Allison R. Eberly, PhD, D(ABMM)

Assistant Professor, Pathology & Immunology

Additional Titles

  • Assistant Medical Director of Clinical Microbiology, Barnes Jewish Hospital
  • Assistant Medical Director of Molecular Infectious Disease Laboratory, Barnes Jewish Hospital


  • BS: Chemistry and Molecular Biology, Chestnut Hill College, Philadelphia, PA (2014)
  • PhD: Microbiology and Immunology, Vanderbilt University, Nashville, TN (2019)
  • Fellowship, Clinical Microbiology: Mayo Clinic, Rochester, MN (2021)

Board Certifications

  • Diplomate, American Board of Medical Microbiology, 2021

Clincal Interests

  • Microbiology
  • Molecular diagnostics of infectious diseases
  • Mycobacteriology
  • Nontuberculous mycobacteria infections
  • Antibiotic stewardship
  • Trainee education
  • Optimizing laboratory test utilization

Research Interests

My research interests, albeit broad, aim to develop more accurate diagnostic tests for infections that are under-/misdiagnosed. I am especially interested in understanding the complexity of biofilms as it pertains to treatment options, including pulmonary nontuberculous mycobacteria (NTM) infections. Antibiotic susceptibility testing typically is performed on planktonically grown microorganisms, though many infections involve biofilms. While an antibiotic may test susceptible, it may not clear the infectious microorganism due to the inability to penetrate the biofilm. In addition to investigating ways to improve treatment of biofilm-associated infections, I plan to continue studying other mechanisms to identify antibiotic resistance beyond phenotypic characteristics, including novel molecular techniques.


Selected Publications:

Floyd KA, Moore JL, Eberly AR, Good JA, Shaffer CL, Zaver H, Almqvist F, Skaar EP, Caprioli RM, Hadjifrangiskou M. Adhesive fiber stratification in uropathogenic Escherichia coli biofilms unveils oxygen-mediated control of type 1 pili. PLoS Pathog. 2015; 11(3):e1004697. (PMID: 25738819)
Floyd KA, Mitchell CA, Eberly AR, Colling SJ, Zhang E, dePas W, Chapman MR, Conover M, Rogers B, Hultgren SJ, Hadjifrangiskou M. The UbiI (VisC) ubiquinone synthase is a biofilm requisite in uropathogenic Escherichia coli that impacts type 1 pili formation and pathogenesis. J Bact. 2016; 198(19):2662-72. (PMID: 27161114)
Eberly, AR, Floyd KA, Beebout CJ, Colling SJ, Fitzgerald MJ, Schmitz JE, Stratton CW, Hadjifrangiskou, M. Biofilm formation by uropathogenic Escherichia coli is favored under conditions that mimic the bladder environment. Intl J Mol Sci. 2017; 18(10), 2077. (PMID: 28973965)
Beebout CJ, Eberly AR, Werby SH, Reasoner SA, Brannon JR, De S, Fitzgerald MJ, Huggins MM, Clayton DB, Cegelski L, Hadjifrangiskou M. Respiratory heterogeneity shapes biofilm formation and host colonization in uropathogenic Escherichia coli. mBio. 2019; 10 (2). (PMID: 30940709)
Eberly AR, Beebout CJ, Tong CMC, Van Horn, GT, Green HD, Fitzgerald MJ, De S, Apple EK, Schrimpe-Rutledge AC, Condreanu SG, Sherrod SD, McLean JA, Clayton DB, Stratton CW, Schmitz JW and Hadjifrangiskou M. Defining a Molecular Signature for Uropathogenic versus Urocolonizing Escherichia coli: The Status of the Field and New Clinical Opportunities. J Mol Biol. 2019; 2836 (9). (PMID:31794727)
Eberly AR, Beebout CJ, Tong CMC, Van Horn, GT, Green HD, Fitzgerald MJ, De S, Apple EK, Schrimpe-Rutledge AC, Condreanu SG, Sherrod SD, McLean JA, Clayton DB, Stratton CW, Schmitz JW and Hadjifrangiskou M. Data highlighting phenotypic diversity of urine-associated Escherichia coli isolates. Data in Brief. 2020; 105833 (31). (PMID: 32566710)
Eberly AR* Challener DW, Shweta FNU, Fida M, Boerger AC, Assi M, O’Horo JC, and Binnicker MJ. Initial SARS-CoV-2 PCR crossing point does not predict hospitalization and duration of PCR positivity. Journal of Microbiology, Immunology, and Infection. 2020; S1684-1182 (20). (PMID:33069621)
Beebout CJ, Sominsky LA, Eberly AR, Van Horn GT, Hadjifrangiskou M. Cytochrome bd promotes Escherichia coli biofilm antibiotic tolerance by regulating accumulation of noxious chemicals. NPJ Biofilms Microbiomes. 2021;7(1):35. (PMID: 33863914
Eberly AR, Germer JJ, Boerger AC, Fernholz EC, Binnicker MJ, and Yao JD. Performance of three polymerase chain reaction-based assays for detection of SARS-CoV-2 in different upper respiratory tract specimens. Diagn Microbiol Infect Dis. 2021; 101(2):115411. Online ahead of print. (PMID:34186320)
Chesdachai S, Eberly AR, Razonable RR. A tale of two unsual anaerobic bacterial infections in an immunocompetent man: a case report and literature review. Anaerobe. 2021; 71:102415. (PMID:34293443)

Dionne Brierton
BJCIH Room 5800