title: Sequence tag-based analysis of microbial population dynamics.
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.
authors.affiliation: 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.
authors.forename: Sören
authors.initials: S
authors.lastname: Abel
authors.affiliation: 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.
authors.forename: Pia
authors.initials: P
authors.lastname: Abel zur Wiesch
authors.affiliation: Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.
authors.forename: Hsiao-Han
authors.initials: HH
authors.lastname: Chang
authors.affiliation: 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.
authors.forename: Brigid M
authors.initials: BM
authors.lastname: Davis
authors.affiliation: Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Lipsitch
authors.affiliation: 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.
authors.forename: Matthew K
authors.initials: MK
authors.lastname: Waldor
mesh_terms: D000818:Animals; D058491:Bacterial Load / Q000235:genetics; D002771:Cholera / Q000382:microbiology*; D020224:Expressed Sequence Tags; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions / Q000235:genetics*; D007422:Intestines / Q000382:microbiology*; D008297:Male; D011817:Rabbits; D014734:Vibrio cholerae / Q000235:genetics* / Q000472:pathogenicity