{"107661":{"#nid":"107661","#data":{"type":"news","title":"Georgia Tech Develops Software for the Rapid Analysis of Foodborne Pathogens","body":[{"value":"\u003Cp\u003E2011 brought two of the deadliest bacterial outbreaks the\nworld has seen during the last 25 years. The two epidemics accounted for more\nthan 4,200 cases of infectious disease and 80 deaths. Software developed at\nGeorgia Tech was used to help characterize the bacteria that caused each\noutbreak. This helps scientists to better understand the underlying\nmicrobiologic features of the disease-causing organisms and shows promise for supporting\nfaster and more efficient outbreak investigations in the future. \u003C\/p\u003E\n\n\u003Cp\u003EFrom 2008 to 2010, a team of bioinformatics graduate\nstudents, led by School of Biology Associate Professor King Jordan, worked in\nclose collaboration with the Centers for Disease Control and Prevention (CDC)\nto create an integrated suite of computational tools for the analysis of\nmicrobial genome sequences.\u0026nbsp; At that\ntime, CDC scientists were in need of a fast and accurate system that could\nautomate the analysis of sequenced genomes from disease-causing bacteria. They\nturned to the Jordan lab at Georgia Tech to help develop such a tool. The\nGeorgia Tech scientists created an open source software package, the \u003Ca href=\u0022http:\/\/jordan.biology.gatech.edu\/jordan\/images\/pubs\/kislyuk-bioinformatics-2010.pdf\u0022\u003EComputational\nGenomics Pipeline\u003C\/a\u003E (CG-pipeline), to help meet CDC\u2019s need. The software\nplatform is now used worldwide in public health research and response efforts. \n\n\u003C\/p\u003E\u003Cp\u003E\u201cDetermining the order of DNA bases for an entire genome has\nbecome relatively cheap and easy in recent years because of technological\nadvancements,\u201d said Jordan. \u201cThe hard part is figuring out what the genome\nsequence information means. Our software takes that next step. It analyzes the sequences,\nfinds the genes and provides clues as to which genes are involved in making\npeople sick. Manually, this process used to take weeks, months or a year. Now\nit takes us about 24 hours.\u201d \u003C\/p\u003E\u003Cp\u003EThe CG-pipeline software has been used to analyze last\nsummer\u2019s outbreak of \u0026nbsp;severe Escherichia coli\n(E. coli) infections that started in Germany and eventually led to illnesses in\n16 European countries, Canada and the United States. It was one of the largest E.\ncoli outbreaks in history, causing 50 deaths and 4,075 confirmed worldwide\ncases. The bacterium was traced to sprouts. Andrey Kislyuk, a graduate of the Bioinformatics\nPh.D. program who helped Jordan create the software, used the CG-pipeline while\nworking at Pacific Biosciences to understand why the strain of the bacteria\nthat caused the outbreak was so virulent. \u003C\/p\u003E\n\n\u003Cp\u003E\u201cThe software was used to determine that genetic material\nfrom two previously distinct strains of E. coli \u003Cem\u003E\u003Cem\u003E\u0026nbsp;\u003C\/em\u003E\u003C\/em\u003Ewas combined in a new, hyper-virulent strain,\u201d said Kislyuk. \u201cThe\nresulting hybrid strain seems to be more lethal than either of the parent\nstrains.\u201d \u003C\/p\u003E\u003Cp\u003EAnother Bioinformatics Ph.D. graduate who helped design and\nimplement the pipeline, Lee Katz, analyzed the bacteria that caused last year\u2019s\noutbreak of listeriosis in the United States while working at the CDC.\u0026nbsp; That outbreak was traced back to cantaloupes\nfrom a single farm in Colorado that were tainted with Listeria. Over the span\nof several months, there were 146 confirmed cases of listeriosis and 30 deaths,\nmaking it the deadliest outbreak of foodborne illness in the U.S. in 25 years.\nUsing the CG-pipeline, Katz was able to identify an important epidemiological genomic\nmarker, which will help track invasive strains of Listeria. \n\n\u003C\/p\u003E\u003Cp\u003EThe CG-pipeline software platform can be used to analyze any\nmicrobial genome sequence. It has already been applied to bacteria that cause a\nvariety of infectious diseases, including cholera, salmonella and bacterial\nmeningitis. \n\n\u003C\/p\u003E\u003Cp\u003EKatz continues to work closely with the Jordan lab to\nimprove the software. This collaboration is important in CDC\u2019s efforts to mine\ngenome sequence information in the service of public health using software\ndeveloped at Georgia Tech.\n\n\u003C\/p\u003E\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E\n\n\u003Cp\u003E\u0026nbsp;\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":[{"value":"Tool can help save lives by quickly tracing origins"}],"field_summary":[{"value":"\u003Cp\u003E2011 brought two of the deadliest bacterial\noutbreaks the world has seen during the last 25 years. The two epidemics accounted\nfor more than 4,200 cases of infectious disease and 80 deaths. Software\ndeveloped at Georgia Tech was used to help characterize the bacteria that\ncaused each outbreak.\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":[{"value":"Georgia Tech software was used to analyze two recent, deadly worldwide outbreaks."}],"uid":"27560","created_gmt":"2012-02-08 14:06:50","changed_gmt":"2016-10-08 03:11:40","author":"Jason Maderer","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2012-02-08T00:00:00-05:00","iso_date":"2012-02-08T00:00:00-05:00","tz":"America\/New_York"},"extras":[],"hg_media":{"83641":{"id":"83641","type":"image","title":"Tech Tower","body":null,"created":"1449178095","gmt_created":"2015-12-03 21:28:15","changed":"1475894700","gmt_changed":"2016-10-08 02:45:00"}},"media_ids":["83641"],"related_links":[{"url":"http:\/\/www.biology.gatech.edu\/graduate-programs\/bioinformatics\/","title":"Computational Biology and Bioinformatics"},{"url":"http:\/\/www.biology.gatech.edu\/","title":"School of Biology"},{"url":"http:\/\/www.cos.gatech.edu\/","title":"College of Sciences"}],"groups":[{"id":"1183","name":"Home"}],"categories":[{"id":"135","name":"Research"}],"keywords":[{"id":"2546","name":"bioinformatics"},{"id":"23381","name":"DNA sequencing"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003EJason Maderer\u003Cbr \/\u003EGeorgia Tech Media Relations\u003Cbr \/\u003E404-385-2966\u003Cbr \/\u003E\u003Ca href=\u0022mailto:maderer@gatech.edu\u0022\u003Emaderer@gatech.edu\u003C\/a\u003E\u003C\/p\u003E","format":"limited_html"}],"email":["maderer@gatech.edu"],"slides":[],"orientation":[],"userdata":""}}}