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Pathogen determination from clinical abscess fluids using metagenomic next-generation sequencing.

Yuxi Zhao1, Jinlian Chen1, Bing Bai1

  • 1Department of Infectious Diseases and Shenzhen Key Laboratory for Endogenous Infection, Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China.

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Metagenomic next-generation sequencing (mNGS) accurately identifies abscess pathogens, including difficult-to-culture bacteria. This advanced method offers a comprehensive view of microbial communities in abscess fluids, aiding clinical treatment decisions.

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Area of Science:

  • Microbiology
  • Infectious Diseases
  • Genomics

Background:

  • Abscesses are localized necrotic tissue collections caused by microbial infections.
  • Accurate pathogen identification is crucial for effective antimicrobial therapy.
  • Conventional methods may fail to detect all causative agents in complex infections.

Purpose of the Study:

  • To evaluate the utility of metagenomic next-generation sequencing (mNGS) for microbial detection in clinical abscess fluid samples.
  • To compare mNGS with conventional bacterial culture for pathogen identification.
  • To assess the ability of mNGS to reveal microbial diversity in abscesses.

Main Methods:

  • Clinical abscess fluid samples from nine patients were analyzed.
  • Pathogen detection was performed using both conventional bacterial culture and mNGS.
  • Microbial composition and abundance were compared between the two methods.

Main Results:

  • mNGS identified dominant pathogens in 8 out of 9 cases, accounting for over 80% of reads.
  • mNGS results were consistent with culture in 6 cases.
  • mNGS detected fastidious anaerobic bacteria missed by culture in 2 cases.
  • mNGS revealed complex polymicrobial infections, including *Parvimonas micra*, not identified by culture.
  • mNGS provided insights into the microbial ecology of abscess fluids.

Conclusions:

  • mNGS is a valuable tool for detecting pathogens in abscess fluids.
  • mNGS offers advantages over conventional culture, especially for identifying fastidious or polymicrobial infections.
  • mNGS can serve as a supplemental diagnostic method for abscesses, guiding antimicrobial treatment.