A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids

Area of Science:

• Genomics
• Molecular Biology
• Bioengineering

Background:

• Optical DNA mapping (ODM) is a key technique for analyzing single DNA molecules, often in nanofluidic channels.
• Bacterial plasmids, extrachromosomal DNA carrying antibiotic resistance genes, require efficient analysis methods.
• Increasing throughput and automation are critical advancements for ODM applications.

Purpose of the Study:

• To develop an automated Optical DNA Mapping (ODM) assay for analyzing bacterial plasmids.
• To design and fabricate a nanofluidic device for parallel sample analysis.
• To demonstrate the device's capability in detecting antibiotic resistance genes in clinical samples.

Main Methods:

• Fabrication of a novel nanofluidic device for parallel sample processing.
• Development of a simple automation routine for high-throughput ODM.
• Application of the ODM assay to plasmids encoding extended-spectrum beta-lactamases (ESBL) from *Escherichia coli* and *Klebsiella pneumoniae*.
• Integration with a rapid plasmid cultivation and extraction protocol from patient fecal samples.

Main Results:

• The designed nanofluidic device enables parallel analysis of up to 10 samples simultaneously.
• Demonstrated multiplexing capability for analyzing diverse resistance genes across multiple samples.
• Successful integration with a rapid protocol for analyzing plasmids directly from clinical fecal samples.
• Enabled same-day analysis of patient samples, significantly advancing ODM for clinical diagnostics.

Conclusions:

• The developed automated ODM system significantly enhances throughput for bacterial plasmid analysis.
• The device effectively identifies antibiotic resistance genes, crucial for clinical diagnostics.
• This advancement facilitates rapid, same-day analysis of patient samples, improving diagnostic capabilities for bacterial infections.