Comparative Study of DNA Extraction Methods for the PCR Detection of Intestinal Parasites in Human Stool Samples
Stool samples typically contain PCR inhibitors; however, helminths are difficult to lyse and can cause false-negative PCR results. We assessed the effective methods for extracting DNA from different kinds of intestinal parasites. We compared the most common DNA extraction methods from stool samples,...
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| Format: | Article |
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MDPI AG
2022-10-01
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| Series: | Diagnostics |
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| Online Access: | https://www.mdpi.com/2075-4418/12/11/2588 |
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| author | Siriporn Srirungruang Buraya Mahajindawong Panachai Nimitpanya Uthaitip Bunkasem Pattama Ayuyoe Surang Nuchprayoon Vivornpun Sanprasert |
| author_facet | Siriporn Srirungruang Buraya Mahajindawong Panachai Nimitpanya Uthaitip Bunkasem Pattama Ayuyoe Surang Nuchprayoon Vivornpun Sanprasert |
| author_sort | Siriporn Srirungruang |
| collection | DOAJ |
| description | Stool samples typically contain PCR inhibitors; however, helminths are difficult to lyse and can cause false-negative PCR results. We assessed the effective methods for extracting DNA from different kinds of intestinal parasites. We compared the most common DNA extraction methods from stool samples, including the phenol-chloroform technique with or without a bead-beating step (P and PB), a QIAamp Fast DNA Stool Mini Kit (Q), and a QIAamp PowerFecal Pro DNA Kit (QB). Genomic DNA was extracted from 85 stool samples collected from patients infected with <i>Blastocystis</i> sp., <i>Ascaris lumbricoides, Trichuris trichiura,</i> hookworm, and <i>Strongyloides stercoralis</i>. DNA quantity and DNA quality were evaluated via spectrophotometry, and DNA integrity was assessed by PCR. We found that P and PB provided higher DNA yields (~4 times) than when using Q and QB. However, P showed the lowest detection rate of PCR (8.2%), wherein only <i>S. stercoralis</i> (7 out of 20 samples) was detected. QB showed the highest detection rate of PCR (61.2%). After plasmid spikes, only 5 samples by QB were negative while 60 samples by P were still negative. Remarkably, QB could extract DNA from all the groups of parasites that we tested. These results indicate that QB is the most effective DNA extraction method for the diagnosis and monitoring of intestinal parasites via PCR. |
| first_indexed | 2024-03-09T19:09:09Z |
| format | Article |
| id | doaj.art-30a88f5889184b54a20bad3fe6ad6211 |
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| issn | 2075-4418 |
| language | English |
| last_indexed | 2024-03-09T19:09:09Z |
| publishDate | 2022-10-01 |
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| record_format | Article |
| series | Diagnostics |
| spelling | doaj.art-30a88f5889184b54a20bad3fe6ad62112023-11-24T04:17:41ZengMDPI AGDiagnostics2075-44182022-10-011211258810.3390/diagnostics12112588Comparative Study of DNA Extraction Methods for the PCR Detection of Intestinal Parasites in Human Stool SamplesSiriporn Srirungruang0Buraya Mahajindawong1Panachai Nimitpanya2Uthaitip Bunkasem3Pattama Ayuyoe4Surang Nuchprayoon5Vivornpun Sanprasert6Lymphatic Filariasis and Tropical Medicine Research Unit, Chulalongkorn Medical Research Center (Chula-MRC), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, ThailandLymphatic Filariasis and Tropical Medicine Research Unit, Chulalongkorn Medical Research Center (Chula-MRC), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, ThailandLymphatic Filariasis and Tropical Medicine Research Unit, Chulalongkorn Medical Research Center (Chula-MRC), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, ThailandLymphatic Filariasis and Tropical Medicine Research Unit, Chulalongkorn Medical Research Center (Chula-MRC), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, ThailandLymphatic Filariasis and Tropical Medicine Research Unit, Chulalongkorn Medical Research Center (Chula-MRC), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, ThailandLymphatic Filariasis and Tropical Medicine Research Unit, Chulalongkorn Medical Research Center (Chula-MRC), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, ThailandLymphatic Filariasis and Tropical Medicine Research Unit, Chulalongkorn Medical Research Center (Chula-MRC), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, ThailandStool samples typically contain PCR inhibitors; however, helminths are difficult to lyse and can cause false-negative PCR results. We assessed the effective methods for extracting DNA from different kinds of intestinal parasites. We compared the most common DNA extraction methods from stool samples, including the phenol-chloroform technique with or without a bead-beating step (P and PB), a QIAamp Fast DNA Stool Mini Kit (Q), and a QIAamp PowerFecal Pro DNA Kit (QB). Genomic DNA was extracted from 85 stool samples collected from patients infected with <i>Blastocystis</i> sp., <i>Ascaris lumbricoides, Trichuris trichiura,</i> hookworm, and <i>Strongyloides stercoralis</i>. DNA quantity and DNA quality were evaluated via spectrophotometry, and DNA integrity was assessed by PCR. We found that P and PB provided higher DNA yields (~4 times) than when using Q and QB. However, P showed the lowest detection rate of PCR (8.2%), wherein only <i>S. stercoralis</i> (7 out of 20 samples) was detected. QB showed the highest detection rate of PCR (61.2%). After plasmid spikes, only 5 samples by QB were negative while 60 samples by P were still negative. Remarkably, QB could extract DNA from all the groups of parasites that we tested. These results indicate that QB is the most effective DNA extraction method for the diagnosis and monitoring of intestinal parasites via PCR.https://www.mdpi.com/2075-4418/12/11/2588DNA extractionbead-beating procedurestool samplesintestinal parasitespolymerase chain reactionPCR inhibitor |
| spellingShingle | Siriporn Srirungruang Buraya Mahajindawong Panachai Nimitpanya Uthaitip Bunkasem Pattama Ayuyoe Surang Nuchprayoon Vivornpun Sanprasert Comparative Study of DNA Extraction Methods for the PCR Detection of Intestinal Parasites in Human Stool Samples Diagnostics DNA extraction bead-beating procedure stool samples intestinal parasites polymerase chain reaction PCR inhibitor |
| title | Comparative Study of DNA Extraction Methods for the PCR Detection of Intestinal Parasites in Human Stool Samples |
| title_full | Comparative Study of DNA Extraction Methods for the PCR Detection of Intestinal Parasites in Human Stool Samples |
| title_fullStr | Comparative Study of DNA Extraction Methods for the PCR Detection of Intestinal Parasites in Human Stool Samples |
| title_full_unstemmed | Comparative Study of DNA Extraction Methods for the PCR Detection of Intestinal Parasites in Human Stool Samples |
| title_short | Comparative Study of DNA Extraction Methods for the PCR Detection of Intestinal Parasites in Human Stool Samples |
| title_sort | comparative study of dna extraction methods for the pcr detection of intestinal parasites in human stool samples |
| topic | DNA extraction bead-beating procedure stool samples intestinal parasites polymerase chain reaction PCR inhibitor |
| url | https://www.mdpi.com/2075-4418/12/11/2588 |
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