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Lymphocytic disorders of the upper and lower gastrointestinal tract seem to cluster in patients. We aimed to assess the frequency of comorbid occurrence of lymphocytic disorders in patients with microscopic colitis (MC).We collected data from the Miraca Life Sciences Database, a large national electronic repository of histopathologic records of patients throughout the United States. In a population of 228,506 patients who underwent bidirectional endoscopy from January 2008 through July 2016, we studied the comorbid occurrence of celiac disease, duodenal intraepithelial lymphocytosis, lymphocytic gastritis, and lymphocytic esophagitis among 3456 patients with MC. Associations were described in terms of their odds ratios (OR) and 95% CIs.Any type of lymphocytic disorder occurred in 13.7% of patients with MC and 5.9% of patients without MC. The ORs of lymphocytic disorders in patients with MC were: 2.56 (95% CI, 2.32–2.82) for any type of lymphocytic disorder, 3.07 (95% CI, 1.25–7.52) for lymphocytic esophagitis, 15.05 (95% CI, 12.31–18.41) for lymphocytic gastritis, 1.73 (95% CI, 1.53–21.96) for duodenal intraepithelial lymphocytosis, and 6.06 (95% CI, 5.06–7.25) for celiac disease. Comorbidities were more common in patients with lymphocytic than collagenous colitis, with an OR of 1.74 (95% CI, 1.42–2.13). Patients with MC with comorbidities were significantly younger and had a lower proportion of men than patients with MC patients without comorbidities. Diarrhea was the predominant symptoms in all patients MC, irrespective of comorbidities.In a retrospective study, we identified lymphocytic disorders of the upper gastrointestinal tract that are significantly more common in patients with than without MC. These associations suggest the existence of an underlying etiology that is common to all lymphocytic disorders and that affects the upper and lower gastrointestinal tract.