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Michail S. Lionakis, M.D., Sc.D.

Photo of Michail S. Lionakis

Chief, Fungal Pathogenesis Unit

Laboratory of Clinical Infectious Diseases

Major Areas of Research

  • Role of chemotactic factors in host defense against invasive candidiasis
  • Role of specific resident and recruited innate immune cells in antifungal host defense against mucosal and systemic fungal challenge
  • Genetic susceptibility to infection in mice and patients with candidiasis
  • Organ-specific immunity in invasive candidiasis
  • Immunological mechanisms of susceptibility to systemic fungal infections in patients with CARD9 deficiency
  • Immunological mechanisms of susceptibility to chronic mucocutaneous candidiasis (CMC) in patients with autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) syndrome
  • Dysbiosis and acquired local immunopathology in the pathogenesis of antibiotic-induced vaginal candidiasis
  • Identification of novel genetic defects in patients with inherited susceptiblity to Candida, Aspergillus, and other mold infections

Program Description

Since the 1990s, fungal infections have emerged as a major cause of morbidity and mortality in immunosuppressed and critically ill patients. The yeast Candida is the most common human fungal pathogen and is responsible for both invasive and mucosal infections. Neutrophils and monocytes/macrophages are critical for host defense against invasive candidiasis, the most common deep-seated human mycosis and the fourth-leading cause of nosocomial bloodstream infection in the United States. Despite administration of antifungal therapy, mortality of patients who develop invasive Candida infection exceeds 40 percent. In stark contrast to the requirement of phagocytes for defense against invasive infection, mucosal candidiasis develops 1) in patients with impaired cellular immunity such as those with AIDS (more than 90 percent of whom develop oral thrush) or inborn errors of immunity leading to chronic mucocutaneous candidiasis (CMC) and 2) in the majority of healthy women, often associated with antibiotic use (vaginal candidiasis). In all of these conditions, detailed knowledge of immunopathogenesis at the molecular and cellular levels is lacking.

Our laboratory research focuses on 1) cellular and molecular factors that regulate the immune response against mucosal and invasive candidiasis in clinically relevant animal models and on 2) better understanding the genetic and immune defects that underlie enhanced susceptibility to mucocutaneous and invasive fungal infections in humans. Our goal is to develop a detailed mechanistic understanding of the molecular and cellular basis of innate and adaptive immune responses against Candida with an aim to devise novel strategies to improve the diagnosis and augment or supplement the current antifungal drug treatment against candidiasis. To this end, we utilize in vitro cell culture systems and clinically relevant mouse models of mucosal and systemic Candida infections to study host-fungal interactions by using a variety of immunological, biological, and imaging approaches.

The first step in mounting any immune response is the effective recruitment and activation of immune cells at the site of infection. Yet, the molecular factors that mediate these processes in the setting of candidiasis are poorly defined. Hence, a major focus of the laboratory is to investigate the role of specific members of the chemoattractant system in mediating trafficking and effector function of specific resident and recruited immune cells in anti-Candida host defense in vivo. Characterization of the role of candidate chemotactic factors in antifungal host defense in mice is then followed by human immunogenomics studies, in which genetic polymorphisms in the identified chemotactic factor genes are tested for correlating effects on biological function and for associations with candidiasis in patients.

Further, an important event that determines the outcome of candidiasis is germination of Candida yeast into hyphae. Hence, Candida mutant strains that are unable to germinate are avirulent in vivo. We have previously demonstrated that in disseminated candidiasis, the innate antifungal immune response is highly idiosyncratic for each infected organ, associated with organ-specific differential ability of Candida to filament in these tissues. Thus, our laboratory is interested in delineating the host factors that govern antifungal resistance versus susceptibility at different anatomical sites. To that end, a major focus of our laboratory is the study of the immunological mechanisms that account for central nervous system (CNS)-targeted susceptibility to systemic candidiasis and other systemic fungal infections in patients with CARD9 mutations. Hence, via an investigational review board (IRB)-approved clinical protocol, our lab is recruiting patients with biallelic CARD9 mutations to NIH to study them immunologically. In parallel, the cellular and molecular basis of enhanced susceptibility to CNS-targeted system fungal diseases in CARD9 deficiency is investigated in Card9-/-mice.

With regard to mucosal candidiasis, the laboratory investigates the mechanisms of Candida susceptibility in inherited immunodeficiencies that lead to CMC and in healthy subjects following antibiotic use. Hence, the laboratory aims to define the immunological mechanisms that account for universal susceptibility to CMC in patients with the autosomal-recessive autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) syndrome. APECED, caused by mutations in autoimmune regulator (AIRE), is the only primary immunodeficiency in which CMC develops in 100 percent of patients and is the only infectious disease phenotype. Hence, our laboratory, via an investigational review board (IRB)-approved clinical protocol, is recruiting APECED patients to the National Institutes of Health to study them immunologically. In parallel, the cellular and molecular basis of enhanced susceptibility to mucosal candidiasis in APECED is investigated in Aire-/- mice.

