• Ami S Bhatt, Samuel S Freeman, Alex F Herrera, Chandra Sekhar Pedamallu, Dirk Gevers, Fujiko Duke, Joonil Jung, Monia Michaud, Bruce J Walker, Sarah Young, Ashlee M Earl, Aleksander D Kostic, Akinyemi I Ojesina, Robert Hasserjian, Karen K Ballen, Yi-Bin Chen, Gabriela Hobbs, Joseph H Antin, Robert J Soiffer, Lindsey R Baden, Wendy S Garrett, Jason L Hornick, Francisco M Marty, and Matthew Meyerson.
• Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
• N. Engl. J. Med.. 2013 Aug 8;369(6):517-28.

BackgroundImmunosuppression is associated with a variety of idiopathic clinical syndromes that may have infectious causes. It has been hypothesized that the cord colitis syndrome, a complication of umbilical-cord hematopoietic stem-cell transplantation, is infectious in origin.MethodsWe performed shotgun DNA sequencing on four archived, paraffin-embedded endoscopic colon-biopsy specimens obtained from two patients with cord colitis. Computational subtraction of human and known microbial sequences and assembly of residual sequences into a bacterial draft genome were performed. We used polymerase-chain-reaction (PCR) assays and fluorescence in situ hybridization to determine whether the corresponding bacterium was present in additional patients and controls.ResultsDNA sequencing of the biopsy specimens revealed more than 2.5 million sequencing reads that did not match known organisms. These sequences were computationally assembled into a 7.65-Mb draft genome showing a high degree of homology with genomes of bacteria in the bradyrhizobium genus. The corresponding newly discovered bacterium was provisionally named Bradyrhizobium enterica. PCR identified B. enterica nucleotide sequences in biopsy specimens from all three additional patients with cord colitis whose samples were tested, whereas B. enterica sequences were absent in samples obtained from healthy controls and patients with colon cancer or graft-versus-host disease.ConclusionsWe assembled a novel bacterial draft genome from the direct sequencing of tissue specimens from patients with cord colitis. Association of these sequences with cord colitis suggests that B. enterica may be an opportunistic human pathogen. (Funded by the National Cancer Institute and others.)

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