Sufian F Al-Khaldi

U.S. Food and Drug Administration, Washington, Washington, D.C., United States

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Publications (30)63.37 Total impact

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    ABSTRACT: 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.
    No preview · Article · Dec 2012 · Applied Spectroscopy
  • Sufian F Al-Khaldi · Magdi M Mossoba · Marc M Allard · E Kurt Lienau · Eric D Brown
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    ABSTRACT: 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 $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.
    No preview · Article · Jan 2012 · Methods in molecular biology (Clifton, N.J.)
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    ABSTRACT: 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.
    Full-text · Article · Aug 2011 · Journal of Food Science
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    ABSTRACT: 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.
    No preview · Article · Jun 2011 · Journal of microbiological methods
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    ABSTRACT: Rapid, accurate and inexpensive analysis of the disease-causing potential of foodborne pathogens is an important consideration in food safety and biodefense, particularly in developing countries. The objective of this study is to demonstrate the use of a robust and inexpensive microarray platform to assay the virulence gene profiles in Salmonella from food and/or the food animal environment, and then use ArrayTrack™ for data analysis. The spotted array consisted of 69 selected Salmonella-specific virulence gene probes (65bp each). These probes were printed on poly-L-lysine-coated slides. Genomic DNA was digested with Sau3AI, labeled with Cy3 dye, hybridized to the gene probes, and the images were captured and analyzed by GenePix 4000B and ArrayTrack™, a free software developed by Food and Drug Administration (FDA) researchers. Nearly 58% of the virulence-associated genes tested were present in all Salmonella strains tested. In general, genes belonging to inv, pip, prg, sic, sip, spa or ttr families were detected in more than 90% of the isolates, while the iacP, avrA, invH, rhuM, sirA, sopB, sopE or sugR genes were detected in 40 to 80% of the isolates. The gene variability was independent of the Salmonella serotype. This hybridization array presents an accurate and cost-effective method for evaluating the disease-causing potential of Salmonella in outbreak investigations by targeting a selective set of Salmonella-associated virulence genes.
    Full-text · Article · Mar 2011 · The Journal of Infection in Developing Countries
  • S.F. Al-Khaldi · M.M. Mossoba · B.J. Yakes · E. Brown · D. Sharma · S. Carnazza
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    ABSTRACT: In an age of molecular genetics, viable but not culturable organisms, and highly sophisticated DNA sequence analysis technologies, is there a chance for a new breakthrough? It is quite extraordinary that 99% of microorganisms not only can't be cultured but are totally unknown to the scientific community. Many bacterial gene functions and identifications in the environment have been uncovered by recent advances in metagenomics or culture-independent genomic analysis in addition to the DNA microarray technology. Our knowledge of detecting and classifying bacterial isolates has been also improved by cutting-edge molecular tools such as biosensors and molecular subtyping as well as phage recombinant probes. Microbial communities, many to be discovered, are slowly revealed by these sharp scientific discoveries.
    No preview · Article · Jan 2011
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    Magdi M Mossoba · Sufian F Al-Khaldi · Brianna Schoen · Betsy Jean Yakes
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    ABSTRACT: 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.
    Preview · Article · Nov 2010 · Applied Spectroscopy
  • J.B. Day · H Nguyen · S.K. Sharma · S.F. Al-Khaldi · Y-Y D Hao
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    ABSTRACT: 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.
    No preview · Article · Dec 2009 · Food Microbiology
  • Sufian F Al-Khaldi · Magdi M Mossoba · Tara L Burke · Frederick S Fry
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    ABSTRACT: 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.
