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Division of Medical Microbiology

Email kcarrol7@jhmi.edu
Phone (410) 955-5077

Karen C. Carroll, M.D.

Director, Division of Medical Microbiology
Primary Appointment in Pathology; Secondary Appointment in Medicine

My research interests include diagnostic test evaluation and development for the detection of microbial pathogens in clinical specimens. Recent projects have included: 1) evaluation of molecular strain typing techniques for epidemiological analysis; 2) use of 16SrDNA-sequencing for identification of non-tuberculous Mycobacteria; 3) epidemiology, diagnosis and pathogenesis of community acquired Staphylococcus aureus; 4) evaluation of new diagnostic instruments.

Riedel S, Neoh KM, Eisinger SW, Dam LM, Tekle T, Carroll KC. 2014. Comparison of commercial antimicrobial susceptibility test methods for testing of Staphylococcus aureus and enterococci against vancomycin, daptomycin, and linezolid. J Clin Microbiol 52:2216-22.

Suwantarat N, Carroll KC, Tekle T, Ross T, Maragakis LL, Cosgrove, Milstone AM. 2014. High prevalence of reduced chlorhexidine susceptibility in organisms causing central line-associated bloodstream infections. Infect Control Hosp. Epidemiol. 35:1183-86.

Salimnia H, Fairfax M, Lephart P, Morgan M, Gilbreath J, Butler-Wu S, Templeton K, Hamilton F, Wu F, Buckner R, Fuller D, Davis T, Abdelhamed A, Jacobs M, Miller A, Pfrommer B, and Carroll KC. 2014. An International, Prospective, Multi-Center Evaluation of the Combination of the AdvanDx Staphylococcus QuickFISH BC with the mecA XpressFISH for the Detection of Methicillin-Resistant Staphylococcus aureus from Positive Blood Culture. J Clin Microbiol 52:3928.

Suwantarat N, Roberts A, R Prestridge A, Seeley R, Speser S, Harmon C, Zhang C, Henciak S, Stamper PD, Ross T, Carroll KC. 2014. Comparison of five chromogenic media for the recovery of vancomycin resistant enterococci (VRE) from fecal samples. J Clin Microbiol 52:4039-42.

Farley JE, Hayat MJ, Sacamano PL, Howard T, Carroll K. 2015. Prevalence and Risk Factors for MRSA in an HIV-positive Cohort. Amer J Infect Control 43:329-35.

Email ambinri@jhmi.edu
Phone (410) 955-8839
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Richard F. Ambinder, M.D., Ph.D.

Primary Appointment in Oncology; Secondary Appointments in Pathology, Pharmacology and Molecular Sciences
Member, Graduate Program in Biochemistry, Cellular and Molecular Biology; Member, Graduate Program in Pharmacology and Molecular Sciences

Epstein-Barr virus is consistently found in association with a variety of tumors including African Burkitt's lymphoma, nasopharyngeal carcinoma, mixed cellularity Hodgkin's disease, post-transplant lymphoma, and AIDS central nervous system lymphoma. Our laboratory studies are aimed at better defining the role(s) of the virus in the pathogenesis of these diseases and the development of strategies to diagnose and treat those malignancies. For example, is there a way to utilize the presence of the virus to specifically target therapy? In patients with EBV-associated Hodgkin's disease, every tumor cell (identified morphologically or by double labeling with CD30) carries the viral genome and expresses the latency membrane protein-1(LMP-1). In non-malignant tissues (including lymph nodes and spleen), there are very few EBV-infected cells and none express LMP-1. In approximately 1/3 of normal volunteers, cytotoxic T cell activity directed against LMP-1 can be detected. Cytotoxic T cells against other EBV antigens are much more common. Cytotoxic T cells directed against EB nuclear antigens (EBNA's)-3A, -3B and -3C can be detected in virtually all normal volunteers. However, these antigens are not expressed in EBV-associated Hodgkin's disease. Can cytotoxic T cells which specifically recognize viral antigens expressed in tumor cells be induced with a therapeutic vaccine, or expanded in vitro from an HLA-matched allogeneic donor and infused in the setting of bone marrow transplantation? Can highly immunogenic viral genes that are not expressed in tumors be induced pharmacologically so as to lead to expression and consequent immune destruction of tumorous cells? Can immuno-suppressive viral gene products such as viral IL-10 be turned off with inhibitors of viral late gene expression and thus render patients more immune competent?

