| Summary: | The molecular epidemiology of giardiasis in Africa remains unclear. A study was carried out across four hospitals in Algeria. A total of 119 fecal samples from 55 children, 37 adults, and 27 individuals of undetermined age, all scored positive for intestinal parasites by microscopy, and were screened by real-time PCR for <i>Giardia</i>. Molecular characterization of <i>Giardia</i> was performed by assemblage-specific PCR and PCR targeting the triose phosphate isomerase gene (<i>tpi</i>). Of the 119 samples, 80 (67%) were <i>Giardia</i>-positive by real-time PCR. For 48 moderately-highly real-time PCR-positive samples, <i>tpi</i> genotyping assigned 22 samples to Assemblage A and 26 to Assemblage B. Contrary to Assemblage A, Assemblage B exhibited substantial genetic diversity and allelic heterozygosity. Assemblage-specific PCR proved to be specific for discriminating Assemblage A or B but not as sensitive as <i>tpi</i> genotyping. We confirmed that real-time PCR is more sensitive than microscopy for detecting <i>Giardia</i> in stool samples and that robust amplification and sequencing of the <i>tpi</i> gene is feasible when moderate-to-strongly real-time PCR-positive samples are used. This study is one of the few performed in Africa providing genotyping data on <i>Giardia</i> infections in humans. Both assemblages A and B were commonly seen and not associated with specific sociodemographic data.
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