    No preview · Article · Aug 2009 · Foodborne Pathogens and Disease
  • Nusrat Siddique · Devang Sharma · Sufian F Al-Khaldi
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    ABSTRACT: Four different food matrices (alfalfa, cilantro, mamey sapote, and mung bean) were contaminated with three different dilutions 10(6), 10(4), and 10(3) cfu/g of Yersinia enterocolitica. DNA was isolated from each food mix and used in chromosomal amplifications. The amplified DNA was used as templates in single PCR reactions of the four genes (virF, ail, yst, and blaA) followed by mixing the four reactions for one PCR primer extension reaction. The presence and the limit of detection of four genes in four food matrices were established by microarray hybridization. Data revealed the diversity of signal intensities. Neither the microarray chip hybridization nor the single PCR amplification could detect virF's presence located on a plasmid. Ail was detected in 10(3) cfu/g, whereas blaA and yst were detected from 10(5) to 10(6) cfu/g in all food matrices. Therefore, the ail gene could be the gene of choice in identifying Y. enterocolitica in alfalfa, cilantro, mamey, and mung bean. Other genes--blaA, yst, virF--exhibited wide variability in hybridization signals, highlighting the need of a better DNA purification step prior to DNA microarray hybridization.
    No preview · Article · Jul 2009 · Current Microbiology
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    M M Mossoba · S F Al-Khaldi · S K Curtis · C F Battrell · F S Fry
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    ABSTRACT: A proof-of-concept study is reported for the differentiation between microcolonies of Enterobacter sakazakii and Klebsiella pneumoniae by means of a novel sample preparation for infrared (IR) analysis. A disposable, IR-transparent, microporous (0.2-microm pores), hydrophobic, polyethylene (PE) membrane (51 microm thick) was plasma treated under an oxygen atmosphere and used to (i) filter (or print microarrays of) dilute aqueous foodborne bacterial suspensions and (ii) subsequently grow bacterial microcolonies when the treated, hydrophilic PE membrane was placed over brain heart infusion agar medium and incubated. Because this unique membrane is transparent to IR light, isolated microcolonies (200 microm) of bacterial cells grown on this PE substrate for the first time could be directly fingerprinted by IR microspectroscopy in the transmission mode. Hence, time-consuming bacterial cell transfer from culture plates to an IR sample holder for subsequent measurement by IR spectroscopy was eliminated. Multivariate analysis of the observed IR spectra for microcolonies allowed the rapid differentiation between E. sakazakii and K. pneumoniae.
    Preview · Article · Jun 2007 · Journal of food protection
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    ABSTRACT: In order to design and validate a method to identify virulence genes of Salmonella typhimurium using DNA microarray, a protocol was developed to label the isolated bacterial DNA directly and to use PCR amplification of limited numbers of genes to validate the hybridization signals. Therefore, a DNA microarray chip of 71 virulence genes of S. typhimurium was developed and evaluated using 10 isolates. Each gene was represented by 65bp oligonucleotide probes (oligoprobes) and immobilized on the surface of chemically modified slides. Whole DNA genomes were digested with Hinf1 and Sau3AI, labeled with a fluorescent tag of Cy3 and then hybridized. The presence of virulence genes in 10 strains of S. typhimurium was established by measuring a fluorescent signal above the background noise of the chip. PCR amplification of 10 genes (orgA, ORF319, ttrB, rmbA, misL, spi4F, spi4H, spi4N, rRNA, and purR) of S. typhimurium was used as a standard to verify the confidence level of the DNA microarray chip. In conclusion, using PCR amplification to increase the confidence level of the microarray hybridization data was successful.
    No preview · Article · Jun 2006 · Molecular and Cellular Probes
  • K.M. Myers · J Gaba · S.F. Al-Khaldi
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    ABSTRACT: A DNA microarray chip of four virulence genes and 16S ribosomal DNA gene conserved region among all Gram negative species, including Yersinia, as a positive control was developed and evaluated using 22 Yersinia enterocolitica isolates. Eight different oligonucleotide probes (oligoprobes) with an average size of 22 bp, complementary to the unique sequences of each gene, were designed and immobilized on the surface of chemically modified slides. Multiplex PCR was used to simultaneously amplify DNA target regions of all five genes, and single stranded DNA (ssDNA) samples for microarray analysis were prepared by using a primer extension of amplicons in the presence of one primer of all genes. The presence of genes in Y. enterocolitica was established by hybridization of the fluorescently labeled ssDNA representing different samples of the microarray gene-specific oligoprobes and confirmed by PCR. Results of the study showed specificity of genotyping Y. enterocolitica using multiple microarray-based assays. Final validation of the chip's ability to identify Y. enterocolitica genes from adulterated pasteurized whole milk was confirmed and successful. The limit of chip detection of virulence genes in pasteurized whole milk was found to be 1000 CFU per hybridization.
