Abstract
Recreational water quality is commonly monitored by means of culture based faecal indicator organism (FIOs) assays. However, these methods are costly and time-consuming; a serious disadvantage when combined with issues such as non-specificity and user bias. New culture and molecular methods have been developed to counter these drawbacks. This study compared industry-standard IDEXX methods (Colilert and Enterolert) with three alternative approaches: 1) TECTA™ system for E. coli and enterococci; 2) US EPA’s 1611 method (qPCR based enterococci enumeration); and 3) Next Generation Sequencing (NGS). Water samples (233) were collected from riverine, estuarine and marine environments over the 2014–2015 summer period and analysed by the four methods. The results demonstrated that E. coli and coliform densities, inferred by the IDEXX system, correlated strongly with the TECTA™ system. The TECTA™ system had further advantages in faster turnaround times (~12 hrs from sample receipt to result compared to 24 hrs); no staff time required for interpretation and less user bias (results are automatically calculated, compared to subjective colorimetric decisions). The US EPA Method 1611 qPCR method also showed significant correlation with the IDEXX enterococci method; but had significant disadvantages such as highly technical analysis and higher operational costs (330% of IDEXX). The NGS method demonstrated statistically significant correlations between IDEXX and the proportions of sequences belonging to FIOs, Enterobacteriaceae, and Enterococcaceae. While costs (3,000% of IDEXX) and analysis time (300% of IDEXX) were found to be significant drawbacks of NGS, rapid technological advances in this field will soon see it widely adopted.
Highlights
Bays, estuaries, and rivers provide ecological, economical, and recreational values to the community [1, 2]; but they are under constant and increasing pressure from urbanisation, population growth, and a changing climate [3]
All sites were compliant with the two State Environment Protection Policy (SEPP) requirements for in-shore segments of Port Phillip Bay [1], having overall geometric mean below 200 most probable numbers (MPNs)/100 mL and 80th-percentile level below 400 MPN/100 mL
As for day-by-day concentration, the lowest levels were observed at ELW, where just 13% of enterococci samples exceeded the 200 MPN/ 100 mL threshold ELW gained the highest assessment category out of the four sites, according to the NHMRC Guidelines for Managing Risks in Recreational Water Quality [22], which establish a gastrointestinal risk (GI risk) of 5%–10% for this category
Summary
Estuaries, and rivers provide ecological, economical, and recreational values to the community [1, 2]; but they are under constant and increasing pressure from urbanisation, population growth, and a changing climate [3]. Techniques based on defined substrate cultures, such as the IDEXX methods [6], are commonly used to quantify indicator levels because of their relative ease of use, low cost, and epidemiological evidence that links such levels to human illness [7]. They have become the effective industry standard in Melbourne, Australia. These techniques have at least four drawbacks: (a) they take at least 18 hours to complete (meaning slower reporting to community about risks, or significant divergences between reported and current risks [8]); (b) they require lab personnel to analyse and report results the following day (so weekend staffing issues often make Friday samples problematic); (c) they can introduce user bias (for example colorimetric systems, by relying on visual comparisons with templates, are prey to systematic or arbitrary error); and (d) they are known to have associated specificity issues [9]
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