Journal
NATURE METHODS
Volume 12, Issue 3, Pages 223-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/NMETH.3253
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Funding
- Swiss Foundation for Grants in Biology and Medicine [PASMP3_142724/1]
- Swiss National Science Foundation [PBEZP3_140163]
- German Academic Exchange Service [D/11/45747]
- National Institute of General Medical Sciences of the US National Institutes of Health (NIH) award [U54GM088558]
- NIH [R37 AI-042347]
- Howard Hughes Medical Institute
- Swiss National Science Foundation (SNF) [PASMP3_142724, PBEZP3_140163] Funding Source: Swiss National Science Foundation (SNF)
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We describe sequence tag-based analysis of microbial populations (STAMP) for characterization of pathogen population dynamics during infection. STAMP analyzes the frequency changes of genetically 'barcoded' organisms to quantify population bottlenecks and infer the founding population size. Analyses of intraintestinal Vibrio cholerae revealed infection-stage and region-specific host barriers to infection and showed unexpected V. cholerae migration counter to intestinal flow. STAMP provides a robust, widely applicable analytical framework for high-confidence characterization of in vivo microbial dissemination.
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