For an up-to-date list and links to articles, please see: Taj’s Google Scholar Page


Taj Azarian, The Importance of Pathogen Whole-Genome Sequencing in Evaluating Interventions to Reduce the Spread of Multidrug-Resistant Organisms in the Healthcare Setting, Clinical Infectious Diseases, Volume 72, Issue 11, 1 June 2021, Pages 1888–1890,

Taj Azarian, Meaningful Use of Pathogen Genomic Data. ASM Journals, doi:


Hassouneh STrujillo AAli SCella E, Johnston CDeRuff KSabeti PAzarian T, 2022. Antigen test swabs are comparable to nasopharyngeal swabs for sequencing of SARS-CoV-2. medRxiv. 2022 June 14; doi: 10.1101/2022.06.09.22276150

Key Publications 

Cella E, Sutcliffe C, Weatherholtz RC, Reid R, Reid A, Quay D, Hammitt L, Azarian T, 2021. Carriage prevalence and genomic epidemiology of Staphylococcus aureus among Native Americans in the southwestern US. 2022 May 13; doi: 10.1099/mgen.0.000806

Azarian T, Cella E, Baines SL, Shumaker MJ, Samel C, Jubair M, Pegues DA and David MZ (2021) Genomic Epidemiology and Global Population Structure of Exfoliative Toxin A-Producing Staphylococcus aureus Strains Associated With Staphylococcal Scalded Skin Syndrome. Front. Microbiol. 12:663831. doi: 10.3389/fmicb.2021.663831

Azarian, T., Martinez, P.P., Arnold, B.J., Grant, L.R., Corander, J., Fraser, C., Croucher, N.J., Hammitt, L.L., Reid, R., Santosham, M. and Weatherholtz, R.C., 2020. Frequency-dependent selection can forecast evolution in Streptococcus pneumoniaePLoS biology. 2020 Oct 22;18(10):e3000878.

Azarian T, Ridgway JP, Yin Z, David MZ. Long-term intrahost evolution of methicillin resistant Staphylococcus aureus among cystic fibrosis patients with respiratory carriage. Frontiers in Genetics. 2019;10.

Azarian T et al., Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci. PLOS Pathog. 14, e1007438 (2018).

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


Mitchell PK, Azarian T, Croucher NJ, Callendrello A, Thompson CM, Pelton SI, Lipsitch M, Hanage WP. Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13. Microbial genomics. 2019 Feb;5(2).

Kuipers, K., Jong, W.S., van der Gaast-de, C.E., Houben, D., van Opzeeland, F., Simonetti, E., van Selm, S., de Groot, R., Koenders, M.I., Azarian, T. et al. Th17-mediated cross protection against pneumococcal carriage by vaccination with a variable antigen. Infection and Immunity. 2017 Jul 17:IAI-00281.

Cella E, Ciccozzi M, Lo Presti A, Fogolari M, Azarian T, Prosperi M, … Angeletti, S. Multi-drug resistant Klebsiella pneumoniae strains circulating in hospital setting: whole-genome sequencing and Bayesian phylogenetic analysis for outbreak investigations. Scientific Reports 2017, 7, 3534. doi:10.1038/s41598-017-03581-4

Azarian T, Ali A, Johnson JA, Jubair M, Cella E, Ciccozzi M, Nolan DJ, Farmerie W, Rashid MH, Sinha-Ray S, Alam MT, Morris JG, Salemi M. Non-toxigenic environmental Vibrio cholerae O1 strain from Haiti provides evidence of pre-pandemic cholera in Hispaniola. Sci Rep. 2016 Oct 27;6:36115. PMCID: PMC5081557.

Rahman M, Jubair M, Alam MT, Weppelmann TA, Azarian T, Salemi M, Sakharuk IA, Rashid MH, Johnson JA, Yasmin M, Morris JG; Ali A. High-frequency Rugose Exopolysaccharide Production by Vibrio cholerae strains Isolated in Haiti. PLoS One. 2014;9:e112853. doi: 10.1371/journal.pone.0112853

Prosperi M, Veras N, Azarian T, Rathore M, Nolan D, Rand K, Salemi M. Molecular Epidemiology of Community-Associated Methicillin-resistant Staphylococcus aureus in the genomic era: a Cross-Sectional Study. Scientific reports, 2012;3,1902. doi:10.1038/srep01902

Akrim M, Lemrabet S, Elharti E, Gray RR, Tardy JC, Cook RL, Salemi M, Andre P, Azarian T, El Aouad R. HIV-1 Subtype distribution in Morocco based on national sentinel surveillance data 2004-2005. AIDS Research and Therapy. 2012;9:5 doi:10.1186/1742-6405-9-5

Azarian T, Winn S, Zaheer S, Buehler J, Hopkins RS. Utilization of Syndromic Surveillance with Multiple Data Sources to Enhance Public Health Response. Advances in Disease Surveillance. 2009;7:1.

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