Adult Infectious Disease and Basic Microbiologic Mechanisms Training Program

Harvard-wide Adult Infectious Diseases Training Grant request for applications

All application materials are due 5:00 PM, Friday, February 1, 2019.

Grant information and application instructions are available in December by request.

The adult Infectious Disease and Basic Microbiological Mechanisms Training Program is a Harvard-wide training program dedicated to the education of those infectious disease fellows and PhD postdoctoral fellows interested in pursuing careers as physician-scientists or scientists with a focus on investigation into important questions in non-HIV microbiology and infectious diseases.

Since 1976, the program has been supported by an National Institutes of Health-funded post-doctoral training grant (T32). The training of infectious disease physician-scientist fellows consists of an initial year in clinical infectious diseases (funded by the hospitals), followed by two or more years of mentored research.

The training grant provides support directly to selected infectious disease fellows during their years of mentored research and, by providing support to selected PhD trainees in Harvard Medical School infectious disease and microbiology laboratories focused on areas that have significant clinical relevance, supports the rich research-training environment for scientists within these laboratories.

Participating Institutions


Adult Infectious Disease and Basic Microbiologic Mechanisms Training Program Faculty

Jonathan Abraham, MD, PhD: Structural biology of viral entry
Assistant Professor of Microbiology, Harvard Medical School

Galit Alter, PhD: Antibody responses to chronic viral and bacterial infections
Professor of Medicine, Harvard Medical School

Caroline Buckee, PhD: Population biology, evolution, and infection dynamics of genetically diverse pathogens
Associate Professor of Epidemiology, Harvard TH Chan School of Public Health

Richelle C. Charles, MD: Protective immunity and diagnostics for Vibrio cholerae and Salmonella enterica serovar Typhi and Paratyphi A
Assistant Professor of Medicine, Harvard Medical School

Isaac M. Chiu, PhD: Role of the nervous system in inflammation and host defense against pathogens
Assistant Professor of Microbiology, Harvard Medical School

Laurie E. Comstock, PhD: Symbiotic relationships among intestinal bacteria
Associate Professor of Medicine (Microbiology and Immunobiology), Harvard Medical School

Joseph El-Khoury, MD: Mechanisms of innate immunity in neuroinflammation
Associate Professor of Medicine, Harvard Medical School

Sarah Fortune, MD: Genetics and molecular pathogenesis of Mycobacterium Tuberculosis
Professor of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health; Associate Member, The Broad Institute; Associate Member, Ragon Institute

Marcia B. Goldberg, MD: Host-pathogen interactions in Shigella infection
Professor of Medicine and Microbiology, Harvard Medical School; Professor of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health; Associate Member, The Broad Institute

Yonatan H. Grad, MD, PhD: Pathogen evolution and spread
Melvin J. and Geraldine L. Glimcher Assistant Professor of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health

Jason B. Harris, MD, MPH: Mucosal immunology of V. cholerae
Associate Professor of Pediatrics, Harvard Medical School

Darren E. Higgins, PhD: Intracellular bacterial pathogenesis in Listeria monocytogenes
Professor of Microbiology, Harvard Medical School

Deborah T. Hung, MD, PhD: Infectious diseases and chemical biology
Associate Professor of Medicine and Genetics, Harvard Medical School; Co-Director, Infectious Disease and Microbiome Program, Broad Institute

Jonathan C. Kagan, PhD: Innate immune response to pathogens
Professor of Pediatrics, Harvard Medical School

James E. Kirby, MD: Antimicrobial development, resistance, and rapid diagnostics
Associate Professor of Pathology, Harvard Medical School

Cammie F. Lesser, MD, PhD: Delivery of bacterial proteins into mammalian cells
Associate Professor of Medicine and Microbiology, Harvard Medical School

Michael K. Mansour, MD, PhD: Host response to invasive fungal pathogens
Assistant Professor of Medicine, Harvard Medical School

John J. Mekalanos, PhD: Molecular mechanisms of virulence of V. cholerae and Pseudomonas aeruginosa
Adele H. Lehman Professor of Microbiology and Immunobiology, Harvard Medical School

Bradley L. Pentelute, PhD: New chemistry for peptide synthesis
Associate Professor of Chemistry, Massachusetts Institute of Technology

