Adult Infectious Disease & Basic Microbiologic Mechanisms Training Program

About the Program

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 a 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

• Beth Israel Deaconess Medical Center, Division of Infectious Diseases
• Brigham and Women's Hospital, Division of Infectious Diseases
• Massachusetts General Hospital, Division of Infectious Diseases
• Harvard Medical School, Department of Microbiology and Department of Immunology
• Harvard School of Public Health, Department of Immunology and Infectious Diseases
• Harvard School of Public Health, Department of Epidemiology
• Massachusetts Institute of Technology, Department of Chemistry

Focus Areas

These areas of infectious diseases and public health are currently 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

Our Faculty

Get to know the talented faculty involved in this program.

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 negative sense 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

How to Apply

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.

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.

Recent Alumni

Grant Writing Workshops

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
Sponsor/Location: 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 pm
This 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.