The gut microbiome and its resistome as predictors of clinical infections and phenotypic antibiotic resistance in hematopoietic stem cell transplant recipients

A relationship among the gut microbiome composition, its resistome, and risk of clinical infections may exist and was explored here by using 663 shotgun-sequenced fecal samples from 276 stem cell transplants. Enterococcus faecium, Escherichia coli, and Enterococcus faecalis were the 3 most prevalent causes of clinical infection, with vancomycin resistance in E faecium as the most common antibiotic resistance feature. Associations among the gut microbiome, resistome, and clinical infections were tested, with significant findings (false discovery rate <0.05) evaluated in multivariable analysis. A 10% increase in gut abundance of E faecium was positively associated with subsequent clinical infection with E faecium (odds ratio, 1.14; P = .02). Additionally, a 1% increase in vanA gene abundance was positively associated with vancomycin-resistant E faecium infection (odds ratio, 1.27; P < .01). Here we used metagenomics to enhance the understanding of infectious sources and to identify patients at risk of clinical infection with antibiotic-resistant bacterial strains.