NimbleGen Systems CGS technique helps identify stomach bacteria

Madison, Wis. - Researchers from Washington University Medical School in St. Louis, using Comparative Genome Sequencing (CGS) from NimbleGen Systems, have identified evolutionary changes in the human pathogen Helicobacter pylori—a bacterium that infects the lining of the stomach and can cause complications such as peptic ulcers and gastric cancer—as it develops resistance to antibiotics, according to a study published online in Nature Methods.

Mutations that adapted H. pylori to increasing levels of the antibiotic metronidazole were rapidly identified in nearly a dozen serially adapted, antibiotic-resistant strains. The characterization of H. pylori strains in this study represents the equivalent of sequencing 3.3 million bases of DNA and identifying 11 confirmed mutations without error. This scale of genomic characterization was achieved in weeks at a cost roughly 80% less than conventional or high-throughput DNA sequencing methods.

To pinpoint the mutations, researchers used NimbleGen's CGS technique, which can find a single point change in millions of bases of DNA with nearly perfect accuracy. The technique uses NimbleGen's high-density DNA microarrays to compare entire microbial genomes for the purpose of strain identification and characterization of genomic changes in response to environmental forces. The technology can be used to track the movement of specific pathogens in human, animal or plant populations, aiding in epidemiology and public health efforts.

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