Escherichia coli is employed as faecal indicator bacteria to indicate recent faecal pollution of water resources. Microbiological water quality monitoring is an integral part of water resource management, as faecal pollution affected not only the environment but also public health. However, E. coli-based monitoring may be affected following the discovery of five monophyletic Escherichia clades (clade I – V). While clade I was a subspecies of E. coli, remaining clades were suggested to represent novel species. Current assessment method would misidentify them as E. coli, as cryptic clades resembled E. coli phenotypically and harboured presumably E. coli-specific genetic markers. Using a watershed consisted of streams connected to a gazetted beach downstream, the distribution of cryptic cl...[ Read more ]

Escherichia coli is employed as faecal indicator bacteria to indicate recent faecal pollution of water resources. Microbiological water quality monitoring is an integral part of water resource management, as faecal pollution affected not only the environment but also public health. However, E. coli-based monitoring may be affected following the discovery of five monophyletic Escherichia clades (clade I – V). While clade I was a subspecies of E. coli, remaining clades were suggested to represent novel species. Current assessment method would misidentify them as E. coli, as cryptic clades resembled E. coli phenotypically and harboured presumably E. coli-specific genetic markers. Using a watershed consisted of streams connected to a gazetted beach downstream, the distribution of cryptic clades and their implication on E. coli population studies was investigated. All cryptic clade isolates belonged to clade II; most were found the upstream watershed, contributed up to 60% of total isolates from periphyton at certain sites. This was contrasted by the presence of E. coli belonging to clonal complexes with potential health risk at the downstream watershed. Genetic exchange of housekeeping genes between clade II and E. coli was limited. Therefore, inclusion of clade II as part of E. coli populations affected the interpretation of gene flow between populations (upstream vs downstream). Considering the implications on water quality monitoring and population studies, rapid identification of cryptic clades was needed. We developed a polymerase chain reaction (PCR) assay targeting bglY gene to identify clade II – V with 100% sensitivity and specificity. Comparing to current cryptic clades identification involving sequencing or multiple PCR assays, the new assay provided a time- and cost-effective method to enhance the reliability of E. coli-based water quality assessment. Furthermore, we simulated a 1:1 cryptic clade to E. coli ratio at various colony density per filter and determined the minimum colony-screening effort that would effectively reflect the actual ratio for each case.