Publications

Editorials

Taj Azarian, Sherry NL, Baker K, Holt KE, Okeke IN. Making microbial genomics work for clinical and public health microbiology. Microb Genom. 2022 Sep;8(9):mgen000900. doi: 10.1099/mgen.0.000900.

Taj Azarian, Meaningful Use of Pathogen Genomic Data. mBio. 2022 Jun 28;13(3):e0031122.

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, https://doi.org/10.1093/cid/ciaa724

Preprints

Shambhu S, Cella E, Azarian T. (2024). Variation in transformation frequency and competence gene expression among serotype 3 Streptococcus pneumoniae. bioRxiv 2024.08.19.608640; doi: https://doi.org/10.1101/2024.08.19.608640

Key Publications

Webb J, Cella E, Sutcliffe CG, Johnston C, Hassouneh SA, Jubair M, Riley DP, Tso C, Weatherholtz RC, Hammitt LL, Azarian T. Multi-strain carriage and intrahost diversity of Staphylococcus aureus among Indigenous adults in the USA. Microb Genom. 2025 Mar;11(3):001367. doi: 10.1099/mgen.0.001367.

Ali S, Azarian T. An ecological study of COVID-19 outcomes among Florida counties. BMC Public Health 2025;25, 579. https://doi.org/10.1186/s12889-025-21764-x.

Ali S, Giovanetti M, Johnston C, Urdaneta-Páez V, Azarian T, Cella E. From Emergence to Evolution: Dynamics of the SARS-CoV-2 Omicron Variant in Florida. Pathogens. 2024; 13(12):1095. https://doi.org/10.3390/pathogens13121095.

Greenman N, Abdelli LS, Hassouneh S, Ali S, Johnston C, Naser SA, Azarian T. Impact of propionic acid-rich diets on microbial composition of the murine gut microbiome. Front. Microbiomes 2024; 3:1451735. doi:10.3389/frmbi.2024.1451735

Greenman N, Hassouneh S, Abdelli LS, Johnston C, Azarian T. Improving bacterial metagenomic research through long read sequencing. Microorganisms. 2024; 12(5):935. https://doi.org/10.3390/microorganisms12050935.

Cella E, Sutcliffe C, ...., Hammitt L, Azarian T. Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001-2018. Microb Genom. 2024 Mar;10(3):001196. doi: 10.1099/mgen.0.001196.

Ali S, Cella E, Johnston C, Rojas AC, Brown AN, Deichen M, Azarian T.  Environmental Surface Monitoring as a Noninvasive Method for SARS-COV-2 Surveillance in Community Settings: Lessons from a University Campus Study.Science of The Total Environment. 2023; 912, 169456. 

Hassouneh S, Trujillo A, Ali S, Cella E, Johnston C, DeRuff K, Sabeti P, Azarian T. Antigen test swabs are comparable to nasopharyngeal swabs for sequencing of SARS-CoV-2. Sci Rep. 2023 Jul 12;13(1):11255.

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

Cella E, Ali S, Schmedes SE, Rife Magalis B, Marini S, Salemi M, Blanton J, Azarian T. Early Emergence Phase of SARS-CoV-2 Delta Variant in Florida, US. Viruses, 2022; 14(4), p.766.

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

Azarian T, Martinez PP, Arnold BJ, Grant LR, Corander J, Fraser C, Croucher NJ, Hammitt LL, Reid R, Santosham M, Weatherholtz RC. Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae. PLoS 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. Front Genet. 2019 Jun 12;10:546.

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, Lo Presti A, 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

Others

Giovanetti M, Ali S, Slavov SN, Azarian T, Cella E. Epidemiological Transitions in Influenza Dynamics in the United States: Insights from Recent Pandemic Challenges. Microorganisms 2025, 13, 469. https://doi.org/10.3390/microorganisms13030469.

Cella E, Fonseca V, Branda F, Tosta S, Moreno K, Schuab G, Ali S, Slavov SN, Scarpa F, Santos LA, Kashima S, Wilkinson E, Tegally H, Mavian C, Borsetti A, Caccuri F, Salemi M, de Oliveira T, Azarian T, de Filippis AMB, Alcantara LCJ, Ceccarelli G, Caruso A, Colizzi V, Marcello A, Lourenço J, Ciccozzi M, Giovanetti M. Integrated analyses of the transmission history of SARS-CoV-2 and its association with molecular evolution of the virus underlining the pandemic outbreaks in Italy, 2019-2023. Int J Infect Dis. 2024 Oct 8:107262. doi: 10.1016/j.ijid.2024.107262

Cella E, Giovanetti M, Benedetti F, Scarpa F, Johnston C, Borsetti A, Ceccarelli G, Azarian T, Zella D, Ciccozzi M. Joining Forces against Antibiotic Resistance: The One Health Solution. Pathogens. 2023 Aug 23;12(9):1074. doi: 10.3390/pathogens12091074. PMID: 37764882; PMCID: PMC10535744.

Kim PY, Kim AY, Newman JJ, Cella E, Bishop TC, Huwe PJ, Uchakina ON, McKallip RJ, Mack VL, Hill MP, Ogungbe IV, Adeyinka O, Jones S, Ware G, Carroll J, Sawyer JF, Densmore KH, Foster M, Valmond L, Thomas J, Azarian T, Queen K, Kamil JP. A collaborative approach to improving representation in viral genomic surveillance. PLOS Glob Public Health. 2023 Jul 19;3(7):e0001935.

Franco EJ, Cella E, Tao X, Hanrahan KC, Azarian T, Brown AN. Favipiravir Suppresses Zika Virus (ZIKV) through Activity as a Mutagen. Microorganisms. 2023 May 19;11(5):1342. doi: 10.3390/microorganisms11051342.

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.