The meaning of the standard fecal coliform test used to monitor water quality has been called into question by Georgia Tech Civil and Environmental Engineering professor Kostas Konstantinidis's new study that identified sources of Escherichia coli bacteria that might not indicate an environmental hazard. Fecal pollution of surface waters is measured by the concentration of E. coli bacteria in the water because E. coli 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 E. coli in water also serves as a marker for other potentially more harmful organisms that may accompany it. Positive E. coli tests may lead to the summertime closing of beaches and other recreational bodies of water.

In this new study, researchers report identifying and sequencing the genomes of nine strains of E. coli that have adapted to living in the environment independent of warm-blooded hosts. These strains are indistinguishable from typical E. coli based on traditional tests and yield a positive fecal coliform result though researchers say they may not represent a true environmental hazard. Konstantinidis and Georgia Tech School of Biology graduate student Chengwei Luo compared the genomes of 25 different strains of E. coli 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 E. coli.

By 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 E. coli and 120 genes specific to the strains commonly found in the gastrointestinal tract of healthy humans, which are called commensal E. coli. They also detected recent genetic exchange of core genes within the environmental E. coli and within the commensal strains, but not from commensal genomes to their environmental counterparts.

This study's findings provide a way to start redefining E. coli species and testing for fecal contamination with procedures based on genomics and ecology. A paper describing the research was published April 11 in the early edition of the journal Proceedings of the National Academy of Sciences. The work was sponsored by the National Science Foundation and the National Institutes of Health.