Detection of bacterial DNA in lymph nodes of Crohn's disease patients

Mechanisms by which bacteria may trigger the development of Crohn’s disease include the presence of a specific micro-organism, which may be common to all patients or vary by the patient’s genetic background; shifts in the microbial composition of the intestinal lumen affecting homeostasis (dysbiosis); and/or a breakdown in the intestinal barrier causing bacterial translocation. Our primary aim was to determine whether or not specific microorganisms were transported selectively to lymph nodes of Crohn’s disease patients by comparing lymph node and mucosal microbial communities from patients with and without Crohn’s disease. We also sought evidence for the presence of dysbiosis and bacterial translocation in these patients.

Lymph nodes, and involved and uninvolved mucosal samples were obtained from bowel resections of 58 patients (29 Crohn’s disease, 8 other- and 21 non-inflammatory bowel disease [IBD]). Universal primers targeting the V1-V3 region of the bacterial 16S rRNA gene were used to amplify bacterial DNA in all samples, the amplicons were sequenced using high-throughput sequencing techniques. Twenty patients (8 Crohn’s disease [28%], 2 other- [25%] and 10 non-IBD [48%]) had PCR-positive lymph nodes and are the subject of this report.

Each sample was covered by an average of 8,720 quality 16S rRNA gene sequences. Lymph node and mucosal samples from the same patient were very similar: there was no evidence for the selective concentration of any microorganisms in lymph nodes. No specific microorganism was present in the lymph nodes of all CD samples. Escherichia/Shigella were common in all patient groups; patients with ileal Crohn’s disease had a significantly greater proportion of E. coli reads in their lymph nodes than other Crohn’s disease patients (p=0.0475). Campylobacter was detected in three Crohn’s disease and one non-IBD patient; Helicobacter in one Crohn’s disease and one non-IBD patient; and Yersinia in one “other-IBD” patient. Mycobacterium and Listeria were not detected in any patient.

Microbial diversity of Crohn’s disease samples was lower than non-IBD (p=0.0062). Dysbiosis was common in all patient groups, but shifts in the microbiota were specific to each individual and no common pattern emerged.

We conclude that it is unlikely that a single bacterium is responsible for the perpetuation of inflammation in late-stage Crohn’s disease; confirm that dysbiosis (decreased microbial diversity) is common; and saw evidence of bacterial translocation in 28% patients with late-stage Crohn’s disease but 48% patients with other non-IBD conditions requiring intestinal resection. In those patients who had bacterial DNA-positive lymph nodes and terminal ileal disease requiring resection, E. coli was present at significantly higher levels (greater relative abundance). We believe that future studies should focus on early disease and viable bacteria in lymph nodes, aphthous ulcers and granulomas of patients with CD, as they may be more relevant in the initiation of inflammation in CD.