The cause of Crohn's disease (CD) has posed a conundrum for at least a century. A large body of work coupled with recent technological advances in genome research have at last started to provide some of the answers. Initially this review seeks to explain and to differentiate between bowel inflammation in the primary immunodeficiencies that generally lead to very early onset diffuse bowel inflammation in humans and in animal models, and the real syndrome of CD. In the latter, a trigger, almost certainly enteric infection by one of a multitude of organisms, allows the faeces access to the tissues, at which stage the response of individuals predisposed to CD is abnormal. Direct investigation of patients' inflammatory response together with genome-wide association studies (GWAS) and DNA sequencing indicate that in CD the failure of acute inflammation and the clearance of bacteria from the tissues, and from within cells, is defective. The retained faecal products result in the characteristic chronic granulomatous inflammation and adaptive immune response. In this review I will examine the contemporary evidence that has led to this understanding, and look for explanations for the recent dramatic increase in the incidence of this disease.
General introductionThe enigma that is the cause of Crohn's disease (CD) has puzzled clinicians and scientists from time immemorial. It is generally accepted that CD results from an aberrant immune response to commensal microflora in genetically susceptible individuals 1 , however, the nature of the immune defects, the responsible microflora and the genetic susceptibility remain incompletely defined and actively debated. With advances in genomic technologies our understanding of this puzzling condition is evolving, and answers forthcoming. The purpose of this article is to undertake a holistic review of the aetiopathogenesis of CD in which historical concepts are integrated with recent discoveries.The bowel mucosa, an interface between faeces and the tissues The distal ileum and colon contain >10 11 bacteria per gram of faecal material 2 , which pose an immediate threat to life if they penetrate into the underlying tissues. The bowel microflora are isolated by a thin film of mucus and a single layer of columnar epithelial cells with a surface area of approximately 32m 2 , 3 . The requirement for the absorption of fluids and nutrients by the bowel mucosa means that the bowel lining cannot simply be a tough impermeable barrier, and as a consequence provision must be made to defend the vulnerable mucosal epithelial cell layer against its contents. Mucus secreted by goblet cells forms a continuous, weak, viscoelastic gel, lining, 5-500 μm thick 4 . In addition to acting as a physical barrier and lubricant, the mucus is the site of action of a variety of antimicrobial mechanisms including secretory IgA, antimicrobial enzymes and peptides 5 and H 2 O 2 generated by the DUOX electron transport chain 6 . Despite these barriers, the separation of the tissues from the gut microbiome...