MBPD: A multiple bacterial pathogen detection pipeline for One Health practices

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Bacterial pathogens pose significant risks to biosafety, environmental health, and agriculture.
• Current 16S rRNA gene sequencing methods for pathogen detection have limitations in taxonomic resolution and database applicability.
• Advanced assessment tools are crucial for effective bacterial pathogen control.

Purpose of the Study:

• To develop and validate a novel pipeline for multiple bacterial pathogen detection (MBPD).
• To improve the identification accuracy and applicability of 16S rRNA gene sequencing for diverse pathogens.
• To support One Health initiatives through comprehensive pathogen monitoring.

Main Methods:

• Creation of a curated database of full-length 16S genes from 1986 bacterial pathogen species (72,685 sequences).
• Development of the MBPD pipeline for identifying animal, plant, and zoonotic pathogens.
• In silico comparison of full-length and variable-region sequencing, identifying V3-V4 as optimal.

Main Results:

• The MBPD pipeline demonstrated superior performance in pathogen detection compared to existing methods (16SPIP, MIP).
• The V3-V4 variable region showed high accuracy (88.37%) for pathogen identification compared to full-length sequencing.
• MBPD successfully identified known pathogens and co-contaminating agents in real-world samples.

Conclusions:

• The MBPD pipeline offers enhanced taxonomic resolution and broader applicability for bacterial pathogen detection.
• Optimized use of the V3-V4 region improves efficiency and accuracy in pathogen identification.
• MBPD provides a valuable tool for integrated agricultural, veterinary, medical, and environmental monitoring under the One Health framework.