ArticleMicrobiology spectrum2023
Pathogen Detection Using Metagenomic Next-Generation Sequencing of Plasma Samples from Patients with Sepsis in Uganda.
Article in Microbiology spectrum, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Establishment and application of a multiplex qPCR panel for multi-host surveillance of tick-Borne pathogens.Emerging microbes & infections · 2026Article
- Article
- Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical sample types, with analysis of paired bronchoalveolar lavage fluid and blood samples.Microbiology spectrum · 2026Article
- Next-Generation Sequencing Dataset Downloader and In Silico Sequence Mining: Graphical-User-Interface-Based Tools for Accessible, Multiprobe Target Mining in Next-Generation Sequencing Data.Computational and structural biotechnology journal · 2026Article
- Article
- Reassessing the promise of NGS in sepsis diagnosis: overcoming scalability barriers.Future microbiology · 2025Article
- Deploying Metagenomics to Characterize Microbial Pathogens During Outbreak of Acute Febrile Illness Among Children in Tanzania.Pathogens (Basel, Switzerland) · 2025Article
- Clinical implement of Probe-Capture Metagenomics in sepsis patients: A multicentre and prospective study.Clinical and translational medicine · 2025Article
- Epstein-Barr Virus in the RIVERA Case-Control Study of Acute Febrile Illness: Acute Mononucleosis Nearly Absent as an Etiology in the Peruvian Amazon.The American journal of tropical medicine and hygiene · 2025Article
- Blood microbiota in HIV-infected and HIV-uninfected patients with suspected sepsis detected by metagenomic next-generation sequencing.BMC infectious diseases · 2024Article
- Article
- Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases.Veterinary sciences · 2024Review
- Anthelmintic resistance in soil-transmitted helminths: One-Health considerations.Parasitology research · 2023Review
- Etiology of Fever and Associated Outcomes Among Adults Receiving Chemotherapy for the Treatment of Solid Tumors in Uganda.Open forum infectious diseases · 2023Article
- Clinical Application and Evaluation of Metagenomic Next-Generation Sequencing for Lower Respiratory Tract Infections and Human Tumor Screening.International journal of general medicine · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Metagenomic sequencing is a promising new method for pathogen detection. We aimed to detect pathogens from archived plasma using metagenomic sequencing in a previously well-characterized cohort of 254 predominantly HIV-infected patients with sepsis in Uganda. We used Illumina sequencing and the Chan Zuckerberg ID metagenomics platform to sequence and identify pathogens. On average, each plasma sample yielded 3,404,737 ± 2,201,997 reads (mean ± standard deviation), of which 220,032 ± 416,691 (6.3% ± 8.6%) were identified as nonhuman reads. Using a background model filter, 414 genus-specific pathogen identifications were found in the 254 samples. Nineteen pathogens were previously detected positive by quantitative PCR (qPCR), compared to sequencing, which demonstrated 30.2% sensitivity and 99.5% specificity. Sensitivity was higher for viral pathogens than nonviral pathogens (37% versus 5%). For example, HIV viremia was detected in 69% of samples using qPCR, and sequencing revealed 70% sensitivity and 92% specificity. There were 75 genus-specific potential pathogens identified by sequencing in this cohort, including hepatitis B and Epstein-Barr virus (EBV), among several others. qPCR showed a prevalence of hepatitis B and EBV viremia of 17% and 45%, respectively. In-hospital mortality was associated with a lower qPCR threshold cycle value for EBV (adjusted odds ratio, 0.85;
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