Rectal Swabs as an Alternative Sample Collection Method to Bulk Stool for the Real-Time PCR Detection of Giardia duodenalis

Abstract

Though bulk stool remains the gold standard specimen type for enteropathogen diagnosis, rectal swabs may offer comparable sensitivity with greater ease of collection for select pathogens. This study sought to evaluate the validity and reproducibility of rectal swabs as a sample collection method for the molecular diagnosis of Giardia duodenalis. Paired rectal swab and bulk stool samples were collected from 86 children ages 0-4 years living in southwest Niger, with duplicate samples collected among a subset of 50 children. Infection was detected using a previously validated real-time PCR diagnostic targeting the small subunit ribosomal RNA gene. Giardia duodenalis was detected in 65.5% (55/84) of bulk stool samples and 44.0% (37/84) of swab samples. The kappa evaluating test agreement was 0.81 (95% CI: 0.54-1.00) among duplicate stool samples (N = 49) and 0.75 (95% CI: 0.47-1.00) among duplicate rectal swabs (N = 48). Diagnostic sensitivity was 93% (95% CI: 84-98) by bulk stool and 63% (95% CI: 49-75) by rectal swabs. When restricting to the lowest three quartiles of bulk stool quantitation cycle values (an indication of relatively high parasite load), sensitivity by rectal swabs increased to 78.0% (95% CI: 64-89, P < 0.0001). These findings suggest that rectal swabs provide less sensitive and reproducible results than bulk stool for the real-time PCR diagnosis of G. duodenalis. However, their fair sensitivity for higher parasite loads suggests that swabs may be a useful tool for detecting higher burden infections when stool collection is excessively expensive or logistically challenging.

Molecular detection of intestinal helminths and protozoa among young children in Dosso Region, Niger

“…Isolation of total DNA from bulk stool and rectal swabs followed a procedure optimized for the qPCR detection of intestinal helminths 11 . Multi-parallel qPCR 7 targeted the following species: the STH Ancylostoma duodenale 6 , Ascaris lumbricoides 12 , Necator americanus 6 , and Trichuris trichiura 6 ; the trematode flukes Schistosoma haematobium 13 and Schistosoma mansoni 13 ; and the protozoan parasite Giardia duodenalis 14 .…”

“…All qPCR assays targeted highly repetitive non-coding elements with the exception of the G. duodenalis assay, which targets the small subunit ribosomal RNA gene. Procedures for sample collection, DNA isolation, qPCR, and quality control followed previously described protocols and standards 11 .…”

Molecular detection of intestinal helminths and protozoa among young children in Dosso Region, Niger

“…All qPCR assays targeted highly repetitive non-coding elements with the exception of the G. duodenalis assay, which targets the small subunit ribosomal RNA gene. Procedures for sample collection, DNA isolation, qPCR, and quality control followed previously described protocols and standards 14 .…”

First-Day-of-Life Rectal Swabs Fail To Represent Meconial Microbiota Composition and Underestimate the Presence of Antibiotic Resistance Genes

“…To advance current knowledge about factors influencing early gut colonization and microbiome development in infants, standardized and easy sampling techniques are needed to increase comparability of the studies and participant recruitment rates. Currently, collecting stool samples is known to be the “gold standard” in gut microbiome studies ( 16 – 18 ). Although stool sampling enables us to obtain a large amount of microbial biomass and is suitable for self-sampling by study participants in a nonclinical setting, several disadvantages emphasize the need for developing alternative sample collection techniques ( 18 ).…”