Eric. J. Rubin, MD, PhD: Molecular pathogenesis of M. tuberculosis
Irene Heinz Given Professor of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health; Assistant Professor of Medicine and Microbiology, Harvard Medical School

Edward T. Ryan, MD: Immune responses and vaccines for enteric bacteria
Professor of Medicine, Harvard Medical School; Associate Professor of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health

Pardis Sabeti, MD, DPhil, MSc: Evolutionary adaptation in humans of viral pathogens
Professor of Immunology and Infectious Disease, Harvard TH Chan School of Public Health; Institute Member, The Broad Institute

Jatin M. Vyas, MD, PhD: Innate immunity to fungal pathogens
Associate Professor of Medicine, Harvard Medical School

Matthew K. Waldor, MD, PhD: Pathogen-host interactions of enteric bacteria
Edward H. Kass Professor of Medicine and Microbiology, Harvard Medical School; Investigator, Howard Hughes Medical Institute; Associate Member, The Broad Institute

Suzanne Walker, PhD: Chemical biology, enzymology, antibiotics, glycosyltransferases, and inhibitors
Professor of Microbiology, Harvard Medical School; Affiliate Faculty Member, Chemistry and Chemical Biology, Harvard University; Associate Member, The Broad Institute

Peter F. Weller, MD: Eosinophils, immunobiology, and leukocyte lipid bodies
Professor of Medicine, Harvard Medical School

Sean Whelan, PhD: Biology of negativesense RNA viruses
Professor of Microbiology, Harvard Medical School

Dyann F. Wirth, PhD: Genomics of malaria transmission
Richard Pearson Strong Professor and Chair, Immunology and Infectious Diseases, Harvard TH Chan School of Public Health; Senior Associate Member, The Broad Institute; Director, Harvard Malaria Initiative, Harvard TH Chan School of Public Health

Priscilla Yang, PhD: Chemistry and biology of host-virus interactions
Associate Professor of Microbiology, Harvard Medical School

Focus Areas

Areas of Infectious Diseases and Public Health addressed by program faculty research

Infectious disease pathogenesis: molecular mechanisms of disease
Abraham, Fortune, Goldberg, Higgins, Hung, Lesser, Mekalanos, Rubin, Waldor, Whelan, Yang

Immune responses to infection: function and mechanisms of host responses
Abraham, Alter, Charles, Chiu, El Khoury, Goldberg, Harris, Higgins, Kagan, Lesser, Mansour, Ryan, Vyas, Weller

Pathogen and host genomics: role of genomic characteristics in infection
Fortune, Grad, Hung, Mekalanos, Rubin, Waldor, Whelan, Wirth

Pathogen transmission, dynamics, and spread: epidemiology and genomics
Buckee, Fortune, Grad, Sabeti, Waldor, Wirth

Antimicrobial resistance: underlying mechanisms, discovery of new antimicrobial targets or drugs
Charles, Goldberg, Hung, Rubin, Walker, Yang

Novel diagnostics: genomic and other approaches for rapid diagnosis of infection and resistance
Goldberg, Hung, Sabeti, Wirth

Emerging and re-emerging infectious diseases: epidemiology and disease mechanisms
Abraham, Buckee, Grad, Sabeti

Microbiome: role in infectious disease pathogenesis and host immunity
Comstock, Goldberg

Nosocomial infections: mechanisms of disease and spread
Hung, Mekalanos, Waldor

Vaccines and immunotherapies: development and analysis
Abraham, Alter, Charles, Harris, Mansour, Pentelute, Ryan


Current Fellows

John Albin, MD, PhD
Under the mentorship of Bradley Pentelute, PhD, at MIT, Dr. Albin is using chemical approaches to develop peptide-based antibiotics, including antibody-bactericide conjugates for the modulation of known antimicrobial agents and synthetic evolution of peptides for the derivation of novel antimicrobial peptides. In this work, he is specifically targeting Pseudomonas aeruginosa, an opportunistic pathogen that commonly affects immunocompromised hosts, including those with cystic fibrosis and neutropenia.

