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Deploying Metagenomics to Characterize Microbial Pathogens During Outbreak of Acute Febrile Illness Among Children in
Shabani Ramadhani Mziray1,2, George Githinji3,4, Zaydah R de Laurent3
1Department of Biochemistry and Molecular Biology, KCMC University, Moshi P.O. Box 2240, Tanzania.
Abstract:
Outbreaks of infectious diseases contribute significantly to morbidity and mortality in resource-limited settings, yet the capacity to identify their etiology remains limited. We aimed to characterize microbes and antimicrobial resistance (AMR) genes in Tanzanian children affected by an acute febrile illness (AFI) outbreak using metagenomic next-generation sequencing (mNGS). A cross-sectional study was conducted on archived blood samples from children who presented with AFI between 2018 and 2019. Total nucleic acids were extracted from 200 µL of blood, and complementary DNA (cDNA), along with enriched pathogenic DNA, was sequenced using the Illumina MiSeq platform. mNGS data were analyzed using CZ-ID Illumina mNGS bioinformatics pipeline v7.0. Results were obtained from 25 participants (mean age: 11.6 years; SD ± 5), of whom 36% had a moderate to high-grade fever. The following five potential microbial causes of AFI were identified: Escherichia coli (n = 19), Paraclostridium bifermentans (n = 2), Pegivirus C (n = 2), Shigella flexneri (n = 1) and Pseudomonas fluorescens (n = 1), with E. coli being the most prevalent. Twelve AMR genes were detected, including mdtC, acrF, mdtF, and emrB. E. coli harbored most of the AMR genes previously associated with resistance to commonly used antibiotics. mNGS offers a promising complementary approach to conventional diagnostics for identifying pathogens and AMR profiles in vulnerable populations.
Insights
Metagenomic sequencing identified microbes and antimicrobial resistance genes in children with acute febrile illness outbreaks in Tanzania. Escherichia coli was the most common pathogen, carrying resistance genes, highlighting mNGS as a valuable diagnostic tool.
Area of Science:
- Infectious Diseases
- Microbiology
- Genomics
Background:
- Infectious disease outbreaks cause significant illness and death in resource-limited areas.
- Identifying the causes of these outbreaks is crucial for effective treatment and control.
- Current diagnostic methods may have limitations in identifying diverse pathogens and antimicrobial resistance.
Purpose of the Study:
- To characterize microbial agents and antimicrobial resistance (AMR) genes in children with acute febrile illness (AFI) during an outbreak in Tanzania.
- To evaluate the utility of metagenomic next-generation sequencing (mNGS) for pathogen and AMR detection in this population.
Main Methods:
- A cross-sectional study analyzed archived blood samples from 25 children with AFI.
- Total nucleic acids were extracted and sequenced using the Illumina MiSeq platform.
- Metagenomic data were analyzed using the CZ-ID Illumina mNGS bioinformatics pipeline.
Main Results:
- Five potential microbial causes of AFI were identified, with *Escherichia coli* being the most prevalent (n=19).
- Twelve antimicrobial resistance genes were detected, with *E. coli* harboring most.
- The study identified *Paraclostridium bifermentans*, *Pegivirus C*, *Shigella flexneri*, and *Pseudomonas fluorescens* in a smaller number of cases.
Conclusions:
- Metagenomic next-generation sequencing is a promising tool for identifying pathogens and AMR profiles in vulnerable populations during disease outbreaks.
- mNGS can complement traditional diagnostic methods, improving etiological diagnosis in resource-limited settings.
