Gut Colonization Preceding Mucosal Barrier Injury Bloodstream Infection: a Strain-Level Analysis

Bloodstream infection (BSI) is a frequent complication of hematopoietic stem cell transplantation (HSCT). The gastrointestinal tract is the predicted reservoir for most of these infections. Whole-genome sequencing and comparative genomics can address gaps in our understanding of the dynamics of gut colonization that precede BSI.Within a prospective cohort study of children (<18 years) undergoing HSCT, 9 subjects met criteria for mucosal barrier injury BSI. We performed shotgun metagenomics of the blood culture isolate and weekly fecal samples preceding the BSI to compare the genetic similarity of BSI isolates to fecal strains.Bacterial strains causing BSIs in pediatric HSCT receipients were observed in the gut microbiota prior to BSI onset, and changes in the abundances of these strains within the gut preceded most BSI episodes. Serial monitoring of the gut microbiota is a promising strategy for identifying HSCT recipients who are high risk for BSI.