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Fecal microbiota transplantation (FMT) is used to treat infection with Clostridium difficile (CDI). Antimicrobial resistance (AMR) gene alterations and potential pathogen load in juvenile FMT recipients are poorly understood. Investigating changes in AMR genes, possible pathogens, species, and functional pathways with FMT in children was the goal of this study.
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All of the kids had recovered from CDI. AMR genes dropped after FMT (P .001), and multidrug resistance genes continued to decline (P .001). After FMT, tetracycline resistance genes increased (P .001). Potential infections were found in very low concentrations in both donors and recipients, with a general decline post-FMT (P .001). None of the recipients experienced any clinical illness, but Prevotella sp. 109 increased in all of them after FMT. Prior to FMT, recipients' alpha diversity was lower than that of donors' (P .001), but it increased afterward (P .002) and remained higher. Beta diversity varied considerably between recipient samples before and after FMT (P .001) Bacterial species Faecalibacterium prausnitzii and Bacteroides ovatus had post-FMT growth and were more prevalent in donors than receivers (P =.008 and P =.040, respectively). Biological processes were prevalent in the donor and post-FMT, the recipient's increased.
Thus, FMT for CDI in kids reduces AMR genes and possible pathogens and modifies the composition and function of the microbiota. However, the acquisition of some AMR genes post-FMT and the low levels of possible pathogens discovered in donors imply that more research into the screening of donors using metagenomics sequencing prior to FMT is necessary.
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