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Nat Methods. 2015 Mar;12(3):223-6, 3 p following 226. doi: 10.1038/nmeth.3253. Epub 2015 Jan 19.

Sequence tag-based analysis of microbial population dynamics.

Author information

1
1] Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA. [2] Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.
2
1] Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA. [2] Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts, USA.
3
Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.
4
1] Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA. [2] Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA. [3] Howard Hughes Medical Institute, Boston, Massachusetts, USA.

Abstract

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.

PMID:
25599549
PMCID:
PMC4344388
DOI:
10.1038/nmeth.3253
[Indexed for MEDLINE]
Free PMC Article

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