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Microarray (phylochip) analysis of freshwater pathogens at several sites along the Northern German coast transecting both estuarine and freshwaters

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Monitoring the quality of drinking water is an important issue for public health. Two of the main objectives of the European Project μAQUA were (i) the development of specific probes to detect and quantify pathogens in drinking water and (ii) the design of standardized sampling programs of water from different sources in Europe in order to obtain sufficient material for downstream analysis. Our phylochip contains barcodes that specifically identify freshwater pathogens for enabling the detection of organisms that can be risks for human health. Monitoring for organisms with molecular tools is rapid, more accurate and more reliable than traditional methods. Rapid detection means that mitigation strategies come into play faster with less harm to the community and to humans. Samples were collected from several waters in France, Germany, Ireland, Italy and Turkey over 2 years. We present microarray results for the presence of freshwater pathogens from brackish and freshwater sites in Northern Germany, and cyanobacterial cell numbers inferred from these sites. In a companion study from the same samples, cyanobacterial toxins were analyzed using two methods and those sites with highest toxin values also had highest cell numbers as inferred from this microarray study.

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This work was supported by the EU μAQUA project (FP7-KBBE-2010-4, 265409).

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Correspondence to Linda K. Medlin.

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LKM declares on behalf of all of the authors that there are no conflicts of interest, no research on humans of animals and no informed consents in this study.

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An erratum to this article is available at

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Baudart, J., Guillebault, D., Mielke, E. et al. Microarray (phylochip) analysis of freshwater pathogens at several sites along the Northern German coast transecting both estuarine and freshwaters. Appl Microbiol Biotechnol 101, 871–886 (2017).

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  • Phylochips
  • Microarray
  • Freshwater pathogens
  • Cyanobacteria
  • Molecular barcodes