Patricia Grace, PhD
Under the co-mentorship of Drs. Galit Alter and Sarah Fortune, Dr. Grace is combing human and mouse immunological approaches to understand the role of antibodies from different disease states in the control of M. tuberculosis infection. Using a mouse model of M. tuberculosis infection, she is testing whether human antibodies from different tuberculosis disease states can confer control of M. tuberculosis growth and/or protection against disease pathology.

Bobby Brooke Herrera, PhD
Under the mentorship of Jonathan Abraham, MD, PhD, at Harvard Medical School, Dr. Herrera is investigating the molecular characterization of Ebola virus antibody responses during asymptomatic infection.

Jacob Lemieux, MD, PhD
Under the mentorship of Dr. Pardis Sabeti, Dr. Lemieux plans to perform genomic and pathogenesis investigations of the human parasites Babesia spp. His work focuses on improving in vitro cultivation techniques, establishing model systems for studying Babesia biology, identifying mechanisms of drug susceptibility and drug resistance in Babesia, and identifying parasite-mediated mechanisms of chronic Babesia infection.

Alaina Ritter, MD
Working with Jason Harris, MD, and Ana Weil, MD, Dr. Ritter is investigating the impact of gut microbiota on the innate immune response during Vibrio cholerae infection. Preliminary data from the Harris lab identified several anaerobic bacteria associated with protection from V. cholerae. Dr. Ritter is assessing the impact of these bacteria on the immune response to V. cholerae.

Fabian Rivera-Chavez, PhD
Under the mentorship of Dr. John Mekalanos, Dr. Rivera-Chavez is investigating the role of complement resistance by Vibrio cholera and other intestinal pathogens during colonization of the intestine.

Pritha Sen, MD
Under the mentorship of Joseph El Khoury, MD at Massachusetts General Hospital, Dr. Sen is investigating how cytomegalovirus infection of immunocompromised hosts alters the host response to other pathogens. Specifically, she plans to focus on evaluating how macrophage and monocyte effector functions important to host defense against pathogens are altered by cytomegalovirus infection.

Swalpa Udit, MD, PhD
Under the mentorship of Dr. Isaac Chiu, Dr. Udit plans to investigate the role of nociceptor sensory neurons in host response to influenza pneumonia. Using a murine model with genetic ablation of nociceptors, Dr. Udit plans to determine the role of pulmonary nocireceptor neurons in host defense and the inflammatory response in influenza infection.


Contact Us

Adult Infectious Disease and Basic Microbiologic Mechanisms Training Program

Massachusetts General Hospital

55 Fruit StreetDivision of Infectious Diseases – GRJ504 Boston, MA 02114
  • Phone: 617-724-7513
  • Fax: 617-726-7416
  • Email Us

Grant Writing

Workshops and courses

  • Are you writing a K? Get practical advice
    Ingrid Bassett, Kenneth Freedberg, Athe Tsibris, Rochelle Walensky
    Special Guest : Robin Huebner, PhD, NIAID Program Officer
    Annually in February or March
    Harvard Medical School
    Joseph B Martin Conference Center
    Space is limited
  • Conquering the K: Applying for an NIH Career Development Award

    MGH Division of Clinical Research
    Annually in February (application in January)
    Sessions over multiple weeks
    Massachusetts General Hospital
    Space is limited

  • Successful Grant Writing Strategies 
    Harvard Catalyst
    Online course, offered periodically
  • Read successful K awards, F32 grants, or other fellowship applications, including the summary statements, with input directly from the grant writers
    Contact Marcia Goldberg

Related Courses

Selected Coursework Taken by T32 Trainees

Analytical and Quantitative Light Microscopy Course
Marine Biological Laboratories, Wood's Hole, MA. Room/board is provided in class fees.
When:Annually, late April, 9 days, 8:00 am to 11:00 pmThis course is designed to provide a foundation in the theory and practice of light microscopy. It consists of dedicated lectures followed by hands-on laboratory sessions building on these lectures. You learn the theory behind the techniques and then get practical experience with expert guidance. It starts with fundamentals of transmitted light microscopy, and works through polarized, darkfield, phase contrast, DIC, fluorescence, TIRF, structured illumination and PALM/STORM microscopy. A commercial faculty is present from the big four microscope companies as well as other imaging companies to help facilitate the laboratory sessions. It is an outstanding course that covers both the major aspects of different types of light microscopy, and the technical details that are so important for proper microscopy.

