Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics
7 affiliations
- 1Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
- 2National Reference Laboratory, Institut National de Santé Publique (INSP) du Burundi, Bujumbura, Burundi
- 3Research 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
- 4Mohammed VI Higher Institute of Biosciences and Biotechnologies, Mohammed VI University of Sciences and Health (UM6SS), Casablanca, Morocco
- 5Mohammed VI Center for Research and Innovation, Rabat, Morocco
- 6National Public Health Institute, Ministry of Public Health Bujumbura, Bujumbura, Burundi
- 7Faculté de Médecine, Université du Burundi, Bujumbura, Burundi
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.
Related
- Whole-Genome Metagenomics Insights Revealed a Uranium Bio-remediating Cross-Domain Microbiome in the Dhala Impact Structure, India
- An FTA card-based CRISPR/Cas12a platform with isothermal amplification for portable tuberculosis diagnosis
- The resistome of European coastal environments revealed by high-resolution targeted metagenomics in oysters
- Delayed diagnosis of Netherton syndrome revealed by hair shaft microscopy.
- Unravelling the role of IRX4 variants in non-syndromic and Down syndrome associated congenital heart disease
BibTeX
@article{jensen2026syndromic,
title = {{Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics}},
author = {Emilie Egholm Bruun Jensen and Néhémie Nzoyikorera and Mirena Ivanova and Pimlapas Leekitcharoenphon and Marie Noelle Uwineza and Idrissa Diawara and Joseph Nyandwi and Frank M. Aarestrup and Saria Otani},
journal = {PLOS Neglected Tropical Diseases},
year = {2026},
month = sep,
doi = {10.1371/journal.pntd.0014175},
url = {https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014175},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics
AU - Emilie Egholm Bruun Jensen
AU - Néhémie Nzoyikorera
AU - Mirena Ivanova
AU - Pimlapas Leekitcharoenphon
AU - Marie Noelle Uwineza
AU - Idrissa Diawara
AU - Joseph Nyandwi
AU - Frank M. Aarestrup
AU - Saria Otani
PY - 2026
DA - 2026/09/01
JO - PLOS Neglected Tropical Diseases
DO - 10.1371/journal.pntd.0014175
UR - https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0014175
AB - 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.
SN - 1935-2735
ER -