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Detection of bacterial DNA in lymph nodes of Crohn's disease patients using high throughput sequencing
  1. Claire L O'Brien1,2,3,
  2. Paul Pavli1,2,
  3. David M Gordon3,
  4. Gwen E Allison2,3
  1. 1IBD Research Group, Canberra Hospital, Canberra, Australia
  2. 2Australian National University Medical School, Canberra, Australia
  3. 3Australian National University Research School of Biology, Canberra, Australia
  1. Correspondence to Dr C O'Brien, Research School of Biology, Australian National University, Bdg 134, Acton, Canberra ACT 0200, Australia; claire.obrien{at}anu.edu.au

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.

Design 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.

  • CROHN'S DISEASE
  • BACTERIAL TRANSLOCATION
  • SURGICAL RESECTION
  • MOLECULAR BIOLOGY
  • RIBOSOMAL RNA

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