Field-based detection of bacteria using nanopore sequencing: Method evaluation for biothreat detection in complex...

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• The Oxford Nanopore Technologies (ONT) MinION offers portability and real-time analysis for microbiological applications.
• Its utility in unbiased pathogen detection is valuable for security and field investigations.

Purpose of the Study:

• To evaluate the impact of different analytical approaches on MinION sequencing outcomes in a field setting.
• To compare the ability of various methods to detect pathogens in complex samples.

Main Methods:

• Multicenter evaluation involving three expert scientific response groups.
• Independent sample preparation using Rapid and/or Rapid PCR kits.
• Sequence data analysis using ONT's WIMP and in-house computational pipelines.

Main Results:

• All participating groups successfully detected all target species, though some at low abundance (<1%).
• Observed microbial community composition diverged from input, with the rapid kit showing less distortion.
• Sequencing output varied significantly between groups, influenced by computational resources and connectivity.

Conclusions:

• The MinION is a useful tool for field-based pathogen detection in mixed samples when used by trained experts with adequate resources.
• Balancing the benefits of rapid, unbiased detection with the complexities of sample preparation and data analysis is essential.
• Further consideration is needed for optimizing unbiased pathogen identification in field settings using MinION sequencing.