In addition, antibiotic use is the most common controllable risk factor for development of vaginal candidiasis in health women. Hence, our laboratory aims to define the microbiomic and immunological perturbations that lead to vaginal candidiasis in antibiotic-treated healthy women. Better understanding of the antibiotic-induced alterations in the commensal flora and mucosal anti-Candida immune response that result in vaginal candidiasis could form the basis for development of targeted probiotic and/or immune-based strategies for the prevention and therapy of vaginal candidiasis in humans.

Last, our lab is working with the NIAID Clinical Genomics Program with a goal to identify novel genetic variants that result in inherited susceptibility to fungal infections by Candida, Aspergillus, and other molds.

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Dr. Lionakis obtained his M.D. and Sc.D. from the University of Crete in Greece. In 2002, he came to the United States and worked as a research fellow at the University of Texas MD Anderson Cancer Center (MDACC) under the mentorship of Dimitrios Kontoyiannis. At MDACC, Dr. Lionakis did clinical research on risk factors, diagnosis, and management of opportunistic fungal infections in cancer patients and bench research focusing on pharmacology and microbial factors in mouse and Drosophila models of invasive aspergillosis, fusariosis, and candidiasis.

After completing his clinical training in Internal Medicine at Baylor College of Medicine and Infectious Diseases at NIAID, Dr. Lionakis joined the Laboratory of Molecular Immunology (LMI) in 2008 and began to work on fungal immunology under the mentorship of Philip Murphy. At LMI, Dr. Lionakis did bench research on how chemotactic factors regulate the innate immune response in invasive candidiasis. In 2010, he was recruited as an Assistant Clinical Investigator in the NIAID Transition Program in Clinical Research and established the Clinical Mycology Unit within LMI. In 2012, Dr. Lionakis was recruited as a tenure-track investigator in the NIAID intramural research program and established the Fungal Pathogenesis Unit within the Laboratory of Clinical Infectious Diseases.


IDWeek Investigator Award (2015); BeHEARD Science Prize Winner, Rare Genomics Institute (2015);​ 50th ICAAC George McCracken Infectious Disease Fellow Award (2010); 49th ICAAC Infectious Disease Fellows Grant Program Award (2009); Henry McIntosh Award for Outstanding Resident in Medicine (2007); Offered Chief Resident position, Baylor College of Medicine (2006); Certificate of Merit, MD Anderson Cancer Center (2004); 1st place Bristol-Myers Squibb Award in Clinical/Translational Research, Trainee Recognition Day, MD Anderson Cancer Center (2004); 43rd ICAAC Program Committee Award for Outstanding Research in the Pathogenesis of Microbial Diseases (2003); Giorgos Gennimatas Scholarship Award (2002); GlaxoWellcome Scholarship Award (2000); Lilian Voudouri Foundation Scholarship Award (2000); The Hellenic National Scholarships' Foundation Scholarship Award (2000); Dretakis Foundation Scholarship Award (2000)


  • American College of Physicians
  • American Society of Microbiology
  • Infectious Diseases Society of America
  • Mycoses Study Group
  • International Immunocompromised Host Society
  • International Society for Human and Animal Mycology
  • American Association of Immunologists
  • Clinical Immunlogy Society
  • American Association for the Advancement of Science

Editorial Boards

  • JCI Insight
  • Journal of Infectious Diseases
  • Infection & Immunity
  • Frontiers in Cellular & Infection Microbiology
  • Virulence
  • Journal of Visualized Experiments

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Research Group

photo of Timothy Break

Timothy Break, Ph.D. Timothy obtained his bachelor's degree in biology from Texas Wesleyan University and then received his Ph.D. from the University of North Texas Health Science Center, studying innate immune responses against Listeria infection in mice. At FPU, Timothy focuses his work on Aire deficiency and the resulting primary immunodeficiency, APECED, which is associated with increased susceptibility to mucosal Candida infection. Using mouse models and clinical samples, he aims to uncover the mechanisms by which APECED leads to universal and specific susceptibility to chronic mucocutaneous candidiasis.

Photo of Jigar Desai, M.S., Ph.D.

Jigar Desai, M.S., Ph.D. Jigar obtained his bachelor's degree and master's degree in pharmacy from the Maharaja Sayajirao University of Baroda in India and Virginia Commonwealth University in Richmond, respectively. He did his Ph.D. at Carnegie Mellon University in Pittsburgh, where he studied the genetic factors that control Candida biofilm formation and the biophysical mechanisms of hyphal invasion. After that, he joined the FPU, where his research focuses on characterizing the Candida and host molecular factors that affect organ-specific fungal virulence.

