Our lab uses pathogen genomics to investigate the emergence and spread of bacterial infectious diseases, with a specific interest in antibiotic-resistant pathogens that are frequent causes of healthcare-associated infections.  To accomplish this, we use a variety of tools including epidemiology, bioinformatics, computational biology, population genomics, and phylogenetics.  Our goal is to understand the factors that contribute to pathogen success and to develop new genomic epidemiological methods to detect, monitor, and combat the growing threat of antimicrobial resistance.

Primary pathogens of interest include Streptococcus pneumoniae, a leading cause of infections in children and adults, as well as methicillin-resistant Staphylococcus aureus (MRSA), a prevalent cause of both community and healthcare-associated infections.  Other pathogens of interest include Vibrio cholerae, Neisseria meningitidis, and the ESKAPE bacteria that are commonly associated with antimicrobial resistance.


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Key Publications:

Azarian T, Grant LR, Arnold BJ, Hammitt LL, Reid R, Santosham M, Weatherholtz R, Goklish N, Thompson CM, Bentley SD, O’Brien KL. The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome. PLoS Pathogens. 2018 Apr 4;14(4):e1006966.

Azarian T, Grant LR, Georgieva M, Hammitt LL, Reid R, Bentley SD, Goldblatt D, Santosham M, Weatherholtz R, Burbidge P, Goklish N, Thompson CM, Hanage WP, Obrien KL, Lipsitch M. Pneumococcal protein antigen serology varies with age and may predict antigenic profile of colonizing isolates. J Infect Dis. 2016; doi: 10.1093/infdis/jiw628

Azarian T, Daum RS, Petty LA, Steinbeck JL, Yin Z, Nolan D, Boyle-Vavra S, Hanage WP, Salemi M, David MZ. Intrahost Evolution of Methicillin-Resistant Staphylococcus aureus USA300 Among Individuals With Reoccurring Skin and Soft-Tissue Infections. J Infect Dis. 2016 Sep 15;214(6):895-905. PMCID: PMC4996148.

Azarian T, Maraqa NF, Cook RL, Johnson JA, Bailey C, Wheeler S, Nolan D, Rathore MH, Morris JG Jr, Salemi M. Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit. PLoS One. 2016 Oct 12;11(10):e0164397. PMCID: PMC5061378.

Azarian T, Presti AL, Giovanetti M, Cella E, Rife B, Lai A, Zehender G, Ciccozzi M, Salemi M. Impact of spatial dispersion, evolution, and selection on Ebola Zaire Virus epidemic waves, Scientific Reports, 2015;5:10170. doi: 10.1038/srep10170. PMCID: PMC4431419

Azarian T, Ali A, Johnson JA, Mohr D, Prosperi M, Veras NM, Jubair M, Strickland SL, Rashid MH, Alam MT, Weppelmann TA, Katz LS, Tarr CL, Colwell RR, Morris JG, Salemi M. Phylodynamic analysis of clinical and environmental Vibrio cholerae from Haiti reveals diversification driven by positive selection. mBio 2014;5:e01824–14–. PMCID: PMC4278535

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