*Applications will be reviewed on a rolling-basis.

A research opportunity is currently available in the Culture-Independent and Metagenomic Subtyping group (CIMS) in the Enteric Diseases Laboratory Branch (EDLB) in the Division of Foodborne, Waterborne, and Environmental Diseases (DFWED) in the National Center for Emerging and Zoonotic Infectious Diseases (NCEZID) at the Centers for Disease Control and Prevention (CDC) in Atlanta, Georgia.

To maintain long-term viability, foodborne enteric pathogen outbreak surveillance systems must transition from culture-based methods, which require extensive laboratory work to isolate pathogens from other microbes in a patient stool sample, to molecular techniques compatible with complex metagenomic samples. CIMS is working closely with PulseNet, the National Antimicrobial Resistance Surveillance Team in EDLB, and other partners to develop complete culture-independent workflows covering specimen collection to final pathogen report. As a part of this work, CIMS is offering a fellowship to support the development and optimization of laboratory procedures utilizing amplicon sequencing and shotgun metagenomic sequencing for culture-independent enteric pathogen surveillance. Activities of the selected participant will include gaining valuable experience and skills in following areas: collaborating with other project scientists to develop project plans, interpreting data, writing protocols, and presenting results to partner public health organizations. The participant will receive extensive laboratory mentoring with the goal of developing a robust molecular and microbiological skillset that will include many techniques commonly used in public health laboratories around the USA. Validated best practices resulting from this project will be distributed to public health laboratories.

Under the guidance of a mentor, the participant will be trained in the following activities:

• Evaluate, develop, and implement a variety of next generation sequencing (NGS) approaches for metagenomic testing of complex specimens for public health deployment
• Operate specialized equipment such as Fluidigm Juno, Perkin-Elmer SciClone, Illumina MiSeq, and Agilent Fragment Analyzer
• Use standard microbiological techniques to safely manipulate primary clinical samples and pathogen isolates
• Extract DNA from pathogen isolates and stool for NGS
• Perform maintenance of shared laboratory spaces and equipment
• Maintain laboratory notebook and other project related records
• Communicate results to other project scientists and external collaborators

This opportunity involves working with human pathogen isolates and human clinical specimens (primarily stool). Relevant vaccinations for working with human clinical samples will be required. Extensive biosafety and chemical safety training and oversite will be provided.

If you have questions, send an email to ORISE.CDC.NCEZID@orau.org. Please include the reference code for this opportunity in your email.