Molecular Identification of Bacteria in Intra-abdominal Abscesses Using Deep Sequencing

Area of Science:

• Microbiology
• Infectious Diseases
• Molecular Diagnostics

Background:

• Intra-abdominal abscesses are localized pus collections often caused by gastrointestinal bacteria.
• Their polymicrobial nature is linked to the primary disease process.
• Standard culture methods struggle to identify the full spectrum of bacteria present.

Purpose of the Study:

• To characterize the bacterial communities in intra-abdominal abscesses using culture-independent methods.
• To compare molecular sequencing results with conventional microbiologic cultures.
• To assess the accuracy of standard techniques in identifying abscess microbes.

Main Methods:

• 16S rRNA Illumina sequencing was employed on 43 abscess samples obtained via percutaneous drainage.
• Samples included both culture-positive and culture-negative specimens.
• Bacterial communities were analyzed and compared to conventional culture results.

Main Results:

• 221 bacterial taxa were identified across samples, averaging 13.1 operational taxonomic units (OTUs) per sample.
• Microbial richness and diversity were significantly higher in culture-positive samples compared to culture-negative ones.
• Cultured isolates represented only a fraction of the total identified microbial composition.

Conclusions:

• 16S rRNA sequencing revealed a polymicrobial and diverse microbiome in intra-abdominal abscesses, largely undetected by standard cultures.
• Molecular techniques offer a more comprehensive view of abscess bacteria, particularly when cultures are negative or after antibiotic treatment.
• Standard culture-based methods underestimate the microbial diversity in these infections.