Clinical OMICS

JAN-FEB 2017

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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24 Clinical OMICs January/February 2017 www.clinicalomics.com the environment) in the NARMS program will help us understand how resistance emerges and spreads." Whole genome-based methodologies such as WGS afford researchers the opportunities to characterize and compare entire microbial genomic sequences to ascertain the spe- cific loci or exact genetic sequence associated resistance. While scientists can be creatures of habit when it comes to certain tech- niques—often following the "if it isn't broke don't fix it" mantra—they are often willing to combine various proven methods together, if they believe it will pro- vide them with greater data out- put, more sensi- tivity, or increased speed (often hoping to get all three attri- butes at once). This is exactly what researchers recently did when studying anti- biotic resistance for tularemia, an acute bacterial infection that causes ulceration of the skin, severe pneumonia, and is often lethal. "We recently applied whole genome-based technologies including DNA microarray and next generation sequencing to characterize an avirulent strain of Francisella tularensis, to the live vaccine strain or LVS, after the strain had been subjected to ciprofloxacin, a commonly used antibiotic to treat bacterial infections," noted Crystal Jaing, Ph.D., group leader of applied genomics at Lawrence Livermore National Laboratory. "Using this approach, we identified both previously known mutations that confer resistance as well mutations that have not been reported previ- ously. These mutations or markers can be used to develop diagnostic tests to rapidly determine if a bacterium is resis- tant to antibiotics, and what alternate treatment strategy can be used." Genomics is not only reshaping how scientists approach the study of antibiotic resistance, but it is also impacting how governmental agencies are collaborating and invest- ing in future research. When speaking to members of the National Institute of Allergy and Infectious Diseases' (NIAID) Office of Genomics and Advanced Technolo- gies (OGAT), they told ClinicalOM- ICS that "NIAID is investing into the application of genomic tech- nologies because we see these as re s e a rc h t o o l s that can be used to understand biolog- ical mechanisms that underlie antibiotic resistance, but also powerful high-throughput assays and cost-effective screens that can be read- ily used to help in the development of new antibiotics and therapeutics." The OGAT members provided numerous examples of ongoing collaborations that they believe will pay out big research dividends. For instance, and alliance between the NIAID Genomic Centers for Infectious Diseases and the NIAID Bioinformatics Resources Centers, or Pathosystems Resource Integration Center (PATRIC) is currently using WGS combined with phylogenom- ics—which uses genomic data to reconstruct evolutionary relation- ships—along with clinical and geographical data to track the pro- gression of resistance on a global scale across various pathogenic species. "This information is being used to understand how pathogens exchange genes, and to develop better diagnostics and therapeutics that take into account this genomic information," OGAT stated. "These data may also inform surveillance and could ultimately lead to improved stewardship. Understanding the biolog- ical mechanisms would enable better responses, however, Genomics is transcending the translational path by helping scientists address the needs of patients, from the development of new molecular diagnostics for improving disease prognosis to pharmacogenomic analyses that identify genetic background that is incompatible with various drug therapies. (continued from page 22) Alkov / Getty Images

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