title: Detection of bacterial DNA in lymph nodes of Crohn's disease patients using high throughput sequencing.
abstract: OBJECTIVE
  Our aim was to determine whether or not specific microorganisms were transported selectively to lymph nodes in Crohn's disease (CD) by comparing node and mucosal microbial communities in patients and controls. We also sought evidence of dysbiosis and bacterial translocation.
  
  
  METHODS
  Lymph nodes, and involved and uninvolved mucosal samples were obtained from resections of 58 patients (29 CD, eight 'other inflammatory bowel disease' (IBD) and 21 non-IBD). Universal primers targeting V1-V3 regions of bacterial 16S rRNA genes were used to amplify bacterial DNA and amplicons sequenced using high throughput sequencing. 20 patients (eight CD (28%), two other IBD (25%) and 10 non-IBD (48%)) had PCR positive nodes.
  
  
  RESULTS
  All samples from an individual were similar: there was no evidence of selective concentration of any microorganism in nodes. No specific microorganism was present in the nodes of all CD samples. Escherichia/Shigella were common in all patient groups but patients with ileal CD had a greater proportion of Escherichia coli reads in their nodes than other CD patients (p=0.0475). Campylobacter, Helicobacter and Yersinia were uncommon; Mycobacterium and Listeria were not detected. Dysbiosis was present in all groups but shifts were specific and no common pattern emerged.
  
  
  CONCLUSIONS
  It is unlikely that a single bacterium perpetuates inflammation in late stage CD; dysbiosis was common and we found no evidence of increased bacterial translocation. We believe that future studies should focus on early disease and viable bacteria in nodes, aphthous ulcers and granulomas, as they may be more relevant in the initiation of inflammation in CD.
authors.affiliation: IBD Research Group, Canberra Hospital, Canberra, Australia Australian National University Medical School, Canberra, Australia Australian National University Research School of Biology, Canberra, Australia.
authors.forename: Claire L
authors.initials: CL
authors.lastname: O'Brien
authors.affiliation: IBD Research Group, Canberra Hospital, Canberra, Australia Australian National University Medical School, Canberra, Australia.
authors.forename: Paul
authors.initials: P
authors.lastname: Pavli
authors.affiliation: Australian National University Research School of Biology, Canberra, Australia.
authors.forename: David M
authors.initials: DM
authors.lastname: Gordon
authors.affiliation: Australian National University Medical School, Canberra, Australia Australian National University Research School of Biology, Canberra, Australia.
authors.forename: Gwen E
authors.initials: GE
authors.lastname: Allison
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification*; D003424:Crohn Disease / Q000382:microbiology*; D004269:DNA, Bacterial / Q000032:analysis*; D005260:Female; D006801:Humans; D007413:Intestinal Mucosa / Q000382:microbiology*; D008198:Lymph Nodes / Q000382:microbiology*; D008297:Male; D008875:Middle Aged; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D055815:Young Adult
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: BACTERIAL TRANSLOCATION; CROHN'S DISEASE; MOLECULAR BIOLOGY; RIBOSOMAL RNA; SURGICAL RESECTION