ArticlemSystems2021
Refined Quantification of Infection Bottlenecks and Pathogen Dissemination with STAMPR.
Article in mSystems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- Zoonotic Streptococcus imports glucose to inhibit stringent response and promote growth during meningitis.Nature microbiology · 2026Article
- Codon bias variation in Staphylococcus aureus.PloS one · 2026Article
- Quantifying host-microbe interactions with bacterial lineage tracing.Science (New York, N.Y.) · 2026Review
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- Mechanisms of bacterial host-to-host transmission.Microbiology and molecular biology reviews : MMBR · 2025Review
- Human microbiome acquisition and transmission.Nature reviews. Microbiology · 2025Review
- Vibrio cholerae motility is associated with inter-animal transmission.Nature communications · 2025Article
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- Patterns of Klebsiella pneumoniae bacteremic dissemination from the lung.Nature communications · 2025Article
- Quantification ofbioRxiv : the preprint server for biology · 2024Article
- Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions.Current protocols · 2024Article
- CRISPR-based functional profiling of the Toxoplasma gondii genome during acute murine infection.Nature microbiology · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Pathogen population dynamics during infection are critical determinants of infection susceptibility and define patterns of dissemination. However, deciphering these dynamics, particularly founding population sizes in host organs and patterns of dissemination between organs, is difficult because measuring bacterial burden alone is insufficient to observe these patterns. Introduction of allelic diversity into otherwise identical bacteria using DNA barcodes enables sequencing-based measurements of these parameters, in a method known as STAMP (Sequence Tag-based Analysis of Microbial Populations). However, bacteria often undergo unequal expansion within host organs, resulting in marked differences in the frequencies of barcodes in input and output libraries. Here, we show that these differences confound STAMP-based analyses of founding population sizes and dissemination patterns. We present STAMPR, a successor to STAMP, which accounts for such population expansions. Using data from systemic infection of barcoded extraintestinal pathogenic E. coli, we show that this new framework, along with the metrics it yields, enhances the fidelity of measurements of bottlenecks and dissemination patterns. STAMPR was also validated on an independent barcoded Pseudomonas aeruginosa data set, uncovering new patterns of dissemination within the data. This framework (available at https://github.com/hullahalli/stampr_rtisan), when coupled with barcoded data sets, enables a more complete assessment of within-host bacterial population dynamics.
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Registered trials
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