PopPIPE

PopPIPE combines reference-free genome analysis methods to split bacterial populations into subclusters and detect plausible transmission events across scales from species-wide clustering to outbreak investigations.

Key Features:

• Population subclustering: Splits whole bacterial populations into subclusters using k-mer sketching to define strains, followed by split k-mer analysis and recombination removal to create alignments and subclusters within strains.
• Transmission detection: Detects plausible transmission events within closely related clusters using genetic distances between bacterial DNA sequences as an additional source of information.
• Reference-free analysis: Employs reference-free methods for sensitive detection of genetic differences, especially among closely related samples found in outbreaks.
• Recombination removal: Accounts for frequent recombination across longer genetic distances by removing recombination effects during alignment creation.
• Interactive visualizations: Generates interactive visualizations for exploring clustering and transmission results.

Scientific Applications:

• Population-wide strain analysis: Creates high-quality subclusters on population-wide datasets, as demonstrated on Streptococcus pneumoniae.
• Nosocomial outbreak investigation: Identifies transmission clusters in hospital settings, as shown with nosocomial vancomycin-resistant Enterococcus faecium samples where it found more epidemiologically plausible clusters than core genome or multilocus sequence typing (MLST) approaches.
• Species-wide to outbreak-scale genomics: Supports analyses spanning species-wide clustering to outbreak investigations in bacterial genomic epidemiology.

Methodology:

PopPIPE uses k-mer sketching to split populations into strains, followed by split k-mer analysis and recombination removal to create alignments and subclusters within these strains.