jmaasch/giardia-swab-detection

Validity of DNA isolation from rectal swabs versus bulk stool for the real-time PCR detection of Giardia duodenalis. Goal: To develop a protocol for DNA isolation from rectal swabs for qPCR detection of enteric parasites and to validate this protocol by comparing the validity of qPCR diagnosis by paired rectal swab and bulk stool samples collected in rural Boboye Department, Dosso Region, Niger. # Rectal swabs as an alternative sample collection method to bulk stool for the real-time PCR detection of *Giardia duodenalis* > *Above:* Real-time PCR sensitivity of rectal swab specimens by corresponding bulk stool Cq value. Rectal swab sensitivity varies when samples are binned by the Cq quartile of the participant’s corresponding *Giardia*-positive bulk stool sample (*N* = 55). ## Project outline **Resulting publications:** A paper resulting from this project can be found in *The American Journal of Tropical Medicine & Hygiene* (doi:10.4269/ajtmh.19-0909). Results were presented at the American Society of Tropical Medicine & Hygiene 68th Annual Meeting (November 2019, National Harbor, Maryland USA) in a poster titled *Rectal swabs for molecular detection of Giardia duodenalis.* **Project goals:** * To develop a protocol for DNA isolation from rectal swabs for qPCR detection of enteric parasites. * To assess the comparative validity and reproducibility of qPCR diagnosis of *Giardia duodenalis* by DNA isolated from paired rectal swab and bulk stool samples collected in rural Boboye Department, Dosso Region, Niger. **Study authors:** Jacqueline R. M. A. Maasch 1 , Ahmed M. Arzika 2 , Catherine Cook 3 , Elodie Lebas 3 , Nils Pilotte 1,4 , Jessica R. Grant 1 , Steven A. Williams 1, 4 , Jeremy D. Keenan 3 , Thomas M. Lietman 3 , Kristen Aiemjoy 3, 5 **Affiliations:** 1. Department of Biological Sciences, Smith College, Northampton, MA, USA 2. The Carter Center, Niamey, République du Niger 3. Proctor Foundation, University of California San Francisco, San Francisco, CA, USA 4. Department of Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA 5. Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA > *Above:* Real-time PCR Cq value correlations by specimen type (A) and sample replicate group (B & C). Plots depict Cq value correlations for paire …