{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T18:10:09Z","timestamp":1788977409508,"version":"build-2803163510"},"update-to":[{"DOI":"10.1371\/journal.pntd.0014175","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000}}],"reference-count":74,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Global Health EDCTP3 Joint Undertaking.","award":["101103059 (GREAT-LIFE)"],"award-info":[{"award-number":["101103059 (GREAT-LIFE)"]}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:sec id=\"sec001\">\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      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\n                      <jats:italic>Vibrio cholerae<\/jats:italic>\n                      is critical, yet cholera-suspected diarrhoea can have multiple infectious causes not captured by targeted diagnostics.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      <jats:italic>V. cholerae<\/jats:italic>\n                      signals were only detected in a subset of suspected cholera cases, while many samples were dominated by alternative bacterial taxa, most frequently\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                      .\n                      <jats:italic>V. cholerae<\/jats:italic>\n                      abundance correlated strongly with detection of the C holera T oxin P hage CTX\u03c6, supporting differentiation between toxigenic signal and background exposure. AMR genes were detected across samples, providing early situational insight into resistance determinants among gastrointestinal bacteria.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec004\">\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pntd.0014175","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T17:49:21Z","timestamp":1788284961000},"page":"e0014175","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics"],"prefix":"10.1371","volume":"20","author":[{"given":"Emilie","family":"Egholm Bruun Jensen","sequence":"first","affiliation":[{"name":"Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark","place":["Kgs Lyngby, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"N\u00e9h\u00e9mie","family":"Nzoyikorera","sequence":"additional","affiliation":[{"name":"National Reference Laboratory, Institut National de Sant\u00e9 Publique (INSP) du Burundi","place":["Bujumbura, Burundi"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mirena","family":"Ivanova","sequence":"additional","affiliation":[{"name":"Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark","place":["Kgs Lyngby, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pimlapas","family":"Leekitcharoenphon","sequence":"additional","affiliation":[{"name":"Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark","place":["Kgs Lyngby, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie","family":"Noelle Uwineza","sequence":"additional","affiliation":[{"name":"National Reference Laboratory, Institut National de Sant\u00e9 Publique (INSP) du Burundi","place":["Bujumbura, Burundi"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Idrissa","family":"Diawara","sequence":"additional","affiliation":[{"name":"Research Laboratory of Microbiology, Infectious Diseases, Allergology and Pathogen Surveillance (LARMIAS), Mohammed VI Faculty of Medicine, Mohammed VI University of Sciences and Health (UM6SS)","place":["Casablanca, Morocco"]},{"name":"Mohammed VI Higher Institute of Biosciences and Biotechnologies, Mohammed VI University of Sciences and Health (UM6SS)","place":["Casablanca, Morocco"]},{"name":"Mohammed VI Center for Research and Innovation","place":["Rabat, Morocco"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph","family":"Nyandwi","sequence":"additional","affiliation":[{"name":"National Public Health Institute, Ministry of Public Health Bujumbura","place":["Bujumbura, Burundi"]},{"name":"Universit\u00e9 du Burundi","place":["Bujumbura, Burundi"],"department":["Facult\u00e9 de M\u00e9decine"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frank","family":"M. 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