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CSTE, in collaboration with CDC, the Association of Schools and Programs of Public Health (ASPPH), and the Health Resources and Services Administration (HRSA), established the Applied Epidemiology Fellowship to train recent graduates in the expanding field of applied epidemiology. The goal of the Fellowship is to provide a high quality training experience and to secure long-term career placement for Fellows at the state or local level. Participating fellows will receive two years of on-the-job training at a state or local health agency under the guidance of an experienced mentor. The Fellowship’s mission is to meet the nation’s ongoing need for applied epidemiology workforce capacity in state and local health departments through a national fellowship-training program.

The Fellowship focuses on balancing three key concepts as identified in Applied Epidemiology and Training Program (AETP) Development Handbook (McDonnell, 2002):

  • Provide service to the sponsoring agency
  • Create and train a core group of public health workers
  • Strengthen capacity in applied epidemiology across public health institutions


The CSTE Applied Epidemiology Fellowship is designed for recent master’s or doctoral level graduates in epidemiology or a related field who are interested in public health practice at the state or local level. The program provides rigorous training for its participants while also being flexible to meet the particular interests of the fellow. Fellows are carefully matched to host agencies based on the fellow’s career interests and the host agency’s available opportunities. Program participants develop a set of core skills through competency-based training.


Closely designed after the Epidemic Intelligence Service (EIS) program and using a mentorship model, the CSTE Fellowship offers a unique opportunity for graduates to acquire and develop epidemiologic skills during a high-quality, on-the-job training program. Fellows work closely with highly trained and experienced epidemiologists at the state and local level, as well as experts working at the federal level. All fellowship graduates have secured permanent positions and most are working in epidemiology at the state or local level.

Mentors and Host Health Agency

Each fellow is assigned to a designated host health agency and two highly trained and experienced mentors (primary and secondary mentors). Host health agencies are approved by CSTE and have demonstrated their ability to provide a fellow with technical training, research opportunities, and practical experience in the application of epidemiologic methods.

Fellowship Application Timeline

2017-2018 Fellowship Application Timeline:

  • October 30, 2017– Fellow application opens. The link to the web-based application will be available on the CSTE website.
  • January 12, 2018– Fellow application closes. All applications and supporting materials must be received; any information received after this date will not be considered.
  • February-March, 2018– Application review. Complete applications are reviewed and evaluated by multiple panels of epidemiologists based on predetermined criteria.
  • April 2018– Matching process. Select finalists are invited to participate in a matching process that includes interviewing with potential host agencies.
  • June 1-August 13, 2018– Fellow placement. New Fellows begin their placements during the summer of 2017.

Applied Epidemiology Fellowship Competencies

Epidemiologic Methods

  1. Design or implement a new, or revise an existing surveillance system
  2. Evaluate a surveillance system and know the limitations of surveillance data
  3. Play a functional role and participate in emergency preparedness and response (training, tabletop exercises, surge capacity, etc.)
  4. Interpret surveillance data
  5. Design an epidemiologic study to address a health problem
  6. Demonstrate an understanding of study design and the advantages and limitations of each type
  7. Design a questionnaire or other data collection tool to address a health problem
  8. Collect health data from appropriate sources (e.g. case interviews, medical records, vital statistics records, laboratory reports, or pathology reports)
  9. Create a database for a health data set
  10. Use statistical software to analyze and characterize epidemiologic data
  11. Interpret findings from epidemiologic studies, including recognition of the limitations of the data and potential sources of bias and/or confounding
  12. Recommend control measures, prevention programs, or other public health interventions based on epidemiologic findings


* Indicates Core Competencies addressed in the fellowship orientation curriculum or in webinar format hosted by CSTE.


