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Clostridium difficile is the most commonly reported infectious diarrhoea in HIV-infected patients in the United States. We set out to determine the incidence, risk factors and clinical presentation of C. difficile infections (CDIs) in a cohort of HIV-infected individuals.We performed a nested, case–control analysis with four non-CDI controls randomly selected for each case.We assessed the incidence of CDI in the Johns Hopkins HIV Clinical Cohort between 1 July 2003 and 31 December 2010. Incident cases were defined as first positive C. difficile cytotoxin assay or PCR for toxin B gene. We used conditional logistic regression models to assess risk factors for CDI. We abstracted data on the clinical presentation and outcomes from case chart review.We identified 154 incident CDI cases for an incidence of 8.3 cases per 1000 patient years. No unique clinical features of HIV-associated CDI were identified. In multivariate analysis, risk of CDI was independently increased for CD4+ cell count of 50 cells/μl or less [adjusted odds ratio (AOR) 20.7, 95% confidence interval (CI) 2.8–151.4], hospital onset CDI (AOR 26.7, 95% CI 3.1–231.2) and use of clindamycin (AOR 27.6, 95% CI 2.2–339.4), fluoroquinolones (AOR 4.5, 95% CI 1.2–17.5), macrolides (AOR 6.3, 95% CI 1.8–22.1), gastric acid suppressants (AOR 3.1, 95% CI 1.4–6.9) or immunosuppressive agents (AOR 6.8, 95% CI 1.2–39.6).The incidence of CDI in HIV-infected patients was twice that previously reported. Our data show that compromised cellular immunity, as defined by CD4+ cell count of 50 cells/μl or less, is a risk factor for CDI. Clinicians should be aware of the increased CDI risk, particularly in those with severe CD4+ cell count suppression.