Abundance of  Bifidobacterium  and  Bacteroides  negatively correlated with that of  C. difficile  at the genus level. CDI patients were clustered using the bacterial composition of the gut: one with high population of  Enterococcus  (cluster 1, n = 12) and another of  Bacteroides  or  Lactobacillus  (cluster 2, n = 14). Cluster1 showed significantly lower bacterial diversity and clinical cure at the end of treatment. Additionally, patients with CDI exhibited increased ARGs; notably,  bla   TEM   , bla   SHV   and  bla   CTX-M   were enriched.  C. difficile  existed in variable proportion of the gut microbiome in CDI patients. CDI patients with  Enterococcus -rich microbiome in the gut had lower bacterial diversity and poorer clinical cure.

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Quantitative characterization of Clostridioides difficile population in the gut microbiome of patients with C. difficile infection and their association with clinical factors