{
  "abstract": "Background: Cholera outbreaks remain a major public-health challenge in sub-Saharan Africa, where diagnostic capacity is limited and clinical case definitions are non-specific and re ly heavily on syndromic diagnosis. Rapid identification of Vibrio cholerae is critical, yet cholera-suspected diarrhoea can have multiple infectious causes not captured by targeted diagnostics. Methods: We evaluated a mobile, culture-independent metagenomic sequencing workflow for on-site detection of gastrointestinal pathogens directly from faecal samples in Burundi. The offline workflow combined long-read Oxford Nanopore Technologies (ONT) sequencing with rapid, laptop-based taxonomic and antimicrobial resistance (AMR) screening and was deployed across a health centre, a district hospital, and a refugee transit camp. The frontline and real-time results were verified using both conventional culturing and in-depth bioinformatic analyses. Results: V. cholerae signals were only detected in a subset of suspected cholera cases, while many samples were dominated by alternative bacterial taxa, most frequently Escherichia coli. V. cholerae abundance correlated strongly with detection of the C holera T oxin P hage CTXφ, supporting differentiation between toxigenic signal and background exposure. AMR genes were detected across samples, providing early situational insight into resistance determinants among gastrointestinal bacteria. Conclusions: Mobile, offline metagenomic sequencing enables rapid frontline characterization of gastrointestinal disease, especially cholera-suspected, in resource-limited settings and complements existing diagnostics by improving etiological resolution and outbreak response. Author summary: Cholera remains a major cause of severe diarrhoeal disease in many low-resource settings, where diagnosis often relies on symptoms and limited laboratory testing. However, patients with suspected cholera may instead harbour other enteric pathogens that are not detected by cholera-specific diagnostic tests. In this study, we evaluated a portable, sequencing-based approach that allows direct identification of pathogens from stool samples at the point of care, without the need for laboratory infrastructure, internet access, or culture. Using this approach in multiple settings in Burundi, including a health centre, hospital, and refugee camp, we found a subset of suspected cholera cases were associated with Vibrio cholerae. Other cases were also dominated by other bacteria, particularly diarrheagenic Escherichia coli. We also detected antimicrobial resistance genes across samples, providing additional information relevant for treatment and surveillance. Our findings demonstrate that mobile metagenomic sequencing can improve the identification of disease causes directly in outbreak settings and help distinguish true cholera cases from other gastrointestinal infections. This approach has the potential to strengthen outbreak response, improve patient management, and support more accurate disease surveillance in resource-limited environments.",
  "abstract_shown": true,
  "affiliations": [
    "Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark",
    "National Reference Laboratory, Institut National de Santé Publique (INSP) du Burundi, Bujumbura, Burundi",
    "Research Laboratory of Microbiology, Infectious Diseases, Allergology and Pathogen Surveillance (LARMIAS), Mohammed VI Faculty of Medicine, Mohammed VI University of Sciences and Health (UM6SS), Casablanca, Morocco",
    "Mohammed VI Higher Institute of Biosciences and Biotechnologies, Mohammed VI University of Sciences and Health (UM6SS), Casablanca, Morocco",
    "Mohammed VI Center for Research and Innovation, Rabat, Morocco",
    "National Public Health Institute, Ministry of Public Health Bujumbura, Bujumbura, Burundi",
    "Faculté de Médecine, Université du Burundi, Bujumbura, Burundi"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Emilie Egholm Bruun Jensen"
    },
    {
      "affs": [
        1
      ],
      "name": "Néhémie Nzoyikorera"
    },
    {
      "affs": [
        2
      ],
      "name": "Mirena Ivanova"
    },
    {
      "affs": [
        3
      ],
      "name": "Pimlapas Leekitcharoenphon"
    },
    {
      "affs": [
        4
      ],
      "name": "Marie Noelle Uwineza"
    },
    {
      "affs": [
        5
      ],
      "name": "Idrissa Diawara"
    },
    {
      "affs": [
        6
      ],
      "name": "Joseph Nyandwi"
    },
    {
      "name": "Frank M. Aarestrup"
    },
    {
      "name": "Saria Otani"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/b8jcpbz1qh39g.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pntd.0014175",
  "fulltext_url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014175",
  "id": "b8jcpbz1qh39g",
  "issns": [
    "1935-2735"
  ],
  "landing_url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014175",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1310|Vibrio bacteria research studies"
    ],
    [
      "plos",
      "/Biology and life sciences/Computational biology/Genome analysis/Genomic databases"
    ],
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      "plos",
      "/Biology and life sciences/Genetics/Genomics/Genome analysis/Genomic databases"
    ],
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      "plos",
      "/Biology and life sciences/Genetics/Genomics/Metagenomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Bacterial pathogens/Escherichia coli"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Bacterial pathogens/Vibrio cholerae"
    ],
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      "/Biology and life sciences/Microbiology/Microbial control/Antimicrobial resistance"
    ],
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    ],
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      "plos",
      "/Medicine and health sciences/Medical conditions/Infectious diseases/Bacterial diseases/Cholera"
    ],
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      "plos",
      "/Medicine and health sciences/Medical conditions/Tropical diseases/Neglected tropical diseases/Cholera"
    ],
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      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Bacterial pathogens/Escherichia coli"
    ],
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      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Bacterial pathogens/Vibrio cholerae"
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      "/Medicine and health sciences/Pharmacology/Antimicrobial resistance"
    ],
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      "/Research and analysis methods/Animal studies/Experimental organism systems/Model organisms/Escherichia coli"
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      "/Research and analysis methods/Animal studies/Experimental organism systems/Prokaryotic models/Escherichia coli"
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  "pdf_url": "https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0014175&type=printable",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-01",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/b8jcpbz1qh39g.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:02Z",
      "native_id": "10.1371/journal.pntd.0014175",
      "source": "plos",
      "url": "https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014175"
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  "subjects": [
    {
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      "origin": "plos:genomics",
      "subfield": "genetics-genomics"
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    {
      "field": "biology",
      "origin": "plos:microbiology",
      "subfield": "microbiology"
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  ],
  "title": "Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics",
  "title_text": "Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:02Z",
  "url": "https://research.draconitic.com/paper/b8jcpbz1qh39g",
  "venue": "PLOS Neglected Tropical Diseases",
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