Evaluating the AllplexTM GI-Bacteria (I) Assay Efficiency to Assess the Diversity of Bacterial Pathogens among Young Children with Diarrhea in Burundi

Abstract

Background Diarrheal infections are caused by many enteric pathogens that infect children as early as birth. Molecular assays are uncommon in routine diagnosis of gastrointestinal bacterial pathogens in Burundi. This study aimed to characterize the diversity of bacterial pathogens among young children with diarrhea in selected healthcare settings and to demonstrate the efficiency of the AllplexTM GI-Bacteria (I) assay over the conventional culture. Methods We conducted a cross-sectional study in seven (7) selected health districts in Burundi. We used a questionnaire to collect sociodemographic information for children ≥ 5 years old whose parents consented to participate. We collected stool samples for both conventional cultures (gold standard) and AllplexTM GI assay. We plated the stool samples shortly after collection and we kept the samples in the fridge between 4–8 ℃ for less than 24 hours before we processed them with the AllplexTM GI kit. We determined the association between sociodemographic factors and carriage of genes using a chi-square test for independence (Pearson's chi-square test or chi-square test of association). A p-value < 0.05 was considered statistically significant. Results 17.6% (18/102) of stool specimens processed with conventional methods were positive for Shigella spp. (13.7%) and Salmonella spp (3.9%). With Allplex GI, 79.4% (81/102) of stool samples were positive for different genes; sh/ei genes were detected in 40.2% (40/102) of the stool samples. An association of two genes namely sh/ei and sal or sh/ei and vib was found. AllplexTM GI-Bacteria(I) PCR Assay had a sensitivity of 94.4% and a negative predictive value (NPV) of 95.2%. There was no association between place of residence, fingernail status, level of education, and being positive for sh/ei, sal, sh/ei and sal and sh/ei and vib. Conclusion We characterized bacterial pathogens in the stool samples and we demonstrated the efficiency of the AllplexTM GI assay over conventional methods. The data could further inform the decision-makers to institute effective prevention and control measures to tackle infectious diarrhea.