Sufian F. Al-Khaldi

Fourier Transform Infrared Bacteria Identification with the Use of a Focal-Plane-Array Detector and Microarray Printing

McGill IR Group, Dept. of Food Science and Agricultural Chemistry, McGill University, Montreal, Quebec, Canada H9X3V9 (J.K., J.S., A.A.I.); and Division of Microbiological Studies, OPDFB (S.F.A.-K.), and Division of General Scientific Support, OSAS, Center for Food Safety and Applied Nutrition (CFSAN) (M.M.M.), Food and Drug Administration (FDA), 5100 Paint Branch Parkway, College Park, Maryland 20740-3835

Survival of Salmonella Typhi and Shigella dysenteriae in Dehydrated Infant Formula

UNLABELLED Powdered infant formula has previously been linked to the transmission of various bacterial pathogens in infants resulting in life-threatening disease and death. Survival studies of 2 common foodborne pathogens, Salmonella enterica serovar Typhi and Shigella dysenteriae, in powdered infant formula have not been previously studied despite the potentially devastating consequences from ingestion of these organisms, particularly by newborns, in case of a natural or deliberate contamination event. Therefore, to better predict the risk of S. Typhi and S. dysenteriae infection from consumption of infant formula, the present study was undertaken to determine survival of these microorganisms in dry infant formula under varying atmospheric conditions. A 2-strain cocktail of S. Typhi and a 3-strain cocktail of S. dysenteriae were stored for up to 12 wk in dehydrated infant formula in an ambient air or nitrogen atmosphere. Viable counts of S. Typhi at 12 wk in infant formula revealed a 2.9- and 1.69-log decrease in ambient air and nitrogen atmosphere, respectively. Viable counts of S. dysenteriae at 12 wk in infant formula revealed a 0.81- and 0.42-log decrease in ambient air and nitrogen atmosphere, respectively. These results show that S. Typhi and S. dysenteriae can remain viable for prolonged periods of time in powdered infant formula, and the presence of nitrogen enhances survival. PRACTICAL APPLICATION Our goal in this work was to study the survival of S. Typhi and S. dysenteriae in dehydrated storage conditions in infant formula. This interest is partially generated by the possibility of using these 2 microorganisms to deliberately contaminate the food supply. The outcome of this study will help us to have a better idea how to respond and react to the risk of deliberate food contamination.

Bacterial Identification and Subtyping Using DNA Microarray and DNA Sequencing

The era of fast and accurate discovery of biological sequence motifs in prokaryotic and eukaryotic cells is here. The co-evolution of direct genome sequencing and DNA microarray strategies not only will identify, isotype, and serotype pathogenic bacteria, but also it will aid in the discovery of new gene functions by detecting gene expressions in different diseases and environmental conditions. Microarray bacterial identification has made great advances in working with pure and mixed bacterial samples. The technological advances have moved beyond bacterial gene expression to include bacterial identification and isotyping. Application of new tools such as mid-infrared chemical imaging improves detection of hybridization in DNA microarrays. The research in this field is promising and future work will reveal the potential of infrared technology in bacterial identification. On the other hand, DNA sequencing by using 454 pyrosequencing is so cost effective that the promise of

Effect of dehydrated storage on the survival of Francisella tularensis in infant formula

1,000 per bacterial genome sequence is becoming a reality. Pyrosequencing technology is a simple to use technique that can produce accurate and quantitative analysis of DNA sequences with a great speed. The deposition of massive amounts of bacterial genomic information in databanks is creating fingerprint phylogenetic analysis that will ultimately replace several technologies such as Pulsed Field Gel Electrophoresis. In this chapter, we will review (1) the use of DNA microarray using fluorescence and infrared imaging detection for identification of pathogenic bacteria, and (2) use of pyrosequencing in DNA cluster analysis to fingerprint bacterial phylogenetic trees.

