Detection of multiple waterborne pathogens using microsequencing arrays



Eric N. Villegas, National Exposure Research Laboratory, US Environmental Protection Agency, Mailstop: 320, 26 W. Martin Luther King Drive, Cincinnati, OH, 45268, USA. E-mail:

R. Paul Schaudies, GenArraytion, Inc. 9700 Great Seneca Hwy, Rockville, MD 20850, USA. E-mail:



A microarray was developed to simultaneously detect Cryptosporidium parvum, Cryptosporidium hominis, Enterococcus faecium, Bacillus anthracis and Francisella tularensis in water.

Methods and Results

A DNA microarray was designed to contain probes that specifically detected C. parvum, C. hominis, Ent. faecium, B. anthracis and Ftularensis. The microarray was then evaluated with samples containing target and nontarget DNA from near-neighbour micro-organisms, and tap water spiked with multiple organisms. Results demonstrated that the microarray consistently detected Ent. faecium, B. anthracis, F. tularensis and C. parvum when present in samples. Cryptosporidium hominis was only consistently detected through the use of shared probes between C. hominis and C. parvum.


This study successfully developed and tested a microarray-based assay that can specifically detect faecal indicator bacteria and human pathogens in tap water.

Significance and Impact of the Study

The use of indicator organisms has become a practical solution for monitoring for water quality. However, they do not always correlate well with the presence of many microbial pathogens, thus necessitating direct monitoring for most pathogens. This microarray can be used to simultaneously detect multiple organisms in a single sample. More importantly, it can provide occurrence information that may be used in assessing potential exposure risks to waterborne pathogens.