The rate of infection by antibiotic-resistant bacteria (ARB) is continuously raising worldwide, particularly because of the selective pressure resulting from the increasing usage of broad-spectrum antibiotics. This burden of ARB is of particular relevance for hematological patients, who undergo frequent antimicrobial prophylaxis and treatments. The prolonged exposure to health care settings may indeed favor the progressive accumulation of antimicrobial resistance genes in the gut microbiome of patients. Consequently, opportunistic ARB can accumulate in intestinal niches, where they can take advantage of the chemotherapy-induced damage to the gut epithelium and the overlapping neutropenia, spreading through the gut wall and causing life-threatening systemic infections.

The gut microbiome of pediatric patients undergoing allo-hematopoietic stem cell transplantation (HSCT) has recently been considered as a potential reservoir of antimicrobial resistance, with important implications in terms of patient mortality rate. By means of shotgun metagenomics, here we explored the dynamics of the gut resistome – i.e. the pattern of antibiotic resistance genes provided by the gut microbiome – in eight pediatric patients undergoing HSCT, half of whom developed acute Graft-versus-Host Disease (aGvHD).