BIOINFORMATICS FELLOW
Population antimicrobial resistance discovery in stools associated with foodborne illness using NGS
Centers for Disease Control and Prevention, Atlanta, GA
A bioinformatics fellowship is 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 in the National Center for Emerging and Zoonotic Infectious Diseases at the Centers for Disease Control and Prevention (CDC).
Antimicrobial resistance (AMR) determinant detection and quantification directly from healthy and disease state stool samples is of strong public health interest. Current AMR assays are culture-based, which has limitations that we are interested in overcoming using shotgun sequencing and AMR-targeted amplicon sequencing in a metagenomic context. The fellow will work with a group of bioinformatics and laboratory scientists in CIMS to develop bioinformatics approaches for the analysis of shotgun sequencing and amplicon sequencing data for AMR content.
In conjunction with the National Antimicrobial Resistance Surveillance Team in EDLB and other partners, CIMS will be generating AMR profiles of stools from healthy individuals as well as individuals who are suffering from cases of bacterial foodborne illness. These AMR profiles will be generated through shotgun metagenomics sequencing of stool DNA using the Illumina HiSeq platform, as well as short (~200 bp) amplicon sequencing of known AMR gene targets amplified from stool DNA.
Questions include:
Activities include:
Qualifications:
Stipend is based on degree attained and other experience. This is a one year fellowship appointment through the Oak Ridge Institute for Science and Education program administered through the Department of Energy. For more information, please contact Andrew Huang care of [email protected].
Population antimicrobial resistance discovery in stools associated with foodborne illness using NGS
Centers for Disease Control and Prevention, Atlanta, GA
A bioinformatics fellowship is 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 in the National Center for Emerging and Zoonotic Infectious Diseases at the Centers for Disease Control and Prevention (CDC).
Antimicrobial resistance (AMR) determinant detection and quantification directly from healthy and disease state stool samples is of strong public health interest. Current AMR assays are culture-based, which has limitations that we are interested in overcoming using shotgun sequencing and AMR-targeted amplicon sequencing in a metagenomic context. The fellow will work with a group of bioinformatics and laboratory scientists in CIMS to develop bioinformatics approaches for the analysis of shotgun sequencing and amplicon sequencing data for AMR content.
In conjunction with the National Antimicrobial Resistance Surveillance Team in EDLB and other partners, CIMS will be generating AMR profiles of stools from healthy individuals as well as individuals who are suffering from cases of bacterial foodborne illness. These AMR profiles will be generated through shotgun metagenomics sequencing of stool DNA using the Illumina HiSeq platform, as well as short (~200 bp) amplicon sequencing of known AMR gene targets amplified from stool DNA.
Questions include:
- How can AMRs be accurately quantified and linked to antimicrobial activity of health consequence from metagenomic shotgun sequencing and AMR amplicon sequencing?
- How much AMR content is found in the stools of Americans without foodborne illness?
- Can AMRs be linked back to their host bacterium using different sequencing strategies?
Activities include:
- Development of pipelines for extraction and quantification of AMR content from metagenomic shotgun sequencing and targeted AMR amplicon NGS data
- Curation of AMR determinant databases both in house and with external collaborators
- Analysis of metagenomic shotgun and amplicon AMR data from hundreds of healthy stool samples to improve understanding of background AMR content
- Analysis of AMR data from outbreak associated stool samples for AMR content associated with foodborne pathogens and commensal organisms
Qualifications:
- Master’s degree in biological sciences, microbiology, bioinformatics, or related field (graduation within last three years)
- Strong UNIX command line bioinformatics tool experience required
- Proven experience with command line NGS data QC, alignment, quantification, and phylogeny tools required
- Experience with Python, Perl, and/or R is desirable
- Experience with metagenomics, comparative genomics, amplicon, and AMR-related research and bioinformatics tools and databases a plus
Stipend is based on degree attained and other experience. This is a one year fellowship appointment through the Oak Ridge Institute for Science and Education program administered through the Department of Energy. For more information, please contact Andrew Huang care of [email protected].