Posted: 12-09-2024

Title: Research Position in Bioinformatics, Microbial Genomics and Antibiotic Resistance

Location: Walter Reed Army Institute of Research

Description:

About us and our mission:
The Walter Reed Army Institute of Research (https://www.wrair.army.mil/) is a World-Class organization that conducts biomedical research that aims to deliver lifesaving medical knowledge, technology, and materials to sustain military readiness. Within WRAIR, the Multidrug-Resistant Organism Repository and Surveillance Network (MRSN) is a unique entity that serves as the primary surveillance organization for antibiotic-resistant bacteria across the Military Healthcare System (MHS). The laboratory receives and processes (routine ID, Antibiotic Susceptibility Testing, and Whole Genome Sequencing) ~1,000 new isolates of ESKAPE+ pathogens every month from military hospitals across the world, and routinely collaborates with other U.S. Government agencies, allied nations, and academic research institutions. Our work directly impacts the DoD and MHS by:

• Providing real-time analysis, at the genomic scale, of the prevalence and mobility of “superbugs”, outbreaks, and antibiotic resistance genes.
• Conducting retrospective and prospective analyses on the emergence of antibiotic resistance and bacterial epidemiology across the entire enterprise.
• Assisting healthcare centers and infection control services to detect and appropriately respond to outbreaks using the most advanced and accurate molecular methods available.

About the position:
The fellow will be trained to perform the comparative genomic analysis of hundreds of epidemiology-linked isolates (ongoing outbreaks in military hospitals) of MDR Enterococcus spp. Staphylococcus spp., Klebsiella spp., Acinetobacter spp., Pseudomonas spp., Enterobacter spp., and Escherichia coli. The successful candidate will employ a variety of bioinformatic tools and software to analyze bacterial genomes for the purpose of outbreak investigations and local, national, and international bacterial epidemiology. The successful candidate will collaborate extensively with internal and external researchers on the molecular genetics of antibiotic-resistant bacteria. In particular, the successful candidate will analyze and research the global dissemination of antibiotic-resistant bacteria and participate in real-time surveillance of these organisms throughout the military healthcare system.

The participant in this program will gain extensive educational experience that will greatly enhance his/her career opportunities. In particular, the participant will gain hands-on knowledge of working with both short-read and long-read DNA sequences using the Illumina Miseq and Nextseq systems and the Oxford Nanopore Minion platform. Furthermore, the participant will be conducting analyses using the most state-of-the-art software and bioinformatics tools, and will also develop hands-on programming experience using Linux, Python, R.

Under the mentorship of WRAIR staff, the selected candidate will help establish a fundamental understanding of translational, military-relevant scientific research. The selected candidate will be highly encouraged to begin expanding their network of scientific colleagues and seek collaborations within the U.S. Department of Defense, academia, and commercial companies. Furthermore, the participant will be challenged to develop new and innovative methods for analyzing bacterial genomes and will have the opportunity to make significant contributions to this emerging field while conducting research in one of the most comprehensive sequencing laboratories in the USA.

Requirements:

• The candidate should have a PhD or be in the process of defending their PhD thesis.
• The candidate must have experience in tissue culture, viral growth and propagation, viral titration, and developing diagnostic or detection assays (e.g. ELISA, neutralization assays, WB, IFA).
• The ideal candidate should also be experienced in basic molecular biology (e.g. DNA/RNA purification, DNA/RNA quantification, PCR, restriction enzyme digestions).
• Experience in DNA/RNA sequencing approaches (nanopore, Illumina) is desired, but not essential.

Level: Graduate