Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome.
BACKGROUND
Immunosuppression 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.


METHODS
We 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.


RESULTS
DNA 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.


CONCLUSIONS
We 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.)
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Ami S
AS
Bhatt
Samuel S
SS
Freeman
Alex F
AF
Herrera
Chandra Sekhar
CS
Pedamallu
Dirk
D
Gevers
Fujiko
F
Duke
Joonil
J
Jung
Monia
M
Michaud
Bruce J
BJ
Walker
Sarah
S
Young
Ashlee M
AM
Earl
Aleksander D
AD
Kostic
Akinyemi I
AI
Ojesina
Robert
R
Hasserjian
Karen K
KK
Ballen
Yi-Bin
YB
Chen
Gabriela
G
Hobbs
Joseph H
JH
Antin
Robert J
RJ
Soiffer
Lindsey R
LR
Baden
Wendy S
WS
Garrett
Jason L
JL
Hornick
Francisco M
FM
Marty
Matthew
M
Meyerson
D001706:Biopsy; D020369:Bradyrhizobium / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D003092:Colitis / Q000276:immunology / Q000382:microbiology*; D003106:Colon / Q000382:microbiology*; D003110:Colonic Neoplasms / Q000382:microbiology; D004269:DNA, Bacterial / Q000032:analysis; D003967:Diarrhea / Q000382:microbiology; D005260:Female; D005312:Fetal Blood; D016680:Genome, Bacterial; D006086:Graft vs Host Disease / Q000382:microbiology; D018380:Hematopoietic Stem Cell Transplantation / Q000009:adverse effects*; D006801:Humans; D016867:Immunocompromised Host; D008297:Male; D009894:Opportunistic Infections / Q000382:microbiology*; D016612:Paraffin Embedding; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial