PACU

PACU performs whole-genome sequencing-based SNP phylogenetic analysis using Illumina and Oxford Nanopore Technologies (ONT) R9/R10 data to support bacterial outbreak investigations.

Key Features:

• Integration of Sequencing Technologies: Supports Illumina short-read and ONT R9 and R10 long-read sequencing data within the same analysis.
• Evaluation Across Bacterial Species: Has been evaluated using outbreak datasets from Shiga toxin-producing Escherichia coli and Listeria monocytogenes.
• Performance Comparison: Performs comparative analyses of ONT R9 and R10 chemistries relative to Illumina to assess accuracy differences.
• Sequencing Time Optimization: Assesses minimum sequencing duration for stable phylogenies, with reported stability at approximately 20 hours for ONT R9 and approximately 8 hours for ONT R10.
• Stable Phylogenomic Results: Integrates datasets sequenced by either Illumina or ONT R10 into unified analyses to produce stable SNP-based phylogenomic results.

Scientific Applications:

• Bacterial SNP-based outbreak investigation: Enables identification and phylogenetic clustering of outbreak-related isolates using whole-genome sequencing data from Illumina and ONT R9/R10.
• Public health surveillance and epidemiology: Supports integration of mixed-platform sequencing datasets for phylogenomic surveillance in clinical and public health settings.

Methodology:

Generates SNP-based phylogenies from Illumina and ONT R9/R10 whole-genome sequencing data, performs comparative analyses between chemistries and against Illumina, and evaluates phylogenetic stability across sequencing durations (≈20 h for R9, ≈8 h for R10).