Moore SM, Cannon JS, Tanhehco YC, Hamzeh FM, Ambinder RF. Induction of Epstein-Barr Virus Kinases to Sensitize Tumor Cells to Nucleoside Analogues. Antimicrob Agents Chemother. 45:2082-2091, 2001.

Murray PG, Swinnen LJ, Flavell JR, Ragni MV, Baumforth KRN, Toomey SM, Filipovich AH, Lowe D, Schnell CS, Young LS, Ambinder RF. Frequent Expression of the Tumor Necrosis Factor Receptor-Associated Factor 1 in Latent Membrane Protein 1-Positive Posttransplant Lymphoproliferative Diseaseand HIV-Associated Lymphomas. Hum Path, 32:963-969, 2001.

Gulley ML, Glaser SL, Craig FE, Borowitz M, Mann RB, Shema SJ, AmbinderRF. Guidelines for interpreting EBER in situ hybridization and LMP1 immunohistochemical tests for detecting Epstein-Barr virus in Hodgkin Lymphoma. Am J Clin Path, 117:259-267, 2002.

Tao Q, Yang J, Swinnen LJ, Ambinder RF. Conservation of Epstein-Barr VirusCytotoxic T Cell Epitopes in Post transplant Lymphomas: Implications for Immune Therapy. Am J Pathol 160:1839-45, 2002.

Email mfowler5@jhmi.edu
Phone (410) 502-0684
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Mary G. Fowler, M.D., M.P.H.

Primary Appointment in Pathology

Dr. Fowler is a Professor in the Department of Pathology. She is a pediatrician by training with a fellowship in developmental pediatrics. She also has a Masters in Public Health from Johns Hopkins U. Bloomberg School of Public Health. Dr. Fowler is a world renowned clinical researcher who has devoted her career to research on prevention of HIV and its treatment. Her area of focus on prevention of mother to child transmission of HIV and among high risk women in international settings;; adherence and resistance; as well as pediatric HIV treatment and developmental outcomes. Before joining the faculty at Johns Hopkins University School of Medicine in 2005, Dr. Fowler previously worked at NIH on pediatric HIV clinical trials; and at CDC overseeing HIV research and programmatic activities in high prevalence sates. She is currently the Principal Investigator for the Johns Hopkins U. Kampala Clinical Trials Unit and is responsible for oversight of two clinical trial units in Kampala Uganda: the Makerere U. Johns Hopkins U. Research Collaboration site and the Baylor-Uganda Clinical Research site.


Email ghayward@jhmi.edu
Phone (410) 955-8686
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Gary S. Hayward, Ph.D.

Primary Appointment in Oncology and in Pharmacology and Molecular Sciences; Secondary Appointment in Pathology
Member, Graduate Program in Biochemistry, Cellular and Molecular Biology; Member, Graduate Program in Cellular and Molecular Medicine; Member, Graduate Programin Pathobiology; Member, Graduate Program in Pharmacology and Molecular Sciences

