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Updated: Jun 29, 2026

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
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Plasma Microbial Cell-Free DNA Sequencing for Pathogen Detection and Quantification in Children With Musculoskeletal

James B Wood1,2, Kelsey Russell1, Tom E Davis3

  • 1Ryan White Center for Pediatric Infectious Diseases and Global Health, Indiana University School of Medicine, Indianapolis, Indiana, USA.

Journal of the Pediatric Infectious Diseases Society
|February 8, 2024
PubMed
Summary

Plasma microbial cell-free DNA (mcfDNA) sequencing shows promise for identifying pathogens in pediatric musculoskeletal infections (MSKIs), especially when samples are collected before surgery. This method offers a longer detection window than traditional blood cultures.

Keywords:
diagnosticsmicrobial cell-free DNA sequencingmusculoskeletal infectionsosteomyelitispediatricsseptic arthritis

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Area of Science:

  • Molecular Diagnostics
  • Pediatric Infectious Diseases
  • Genomic Medicine

Background:

  • Pediatric musculoskeletal infections (MSKIs) frequently present as culture-negative, limiting accurate diagnosis.
  • Plasma microbial cell-free DNA (mcfDNA) sequencing offers a non-invasive alternative to culture, bypassing common diagnostic barriers.

Purpose of the Study:

  • To evaluate the diagnostic performance of plasma mcfDNA sequencing in pediatric MSKIs.
  • To compare the pathogen detection duration of mcfDNA sequencing with traditional blood cultures.
  • To assess the impact of sample timing (pre- vs. post-surgery) on mcfDNA sequencing concordance.

Main Methods:

  • Prospective study of children (6 months–18 years) with MSKIs from July 2019 to May 2022.
  • Serial plasma mcfDNA sequencing samples were collected and compared with concurrent blood cultures.
  • Analysis included pathogen recovery rates, concordance, and duration of detection.

Main Results:

  • mcfDNA sequencing identified pathogens in 81% of cases, compared to 68% for culture.
  • Concordance with culture was higher when samples were obtained pre-surgery (82%) versus post-surgery (20%).
  • mcfDNA sequencing detected pathogens for a significantly longer interval (median 2 days) than blood culture (median 1 day).

Conclusions:

  • Plasma mcfDNA sequencing is a valuable tool for diagnosing culture-negative pediatric MSKIs, particularly when samples are collected pre-surgery.
  • Frequent detection of multiple pathogens necessitates careful interpretation and diagnostic stewardship.
  • mcfDNA sequencing extends the window for pathogen detection compared to blood cultures.