Evaluation of two DNA extraction methods for the PCR-based detection of eukaryotic enteric pathogens in fecal samples

• DOI: 10.1186/s13104-018-3300-2
• Publication Date: 2018-04-04T00:44:04Z
• Authors: Estelle Menu; Charles Mary; Isabelle Toga; Didier Raoult; Stéphane Ranque; Fadi Bittar
• Keywords: Science (General); QH301-705.5; Enteric parasites; Polymerase Chain Reaction; Sensitivity and Specificity; Q1-390; Feces; 03 medical and health sciences; 0302 clinical medicine; Humans; Protozoa; Biology (General); DNA extraction; [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases; Cryptosporidium parvum; [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases; Protozoan Infections; R; Eukaryota; Reproducibility of Results; DNA, Protozoan; [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology; Cyclospora; 3. Good health; qPCR; Research Note; Molecular Diagnostic Techniques; Blastocystis; Microsporidia; Medicine; [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology; Giardia lamblia

Efficient and easy-to-use DNA extraction and purification methods are critical in implementing PCR-based diagnosis of pathogens. In order to optimize the routine clinical laboratory diagnosis of eukaryotic enteric pathogens, we compare, via quantitative PCR cycle threshold (Ct) values, the efficiency of two DNA extraction kits: the semi-automated EZ1® (Qiagen) and the manual QIAamp® DNA Stool Mini Kit (Qiagen), on six protozoa: Blastocystis spp., Cryptosporidium parvum/hominis, Cyclospora cayetanensis, Dientamoeba fragilis, Giardia intestinalis and Cystoisospora belli and one microsporidia: Enterocytozoon bieneusi.Whereas EZ1® (Qiagen) and QIAamp® DNA Stool Mini Kit (Qiagen) yielded similar performances for the detection of Cryptosporidium spp. and D. fragilis, significant lower Ct values (p < 0.002) pointed out a better performance of EZ1® on the five remaining pathogens. DNA extraction using the semi-automated EZ1® procedure was faster and as efficient as the manual procedure in the seven eukaryotic enteric pathogens tested. This procedure is suitable for DNA extraction from stools in both clinical laboratory diagnosis and epidemiological study settings.