CDC Development of Genomic Tools and Pipelines to Support Molecular Epidemiology of Bacterial Pathogens

CDC Office and Location: A research and training opportunity is available in the Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP) of the National Centers for Emerging and Zoonotic Infectious Diseases (NCEZID) at the Centers for Disease Control and Prevention (CDC) located in Atlanta, Georgia.

The Centers for Disease Control and Prevention (CDC) is one of the major operation components of the Department of Health and Human Services. CDC protects America from health, safety and security threats, both foreign and in the U.S. Whether diseases start at home or abroad, are chronic or acute, curable or preventable, human error or deliberate attack, CDC fights disease and supports communities and citizens to do the same. CDC increases the health security of our nation. As the nation’s health protection agency, CDC saves lives and protects people from health threats. To accomplish its mission, CDC conducts important science and provides health information that protects our nation against expensive and dangerous health threats, and responds when these arise.

Research Project: BSPB serves as a national reference laboratory for several high consequence bacterial pathogens, including Bacillus anthracis, Burkholderia mallei and pseudomallei, Brucella spp., as well as over 500 rare and unusual bacterial pathogens. A major component of the research done within BSPB is developing and maintaining bioinformatic tools to help BSPB and its partners (both national and international) to investigate outbreaks, conduct surveillance, and identify novel species of bacterial pathogens.

BSPB is looking for a fellow to gain experience in the data management, bioinformatic pipeline development, analysis and visualization projects related to genomic and metagenomic data for bacterial pathogens. The fellow will train as a part of containerizing specialized bioinformatic pipelines, currently in use within the branch, so that standardized bioinformatic tools may be deployed to partner labs unable to perform their own genomic analysis. This will increase both national and international capacity and ensure that genomic analysis is being performed in a consistent and reproducible manner between multiple laboratories. This fellowship will also collaborate with MicrobeNet, a free online virtual reference laboratory run within BSPB, to create an organized state and national surveillance network of diseases which are not currently captured by active systems. 

Learning Objectives: 

• Learn about high-consequence bacterial pathogens and the role of national reference laboratories in public health surveillance and outbreak response.
• Gain experience with genomic and metagenomic data related to bacterial pathogens.
• Develop bioinformatics skills in data management, pipeline development, analysis, and scientific data visualization.
• Learn how bioinformatic tools are used to investigate outbreaks, support disease surveillance, and identify novel bacterial species.
• Gain training in developing and containerizing bioinformatic pipelines to support standardized and reproducible genomic analyses across laboratories.
• Develop experience with collaborative public health and laboratory networks that support national and international pathogen surveillance efforts.
• Learn principles of reproducibility, standardization, and scalable computational workflows in bioinformatics research.
• Participate in projects supporting MicrobeNet and virtual reference laboratory systems for pathogen identification and disease monitoring.
• Gain interdisciplinary exposure to microbiology, genomics, bioinformatics, public health, and infectious disease surveillance.
• Learn how genomic technologies contribute to improving laboratory capacity, disease tracking, and public health preparedness.

Mentor(s): The mentor for this opportunity is Zach Weiner (xxd7@cdc.gov). If you have questions about the nature of the research please contact the mentor(s).

Anticipated Appointment Start Date: October 1, 2026. Start date is flexible and will depend on a variety of factors.

Appointment Length: The appointment will initially be for one year, but may be renewed upon recommendation of CDC and is contingent on the availability of funds.

Level of Participation: The appointment is full time.

Participant Stipend: Stipend rates may vary based on numerous factors, including opportunity, location, education, and experience. If you are interviewed, you can inquire about the exact stipend rate at that time and if selected, your appointment offer will include the monthly stipend rate.

Citizenship Requirements: This opportunity is available to U.S. citizens only.

ORISE Information: This program, administered by ORAU through its contract with the U.S. Department of Energy (DOE) to manage the Oak Ridge Institute for Science and Education (ORISE), was established through an interagency agreement between DOE and CDC. Participants do not become employees of CDC, DOE or the program administrator, and there are no employment-related benefits. Proof of health insurance is required for participation in this program. Health insurance can be obtained through ORISE.

The successful applicant(s) will be required to comply with Environmental, Safety and Health (ES&H) requirements of the hosting facility, including but not limited to, COVID-19 requirements (e.g. facial covering, physical distancing, testing, vaccination).

Questions: Please visit our Program Website. After reading, if you have additional questions about the application process please email CDCrpp@orau.org and include the reference code for this opportunity.

Qualifications

The qualified candidate should be have received a master's in the one of the relevant fields. Degree must have been received within the past five years.

Public health informatics majors would be the most natural fit. 

Preferred skills:

• Proficient in Linux
• Proficient in Bash and Python scripting
• Experience with package managers (e.g., conda)
• Use of project version control with git
• Interest to learn Clarity LIMS for data management
• Interest to learn Nextflow for genomics and metagenomics data processing
• Understanding of generating computer algorithms for disease trends is desired.
• Informatics experience, including software applications for public health analysis.
• Background in information technology is considered helpful.
• Communications skills and a desire to learn and grow.