Unlocking the Hidden Causes of Sepsis in Children

How Genetic Detective Work is Revolutionizing Medicine

mNGS Technology Pediatric Sepsis Genetic Diagnostics

The Tiny Patients and the Diagnostic Dilemma

Pediatric Mortality Range

5-20%

Mortality rate for pediatric sepsis patients 1

Annual Infant Deaths

3 Million

Sepsis-related deaths in premature infants annually 1

Sepsis, a life-threatening organ dysfunction caused by a dysregulated host response to infection, remains a formidable foe in pediatric and neonatal medicine. It's one of the main causes of mortality and morbidity in these vulnerable age groups 1 .

Diagnostic Challenge: Traditional culture-based methods have low sensitivity and specificity with high rates of false positives and negatives 1 3 8 .

For clinicians, the clock starts ticking the moment a child presents with potential sepsis. Timely and appropriate antibiotic therapy is crucial for survival, yet traditional culture-based diagnostic methods have significant limitations 1 3 .

The mNGS Revolution: From Genetic Fragments to Diagnostic Answers

What is Metagenomic Next-Generation Sequencing?

At its core, mNGS is a sophisticated method that enables comprehensive analysis of all genetic material in a clinical sample. Unlike traditional tests, mNGS takes an unbiased, hypothesis-free approach 5 8 .

Pathogens Detectable by mNGS
Why mNGS Matters for Pediatric Sepsis
  • Detects polymicrobial infections 1
  • Identifies unusual pathogens
  • Works despite prior antibiotic treatment 3 8
  • Provides rapid, precise pathogen identification

A Closer Look at the Evidence: Systematic Review Findings

Systematic Review Overview

5

Studies Analyzed

462

Patients Included

Recent research has begun to systematically evaluate the real-world performance of mNGS in pediatric sepsis diagnosis. A 2023 systematic review examined five studies including 462 patients 1 .

Key Finding: mNGS improves etiological identification in neonatal and pediatric sepsis, especially for negative cultures and unusual microorganisms 1 .

The potential clinical impact is substantial—more accurate and rapid diagnosis could significantly improve the rational use of antibiotics in this vulnerable population 1 .

Inside a Groundbreaking Study: Integrated Host-Microbe Metagenomics

Methodology: A Dual Approach to Sepsis Diagnosis

One of the most innovative applications of mNGS in sepsis comes from a 2022 study that took a revolutionary dual approach 6 . Rather than just looking for pathogens, researchers performed integrated host and pathogen metagenomic RNA and DNA sequencing from whole blood and plasma 6 .

Study Patient Categories:
SepsisBSI

Sepsis with microbiologically confirmed bloodstream infection

Sepsisnon-BSI

Sepsis with microbiologically confirmed non-bloodstream infection

Sepsissuspected

Suspected sepsis with negative clinical microbiologic testing

No-sepsis

No evidence of sepsis with clear alternative diagnosis

Indeterminate

Uncertain status 6

Results and Analysis: Unlocking New Diagnostic Insights

Classifier Type Sample Source Training AUC Validation AUC
Host Transcriptional Whole Blood 0.81 0.82
Host Transcriptional Plasma RNA 0.97 0.77
Viral Detection Plasma 0.94 0.96
Host Response Signature

Researchers identified 5,807 differentially expressed genes between patients with confirmed sepsis and those without infection 6 .

Integrated Diagnostic Model

Combined host and pathogen analysis identified 99% of microbiologically confirmed sepsis cases 6 .

mNGS in Action: Clinical Impact on Patient Outcomes

A 2025 multicenter prospective study of 859 adult sepsis patients compared conventional microbiological testing (CMT) alone versus CMT plus mNGS 8 .

92.0%

Positive Percent Agreement

mNGS vs composite reference standard 8

29.2%

Antibiotic Changes

Based on mNGS results 8

5.2%

7-Day Mortality

CMT + mNGS group vs 8.6% in CMT-only group 8

Outcome Measure CMT Only Group CMT + mNGS Group Statistical Significance
7-Day Mortality 8.6% 5.2% HR 0.44, p=0.004 8
28-Day Mortality Not reported Not reported No significant difference 8
Pathogen Detection 51.1% 92.0% p<0.001 8
Therapeutic Changes Not applicable 29.2% Not applicable 8
Clinical Impact: The dramatic reduction in early mortality highlights how rapid pathogen identification can influence the most critical early phase of sepsis management 8 .

The mNGS Toolkit: Essential Components for Success

Tool/Reagent Function Application in mNGS
16S rRNA Primers Amplify hypervariable regions of bacterial 16S gene Bacterial identification and phylogenetic analysis 7
Nextera DNA Flex Kit Library preparation for DNA sequencing Fragmentation and adapter addition for Illumina platforms 8
Ovation Trio RNA-Seq Kit cDNA generation and library prep from RNA Transcriptomic analysis and RNA virus detection 8
Host Depletion Reagents Remove human nucleic acids Improve sensitivity by reducing host background 5
Bioinformatics Pipelines Taxonomic classification and resistance gene detection Translate raw data into clinically actionable results 5
mNGS Workflow
  1. Sample preparation
  2. Nucleic acid extraction
  3. Library preparation
  4. Sequencing
  5. Bioinformatic analysis 4
Targeted NGS Approaches
  • Hybrid capture-based methods: Use solution-phase probes to enrich target sequences 4
  • Amplification-based approaches: Use PCR to amplify specific regions 4

Conclusion: The Future of Pediatric Sepsis Diagnosis

The Paradigm Shift in Sepsis Diagnosis

Metagenomic next-generation sequencing represents a paradigm shift in how we approach the diagnostic challenge of pediatric and neonatal sepsis.

Rapid Diagnosis Precise Identification Targeted Therapies Improved Outcomes

By moving beyond century-old culture techniques to comprehensive genetic analysis, mNGS offers the potential for rapid, precise pathogen identification even in the most complex cases.

The Future Vision: As these technologies evolve, they hold the promise of transforming sepsis from a deadly diagnostic puzzle into a manageable condition with precisely targeted therapies.

References