**5. Conclusions**

Proteomics methods have been developed and extensive databases created allowing the identification of microorganisms directly in complex samples. Several studies have shown how MALDI‐TOF‐MS (Matrix‐Assisted Laser Desorption Ionisation Time‐of‐flight Mass Spectrometry) can be employed to identify organisms at species level, and detect virulence and resistance markers in environmental waters [62, 63]. A study by Loff [64] compares proteomics analysis with molecular and biochemical methods for the detection of microorganisms commonly associated with water safety. It can be expected that future developments of this technology will widen its application in many diagnostic and analytical applications. It has to be noted that the identification of organisms and detection of virulence or resistance by both molecular and proteomics approaches relies on the comparison of results with existing databases. This limits to the identification of known strains and characterised genes and proteins and is thus unlikely to achieve detection of uncultivable microorganisms. However, a combination of recent advances in bioinformatics and novel methods like the one described by Kaeberlein [65] have increased our knowledge about the microbial world and extended our database resources. Molecular and proteomics methods have shown great potential in the identification in temporal and special distribution of microorganisms in the aquatic environment and to combine species identification with detection of virulence and drug resistance. Future developments are likely to combine the best of both worlds to achieve robust assessment of water quality by quantifying indicator organisms to detect contamination and identify virulence and resistance markers to assess public health risks and inform stakeholders on

132 *Escherichia coli* Escherichia coli - Recent Advances on Physiology, Pathogenesis and Biotechnological Applications - Recent Advances on Physiology, Pathogenesis and Biotechnological Applications

the need and nature of required interventions.

**contamination**

**4. Disadvantages in relying solely on** *E. coli* **to monitor water** 

Although historically total coliforms, faecal coliforms, *Enterococci* and *E. coli* have all been used as indicator organism for faecal water pollution and currently employed methods continue to largely rely on these, it is clear that alternative indicators need to be developed to address limitations in identifying other water contaminants of considerable public health concerns. Water‐borne diseases including diarrhoea and gastrointestinal illness can be caused by bacteria, viruses and protozoa [4]. Approximately 3.4 million people, mainly children, die from water‐borne diseases [66] and solely relying on *E. coli* can result in misleading information [67]. Major etiological agents including *Giardia*, *Cryptosporidium*, *Vibrio cholerae* and *Salmonella* would be missed by current testing procedures. Often outbreaks are due to local flood or storm events or releases of untreated sewage which result in significant contamination of environmental water. Worldwide morbidity and mortality caused by contaminated drinking water is of considerable magnitude. The WHO ranks diarrhoeal diseases sixths highest in the list of causes of environmental deaths with an estimate of 846,000 deaths annually [68]. This highlights the need for a concentrated effort to make both recreational and drinking water safe in both developing and developed countries [4]. The development of methods detecting a wide range of significant pathogens is most likely to be achieved by extraction and antibody based detection, as described for pathogenic protozoa [69] or molecular techniques such as PCR, shown for *Cryptosporidium parvum* and *Giardia lamblia* [70], and Sensitive and frequent monitoring of environmental waters is essential to minimise adverse effect on human health. The current approach to monitoring for contamination in environmental waters is shown in **Figure 1**.

**Figure 1.** Current approach to monitoring and identifying bacteria in environmental water.

A wide range of techniques are now available for monitoring but culture-based techniques are used to define the legally accepted limits of environmental water contamination. The quantification of the indicator organisms *E. coli* and *Enterococci* are used to detect faecal pollution. Routine analysis is still largely based on the enumeration of these two intestinal organisms by culture coupled with the detection of β‐D‐galactosidase and β‐D‐glucuronidase activity. A secondary objective of environmental monitoring is the identification and quantification of bacteria present in water samples and this is best achieved by molecular methods. Whereas culture methods have the limitation of only providing information the day after collection of the sample, all the other methods currently available have some limitations as well when used for environmental samples. In the case of molecular methods this is the need to concentrate the sample or amplify the DNA, further the highly specific target sequences that are used could result in an underestimation of the actual level of indicator organism. The most promising area is the development of a wide range of biosensor systems which show promising simplicity for direct and *in situ* analysis.

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*E. coli* as an Indicator of Contamination and Health Risk in Environmental Waters

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