{
  "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.",
  "authors": [
    {
      "affiliations": [
        "Defence Science and Technology Laboratory Porton Down, Salisbury, UK",
        "Norwich Medical School, University of East Anglia, Norwich, UK"
      ],
      "name": "Carl Halford"
    },
    {
      "affiliations": [
        "Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK",
        "Army Medical Services, Royal Military Academy Sandhurst, Camberley, UK"
      ],
      "name": "Romeo Toriro"
    },
    {
      "affiliations": [
        "Defence Science and Technology Laboratory Porton Down, Salisbury, UK"
      ],
      "name": "Emily Rowlands"
    },
    {
      "affiliations": [
        "Quadram Institute Bioscience, Norwich, UK"
      ],
      "name": "Thanh Le Viet"
    },
    {
      "affiliations": [
        "Defence Science and Technology Laboratory Porton Down, Salisbury, UK"
      ],
      "name": "Stephanie Schaap"
    },
    {
      "affiliations": [
        "Centre for Defence Pathology, Royal Centre for Defence Medicine, Birmingham, UK",
        "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK"
      ],
      "name": "Matthew K O’Shea"
    },
    {
      "affiliations": [
        "Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK",
        "Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK"
      ],
      "name": "Thomas Fletcher"
    },
    {
      "affiliations": [
        "Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK"
      ],
      "name": "Nicholas J Beeching"
    },
    {
      "affiliations": [
        "Centre for Defence Pathology, Royal Centre for Defence Medicine, Birmingham, UK",
        "Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK"
      ],
      "name": "Stephen Woolley"
    },
    {
      "affiliations": [
        "Defence Science and Technology Laboratory Porton Down, Salisbury, UK"
      ],
      "name": "Roman Lukaszewski"
    },
    {
      "affiliations": [
        "Norwich Medical School, University of East Anglia, Norwich, UK",
        "Quadram Institute Bioscience, Norwich, UK"
      ],
      "name": "Matthew Gilmour"
    },
    {
      "affiliations": [
        "Defence Science and Technology Laboratory Porton Down, Salisbury, UK"
      ],
      "name": "Simon A Weller"
    }
  ],
  "title": "Detection of Cryptosporidium hominis by clinical metagenomics in stool samples from an outbreak of diarrhoea among British military personnel in Kenya",
  "uid": "cca4d486-4350-5e19-8822-66b7748dd376"
}