Fig. 2

Effect of faecal microbiota transplantation on prevalence and abundance of cultured multidrug resistant bacteria. Stool samples of recurrent C. difficile infected (rCDI) patients were selectively cultured to assess the prevalence of multidrug-resistant (MDR) bacteria before and after faecal microbiota transplantation (FMT). We called samples MDR positive if at least one MDR bacterium was detected. Cultured isolates were subjected to whole-genome sequencing, and metagenomic sequencing data from the same stool samples were mapped to the assembled genomes to quantify the MDR bacteria in the metagenomes. A Prevalence of MDR bacteria in 87 rCDI patients. B Colonisation rates in 22 patients of whom long-term follow-up (~ 1–3 years after FMT) samples were collected. C Abundance of MDR bacteria based on metagenome data. D Breadth of coverage and relative abundance of MDR bacteria in metagenomic sequencing data per species. Asterisks indicate statistically significant differences, *: p < 0.05; **: p < 0.01; n.s.: not significant, MDR: multidrug resistant, FMT: faecal microbiota transplantation, LTFU: long-term follow-up