Rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach.

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Prompt identification of biothreat agents is critical for emergency response.
• Existing high-throughput sequencing (HTS) methods for unknown samples take days to weeks, which is too slow for emergency scenarios.
• Genetic identification of novel or engineered agents presents significant challenges.

Purpose of the Study:

• To develop a rapid, HTS-based approach for identifying unknown biothreat agents within a working day.
• To demonstrate the feasibility of rapid genetic identification in environmental samples.

Main Methods:

• Utilized a rapid library preparation procedure for high-throughput sequencing (HTS).
• Employed short-length sequencing and prompt bioinformatics comparison against comprehensive microbial genomic databases.
• Applied the method to detect spiked-in biothreat agents in environmental samples.

Main Results:

• Successfully identified two biothreat agents, *Bacillus anthracis* and *Yersinia pestis*, in environmental samples.
• Achieved detection within an eight-hour timeframe, significantly faster than previous methods.
• Demonstrated the approach's sensitivity at relevant concentrations.

Conclusions:

• The developed HTS-based approach enables rapid genetic identification of biothreat agents within eight hours.
• This method is suitable for emergency scenarios requiring swift confirmation and countermeasure deployment.
• The approach offers a significant advancement in rapid microbial identification for biosecurity applications.