{"65520":{"#nid":"65520","#data":{"type":"news","title":"Study Provides New Means for Classifying E. Coli Bacteria \u0026 Testing for Fecal Contamination","body":[{"value":"\u003Cp\u003EThe meaning of the standard fecal coliform test used to monitor water quality has been called into question by a new study that identified sources of \u003Cem\u003EEscherichia coli\u003C\/em\u003E bacteria that might not indicate an environmental hazard. \u003C\/p\u003E\n\u003Cp\u003EFecal pollution of surface waters is measured by the concentration of \u003Cem\u003EE. coli\u003C\/em\u003E bacteria in the water because \u003Cem\u003EE. coli\u003C\/em\u003E is believed to live only in the intestines and waste of humans and other warm-blooded animals, and quickly dies outside its host. The presence of \u003Cem\u003EE. coli\u003C\/em\u003E in water also serves as a marker for other potentially more harmful organisms that may accompany it. Positive \u003Cem\u003EE. coli\u003C\/em\u003E tests may lead to the summertime closing of beaches and other recreational bodies of water.\n\u003C\/p\u003E\n\u003Cp\u003EIn this new study, researchers report identifying and sequencing the genomes of nine strains of \u003Cem\u003EE. coli\u003C\/em\u003E that have adapted to living in the environment independent of warm-blooded hosts. These strains are indistinguishable from typical \u003Cem\u003EE. coli\u003C\/em\u003E based on traditional tests and yield a positive fecal coliform result though researchers say they may not represent a true environmental hazard.\n\u003C\/p\u003E\n\u003Cp\u003E\u0022The basis for \u003Cem\u003EE. coli\u003C\/em\u003E\u2019s widespread use as a fecal pollution indicator is the traditional thinking that \u003Cem\u003EE. coli\u003C\/em\u003E cannot survive for extended periods outside a host or waste, but this study indicates that\u0027s not true,\u0022 said Kostas Konstantinidis, an assistant professor in the Georgia Tech School of Civil and Environmental Engineering. \u0022These results suggest the need to develop a new culture-independent, genome-based coliform test so that the non-hazardous environmental types of \u003Cem\u003EE. coli\u003C\/em\u003E are not counted as fecal contamination.\u0022\n\u003C\/p\u003E\n\u003Cp\u003EA paper describing the research was published April 11 in the early edition of the journal \u003Cem\u003EProceedings of the National Academy of Sciences\u003C\/em\u003E. The work was sponsored by the National Science Foundation and the National Institutes of Health.\n\u003C\/p\u003E\n\u003Cp\u003EKonstantinidis and Georgia Tech School of Biology graduate student Chengwei Luo compared the genomes of 25 different strains of \u003Cem\u003EE. coli\u003C\/em\u003E and close relatives, which were sequenced by the Center for Microbial Ecology at Michigan State University, the Broad Institute in Massachusetts, or were publicly available in the National Center for Biotechnology Information database. Nine strains that were recovered primarily from environmental sources encoded all genes required for classification as \u003Cem\u003EE. coli\u003C\/em\u003E.\u003C\/p\u003E\n\u003Cp\u003E\u0022The orders-of-magnitude higher abundances of the group of organisms represented by these nine strains in environmental samples relative to those in human feces and the clinic indicate that they represent truly environmentally adapted organisms that are not associated primarily with mammal hosts,\u0022 explained Konstantinidis, who also holds a joint appointment in the Georgia Tech School of Biology.\n\u003C\/p\u003E\n\u003Cp\u003EBy comparing the full genomes of the samples, the Georgia Tech researchers identified 84 genes specific to or highly enriched in the genomes of the environmental \u003Cem\u003EE. coli\u003C\/em\u003E and 120 genes specific to the strains commonly found in the gastrointestinal tract of healthy humans, which are called commensal \u003Cem\u003EE. coli\u003C\/em\u003E. They also detected recent genetic exchange of core genes within the environmental \u003Cem\u003EE. coli\u003C\/em\u003E and within the commensal strains, but not from commensal genomes to their environmental counterparts.