American Association of Immunologists Advanced Course in Immunology
Sponsor/Location: American Association of Immunologists, Seaport World Trade Center, Boston, MA
When: Annually, in July-August
This intensive course is directed toward advanced trainees and scientists who wish to expand or update their understanding of the field of Immunology. Leading experts present recent advances in the biology of the immune system and address its role in health and disease. Each day consists of a series of lectures on various topics in the field of Immunology. The overall quality of the course was excellent and assumes each participant has a firm understanding of the principles of immunology.

Boston Area Antibiotic Resistance Network (BAARN)
Sponsor/Location: American Academy of Arts and Science, Somerville, MA
When: Annually, date varies
This small (~200 attendees), focused, one-day meeting includes talks on a range of topics related to antimicrobial resistance. Presenters are from industry, academia, and the NIH. Topics include novel therapeutics, diagnostics, and funding mechanisms. There is ample time for networking as well as a poster session at the end of the day. I would highly recommend this meeting for anyone in the field because of its focus and limited size, which facilitates networking. For questions, please contact Thea Brennan-Krohn.

Harvard University CFAR Workshop on Metagenomics and Transcriptomics
Sponsor/Location: Harvard University Center for AIDS Research, Joseph B. Martin Conference Center Harvard Medical School Boston, MA
When: Annually, in September
The focus of this five-day intensive workshop was to provide an introduction to fundamental computational skills, genomics study design, and data interpretation. Specific topics covered included an introduction to Unix and R, an overview of metagenomics study design and data analysis tools with a focus on QIIME, and transcriptomics study design and data analysis pipelines. Each day consisted of lectures in the morning and laboratory sessions in the afternoon with access to teacher assistants.

High-Throughput Biology: From Sequence to Networks
Sponsors/ Location: Cold Spring Harbor Laboratory, Canadian Bioinformatics Workshops, New York Genome Center
When: In the Spring
This week-long intensive course covered the bioinformatics concepts and tools required to analyze DNA and RNA-sequence reads using a reference genome. Two days were focused on DNA sequencing data analysis with topics including reference genome alignment, data visualization, De Novo assembly, small variant calling and annotation, and structural variation calling. The next two days were devoted the RNA-seq analysis with topics including alignment and visualization, expression and differential expression analysis, and isoform discovery and alternative expression. While the course included an introduction to the Galaxy environment, it predominantly focused on the use of command-line tools in the Unix and R environment for carrying out analyses. Data visualization tools were also reviewed. Following the DNA and RNA-seq analysis course segments, two and half days were devoted to pathway and network analysis along with gene function prediction and gene regulation network analysis. Each day consisted of didactic lectures followed by hands-on tutorials using example data sets provided by the course. In the evenings, there were optional hands-on tutorials with additional data sets. Overall, this was an excellent course with outstanding instructors. Basic working knowledge of Unix and R is a prerequisite.

Introduction to Network Medicine
Sponsors/ Location: Harvard Catalyst
When: Periodically
This three-day survey course serves as a 10,000-foot overview of network medicine (i.e., systems biology) and provides a useful introduction to the use of network science to make sense of the massive amounts of data generated by modern -omics approaches. The quality of the sessions was variable, and this is clearly still a field still in its infancy, but the core sessions delivered by Harvard faculty were valuable. No coding background is required. After this course, I am now broadly familiar with the approaches used in this field, and now have a sense of the kinds of data to which these analyses could be applied, though probably would not feel comfortable analyzing data de novo and would require a collaborator. For questions, please contact Jacob Lazarus.

MassBioSciences Career Development Workshop
Sponsor/Location: Postdoctoral Associations at Boston Children’s Hospital, Harvard School or Public Health, Tufts University, Dana-Farber Cancer Institute and The Broad Institute hosted at The Broad Institute
When: In the Spring
This workshop was organized to bring together area scientists, mostly targeted at postdocs and graduate students. This was a two-day training event to learn about transferable skills, leadership and management styles, non-academic alternative career paths and networking skills. They also provided tools and information to further career development after the workshop.

