Prospective evaluation of different faecal preservation media for travellers' diarrhoea diagnostic application with multiplex PCR BioFire FilmArray in resource-limited settings.

Abstract

Introduction. Immediate identification of travellers' diarrhoea-causing pathogens may not be possible in remote settings, but samples can be stored for epidemiological and related research. We collected pilot data to evaluate the utility of three different preservation media for testing stored faecal samples compared to immediate testing of fresh samples using the BioFire^® FilmArray^® multiplex PCR gastrointestinal panel (bioMérieux).Gap statement. No previous studies have demonstrated the utility of testing faecal samples directly by PCR BioFire^® FilmArray^® following prolonged storage and transportation in OMNIgene^®, DNA^™ shield and FTA^™ cards.Aims. To evaluate the reliability of OMNIgene^®, DNA shield^™ and FTA^™ card faecal storage and transport media in parallel, compared to initial testing of fresh faeces obtained from the same individuals at the time of presentation with diarrhoea in the field compare the results of faecal samples stored and transported at ambient temperature in OMNIgene^®, DNA shield^™ and FTA^™ cards then tested using PCR BioFire^® FilmArray^® 6-18 months later with those obtained from fresh faecal samples during a diarrhoea outbreak.Methodology. Fresh faecal samples were obtained from British military personnel who developed diarrhoea during deployment to Kenya between February-April 2022. Unpreserved fresh samples were tested onsite using PCR BioFire^® FilmArray^® and corresponding samples were stored at ambient temperature in OMNIgene^®200 (DNAgenotek^®), DNA/RNA shield DX^™ (Zymo Research) and Whatman FTA™ Elute cards (GE Healthcare) then repatriated to the UK for direct testing by PCR BioFire^® FilmArray^®, 6-18 months later. The most common enteropathogens evaluated were: Cryptosporidium spp., Enteroaggregative Escherichia coli (E. coli; EAEC), Enteropathogenic E. coli (EPEC), Shiga toxin-producing E. coli (STEC) and Campylobacter spp. Test results for the three storage modalities were compared to the fresh sample tests as a reference standard.Results. Samples from 60 individuals [80% male; median (interquartile range) age 24 (22-28) years] were analysed. Test sensitivity for Campylobacter spp. and EAEC was high across all three storage modalities (86.4-100%). OMNIgene^®200 and DNA/RNA shield^™ showed significant concordance with the reference standard test for other pathogens, but FTA^™ Elute card tests had low sensitivity for STEC and poor specificity for Campylobacter spp. Agreement between FTA^™ Elute cards and the reference standard test was low-moderate (kappa coefficient ≤0-0.49) for all enteropathogens.Conclusions. This study demonstrates successful PCR BioFire^® FilmArray^® utility in testing samples stored in different media and is the first to compare the use of OMNIgene^®200, DNA/RNA shield^™ and FTA^™ Elute cards simultaneously with the results of clinical samples. Stored samples were tested up to 18 months later with significant concordance observed in OMNIgene^®200 and DNA/RNA shield^™ compared to reference standard testing. The distorted performance of FTA^™ Elute card testing requires further optimisation. Testing of samples stored in these media is suitable for research studies, but their applicability with other molecular diagnostic platforms, or clinical diagnostics, requires confirmation.