Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection.
BACKGROUND
Bacteremia, or bloodstream infection (BSI), is a leading cause of death among patients with certain types of cancer. A previous study reported that intestinal domination, defined as occupation of at least 30 % of the microbiota by a single bacterial taxon, is associated with BSI in patients undergoing allo-HSCT. However, the impact of the intestinal microbiome before treatment initiation on the risk of subsequent BSI remains unclear. Our objective was to characterize the fecal microbiome collected before treatment to identify microbes that predict the risk of BSI.


METHODS
We sampled 28 patients with non-Hodgkin lymphoma undergoing allogeneic hematopoietic stem cell transplantation (HSCT) prior to administration of chemotherapy and characterized 16S ribosomal RNA genes using high-throughput DNA sequencing. We quantified bacterial taxa and used techniques from machine learning to identify microbial biomarkers that predicted subsequent BSI.


RESULTS
We found that patients who developed subsequent BSI exhibited decreased overall diversity and decreased abundance of taxa including Barnesiellaceae, Coriobacteriaceae, Faecalibacterium, Christensenella, Dehalobacterium, Desulfovibrio, and Sutterella. Using machine-learning methods, we developed a BSI risk index capable of predicting BSI incidence with a sensitivity of 90 % at a specificity of 90 % based only on the pretreatment fecal microbiome.


CONCLUSIONS
These results suggest that the gut microbiota can identify high-risk patients before HSCT and that manipulation of the gut microbiota for prevention of BSI in high-risk patients may be a useful direction for future research. This approach may inspire the development of similar microbiome-based diagnostic and prognostic models in other diseases.
['Montassier|Emmanuel|E|', 'Al-Ghalith|Gabriel A|GA|', 'Ward|Tonya|T|', 'Corvec|Stephane|S|', 'Gastinne|Thomas|T|', 'Potel|Gilles|G|', 'Moreau|Phillipe|P|', 'de la Cochetiere|Marie France|MF|', 'Batard|Eric|E|', 'Knights|Dan|D|']
D000970:Antineoplastic Agents D016470:Bacteremia D001419:Bacteria D005243:Feces D005260:Female D000069196:Gastrointestinal Microbiome D014644:Genetic Variation D018380:Hematopoietic Stem Cell Transplantation D006801:Humans D015994:Incidence D008228:Lymphoma, Non-Hodgkin D000069550:Machine Learning D008297:Male D008875:Middle Aged D012336:RNA, Ribosomal, 16S D012189:Retrospective Studies D012307:Risk Factors D017423:Sequence Analysis, RNA
Prediction Bloodstream infection Intestinal microbiome Chemotherapy