Strategies and techniques for analyzing microbial population structure
Sponsor/Location: Marine Biological Laboratories, Wood's Hole, MA. Room/board is provided in class fees.
When: Annually in August, 10 days from 8:00 am to 9:00 pm, with one day off.
The course is focused on concrete skills for analyzing genomic data of biological populations generated by next-generation sequencing technology ("big data"). The theory, technical aspects, and best practices of data generation and analysis are discussed by experts in the field. Most valuable are the daily programming computer labs with excellent TAs to help with questions. Although prior experience in programming is not required, participants with some familiarity with Unix or R will be able to complete more of the class material.

Note that participants are often accepted after the deadline listed on the website.
For questions, please contact Ana Weil.

Workshop on Molecular Evolution 
Sponsor/Location: Marine Biological Laboratories, Wood's Hole, MA. Room/board is provided in class fees.
When: Annually in August, 10 days from 8:00 am to 9:00 pm
Taught by a group of some of the foremost evolutionary biologists in the world, and up and coming stars. Covers many of the phylogenetic inference methods seen in the literature as well as the history behind them. Helps to have a quantitative background but not absolutely necessary. Students from all over the world with an incredible array of experiences. For questions, please contact Sanjat Kanjilal.


Recent Alumni

Jonathan Abraham, MD, PhD, 2016 Trainee:
Dr. Abraham transitioned to an NIH Director's Early Independence (DP5) award and a Burroughs-Wellcome Fund Career Award for Medical Scientists. He is currently a faculty member in the Department of Microbiology at Harvard Medical School. His work focuses on profiling the human antibody response in survivors of viral hemorrhagic fevers, the development of antibody therapies for human viral hemorrhagic fevers, and the prevention of late neurological complications of these infections.

Kelly Bachta, MD, PhD, 2014-2016 Trainee: 
Under the mentorship of Dr. John Mekalanos, Dr. Bachta’s project focused on the mechanisms of multi-drug resistance in Pseudomonas aeruginosa. Pseudomonas aeruginosa is an opportunistic pathogen that commonly affects immunocompromised hosts, including those with cystic fibrosis or neutropenia, who frequently receive multiple courses of antibiotics. As a result, P. aeruginosa is serially exposed to selective pressure to develop and maintain mechanisms of antibiotic resistance. One such mechanism involves the coordination of drug-efflux pumps. P. aeruginosa has several known multi-drug efflux pumps which efflux a variety of antibiotics including beta-lactams, fluoroquinolones and aminoglycosides. Dr. Bachta’s project characterized these efflux pumps with the hope of developing novel inhibitors to expand the array of clinically useful anti-pseudomonal therapies. Dr. Bachta is currently conducting additional mentored postdoctoral training at Northwestern Memorial Hospital.

Roby Bhattacharyya, MD, PhD, 2012-2013 Trainee:
Dr. Bhattacharyya transitioned to a Foundation for Medical Discovery individual fellowship from the Mass General Executive Committee on Research and an NIH K08. He is currently an Instructor in Medicine in the Division of Infectious Diseases at Massachusetts General Hospital. Dr. Bhattacharyya is working with Dr. Deborah Hung to develop rapid, non-culture based diagnostics for a variety of pathogens and from a range of human samples. This group showed that RNA expression signatures can be used to identify a variety of common pathogens rapidly and specifically using RNA probes that target sequences highly conserved within but not shared between pathogenic species. Targeting RNA expression signatures of stress response pathways that respond early to antibiotic therapy enables discrimination of susceptible strains from resistant ones. The development of rapid diagnostic methods for important human pathogens has the potential to revolutionize early diagnosis and treatment, particularly in resource-poor settings, with enormous impact on the control and prevention of transmission of infectious diseases.

Tyler Bold, M.D., M.D., Ph.D., 2017-2018 Trainee:
Dr. Bold is currently Assistant Professor, University of Minnesota Medical School. A hallmark of Mycobacterium tuberculosis infection is bacterial persistence, which may cause chronic T cell antigenic stimulation that results in the development of T cell exhaustion phenotypes, which limit the efficacy of effector and memory immune responses. Under the mentorship of Dr. Eric Rubin, Dr. Bold investigated the hypothesis that T cell exhaustion contributes to the inability of endogenous adaptive immunity to eradicate M. tuberculosis and prevent future infection.

