DA Whole Genome Sequencing Fellowship

APPLICATION DEADLINE: September 15, 2019 3:00PM ET

https://www.zintellect.com/Opportunity/Details/FDA-CFSAN-2019-0036

*Applications will be reviewed on a rolling-basis.

A research opportunity is currently available at the U.S. Food and Drug Administration (FDA), Center for Food Safety and Applied Nutrition (CFSAN), Office of Regulatory Science (ORS) located in College Park, Maryland.

Whole genome sequencing is an essential tool for tracing which bacteria have contaminated foods and identifying whether these bacteria pose serious public health threats because they carry virulence factors. Closing bacterial genomes provide a comprehensive view of their genetic composition that allows the generation of: 1) high quality reference genomes for source tracking during a foodborne outbreak investigation, 2) understanding long-term evolution of foodborne pathogens, 3) new insights in drug resistance and transmission of mobile elements carrying antimicrobial resistance markers, and 4) information about the contribution of DNA modification on pathogenesis. Currently, the only instrument that can reliably complete that task is the Pacific Bioscience (PacBio) Sequencer. Unfortunately, this equipment is expensive, requires specialized laboratories, needs significant quantities of DNA, and produce reads of around 30 kilo base(kb) in size at a time, making it challenging to correctly assemble the genomes of bacteria and the plasmids they may carry if they have high repetitive regions (e.g. E. coli). We need accessible technology that can produce longer reads so we can quickly help solve these problems. We propose to evaluate a relatively new alternative to SMRT sequencing, the MinION (Oxford Nanopore), which needs much less DNA to run, and can produce much longer reads. The MinION has been in testing for several years, is much less expensive, can be carried in one hand, and can be operated by regular lab staff. We will test the efficiency and accuracy of the MinION on strains of Escherichia coli and Clostridium botulinum.

We would like to sequence 200 selected strains (100 STECs E. coli from diverse serotypes and 100 C. botulinum representing groups I (proteolytic serotypes A-G) and II (non-proteolytic), isolated from both clinical and food samples) using an alternative platform: the MinION and GridION nanopore sequencer (Oxford Nanopore, Oxford, UK). Our goal is to develop a pipeline that could be used by other FDA researchers to perform real-time calling for sequences of interest, suitable for metagenomics, studies of antimicrobial resistance and virulence, and the detection/identification of BoTN toxins. We believe that such a MinION-based pipeline can help reduce the cost of closing genomes and simultaneously enable more laboratories to perform such analyses, since it would eliminate barriers posed by cumbersome technologies that require specialized bioinformatics.

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

• Test and evaluate MinION and GridION using systems for sequencing complete bacterial genomes and to develop a pipeline to analyze the output data as an alternative to the PacBio for rapid detection of virulence markers (Ecoli), antimicrobial resistance features (Ecoli), and toxin genes (Cbot) among food isolates and shotgun metagenomics samples
• Test the effectiveness of new MinION sequencing kits and flow cells using 8 genomes that have already been sequenced by PacBio or Sanger methods
• Data captured in reports and presentation in meetings
• Etc.

Qualifications

The qualified candidate should have received a master's or doctoral degree in one of the relevant fields. Degree must have been received within five years of the appointment start date.

Preferred skills:

• Sequencing experience
• Extensive Microbiology or molecular biology active lab experience
• Experience and knowledge of next generation sequencing and basic Bioinformatics tools and where to source them from
• Previous experience with foodborne pathogens in a laboratory setting

For a full description of this opportunity and to submit your application, visit https://www.zintellect.com/Opportunity/Details/FDA-CFSAN-2019-0036.

If you have any questions, send an email to ORISE.FDA.CFSAN@orau.org.  Please include the reference code for this opportunity (FDA-CFSAN-2019-0036) in your email.