Nanoparticle Probes and Mid-Infrared Chemical Imaging for DNA Microarray Detection

Francisella tularensis is a Gram-negative bacterium that can cause gastrointestinal or oropharyngeal tularemia in humans from ingestion of contaminated food or water. Despite the potential for accidental or intentional contamination of foods with F. tularensis, there are few studies on the long-term survivability of this organism in food matrices. Infant formula has previously been implicated as a vehicle for the transmission of a variety of bacterial pathogens in infants. In this study, we investigated the survival of F. tularensis in dehydrated infant formula under various storage conditions. F. tularensis was stored for up to 12 weeks in dehydrated infant formula in an ambient air, dry or nitrogen atmosphere. Viable counts of fresh F. tularensis at 12 weeks in infant formula revealed a 4.15, 3.37 and 3.72-log decrease in ambient air, dry and nitrogen atmosphere, respectively. D-values were calculated (in weeks) as 3.99, 4.68 and 4.47 in air, dry and nitrogen atmosphere, respectively.

Differentiation of Whole Bacterial Cells Based on High-Throughput Microarray Chip Printing and Infrared Microspectroscopic Readout

To date most mid-infrared spectroscopic studies have been limited, due to lack of sensitivity, to the structural characterization of a single oligonucleotide probe immobilized over the entire surface of a gold-coated slide or other infrared substrate. By contrast, widely used and commercially available glass slides and a microarray spotter that prints approximately 120-μm-diameter DNA spots were employed in the present work. To our knowledge, mid-infrared chemical imaging (IRCI) in the external reflection mode has been applied in the present study for the first time to the detection of nanostructure-based DNA microarrays spotted on glass slides. Alkyl amine-modified oligonucleotide probes were immobilized on glass slides that had been prefunctionalized with succinimidyl ester groups. This molecular fluorophore-free method entailed the binding of gold-nanoparticle–streptavidin conjugates to biotinylated DNA targets. Hybridization was visualized by the silver enhancement of gold nanoparticles. The adlayer of silver, selectively bound only to hybridized spots in a microarray, formed the external reflective infrared substrate that was necessary for the detection of DNA hybridization by IRCI in the present proof-of-concept study. IRCI made it possible to discriminate between diffuse and specular external reflection modes. The promising qualitative results are presented herein, and the implications for quantitative determination of DNA microarrays are discussed.

Identification of Mycoplasmas Using a Fluorophore-Free Microarray and Infrared Chemical Imaging (IRCI)☆

Using robotic automation, a microarray printing protocol for whole bacterial cells was developed for subsequent label-free and nondestructive infrared microspectroscopic detection. Using this contact microspotting system, 24 microorganisms were printed on zinc selenide slides; these were 6 species of Listeria, 10 species of Vibrio, 2 strains of Photobacterium damselae, Yersinia enterocolitica 289, Bacillus cereus ATCC 14529, Staphylococcus aureus, ATCC 19075 (serotype 104 B), Shigella sonnei 20143, Klebsiella pneumoniae KP73, Enterobacter cloacae, Citrobacter freundii 200, and Escherichia coli. Microarrays consisting of separate spots of bacterial deposits gave consistent and reproducible infrared spectra, which were differentiated by unsupervised pattern recognition algorithms. Two multivariate analysis algorithms, principal component analysis and hierarchical cluster analysis, successfully separated most, but not all, the bacteria investigated down to the species level.

Enhanced Mid-Infrared Chemical Imaging (IRCI) Detection of DNA Microarrays

A novel application of mid-infrared chemical imaging (IRCI) for the fluorophore-free detection and identification of mycoplasma species is reported for the first time. The PCR-amplified biotinylated targets hybridized to microarray probes were treated with streptavidin-gold nanoparticles followed by silver enhancement. This modification has the potential to expand the implementation of DNA microarray techniques in laboratories involved in the detection of cell substrates, other biological products, and clinical materials for the presence of mycoplasmas.

Multipathogen oligonucleotide microarray for environmental and biodefense applications

We report on the optimization of a recently proposed mid-infrared chemical imaging (IRCI) detection method for the analysis of DNA microarrays. The improved protocol allowed for a ten-fold reduction in the time needed to generate a mosaic image of an entire microarray and the production of IR images with high contrast that would facilitate data analysis and interpretation. Advantages of using this protocol were evaluated by applying it to the analysis of four virulence genes in the genomes of 19 strains of the food bacterial pathogen Yersinia enterocolitica.