  1. Write a field investigation report resulting from participation in an outbreak investigation or a time-sensitive field investigation
  2. Write a surveillance report
  3. Understand the basic process for preparing a manuscript for publication*
  4. Make an oral presentation using appropriate media
  5. Present data graphically and know how to use graphic software
  6. Understand the basics of health risk communication and communicate epidemiologic findings in a manner easily understood by lay audiences
  7. Masters-level Fellows: present at a national or regional meeting, publish a technical report, or prepare a manuscript for publication in a peer-reviewed journal
  8. Doctoral-level fellows: prepare a manuscript for publication in a peer reviewed journal

* Indicates Core Competencies addressed in the fellowship orientation curriculum or in webinar format hosted by CSTE.

Public Health Practice, Policy and Legal Issues

  1. Understand the basics of public health law
  2. Understand the Health Insurance Portability and Accountability Act of 1996 (HIPPA)*
  3. Distinguish between public health research and public health practice*
  4. Understand policies for the protection of human subjects in research and the role of an Institutional Review Board (IRB)*
  5. Know the essential public health functions*
  6. Understand the roles of local, state, and federal public health agencies*
  7. Appreciate the diversity of how epidemiology is used in different program areas
  8. Understand and demonstrate cultural sensitivity and its relevance to public health practice

* Indicates Core Competencies addressed in the fellowship orientation curriculum or in webinar format hosted by CSTE.

Optional Experiences

  1. Provide epidemiologic input into an assessment of a local public health priority or issue
  2. Fellow to work with another AEF fellow or other public health trainee to complete a similar project and provide support to each other during the project phase
  3. Fellow to complete a visit to a lab or a different type of STLT agency than his/her placement; a fellow may also seek to complete an in-person hands-on experience (up to 5 days) in a different area than where he or she works to assist with a short term project or assignment
  4. Fellows to complete a report, presentation, brief, etc. related to one of the following activities: (1) Demonstrate knowledge of non-ID data sources and work on a project around this source; (2) Assist a non-ID department with a grant writing opportunity

* Indicates Core Competencies addressed in the fellowship orientation curriculum or in webinar format hosted by CSTE.

Fellowship Details

Fellows with a masters-level degree will be paid a bimonthly stipend of up to $41,000 annually. Doctoral-level candidates will be paid up to $56,000.

In addition to the stipend, up to $370 per month ($4,440 per year) will be available to defray the costs for individual health insurance coverage selected by the fellow. These funds are to be used for medical and/or dental coverage.

Moving/Relocation Expenses:
Up to $1,000 will be provided for moving related expenses.

Professional Development:
$970 per year is provided to each fellow for professional development. This stipend can be used for travel to meetings or conferences, short-term training programs, purchasing work-related books, and classes intended to aid in work-related projects.

Fellow Activities:

  • Orientation: All incoming fellows participate in a five-day orientation in Atlanta, Georgia. The orientation covers various topics related to developing the Applied Epidemiology Core Competencies. The curriculum is taught by CSTE and CDC epidemiologists as well as faculty from Schools of Public Health.
  • Plan of Action: After starting at the host health agency, the fellow and mentors develop a mutually agreed upon plan for fulfilling the Applied Epidemiology Core Competencies. By the end of the third month of the fellowship, the fellow and mentors submit a formal “Plan of Action” that outlines how the fellow will complete the required core activities and address the competencies.
  • Progress Reports/Evaluations: Each fellow completes quarterly progress reports updating the activities from his/her Plan of Action. Reports describe completed activities, accomplishments to date, and any new activities. Additionally, each fellow works with his/her mentors to complete biannual evaluations. These evaluations assess the fellow’s performance and outline progress toward meeting the required core activities.
  • Certification: A certificate from CSTE is awarded to each fellow at the end of the two-year fellowship, provided they demonstrate completion of all required core activities, submit a final report to CSTE, and perform satisfactorily during the fellowship according to their supervisors.
  • CSTE Annual Conference: Fellows are required to attend the CSTE Annual conference each year of their fellowship. Fellows are required to submit abstracts for the conference. Fellows are not expected to use their professional development allowance to attend the conference.

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