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Allison Carey

Assistant Professor of Clinical Pathology

Mycobacteria, Tuberculosis, Microbial Genomics, Antibiotic Resistance, Virulence

Allison Carey


Molecular Biology Program


B.S. Pennsylvania State University

M.D., Ph.D. Yale University School of Medicine




My lab’s research focus is pathogenic mycobacteria, including the causative agent of tuberculosis, Mycobacterium tuberculosis, and non-tuberculous mycobacteria such as Mycobacterium avium. Our goal is to understand how bacterial strain diversity impacts clinically relevant phenotypes, such as antibiotic resistance, virulence, and vaccine escape. We utilize a combination of high-throughput forward genetic tools, bacterial population genomics, and in vitro and in vivo models to address these questions.


  1. Carey AF, Wang X, Cicchetti N, Spaulding CN, Liu Q, Hopkins F, Brown J, Sixsmith J, Sutiwisesak R, Behar SM, Loerger TR, Fortune SM. Multiplexed Strain Phenotyping Defines Consequences of Genetic Diversity in Mycobacterium tuberculosis for Infection and Vaccination Outcomes. ASM Journals. 2022 Apr 18; 7(3) DOI:
  2. Hicks ND, Carey AF, Yang J, Zhao Y, Fortune SM. Bacterial Genome-Wide Association Identifies Novel Factors That Contribute to Ethionamide and Prothionamide Susceptibility in Mycobacterium tuberculosis. mBio. 2019 Apr 23;10(2):e00616-19. doi: 10.1128/mBio.00616-19. PMID: 31015328; PMCID: PMC6479004.
  3. Carey AF, Rock JM, Krieger IV, Chase MR, Fernandez-Suarez M, Gagneux S, Sacchettini JC, Ioerger TR, Fortune SM. TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities. PLoS Pathog. 2018 Mar 5;14(3):e1006939. doi: 10.1371/journal.ppat.1006939. Erratum in: PLoS Pathog. 2019 Jun 4;15(6):e1007846. PMID: 29505613; PMCID: PMC5854444.
  4. Cadena AM, Hopkins FF, Maiello P, Carey AF, Wong EA, Martin CJ, Gideon HP, DiFazio RM, Andersen P, Lin PL, Fortune SM, Flynn JL. Concurrent infection with Mycobacterium tuberculosis confers robust protection against secondary infection in macaques. PLoS Pathog. 2018 Oct 12;14(10):e1007305. doi: 10.1371/journal.ppat.1007305. PMID: 30312351; PMCID: PMC6200282.
  5. Martin CJ, Carey AF, Fortune SM. A bug's life in the granuloma. Semin Immunopathol. 2016 Mar;38(2):213-20. doi: 10.1007/s00281-015-0533-1. Epub 2015 Nov 17. PMID: 26577238; PMCID: PMC4834868.
Last Updated: 7/11/23