STAMPR

STAMPR reconciles DNA barcode frequency changes from sequencing data to quantify within-host bacterial population dynamics and estimate founding population sizes and dissemination patterns across host organs.

Key Features:

• Barcode frequency reconciliation: Reconciles differences in barcode frequencies between input and output sequencing libraries to adjust for changes arising during infection.
• Unequal expansion correction: Accounts for unequal expansion rates of bacteria within host organs to correct bottleneck and burden estimates.
• DNA barcoding and allelic diversity: Leverages allelic diversity introduced by DNA barcoding of otherwise genetically identical bacteria to enable sequencing-based tracking of populations.
• Founding population and dissemination estimation: Estimates founding population sizes and infers pathogen dissemination patterns across organs from barcode data.
• Validation on bacterial datasets: Validated on systemic infections with barcoded extraintestinal pathogenic E. coli and independently on barcoded Pseudomonas aeruginosa.
• Improved bottleneck metrics: Enhances the fidelity of bottleneck measurements and provides metrics for more complete assessment of within-host bacterial population dynamics.

Scientific Applications:

• Bacterial burden quantification: Quantifying bacterial burden and population dynamics in host-pathogen interaction studies.
• Dissemination mapping: Tracing pathogen dissemination across host organs to reveal organ-specific expansion and spread patterns.
• Bottleneck analysis: Estimating transmission and colonization bottlenecks via calculation of founding population sizes.
• Barcode-based tracking across systems: Applying barcode-based tracking to studies of pathogens and symbionts, including studies involving E. coli and Pseudomonas aeruginosa.

Methodology:

Performs sequencing-based measurement of DNA barcodes and reconciles barcode frequency differences between input and output libraries to account for differential expansion and estimate founding population sizes and dissemination patterns.