\n\u003C\/p\u003E\n\u003Cp\u003EThe environment-specific bacteria included genes important for resource acquisition and survival in the environment, such as the genes required to utilize energy sources and to break down dead cellular material. In contrast, the gastrointestinal \u003Cem\u003EE. coli\u003C\/em\u003E included several genes involved in the transport and use of nutrients thought to be abundant in the gut.\n\u003C\/p\u003E\n\u003Cp\u003E\u0022The genomic data suggest that the environmental \u003Cem\u003EE. coli\u003C\/em\u003E are better at surviving in the external environment, but are less effective competitors in the gastrointestinal tract than commensal E. coli, which tells us that the environmental bacteria are highly unlikely to represent a risk to public health,\u0022 explained Konstantinidis.\n\u003C\/p\u003E\n\u003Cp\u003ECollectively, this data also indicates that the environmental \u003Cem\u003EE. coli\u003C\/em\u003E strains represent a distinct species from their commensal \u003Cem\u003EE. coli\u003C\/em\u003E counterparts even though they are identified as \u003Cem\u003EE. coli\u003C\/em\u003E based on the standard taxonomic methods. This work is consistent with a more stringent and ecologic definition for bacterial species than the current definition and suggests ways to start replacing traditional, culture-based approaches for defining diagnostic phenotypes of new species with genomic-based procedures.\u003C\/p\u003E\n\u003Cp\u003EThe scientific, medical, regulatory and legal communities expect species to reasonably reflect the traits and habitat of an organism -- especially an organism like \u003Cem\u003EE. coli\u003C\/em\u003E that has ramifications for diagnostic microbiology and for assessing fecal pollution of natural ecosystems. Efforts toward a more refined definition of this bacterial species are needed, according to Konstantinidis.\n\u003C\/p\u003E\n\u003Cp\u003EThis study\u0027s findings provide a way to start redefining \u003Cem\u003EE. coli\u003C\/em\u003E species and testing for fecal contamination with procedures based on genomics and ecology.\n\u003C\/p\u003E\n\u003Cp\u003E\u0022We are now working to develop a molecular assay that uses the gastrointestinal-specific genes as robust biomarkers to count commensal \u003Cem\u003EE. coli\u003C\/em\u003E cells in environmental samples more accurately than current methods,\u0022 added Konstantinidis.\n\u003C\/p\u003E\n\u003Cp\u003E\u003Cem\u003EThis project is supported by a National Science Foundation (NSF) award to Georgia Tech and Michigan State University (Award No. DEB0516252) and a National Institutes of Health (NIH\/NIAID) award to the Broad Institute (Award No. HHSN2722009000018C). The content is solely the responsibility of the principal investigators and does not necessarily represent the official views of NSF or NIH.\u003C\/em\u003E\n\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EResearch News \u0026amp; Publications Office\u003Cbr \/\u003E\nGeorgia Institute of Technology\u003Cbr \/\u003E\n75 Fifth Street, N.W., Suite 314\u003Cbr \/\u003E\nAtlanta, Georgia  30308  USA\u003C\/strong\u003E\n\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EMedia Relations Contacts:\u003C\/strong\u003E Abby Robinson (abby@innovate.gatech.edu; 404-385-3364) or John Toon (jtoon@gatech.edu; 404-894-6986)\n\u003C\/p\u003E\n\u003Cp\u003E\u003Cstrong\u003EWriter:\u003C\/strong\u003E Abby Robinson\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003EThe meaning of the standard fecal coliform test used to monitor water quality has been called into question by a new study that identified sources of Escherichia coli bacteria that might not indicate an environmental hazard.