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United States Department of Agriculture

Agricultural Research Service

Research Project: Optical Detection of Food Safety and Food Defense Hazards

Location: Quality and Safety Assessment Research Unit

Title: Hyperspectral imaging for differentiating colonies of non-O157 shiga-toxin producing echerichia coli (STEC) serogroups on spread plates of pure cultures

Authors
item Yoon, Seung-Chul
item Windham, William
item Ladely, Scott -
item Heitschmidt, Gerald
item Lawrence, Kurt
item Park, Bosoon
item Narang, Neelam
item Cray Jr, William

Submitted to: Journal of Near Infrared Spectroscopy
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 20, 2013
Publication Date: March 28, 2013
Citation: Yoon, S.C., Windham, W.R., Ladely, S.R., Heitschmidt, G.W., Lawrence, K.C., Park, B., Narang, N., Cray Jr, W.C. 2013. Hyperspectral imaging for differentiating colonies of non-O157 shiga-toxin producing echerichia coli (STEC) serogroups on spread plates of pure cultures. Journal of Near Infrared Spectroscopy. 21(2):81-95.

Interpretive Summary: Direct plating of microorganisms on solid agar media has been widely used for screening foodborne pathogens although it is laborious and time-consuming because directing plating involves manual selection of presumptive-positive colonies one-by-one for further confirmatory testing. The USDA ARS scientists have been developing new non-contact optical imaging technology, called hyperspectral imaging, for rapid presumptive positive screening of colonies grown on agar plates. This study reports research results involving model development for discriminating colonies of the “Big Six” non-O157 Shiga-toxin producing Escherichia coli (STEC) serogroups such as O26, O111, O45, O121, O103, and O145 on Rainbow agar plates using hyperspectral imaging. A set of prediction models were developed from 1,421 colonies on 24 hyperspectral images obtained from spread plates individually inoculated with pure non-O157 STEC cultures. The best overall mean classification accuracy of 95.06% was achieved by a prediction model that adopted a k-nearest neighbor classifier of principal component scores. The study showed the potential of hyperspectral imaging for objective, rapid and accurate screening of non-O157 STEC colonies.

Technical Abstract: Direct plating onto solid agar media has been widely used in microbiology laboratories for presumptive-positive pathogen detection in spite of the fact that it is often subjective, labor intensive and time consuming. Rainbow agar is a selective and chromogenic medium that helps to detect pathogenic Escherichia coli (E. coli) strains. However, it is challenging to rapidly and accurately differentiate the well-known six pathogenic non-O157 Shiga-toxin producing E. coli (STEC) serogroups (O26, O45, O103, O111, O121, and O145) by human eyes due to the variability in STEC populations and the presence of background microflora. Therefore, there is a need for objectively, rapidly and accurately performing high-throughput screening of pathogen colonies on agar plates. In this paper, we report the development of a visible and near-infrared (VNIR) hyperspectral imaging technique and prediction model for objective, rapid and accurate differentiation of the six non-O157 STEC colony identities from pure cultures individually inoculated on Rainbow agar, which adopted supervised linear classification of factor sores obtained by principal component analysis (PCA). Both PCA-MD (Mahalanobis distance) and PCA-kNN (k-nearest neighbor) classifiers were used for model development. The number of spectral samples collected from semi-automatically defined 1,421 colony regions was 51,173, which were on 24 hyperspectral images from two replicates. Chemometric preprocessing methods and other operating parameters such as scatter correction, first derivative, moving average, sample size and number of principal components (PCs) were compared using a classification and regression tree (CART) method and followed by brute-force searching from candidates selected by the CART. The number of PCs, scatter correction and moving average were selected as the most important elements to consider before selecting a set of candidate models. Cross-validation (CV) such as hold-out and k-fold CV was used to validate the prediction performance of candidate models. Serogroups O111 and O121 showed consistently over 99% accuracy regardless of the classification algorithms. However, the classification accuracies of serogroups O26, O45, O103, and O145 showed varying results from 84% up to 100%, depending on which preprocessing treatment and prediction model were adopted. The best overall mean classification accuracy of 95.06% was achieved with PCA-kNN (k = 3), 6 PCs, 5 pixel sample size defined around each colony center, standard normal variate and detrending, first derivative with 11 point gaps and moving average with 11 point gaps. Future studies will focus on automating colony segmentation, further improving detection accuracy of the developed models, expanding the spectral library to include background microflora from ground beef and developing prediction models to detect the target bacteria in the presence of these background microorganisms.

Last Modified: 8/1/2014
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