Acute gastroenteritis in Rwandan children under five years of age investigated by real-time PCR

Abstract: Acute gastroenteritis is a major cause of illness and death among children in developing countries. Knowledge about the aetiology is important to make the right priorities regarding preventive measures, and for the recommendation to use or not use antibiotics. The objective of this thesis was to investigate causes of acute diarrhea in children in Rwanda by real-time PCR targeting a wide range of infectious agents. By analysing 326 paired faecal samples we found that rectal swabs provided equal rates of PCR detection of 10 different pathogens as usual stool samples, and correlating Ct values indicated that rectal swabs also may be used for quantitative measurements. PCR findings in 544 children with acute diarrhea and 162 controls showed a higher prevalences in children with than without diarrhea only for rotavirus and the enterotoxigenic E. coli (ETEC-estA) (42% vs. 2%, and 21% vs. 9%). Other agents were detected at similar rates in sick and healthy children (adenovirus, 39% vs. 36%; ETEC-eltB, 29% vs. 30%, Campylobacter, 14% vs. 17%, Shigella, 13% vs. 10%). Lower Ct values for ETEC-estA, Shigella and norovirus GII indicate that measuring pathogen concentration in faeces may help to identify clinically relevant infections. At least one pathogen was detected in 92% of 880 children with diarrhea. Rotavirus and ETEC-estA were associated with more severe dehydration, Shigella with bloody diarrhoea and higher CRP, and concentrations in faeces of rotavirus, ETEC-estA and Shigella were associated with more severe symptoms. Rotavirus and ETEC-estA were more common in younger, Shigella more a common in older children. Antibiotics were given to 42% of children, mainly those with fever and more severe dehydration, and without any logical connection with the causative organism. The conclusions of this thesis are (i) that rectal swabs are as good as conventional stool samples for pathogen detection by PCR, (ii) that rotavirus, ETEC-estA and Shigella were the major causes of gastroenteritis, (iii) that higher concentrations of rotavirus, ETEC-estA, Shigella and norovirus GII were associated with symptoms, and that Ct value cut-offs for these agents improved identification of them as causes of disease, (iv) that antibiotics were used extensively and in a seemingly irrational manner, and (v) highly sensitive multiple real-time PCR was efficient and informative and that its use in future studies may provide valuable new information about the clinical significance and epidemiology of these infections.

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