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Updated: Apr 28, 2026

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
Molecular revolution in the diagnosis of microbial brain abscesses
A K Mishra1, H Dufour, P-H Roche
1URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.
Abstract:
A brain abscess is a life-threatening infection, frequently with serious sequelae. Culture-based methods present many limitations and do not enable an exhaustive documentation of the bacterial flora. 16S rRNA-based amplification, cloning, and high-throughput sequencing have dramatically increased the number of identified agents of brain abscesses, showing that the causative flora is polymicrobial in up to 40 % of cases, with the presence of at least one anaerobic bacterium. In contrast, real-time polymerase chain reaction (PCR) technology is an appealing alternative to culture-based methods for diagnosing brain abscesses due to its speed, sensitivity, and specificity. Molecular typing is available for several bacterial and fungal genera, and this user-friendly tool is accessible for the clinical microbiology laboratory to diagnose microbes involved in a brain abscess. This article reviews the applications of the currently available tools for the etiological diagnosis of a brain abscess.
Insights
Diagnosing brain abscesses is challenging due to limitations in traditional culture methods. Molecular techniques like 16S rRNA sequencing and real-time polymerase chain reaction (PCR) offer faster, more accurate identification of polymicrobial infections.
Area of Science:
- Microbiology
- Infectious Diseases
- Neurology
Background:
- Brain abscesses are severe infections with potential for lasting neurological damage.
- Traditional culture methods for identifying causative agents are often insufficient and time-consuming.
- Emerging molecular techniques offer improved diagnostic capabilities for brain abscesses.
Purpose of the Study:
- To review current molecular tools for the etiological diagnosis of brain abscesses.
- To highlight the limitations of culture-based methods in identifying polymicrobial flora.
- To discuss the advantages of real-time polymerase chain reaction (PCR) and sequencing in diagnosing brain infections.
Main Methods:
- Review of literature on molecular diagnostic techniques for brain abscesses.
- Comparison of culture-based methods with 16S rRNA sequencing and real-time PCR.
- Analysis of the utility of molecular typing for microbial identification.
Main Results:
- 16S rRNA sequencing has identified polymicrobial etiology in up to 40% of brain abscesses, often including anaerobic bacteria.
- Real-time PCR provides a rapid, sensitive, and specific alternative to culture for diagnosing brain abscesses.
- Molecular typing tools are becoming accessible for clinical microbiology laboratories.
Conclusions:
- Molecular methods significantly enhance the identification of causative agents in brain abscesses compared to traditional cultures.
- Real-time PCR and sequencing are valuable tools for rapid and comprehensive etiological diagnosis.
- Accurate identification of polymicrobial infections is crucial for effective brain abscess management.
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