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Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
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Identification of prosthetic joint infections with 16S amplicon metagenomic sequencing - comparison with standard

Aleksander Mahnic1, Mitja Rak2, Rihard Trebše3

  • 1National Laboratory of Health, Environment and Food, Department for Microbiological Research, Maribor, Slovenia.

Diagnostic Microbiology and Infectious Disease
|February 10, 2024
PubMed

Insights

Amplicon metagenomic sequencing (16S AS) offers greater microbial diversity detection for prosthetic joint infections (PJIs) than traditional cultures. However, confirming bacterial presence with 16S AS remains challenging, indicating a need for improved diagnostic methods.

Area of Science:

  • Microbiology
  • Infectious Diseases
  • Genomics

Background:

  • Prosthetic joint infections (PJIs) pose significant clinical challenges.
  • Current diagnostic methods, primarily culture-based, may fail to detect all causative pathogens, especially fastidious or anaerobic bacteria.
  • Accurate and timely diagnosis is crucial for effective patient management and treatment strategies.

Purpose of the Study:

  • To compare the diagnostic performance of amplicon metagenomic sequencing (16S AS) against traditional culture methods for detecting pathogens in PJI sonicate fluid.
  • To evaluate the ability of 16S AS to identify a broader range of microbial diversity, including difficult-to-grow organisms.
  • To assess the potential of 16S AS as an enhanced tool for clinical decision-making in PJI diagnosis.

Main Methods:

  • Analysis of sonicate fluid samples from 27 patients undergoing revision arthroplasty.
  • Application of both traditional culture techniques and 16S amplicon metagenomic sequencing.
  • Utilized algorithms and rigorous controls to distinguish between contaminants and true microbial presence.

Main Results:

  • Moderate agreement was observed between 16S AS and culture methods (Cohen's kappa = 0.490), with significant variation across bacterial genera.
  • 16S AS demonstrated higher sensitivity (81%) compared to culture, revealing greater microbial diversity, including anaerobic genera.
  • Several culture-negative PJI samples yielded positive results with diverse bacterial identification via 16S AS.

Conclusions:

  • 16S AS provides a more comprehensive view of the microbial landscape in PJI sonicate fluid compared to standard cultures.
  • While promising for detecting a wider array of pathogens, challenges remain in confirming bacterial presence and differentiating contaminants using 16S AS.
  • Further development of next-generation sequencing (NGS) techniques and interpretation algorithms is necessary for its routine clinical application in PJI diagnostics.
Keywords:
Amplicon metagenomic sequencingCultivationPathogen detectionProsthetic joint infection

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