Microbiological methodologies: Comparative evaluation of microbial community and enhanced antibiotic susceptibility testing

Abstract

Background

This study provides a comparative analysis of microbial community profiling and antibiotic susceptibility testing (AST) methodologies.

Microbial community profiling

Methods such as Shotgun Metagenomics and 16S rRNA sequencing were evaluated based on criteria including resolution, throughput, cost, and reproducibility. Shotgun Metagenomics was found to offer the highest resolution and detailed insights into microbial diversity, though at a higher cost and complexity. In contrast, 16S rRNA Sequencing provided a more cost-effective and high-throughput alternative, suitable for large-scale studies despite lower taxonomic resolution. Culturomics, while offering unique phenotypic data, showed variability in reproducibility and required more labor-intensive processes.

Antibiotic susceptibility testing (AST)

Traditional methods such as disk diffusion and broth microdilution were compared to emerging molecular and automated AST technologies. Traditional methods were noted for their precision in determining minimum inhibitory concentrations (MICs), crucial for guiding effective antimicrobial therapy. However, the emerging methods provided faster turnaround times and higher throughput, which are increasingly important in clinical settings focused on antimicrobial stewardship.

Conclusions

The study underscores the importance of selecting appropriate methodologies based on specific research or clinical needs, balancing factors such as cost, sensitivity, and throughput. The integration of multiple methodologies is recommended to overcome the limitations of individual techniques, providing a more comprehensive understanding of microbial ecosystems and resistance profiles. These findings are crucial for enhancing both research and clinical practices, particularly in the context of the global challenge posed by antimicrobial resistance.

How to cite: Yakobi SH, Nwodo UU. Microbiological methodologies: Comparative evaluation of microbial community and enhanced antibiotic susceptibility testing. Electron J Biotechnol 2025;74. https://doi.org/10.1016/j.ejbt.2025.01.001.