The successful candidate will be a full-time employee of IHRC, Inc. and will be assigned to the Enteric Diseases Laboratory Branch (EDLB) within the Division of Foodborne, Waterborne, and Environmental Diseases (DFWED) at the US Centers for Disease Control and Prevention (CDC), 1600 Clifton Road, Atlanta, GA.
The successful candidate will be assigned to EDLB to provide bioinformatics support services for the identification of genetic markers extracted from whole genome sequences obtained using next generation sequencing devices that might be useful in the identification and subtyping of foodborne bacterial pathogens. The analysis will be performed on CDC-generated and publicly available sequences from a variety of foodborne bacterial pathogens including Shiga toxin-producing E. coli, Salmonella, Listeria and Campylobacter, among others. The main goal of this project is to develop whole genome sequencing and bioinformatic approaches that will enable the rapid detection and identification of foodborne bacterial pathogens from complex matrices without the need to culture them. The candidate will perform all or a subset of the following duties in support of EDLB’s objectives for this project.
Scope of Work
The Enteric Diseases Laboratory Branch is seeking bioinformatics support services to develop tools that will aid in the identification of potential culture-independent (genetic) targets useful for the characterization and subtyping of enteric bacterial pathogens using WGS data. Functions require expertise in bioinformatics, molecular analytical methods, and the ability to communicate essential information concerning the evaluation of analytical assays to members of the Branch. Whole genome sequences will be assembled, annotated, and analyzed for the most relevant foodborne bacterial pathogens impacting human health. Targets for subtyping and strain characterization will be identified for future development of highly discriminatory genotyping assays assess how genetic markers obtained from WGS analysis correlated with traditional epidemiological findings. Independent thought and experience are essential to successfully carry out the multiple tasks and responsibilities that pertain to these requirements.
a. Assist in the research and development approaches for the identification of unique genetic markers for the identification of foodborne bacteria pathogens.
b. Work with molecular microbiologists in the laboratory to address public health-related scientific questions as it relates to virulence factors, potential antimicrobial susceptibility markers and bioinformatics analyses.
c. Develop practical bioinformatic schemes to link subtyping, virulence, and susceptibility determinants to specific organisms, serotypes, and subtypes.
d. Manage large bacterial genome sequence files and databases to include upload of information to NCBI or similar data banks.
e. Create novel computational approaches and analytical tools as required by research goals.
f. Perform the quality control, assembly, annotation, and analysis of bacterial whole genome sequences.
g. Communicate research results through presentations, scientific publications, or project reports.
MAJOR DUTIES AND RESPONSIBILITIES:
Function 1: Analyze genetic sequencing data utilizing new methodologies or existing techniques that have been properly revised and validated.
Function 2: Develop, evaluate, and validate bioinformatics tools to establish correlations between unique genetic markers (extracted from whole genome sequences) and the species/serotype of foodborne bacterial pathogens.
Function 3: Assist laboratory personnel with the development and implementation of schemes designed to rapidly identify and subtype bacterial pathogens from complex matrices using the genetic markers identified in “Function 2” above.
Function 4: Assist with the establishment of schemes for the identification of potential antimicrobial resistance markers.
Function 5: Assist with the establishment of procedures for Quality Assurance (QA) and Quality Control (QC) of sequence data analysis in the context of this project.
Function 6: Prepare reports, charts, graphs, and presentations as required.