Daniel Bourque, MD, 2014-2016 Trainee:
Under the mentorship of Dr. Jason Harris, Dr. Bourque investigated the mechanisms that promote long-term immunity from natural infection to Vibrio cholerae. The aims of his research were to identify mucosal innate immune pathways and early B cell responses, which lead to the development of long lasting B cell memory after natural infection as compared to oral vaccination.

Thea Brennan-Krohn, MD, Trainee 2017-2018: Dr. Brennan-Krohn transitioned to an NIH K08 award under the mentorship of James Kirby, MD, at Beth Israel-Deaconess Medical Center. Dr. Brennan-Krohn is working to develop new antimicrobial strategies for treatment of carbapenem resistant Enterobacteriacae (CRE), which are among the most drug-resistant bacteria known. Her work is based on the observation that treatment with more than one antibiotic in combination is associated with better patient outcomes. Dr. Brennan-Krohn's project involves the development of new methods to test for synergy and investigation of the impact of drug combinations in a mouse model of CRE infection.

Allison Carey, MD, 2015-2017 Trainee:
Dr. Carey transitioned to an NIH K08 award. Under the mentorship of Sarah Fortune, MD, Dr. Carey is investigating the modulating features and genetic determinants of tuberculosis infection. Tuberculosis, the disease caused by the pathogen Mycobacterium tuberculosis, is a global health crisis, with over 9 million new cases of active disease and more than a million deaths annually. Tuberculosis was long thought to be a genetically monomorphic pathogen, but recent work uncovered substantial genetic diversity among circulating clinical strains. Dr. Carey uses genome-wide genetic screening and quantitative molecular tools to explore the impact of genetic diversity among clinical strains in the settings of reinfection and vaccination.

Heather Eshleman, PhD, 2016-2017 Trainee:
Under the mentorship of Marcia Goldberg, MD, at Massachusetts General Hospital, Dr. Eshleman investigated the mechanism of action of the Shigella flexneri effector protein OspB. Shigella spp. deliver into host cells effector proteins that alter the function of host cell pathways in ways that promote infection. OspB induces cell proliferation of host cells. Dr. Eshleman worked on defining the pathway that is impacted by OspB and the mechanism by which OspB manipulates it.

Sanjat Kanjilal, MD, MPH, 2015-2017 Trainee:
Under the mentorship of Marc Lipsitch, PhD, and Yonatan Grad, MD PhD, Dr. Kanjilal worked to define population dynamics and genotypic correlates of invasion and antibiotic resistance of methicillin-resistant Staphylococcus aureus (MRSA). With the goal of defining S. aureus genes and regulatory networks that underlie clinically important phenotypes and of defining patterns of transmission through human populations, Dr. Kanjilal investigated the population structure, antibiotic resistance, and virulence factors of MRSA, using phylogenetic and statistical tools to analyze a data set of over 1400 genomes from well-characterized isolates.

Jacob Lazarus, MD, PhD, 2017-2018 Trainee:
Dr. Lazarus transitioned to a KL2 MeRIT fellowship. Under the mentorship of Dr. Matthew Waldor, Dr. Lazarus is working to identify host and pathogen factors that influence induction of antibiotic resistance, the switch from commensal to pathogen, and bloodstream translocation by Enterobacteriaceae, a large group of Gram-negative bacteria than can both colonize the human gut as commensals and cause life-threatening infections as invasive pathogens. Enterobacteriaceae frequently acquire resistance to multiple antibiotics, especially extended-spectrum beta-lactams and carbapenems, making them challenging and occasionally impossible to treat successfully.

Philip Lederer, MD, 2015-2016 Trainee:
Under the mentorship of Dr. Edward Nardell, Dr. Lederer worked to evaluate the impact of a novel approach to identify and treat individuals with tuberculosis on ruducing delays in tuberculosis treatment and on health care worker infections in Peru.