\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":[{"value":"The meaning of standard fecal coliform test is called into question."}],"uid":"27206","created_gmt":"2011-04-11 00:00:00","changed_gmt":"2016-10-08 03:08:34","author":"Abby Vogel Robinson","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2011-04-11T00:00:00-04:00","iso_date":"2011-04-11T00:00:00-04:00","tz":"America\/New_York"},"extras":[],"hg_media":{"65521":{"id":"65521","type":"image","title":"Kostas Konstantinidis \u0026 Chengwei Luo","body":null,"created":"1449176863","gmt_created":"2015-12-03 21:07:43","changed":"1475894579","gmt_changed":"2016-10-08 02:42:59","alt":"Kostas Konstantinidis \u0026 Chengwei Luo","file":{"fid":"192266","name":"tpq51670.jpg","image_path":"\/sites\/default\/files\/images\/tpq51670_0.jpg","image_full_path":"http:\/\/www.tlwarc.hg.gatech.edu\/\/sites\/default\/files\/images\/tpq51670_0.jpg","mime":"image\/jpeg","size":1726161,"path_740":"http:\/\/www.tlwarc.hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/tpq51670_0.jpg?itok=dekNP5qZ"}},"65522":{"id":"65522","type":"image","title":"Konstantinidis \u0026 Luo","body":null,"created":"1449176863","gmt_created":"2015-12-03 21:07:43","changed":"1475894579","gmt_changed":"2016-10-08 02:42:59","alt":"Konstantinidis \u0026 Luo","file":{"fid":"192267","name":"tys51670.jpg","image_path":"\/sites\/default\/files\/images\/tys51670_0.jpg","image_full_path":"http:\/\/www.tlwarc.hg.gatech.edu\/\/sites\/default\/files\/images\/tys51670_0.jpg","mime":"image\/jpeg","size":1404480,"path_740":"http:\/\/www.tlwarc.hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/tys51670_0.jpg?itok=pwrGggmn"}},"65523":{"id":"65523","type":"image","title":"Konstantinidis \u0026 Luo","body":null,"created":"1449176863","gmt_created":"2015-12-03 21:07:43","changed":"1475894579","gmt_changed":"2016-10-08 02:42:59","alt":"Konstantinidis \u0026 Luo","file":{"fid":"192268","name":"ttn51670.jpg","image_path":"\/sites\/default\/files\/images\/ttn51670_0.jpg","image_full_path":"http:\/\/www.tlwarc.hg.gatech.edu\/\/sites\/default\/files\/images\/ttn51670_0.jpg","mime":"image\/jpeg","size":1829367,"path_740":"http:\/\/www.tlwarc.hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/ttn51670_0.jpg?itok=-0ZoSHPw"}}},"media_ids":["65521","65522","65523"],"related_links":[{"url":"http:\/\/www.ce.gatech.edu\/people\/faculty\/711\/overview","title":"Kostas Konstantinidis"},{"url":"http:\/\/www.ce.gatech.edu\/","title":"School of Civil and Environmental Engineering"},{"url":"http:\/\/www.biology.gatech.edu\/","title":"School of Biology"}],"groups":[{"id":"1188","name":"Research Horizons"}],"categories":[{"id":"145","name":"Engineering"},{"id":"154","name":"Environment"},{"id":"146","name":"Life Sciences and Biology"},{"id":"135","name":"Research"}],"keywords":[{"id":"12762","name":"Commensal Bacteria"},{"id":"12760","name":"E. Coli"},{"id":"12761","name":"E. Coli Bacteria"},{"id":"12765","name":"environmental bacteria"},{"id":"12766","name":"environmental e. coli"},{"id":"12759","name":"Escherichia Coli"},{"id":"12763","name":"fecal coliform test"},{"id":"12764","name":"fecal pollution"},{"id":"12767","name":"Genome Sequencing"},{"id":"12758","name":"Kostas Konstantinidis"},{"id":"167864","name":"School of Civil and Environmental Engineering"},{"id":"12768","name":"Taxonomy"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003E\u003Cstrong\u003EAbby Robinson\u003C\/strong\u003E\u003Cbr \/\u003EResearch News and Publications\u003Cbr \/\u003E\u003Ca href=\u0022http:\/\/www.gatech.edu\/contact\/index.html?id=avogel6\u0022\u003EContact Abby Robinson\u003C\/a\u003E\u003Cbr \/\u003E\u003Cstrong\u003E404-385-3364\u003C\/strong\u003E\u003C\/p\u003E","format":"limited_html"}],"email":["abby@innovate.gatech.edu"],"slides":[],"orientation":[],"userdata":""}}}