Detection of Cryptosporidium hominis by clinical metagenomics in stool samples from an outbreak of diarrhoea among British military personnel in Kenya

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Halford, Carl, Toriro, Romeo, Rowlands, Emily, Le Viet, Thanh, Schaap, Stephanie, O’Shea, Matthew K., Fletcher, Thomas, Beeching, Nicholas J., Woolley, Stephen, Lukaszewski, Roman, Gilmour, Matthew and Weller, Simon A. (2026) Detection of Cryptosporidium hominis by clinical metagenomics in stool samples from an outbreak of diarrhoea among British military personnel in Kenya. BMJ Military Health. ISSN 2633-3767

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Abstract

Introduction: Traveller's diarrhoea is a common complaint among deployed military personnel. Maintaining sample integrity prior to diagnostic testing is a key challenge in resource-limited environments. We report the comparison of three long-term ambient temperature stool sample stabilisation matrices for the detection of Cryptosporidium hominis from samples collected during an outbreak among British military personnel stationed in Kenya.  Methods: A retrospective cohort of stool samples, each stabilised for more than 12 months at ambient temperatures using Flinders Technical Associate (FTA) cards, OMNIgene GUT tubes and DNA Shield faecal collection tubes, were analysed by Nanopore-based clinical metagenomic (CMgs) DNA sequencing and quantitative real-time PCR (qPCR) in the UK. The results were compared with BioFire FilmArray Gastrointestinal Panel testing carried out at the point of sampling in Kenya.  Results: Cryptosporidium DNA was detected in 13/24 (54.2%) OMNIgene GUT samples by CMg following long-term storage, compared with 9/24 (37.5%) of DNA Shield samples. Samples stored on FTA cards did not identify Cryptosporidium DNA by CMg in any sample. OMNIgene GUT samples also had the highest rate of detection of C. hominis DNA by qPCR, with 23/24 samples testing positive, compared with 21/24 and 17/20 of DNA Shield and FTA samples, respectively.  Conclusions: Samples stored in OMNIgene GUT tubes retained detectable levels of Cryptosporidium DNA in a higher proportion of samples following long-term storage. This study demonstrates the importance of selecting the optimal sample collection and stabilisation matrix for CMg and qPCR based diagnostic testing in austere environments.

Item Type: Article
Additional Information: Data availability statement: Data are available upon reasonable request.
Uncontrolled Keywords: gastrointestinal infections,infectious diseases,military personnel,molecular biology,molecular diagnostics,public health, environmental and occupational health,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/2700/2739
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups: Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
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Depositing User: LivePure Connector
Date Deposited: 25 Aug 2026 15:50
Last Modified: 30 Aug 2026 23:03
URI: https://ueaeprints.uea.ac.uk/id/eprint/104350
DOI: 10.1136/military-2026-003248

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