Variation of the Microbiome in Paediatric Crohn’s Disease
Document TypePhD thesis
Access StatusOpen Access
© 2019 Shivani Kansal
Introduction: Crohn’s Disease (CD) is a chronic, relapsing condition of the human gastrointestinal system with several significant extraintestinal manifestations. It can affect any age group; 10% of patients being diagnosed prior to their 18th birthday. Pediatric CD is known to have a more severe and difficult to manage phenotype. A rising incidence has been observed in recent years although the disease phenotype has remained largely unchanged. There is a growing body of literature describing dysbiosis in patients with CD. Despite extensive research, the role and behaviour of the gut microbiome in pediatric CD is not well understood. Aims: We aimed to characterize the microbiome in patients with CD longitudinally and compare it with non-IBD patients. We also sought to explore if there were any microbiome differences between ASCA positive and ASCA negative patients. Methods: We analysed the microbiome of 345 biopsies from 204 patients, including 88 CD first diagnosis (CDFD) patients, 38 patients in relapse (CDRL), 12 patients in remission (CDRM), and 66 controls. Species identification was conducted using oligotyping in combination with ARB/SILVA taxonomic annotation. Comparison was also made between ASCA status, microbial diversity and clinical characteristics. Results: We observed 45 bacteria to be statistically different between CDFD samples and controls, with Fusobacterium being the most implicated species in CDFD patients. We also identified gender specific differences in CD. Five species showed a strong association with patients with CD in relapse and 10 species in patients with CD in remission. Three taxa showed a positive co-occurrence across the two groups. Hespellia porcina (closest taxonomic neighbor to Clostridium oroticum) had the strongest association with samples from patients with CD in relapse. Interestingly, Fusobacterium was not part of the CD relapse associated taxa group. Faecalibacterium prausnitzii was equally present in CDFD and in control samples. ASCA was highly specific but poorly sensitive for the diagnosis of CD. In patients with CD, ASCA positivity was more likely to be present in patients older than 10 years, and associated with increased likelihood of ileocolonic disease distribution and long-term risk of surgery. Microbial alpha and beta diversity were similar in patients with CD with or without ASCA, but significantly less when compared to non-IBD controls. 14 bacterial species were statistically associated with ASCA positive patients with CD and 14 species with ASCA negative patients (p< 0.05). By using a false discovery rate corrected P value, two species remained statistically associated with both the groups. Ruminococcus torques and bacterium Yersinia enterocolitica were statistically associated with CD ASCA positive patients (p = 0.0178). Enterobacter cloacae and Faecalibacterium prausnitzii were statistically associated with CD ASCA negative patients (p = 0.0178 and 0.0342, respectively). Conclusions: This is the first study to investigate gut mucosal microbiome in a pediatric CD cohort with longitudinal sampling. Significant differences in microbiome were observed between treatment naïve patients with CD, patients with CD in relapse, patients with CD in remission and non-IBD patients. We also identified differences in the gut microbiome between patients with CD depending on presence of ASCA.
KeywordsPediatrics; Crohns Dsiease; Microbiome; bacteria; PTP; ASCA; genetics; endoscopic; alpha diversity; beta diversity
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