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Real-time PCR Identification of Agents Causing Diarrhea in Rwandan Children Less Than 5 Years of Age

Kabayiza, Jean-Claude MD, PhD*†; Andersson, Maria E. BSc; Nilsson, Staffan PhD; Bergström, Tomas MD, PhD; Muhirwa, Gregoire MD, PhD§; Lindh, Magnus MD, PhD

The Pediatric Infectious Disease Journal: October 2014 - Volume 33 - Issue 10 - p 1037–1042
doi: 10.1097/INF.0000000000000448
Original Studies

Background: Knowledge about causes of acute diarrhea among children in developing countries is insufficient. Molecular methods might improve diagnostics of infectious gastroenteritis, but due to the high sensitivity, findings may be difficult to interpret.

Methods: Feces samples from Rwandan children 0.5–5.0 years of age, with diarrhea for <96 hours (patients, n = 544) or without diarrhea for 14 days (controls, n = 162), were analyzed by real-time polymerase chain reaction targeting 17 pathogens.

Results: At least 1 agent was detected in 94% of patients and in 79% of controls, with higher rates in sick children for rotavirus (42% vs. 2%, P < 0.0001) and enterotoxigenic Escherichia coli (ETEC)-estA (21% vs. 9%, P = 0.0006). Detection rates did not differ significantly for adenovirus (39% vs. 36%), ETEC-eltB (29% vs. 30%), Campylobacter (14% vs. 17%) or Shigella (13% vs. 10%), but for Shigella the threshold cycle (Ct) values were lower (pathogen loads were higher) in sick children than in controls. By multivariate analysis, including gender and age, detection of rotavirus (P < 0.0001), ETEC-estA (P = 0.001), Shigella (P = 0.004) and norovirus genogroup II (P = 0.009) was associated with symptomatic infection, and a Ct value below a cutoff (in the range 28–29) improved identification of ETEC-estA, Shigella and norovirus genogroup II.

Conclusion: Real-time polymerase chain reaction can detect essentially all diarrheagenic agents, and provides Ct values that improve identification of clinically relevant infections.

Supplemental Digital Content is available in the text.

From the *Department of Paediatrics, National University of Rwanda, Butare, Rwanda; Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden; Chalmers University of Technology, Gothenburg, Sweden; and §Department of Clinical Biology, National University of Rwanda, Butare, Rwanda.

Accepted for publication April 16, 2014.

This work was supported by grants from the Swedish International Development Cooperation Agency (SIDA).

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The authors have no conflicts of interest to disclose

Address for correspondence: Magnus Lindh, PhD, Department of Infectious Diseases, University of Gothenburg, Guldhedsgatan 10B, 413 36 Gothenburg, Sweden. E-mail:

© 2014 by Lippincott Williams & Wilkins, Inc.