Sample Adequacy Controls for Infectious Disease Diagnosis by Oral Swabbing

Abstract

Oral swabs are emerging as a non-invasive sampling method for diagnosis of infectious diseases such as Ebola and tuberculosis. This project evaluated quality assurance strategies to assure proper sample collection. Two sample adequacy controls (SAC) that detect substances that are differentially present in properly versus improperly collected samples were assessed. One control detected oral microbial flora (Streptococcus species DNA) and the other, human cells (human mitochondrial DNA, mtDNA). Quantitative PCR (qPCR) assays for the two targets were applied to swabs of buccal and hand regions (representing properly improperly collected samples, respectively) collected from 51 healthy human volunteers in Seattle, WA, USA. Quantification cycle (Cq) cutoffs that maximized Youden’s index were established for each assay. The streptococcal target at a Cq cutoff of 34.9 had 99.0% sensitivity and specificity, whereas human mtDNA perfectly distinguished between hand and mouth swabs at Cq=31.3. The mtDNA test was then applied to buccal, tongue, and gum swabs collected from suspected tuberculosis patients in Worcester, South Africa. The three oral sites yielded indistinguishable amounts of human mtDNA, however PurFlockTM swabs collected slightly more human DNA than OmniSwabsTM (p = 0.035). Participant characteristics such as HIV status, TB status and gender did not influence Cq values for any swab type or mouth region. Quantitative PCR detection of human mtDNA can reliably distinguish proper sample collection from casual skin contact, and thereby serve as a sample adequacy control for oral swab-based diagnostics.