Herpes viruses have developed successful genetic strategies that allow them to target to specific cell types or tissues where they can reside temporarily in a quiescent or latent state without damaging the host cell. However, immuno suppression, allograft transplantation and other stress conditions often lead to accelerated reactivation and disseminated spread of lytic or abortive infection with associated serious pathology and disease. The molecular mechanisms used by herpes simplex virus and Epstein Barr virus to establish and reactivate from latency in sensory neurons and immortalized B lymphocytes are now relatively well understood. However, in recent years it has also become apparent that cytomegalovirus (CMV), HHV 6/7 and Kaposi's sarcoma herpes virus (HHV 8) are harbored as widespread latent infections in monocytes, T cells and vascular endothelial cells and can be associated with or causative agents of chronic disease after immunosuppression and organ transplantation. Our group is especially interested in molecular mechanisms involved in herpes virus host cell interactions in vascular tissue and myeloid cells in the settings of cardiac, lung and renal transplants and AIDS. This includes study of the roles of viral encoded angiogenic cytokines and chemokine receptors, effects of viral immediate-early genes on cell cycle regulation and very early events in the nucleus including alterations in subnuclear compartments involving PML and SUMO-modification mechanisms. Potential pathogenic variants of specific viral genes are also being evaluated.

Wu F., Ahn J-H, Alcendor D, Jang W-J, Xiao J, Hayward SD, Hayward GS. OriginIndependent Assembly of Kaposi's Sarcoma-associated Herpesvirus DNAReplication Compartments in Transient Cotransfection Assays and Association with the ORF-K8 Protein and Cellular PML. J. Virol. 75:1487-1506, 2001.

Ciufo DM, Cannon JS, Poole LJ, Wu F, Murray P, Ambinder RF, Hayward GS. Spindle Cell Conversion by Kaposi's Sarcoma-Associated Herpesvirus: Formation of Colonies and Plaques with Mixed Lytic and Latent Gene Expression in Infected Primary Dermal Microvascular Endothelial Cell Cultures. J. Virol.75:5614-5626, 2001.

Poole L., Yu Y, Kim P, Zheng QZ, Pevsner J, Hayward GS. Altered Patternsof Cellular Gene Expression in Dermal Microvascular Endothelial Cells Infected with the Kaposi's Sarcoma Associated Herpesvirus. J. Virol.76:3395-3420, 2002.

Chiou C-J, Poole L, Kim P, Ciufo DM, Cannon JS, ap Rhys CM, Alcendor DJ,Zong J-C, Ambinder RF, Hayward GS. Patterns of Gene Expression and a Transactivation Function Exhibited by the vGCR (ORF 74) Chemokine Receptor Protein of Kaposi's Sarcoma-Associated Herpesvirus. J. Virol. 76:3421-3439,2002.

Email nparrish@jhmi.edu
Phone (410) 550-3525
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Nicole M. Parrish, Ph.D.

Primary Appointment in Pathology

Tuberculosis continues to be the leading cause of death worldwide due to an infectious agent. Of greater concern in recent years, is the emergence of multi-drug resistance and the increasing incidence of infection with atypical mycobacteria in immunocompromised patients. These factors have highlighted the need for new antibiotics targeting these organisms. My primary research focus is aimed at characterization of the mechanism of action of a novel class of antimycobacterial compounds which have demonstrated potent in vitro efficacy against pathogenic mycobacteria, including multi-drug resistant strains. A variety of methods lead this approach including, proteomics, protein and lipid biochemistry as well as current molecular techniques.


Parrish, N.M., F.P. Kuhajda, H.S. Heine, W.R. Bishai, and J.D. Dick. 1999. Antimycobacterial activity of cerulenin and its effects on lipid biosynthesis. Journal of Antimicrobial Chemotherapy. 43: 219-226.

Jones, P.B., N.M. Parrish, T.A. Houston, A. Stapon, N.P. Bansal, J.D. Dick, and C.A.Townsend. 2000. A new class of antituberculosis agents. J. Med. Chem. 43(17): 3304-14.

Parrish, N.M, C. Townsend, P. Jones, T. Houston, and J. Dick. 2001. In vitro activity of a novel antimycobacterial compound, N-octanesulfonylacetamide, and its effects on lipid and mycolic acid synthesis. Antimicrob. Agents Chemother. 45:1143-1150.

Parrish, N.M., C.A. Townsend, C.G. Ko, and J.D. Dick. 2004. Effect of n-Octanesulfonylacetamide (OSA) on ATP and protein expression in Mycobacterium bovis BCG. J. Antimicrob. Chemother. 54(4): 722-9.

