CFSAN SNP Pipeline 2 (CSP2)

CFSAN SNP Pipeline 2 (CSP2) extracts single nucleotide polymorphisms (SNPs) directly from bacterial genome assemblies for rapid and accurate genetic distance estimation in public health surveillance and outbreak investigation.

Key Features:

• Rapid SNP extraction: CSP2 extracts SNPs directly from genome assemblies in seconds through MUMmer whole-genome alignment and parallel processing.
• Quality control measures: Data processing steps include density filtering and missing data handling mirroring the CFSAN SNP Pipeline (CSP1).
• Assembly compatibility: High quality assemblies from SKESA contain sufficient information for accurate, high resolution SNP distance estimation.
• Performance validation: CSP2 SNP distances for 150 real-world clusters of E. coli, Listeria monocytogenes, and S. enterica were highly correlated with CSP1 and the NCBI Pathogen Detection pipeline.

Scientific Applications:

• Public health surveillance: Accurate genetic distance estimation from pathogen whole-genome sequence data provides critical information for traceback and outbreak investigations of foodborne bacterial pathogens.
• Large cluster analysis: CSP2 facilitates rapid analysis of whole-genome sequencing (WGS) data for large clusters containing hundreds or thousands of isolates of common pathogens such as Escherichia coli and Salmonella enterica.
• SNP distance estimation: The pipeline enables high resolution SNP distance estimation comparable to accepted methods including CSP1 and the NCBI Pathogen Detection pipeline.

Methodology:

CSP2 is coded in Nextflow and Python and uses MUMmer whole-genome alignment followed by parallel processing. After genome alignment, data processing includes density filtering and missing data handling.