Detection of <i>Cryptosporidium hominis</i> by clinical metagenomics in stool samples from an outbreak of diarrhoea among British military personnel in Kenya
Halford et al.
The finding, in our words
A study limited by sample size found OMNIgene GUT tubes preserved Cryptosporidium DNA better than DNA Shield and FTA cards after year-long ambient storage. qPCR detected DNA in 23/24 OMNIgene, 21/24 DNA Shield, and 17/20 FTA samples, while metagenomics detected it in 13/24, 9/24, and 0/24 samples respectively, guiding decentralised sampling choices.
A paraphrase to the Library’s standard, never the abstract. The source is one link away and is always the authority.
In a field cohort of 60 adults with diarrhoea, OMNIgene 200 and DNA/RNA shield maintained high sensitivity and concordance with fresh samples for most pathogens, while FTA cards showed low sensitivity for STEC and poor specificity for Campylobacter. This supports the use of stabilised stool media for decentralised PCR testing after prolonged ambient transport.
Taxonomic and diversity profiles differed between unstabilised swabs and stabilised OmniGene kits, with transport time disproportionately affecting swab samples; the collection method had a greater impact on taxa and diversity than transport time, highlighting the need for standardised stool collection in decentralised microbiome studies.
The study found significant gut microbiota alterations in systemic lupus erythematosus patients, with different beta diversity, p=0.001, and shifts in phyla abundance compared to controls. Specific microbial profiles were associated with clinical subgroups, though the authors note the clinical relevance of species-level alterations requires further validation.
This study compared OMNIgene Gut tubes and FTA cards for stool collection in a deployed setting, finding that OMNIgene yielded higher nucleic acid concentrations while both methods detected the majority of microbial genera. The authors conclude that distinct microbial abundance profiles between the two methods necessitate standardised protocols for field research.
This study compared two preservatives for stool samples and found that OMNIgene GUT OMR-200 produced less variation in metagenomic taxonomic data across different storage temperatures, supporting its use in decentralised field studies. The authors recommend absolute quantification to address bias in microbial measurements.