Multitiered Approach Using Quantitative PCR To Track Sources of Fecal Pollution Affecting Santa Monica Bay, California

The ubiquity of fecal indicator bacteria such as Escherichia coli and Enterococcus spp. in urban environments makes tracking of fecal contamination extremely challenging. A multitiered approach was used to assess sources of fecal pollution in Ballona Creek, an urban watershed that drains to the Santa Monica Bay (SMB) near Los Angeles, Calif. A mass-based design at six main-stem sites and four major tributaries over a 6-h period was used (i) to assess the flux of Enterococcus spp. and E. coli by using culture-based methods (tier 1); (ii) to assess levels of Enterococcus spp. by using quantitative PCR and to detect and/or quantify additional markers of human fecal contamination, including a human-specific Bacteroides sp. marker and enterovirus, using quantitative reverse transcriptase PCR (tier 2); and (iii) to assess the specific types of enterovirus genomes found via sequence analysis (tier 3). Sources of fecal indicator bacteria were ubiquitous, and concentrations were high, throughout Ballona Creek, with no single tributary dominating fecal inputs. The flux of Enterococcus spp. and E. coli averaged 10 9 to 10 10 cells h 1 and was as high at the head of the watershed as at the mouth prior to discharge into the SMB. In addition, a signal for the human-specific Bacteroides marker was consistently detected: 86% of the samples taken over the extent during the study period tested positive. Enteroviruses were quantifiable in 14 of 36 samples (39%), with the highest concentrations at the site furthest upstream (Cochran). These results indicated the power of using multiple approaches to assess and quantify fecal contamination in freshwater conduits to high-use, high-priority recreational swimming areas. The Santa Monica Bay (SMB), California, is home to some of the most popular beaches in the world. It is located adjacent to metropolitan Los Angeles, and more than 50 million beachgoers visit SMB shorelines every year—more than those visiting all other beaches in California combined (38). However, there are serious concerns about beach water quality because of continued exceedances of water quality thresholds based on fecal indicator bacteria such as total coliforms, fecal coliforms, or Escherichia coli and Enterococcus spp., particularly in areas impacted by urban runoff. Thirteen percent of the shoreline mile-days in the SMB exceeded water quality thresholds between 1995 and 2000, with over 50% of these exceedances located near storm drains (37). The public health risk associated with urban runoff has been directly demonstrated through epidemiology studies. Haile et al. (19) demonstrated that swimmers near storm drain discharges in the SMB had a higher likelihood of respiratory and/or gastrointestinal symptoms than swimmers more than 400 m from a storm drain. Despite the impairment of water quality and risks to human health, identification and elimination of the sources of bacteria responsible for the beach warnings remain elusive. The difficulty in identifying and eliminating the sources of bacteria results from three important factors. First, the traditional indicators of fecal pollution on the basis of which the water quality thresholds were developed are not specific to humans.