Kelly Miller, PhD, 2014-2016 Trainee:
Under the mentorship of Marcia Goldberg, MD, Dr. Miller characterized interactions of Shigella flexneri and host cells at the molecular level to better understand Shigella pathogenesis. S. flexneri is an intracellular bacterial pathogen that is the most common cause of diarrheal disease worldwide. To establish successful infection bacteria must induce uptake into human colonic epithelial cells, evade host innate immune responses, and spread into neighboring cells within the epithelium. Many steps in this process require the activity of bacterial “effector” proteins that are translocated into host cells using a conserved syringe-like secretion apparatus called a type three secretion system. Dr. Miller investigated how interaction of bacterial effector proteins and host proteins interfere with the host cell innate immune response during Shigella infection.

Anne Piantadosi, MD, PhD, 2016 Trainee:
Dr. Piantadosi transitioned to a KL2 MeRIT fellowship. Under the mentorship of Dr. Pardis Sabeti, she is using next-generation sequencing to identify known and unknown viral pathogens in infectious encephalitis and is then characterizing a selected subset of these pathogens.

Jennifer Reedy, MD, PhD, 2012-2014 Trainee:
Dr. Reedy transitioned to a KL2 MeRIT fellowship. Under the mentorship of Jay Vyas, MD, PhD, Dr. Reedy investigated how the innate immune system recognizes and responds to fungal pathogens. Her research focused on the dematiaceous mold Exserohilum rostratum and elucidating the mechanisms by which the innate immune system recognizes and responds to this fungus. Specifically, she analyzed the carbohydrate composition of spores and hyphae of E. rostratum and evaluated the cytokine response elicited by macrophages in response to E. rostratum.

Chanu Rhee, MD, MPH, 2014-2015 Trainee:
Dr. Rhee is a faculty member in the Department of Population Medicine, Brigham and Women’s Hospital. Under the mentorship of Richard Platt, MD, MSc, Dr. Rhee focused on the epidemiology, surveillance, and prevention of healthcare-associated infections, particularly in critically ill patients. His research project, a multicenter observational study being conducted with the CDC Prevention Epicenters, used objective clinical data captured by electronic health records to improve the public health system’s capacity to accurately track the incidence and burden of severe sepsis and septic shock.

Jonathan Robbins, MD, PhD, 2014-2017 Trainee:
Now a Medical Director at Merck & Co., Dr. Robbins studied malaria, a parasitic disease responsible for hundreds of thousands of deaths each year, under the mentorship of Jeffrey Drovin, MD PhD. Dr. Robbins used a combination of forward and reverse genetic approaches to better understand the cell division cycle of P. falciparum.

William Robins, PhD, 2012-2013 Trainee:
Dr. Robins is working with John Mekalanos, PhD, to characterize the transcriptional regulation of V. cholerae, the agent of cholera, during its exit from the host into the environment. Where cholera is present, a substantial number of environmental V. cholerae organisms exist as clumps of metabolically-inhibited cells that persist for weeks or months. These conditionally viable environmental cells resist growth under standard conditions, but revert to an infectious and virulent form when introduced into animals. Dr. Robins’ seeks to uncover the transcriptional patterns occurring in conditionally viable environmental cholera as they form and persist in environmental water and then as they are resuscitated by exposure to autoinducers.

Brian Russo, PhD, 2014-2016 Trainee:
Under the mentorship of Marcia Goldberg, MD, Dr. Russo works to define molecular mechanisms required for the virulence of the bacterium Shigella, the most common cause of diarrhea worldwide. To establish disease, Shigella infects epithelial cells lining the intestine and spreads to adjacent cells. Effector proteins, delivered into the epithelial cells by Shigella, usurp host signaling in ways that promote infection. Dr. Russo is investigating the mechanisms by which the host cell activates type 3 secretion, including the role of cellular intermediate filaments and actin polymerization.

Ana Weil, MD, 2014-2015 Trainee:
Dr. Weil is currently supported on a K08 and is a junior faculty member in the Division of Infectious Diseases at Massachusetts General Hospital. Under the mentorship of Edward Ryan, MD, and Regina LaRocque, MD, Dr. Weil investigates factors that modulate the spread of cholera among humans, focusing on the human gut microbiome. Analyzing the microbial population structure of samples taken from household contacts of cholera patients, she determined specific bacterial groups associated with a higher likelihood of becoming infected with V. cholerae.

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