Comparison of rectal swabs and faeces for real-time PCR detection of enteric agents in Rwandan children with gastroenteritis

Abstract

BackgroundMolecular diagnostics have emerged as an efficient and feasible alternative for broad detection of pathogens in faeces. However, collection of stool samples is often impractical in both clinical work and in epidemiology studies. The aim of this study was to investigate the diagnostic performance of rectal swabs as compared with traditional faeces samples for detection of enteric agents by PCR.MethodThree hundred twenty-six pairs of rectal swab and stool samples, obtained from Rwandan children aged 0.5-4.99 years, with or without diarrhoea, were analysed by multiple real-time PCR amplifying 3 viral, 6 bacterial and one protozoan target.ResultsFor all agents there was a significant correlation (R2 0.31-0.85) between Ct values in faeces and rectal swabs. For most agents the Ct values, a marker for target concentration, were significantly lower (by 1–3 cycles) in faeces, indicating pathogen content up to ten times higher than in rectal swabs. Despite this, there was no significant difference in detection rate between faeces and rectal swabs for any agent, reflecting that pathogen concentration was far above the limit of detection in the majority of cases.ConclusionThe similar detection rates and the Ct value correlations as compared with traditional faeces samples indicate that rectal swabs are accurate for real-time PCR-based identification of enteric agents and may be used also for quantitative estimation of pathogen load.

Evaluation of Anatomically Designed Flocked Rectal Swabs for Molecular Detection of Enteric Pathogens in Children Admitted to Hospital with Severe Gastroenteritis in Botswana

“…However, this potential difference in E. his- tolytica detection by preanalytical method is unlikely to affect the results of the swab and bulk stool comparison, as all matching samples were processed identically, and neither viral nor bacterial target amplification was affected by extraction methods. A similar study carried out with children presenting with diarrhea in Rwanda compared regular flocked swabs to bulk stool PCR and found similar yields for the qualitative detection of multiple bacterial, viral, and parasitic pathogens (18). Our swab showed similar detection rate for most pathogen targets but actually had a higher yield for several bacterial targets.…”

Pattern of Circulation of Norovirus GII Strains during Natural Infection

“…previous studies where NoV was detected in 4 to 11% of asymptomatic participants (25)(26)(27). NoVs are considered an important cause of viral gastroenteritis in all age groups.…”

Norovirus prevention and the prevalence of asymptomatic norovirus infection in kindergartens and primary schools in Changzhou, China: Status of the knowledge, attitudes, behaviors, and requirements

“…These settings were from 1 urban district (also randomly selected) and 3 suburban counties. Rectal swabs are as accurate as stool samples for polymerase chain reaction-based identification of NoV. 12,13 Swab samples were taken from healthy students with no diarrhea or vomiting or other gastroenteritis symptoms (eg, stomach cramps, fever, headache, and muscle aches) for at least 72 hours before and 48 hours after the day of sampling. This asymptomatic infection was defined based on previous studies.…”