Parrish, N.M., C.A. Townsend, C.G. Ko, and J.D. Dick. 2004. Congo red agar colony morphotypes and antibiotic susceptibility testing of M. avium subspecies paratuberculosis. 2004. Clinical Medicine and Research. 2: 107-114.

Email mreller1@jhmi.edu
Phone (410) 955-5077
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Megan E. Reller, M.D.

Primary Appointment in Pathology


Email sriedel2@jhmi.edu
Phone (410) 550-0648
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Stefan Riedel, M.D., Ph.D.

Primary Appointment in Pathology
Director, Clinical Pathology Laboratories, Johns Hopkins Bayview Medical Center

My research interests are focused on the epidemiology of emerging bacterial resistance, mechanisms and laboratory detection of antimicrobial resistance, with a particular interest in gram-negative organisms (e.g. Acinetobacter baumanii and Pseudomonas aeruginosa). Additional areas of my research are focusing on the early detection of blood stream infections, the evaluation of bacteremia/sepsis and the clinical impact of laboratory testing with regard to a cost-effective and clinically relevant management of the laboratory. Recent studies include the development and evaluation of novel diagnostic methods in clinical microbiology for the evaluation of sepsis.

Riedel S, Bourbeau P, Swartz B, Brecher S, Carroll KC, Stamper PD, Dunne M Wm, McCardle T, Walk N, Fiebelkorn K, Sewell D, Richter SS, Beekmann S, and Doern GV. The Timing of Specimen Collection for Blood Cultures in Febrile Patients with Bacteremia. Journal of Clinical Microbiology; April 2008; 46 (4): 1381-1385

Lockhart S, Abramson M, Beekmann S, Gallagher G, Riedel S, Diekema D, Quinn J, Doern GV Antimicrobial resistance among gram negative bacilli as causes of infections in intensive care unit patients in the United States between 1993 and 2004 Journal of Clinical Microbiology; 2007; 45(10): 3352-3359

Riedel S, Beekmann S, Heilmann K, Richter S, Garcia-de-Lomas J, Ferech M, Goossens H, Doern GV. Antimicrobial Use in Europe and Antimicrobial Resistance with Streptococcus pneumoniae European Journal of Microbiology & Infectious Diseases; 2007; 26(7): 485-490

Riedel S, Siwek G, Beekmann S, Richter S, Raife T, Doern GV. Comparison of the BACTEC and the BacT/Alert Blood Culture System for Detection of Bacterial Contamination of Platelet Concentrates Journal of Clinical Microbiology, 2006; 44 (6): 2262-2264

Riedel S. Edward Jenner and the history of smallpox and vaccination Baylor University Medical Center Proceedings, 2005; 18 (1): 21-25

Email psimner1@jhmi.edu
Phone (410) 955-5077
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Patricia J. Simner, Ph.D.

Primary Appointment in Pathology

My research interests include, 1) evaluating and developing novel diagnostic technologies for the detection of microorganisms from culture and direct from clinical specimens and 2) understanding the epidemiology, transmission, molecular resistance mechanisms, treatment, and prevention of multidrug-resistant pathogens, in particular β-lactamase-producing Gram-negative bacilli. My recent studies include 1) Elucidating an efficient workflow to screen for and confirm the presence of carbapenemase-producing Gram-negative bacilli in the clinical laboratory, 2) Evaluating the novel PCR-Electrospray Ionization Mass Spectrometry method for detection of yeasts from formalin-fixed, paraffin-embedded tissues, 3) Evaluating the novel PCR-Electrospray Ionization Mass Spectrometry method for detection of Mycobacterium species and Mycobacterium tuberculosis Complex Resistance Determinants, 4) Evaluating the novel PCR-Electrospray Ionization Mass Spectrometry method for detection and identification of fungi.