Photo of Rebecca Drummond

Rebecca Drummond, Ph.D. Rebecca obtained her bachelor's degree in immunology at the University of Edinburgh. Rebecca joined the FPU after completing her Ph.D. at the University of Aberdeen, where she worked on C-type lectin receptors in antifungal immunity. Her research at the FPU tries to understand the immune mechanisms that protect against infections caused by the fungal pathogen Candida albicans and how acquired and inherited susceptibility factors (such as antibiotic usage and genetic mutations) impair antifungal host defense.​

Photo of Elise Ferré, PA-C, M.P.H.

Elise Ferré, PA-C, M.P.H. Elise obtained a Master of Science in health sciences for physician assistant studies from George Washington University, as well as a Master of Public Health with a concentration in community-oriented primary care. At FPU, Elise focuses her work on clinical care and clinical research in patients with inherited (e.g., APECED, CARD9 deficiency) and acquired (e.g., antibiotic-induced vaginal candidiasis) susceptibility to fungal disease.

Photo of Mukil Natarajan, M.D.

Mukil Natarajan, M.D. Mukil obtained his bachelor’s degree in bioengineering from Rice University in Houston, TX, and his M.D. from Duke University in Durham, NC. He then did his internal medicine residency at the University of Michigan in Ann Arbor. After completing a clinical fellowship in infectious diseases at NIH, Mukil joined the Fungal Pathogenesis Unit. His research in the FPU focuses on better understanding the role of microbiota in promoting antimicrobial host defense and organ-specific autoimmunity in patients with APECED. In addition, he is aiming to elucidate the genetic and immunological defects that underlie susceptibility to invasive fungal infections of the central nervous system.

Photo of Muthulekha Swamydas, Ph.D.

Muthulekha Swamydas, Ph.D. Muthulekha obtained her bachelor of medicine and bachelor of surgery from India and her Ph.D. in anatomy and cell biology from Wayne State University in Detroit. Her work at FPU focuses on understanding the in vivo role of phagocyte-targeted chemoattractant receptors in host defense against invasive candidiasis in mice.


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Selected Publications

Swamydas M, Gao JL, Break TJ, Johnson MD, Jaeger M, Rodriguez CA, Lim JK, Green NM, Collar AL, Fischer BG, Lee CR, Perfect JR, Alexander BD, Kullberg BJ, Netea MG, Murphy PM, Lionakis MS. CXCR1-mediated neutrophil degranulation and fungal killing promotes Candida clearance and host survival. Sci Transl Med. 2016. 2016 Jan 20;8(322):322ra10.

Drummond RA, Collar AL, Swamydas M, Rodriguez CA, Lim JK, Mendez LM, Fink DL, Hsu AP, Zhai B, Karauzum H, Mikelis CM, Rose SR, Ferre EM, Yockey L, Lemberg K, Kuehn HS, Rosenzweig SD, Lin X, Chittiboina P, Datta SK, Belhorn TH, Weimer ET, Hernandez ML, Hohl TM, Kuhns DB, Lionakis MS. CARD9-dependent neutrophil recruitment protects against fungal invasion of the central nervous system. PLoS Pathog. 2015 Dec 17;11(12):e1005293.

Lionakis MS, Swamydas M, Fischer B, Plantinga T, Johnson MD, Jaeger M, Masedunskas A, Weigert R, Mikelis C, Wan W, Richard Lee CC, Lim JK, Rivollier A, Yang J, Laird G, Wheeler RT, Alexander BD, Perfect J, Gao JL, Kullberg BJ, Netea MG, Murphy PM. CX3CR1-dependent renal macrophage survival promotes Candida control and host survival. J Clin Invest. 2013 Dec 2;123(12):5035-51.

Lionakis MS, Holland SM. CARD9: at the intersection of mucosal and systemic antifungal immunity. Blood. 2013 Mar 28;121(13):2377-8.

Lionakis MS, Netea MG. Candida and host determinants of susceptibility to invasive candidiasis. PLoS Pathog. 2013 Jan;9(1):e1003079

Lionakis MS, Fischer B, Lim JK, Swamydas M, Wan W, Richard Lee CC, Cohen J, Scheinberg P, Gao J, Murphy PM. Chemokine receptor Ccr1 drives neutrophil-mediated kidney immunopathology and mortality in invasive candidiasis. PLoS Pathog. 2012. Aug;8(8):e1002865.

Visit PubMed for a complete publication listing.

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Protocols and Patents

Clinical research protocols

Microbiomic and Immunologic Profiling of Women With Antibiotic-Induced Vaginal Candidiasis, #13-I-0181

The Natural History and Pathogenesis of Human Fungal Infections, #11-I-0187

Research patent

Kontoyiannis DP, Arap W, Pasqualini R, Lionakis MS, Lahdenranta J, inventors; Board of Regents, The University of Texas System, assignee. Biopanning as an approach to study the pathogenesis of and produce novel treatment modalities for invasive Aspergillosis. United States patent application US 20050187161. 2005 Aug 25.

Last Updated February 01, 2016