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Application of Oligonucleotide Microarrays for Bacterial Source Tracking of Environmental Enterococcus sp. Isolates
U.S. Army Engineer Research and Development Center, Waterways Experiment Station, 3909 Halls Ferry Road, Vicksburg, MS 39180, USA
CSC, 3530 Manor Drive, Vicksburg, MS 39180, USA
Analytical Services, Inc., 555 Sparkman Drive, Huntsville, Alabama 35816, USA
* Author to whom correspondence should be addressed.
Received: 15 November 2004; Accepted: 6 February 2005 / Published: 30 April 2005
Abstract: In an effort towards adapting new and defensible methods for assessing and managing the risk posed by microbial pollution, we evaluated the utility of oligonucleotide microarrays for bacterial source tracking (BST) of environmental Enterococcus sp. isolates derived from various host sources. Current bacterial source tracking approaches rely on various phenotypic and genotypic methods to identify sources of bacterial contamination resulting from point or non-point pollution. For this study Enterococcus sp. isolates originating from deer, bovine, gull, and human sources were examined using microarrays. Isolates were subjected to Box PCR amplification and the resulting amplification products labeled with Cy5. Fluorescent-labeled templates were hybridized to in-house constructed nonamer oligonucleotide microarrays consisting of 198 probes. Microarray hybridization profiles were obtained using the ArrayPro image analysis software. Principal Components Analysis (PCA) and Hierarchical Cluster Analysis (HCA) were compared for their ability to visually cluster microarray hybridization profiles based on the environmental source from which the Enterococcus sp. isolates originated. The PCA was visually superior at separating origin-specific clusters, even for as few as 3 factors. A Soft Independent Modeling (SIM) classification confirmed the PCA, resulting in zero misclassifications using 5 factors for each class. The implication of these results for the application of random oligonucleotide microarrays for BST is that, given the reproducibility issues, factor-based variable selection such as in PCA and SIM greatly outperforms dendrogram-based similarity measures such as in HCA and K-Nearest Neighbor KNN.
Keywords: bacterial sourcing tracking; Enterococcus; oligonucleotides microarrays; principal components analysis
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Indest, K.J.; Betts, K.; Furey, J.S. Application of Oligonucleotide Microarrays for Bacterial Source Tracking of Environmental Enterococcus sp. Isolates. Int. J. Environ. Res. Public Health 2005, 2, 175-185.
Indest KJ, Betts K, Furey JS. Application of Oligonucleotide Microarrays for Bacterial Source Tracking of Environmental Enterococcus sp. Isolates. International Journal of Environmental Research and Public Health. 2005; 2(1):175-185.
Indest, Karl J.; Betts, Kelley; Furey, John S. 2005. "Application of Oligonucleotide Microarrays for Bacterial Source Tracking of Environmental Enterococcus sp. Isolates." Int. J. Environ. Res. Public Health 2, no. 1: 175-185.