Simner PJ, H Adam, M Baxter, M McCraken, G. Golding, JA Karlowksy, K Nichol, P Lagacé-Wiens, MW Gilmour, Canadian Antimicrobial Resistance Alliance-CARA, DJ Hoban and GG Zhanel. 2015. Epidemiology of Vancomycin-Resistant Enterococci (VRE) in Canadian Hospitals: CANWARD 2007-2013. Submitted to Antimicrob. Agents Chemotherapy.

Simner PJ, MW Gilmour, P DeGagne, K Nichol and JA Karlowsky. 2014. Evaluation of Five Chromogenic Agar Media and the Rosco Rapid Carb Screen Kit for Detection and Confirmation of Carbapenemase Production in Gram-Negative Bacilli. J Clin Microbiol. 53:105-12.

Simner PJ, SP Buckwalter, JR Uhl, NL Wengenack and BS Pritt. 2013. Detection and Identification of Yeasts from Formalin-Fixed, Paraffin-Embedded Tissue Using PCR-Electrospray Ionization. J Clin Microbiol. 51:3731-4.

Simner PJ, SP Buckwalter, JR Uhl and NL Wengenack. 2013. Identification of Mycobacterium species and Mycobacterium tuberculosis Complex Resistance Determinants Using PCR-Electrospray Ionization Mass Spectrometry. J Clin Microbiol. 51:3492-8.

Simner PJ, JR Uhl, L Hall, MM Weber, RC Walkchak, S Buckwalter and NL Wengenack. 2013. Broad-Range Direct Detection and Identification of Fungi Using the PLEX-ID PCR-Electrospray Ionization Mass Spectrometry (ESI-MS) System. J Clin Microbiol. 51:1699-1706.

Email avalsam1@jhmi.edu
Phone (410) 955-5077

Related Websites
Molecular Diagnostics Laboratories

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Alexandra Valsamakis, M.D., Ph.D.

Primary Appointment in Pathology; Joint Appointment in Molecular Medicine and Immunology (BSPH)
Member, Graduate Program in Molecular Microbiology and Immunology (BSPH)

My research is focused on the detection, identification, and therapeutic monitoring of infectious diseases, particularly viral infections. My current work entails 1) improving molecular assays that are critical for the management of hepatitis C and hepatitis B infections, 2) devising quantitative assays for viral infections and studying their clinical utility particularly in immunocompromised patients, and 3) investigation of the performance and utility of automated nucleic acid preparation instrumentation in the clinical laboratory. We utilize a variety of conventional (cell culture, antigen detection) and molecular techniques (nucleic acid amplification, primarily PCR and real time PCR).


Forman, M.S. and A. Valsamakis. Increased sensitivity of the Roche COBAS AMPLICOR HCV test v.2.0, using modified extraction techniques. J. Molec. Diag. 6:225-30, 2004.

Forman, M.S. and A. Valsamakis. Verification of an assay for quantification of HCV RNA using an analyte specific reagent and two different extraction methods. J. Clin. Micro. 42:3581-8, 2004.

Elbeik T, J Surtihadi, M Destree, J Gorlin, M Holodniy, S Jortani, K Kuramoto, V Ng, R Valdes, A Valsamakis, N Terrault. Multicenter evaluation of the performance characteristics of the Bayer VERSANT‘ HCV RNA 3.0 assay (bDNA). J. Clin. Micro. 42:563-9, 2004

Knepp, J.H., M.A. Geahr, M.S. Forman, and A. Valsamakis. Comparison of Automated and Manual Nucleic Acid Extraction Methods for the Detection of Enterovirus RNA. J. Clin. Microbiol. 41: 3532-3536, 2003.

Dumler, J.S. and A. Valsamakis. Molecular diagnostics of infectious diseases: complementary tools for a new era of clinical microbiology. Am J Clin Path 112: S33-S39, 1999.

Email szhang28@jhmi.edu
Phone (410) 955-5077
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Sean X. Zhang, Ph.D.

Primary Appointment in Pathology



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