    No preview · Article · May 2006 · Molecular and Cellular Probes
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    ABSTRACT: Fourier transform infrared (FTIR) spectroscopy has been established as a rapid bacteria identification technique. To increase the throughput of this methodology, the feasibility of applying contact deposition microarray technology to print intact bacterial cells as arrayed deposits (150 μm diameter) on optical substrates and on agar slides was demonstrated for the first time. This contact deposition technology delivers nanoliter (nL) droplets of bacterial suspensions from a microtiter plate onto a slide surface. Protocols for printing microarrays of whole-cells on agar and on infrared (IR)-transparent slides were evaluated and optimized for subsequent measurement by IR microspectroscopy and IR imaging. Parameters that were investigated included pin capacity, deposition mode, and spatial distribution of microarrays. Bacteria representing eight genera (Yersinia, Staphylococcus, Salmonella, Listeria, Enterobacter, Citrobacter, Klebsiella, and Escherichia) were used in this proof-of-concept study. The resulting dendrograms generated by hierarchical cluster analysis (HCA) demonstrated clustering of the descendants of the foodborne bacteria investigated into their respective branches. The suitability of microarray printing coupled to focal-plane-array (FPA) FTIR detection for the rapid identification of bacteria was demonstrated.
    No preview · Article · Jul 2005 · Vibrational Spectroscopy
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    ABSTRACT: Capillary gas chromatography (GC) with flame ionization detection was used to determine the cellular fatty acid profiles of various food-borne microbial pathogens and to compare the fatty acid profiles of spores and vegetative cells of the same endospore-forming bacilli. Fifteen bacteria, representing eight genera (Staphylococcus, Listeria, Bacillus, Yersinia, Salmonella, Shigella, Escherichia, and Vibrio) and 11 species were used to compare the extracted fatty acid methyl esters (FAMEs). Endospore-forming bacilli were processed to obtain pure spores and whole cell FAMEs for GC analysis. A data set for each bacterial agent was prepared using fatty acid profiles from five replicates prepared on different days. The results showed that these fatty acid intensity profiles were unique for each of the 11 species and that they could be used as a fingerprint for the organisms. The cellular fatty acid profiles for Bacillus anthracis and Bacillus cereus show that there are two branched chain fatty acids, iso 17:1 omega10c and 17:1 anteiso, which are unique in these species. Iso 17:1 omega10c is present in B. cereus vegetative cells and spores but is not observed in B. anthracis. The 17:1 anteiso fatty acid is present in B. anthracis cells but not in B. cereus cells. Fatty acids 16:0 2OH and 17:0 iso 3OH are present in B. anthracis and B. cereus spores but not in the vegetative cells. In summary, analysis of FAMEs from bacteria and spores can provide a sensitive procedure for the identification of food-borne pathogens.
    Preview · Article · Jun 2005 · Journal of Agricultural and Food Chemistry
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    S F Al-Khaldi · K M Myers · A Rasooly · V Chizhikov
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    ABSTRACT: A microarray-based method for characterization of six Clostridium perfringens toxin genes: iA (iota toxin), cpa (alpha toxin), cpe (enterotoxin E), etxD (epsilon toxin), cpb1 (beta toxin 1),and cpb2 (beta toxin 2) was developed and evaluated using 17 C. perfringens isolates. Three individual oligonucleotide probes (oligoprobes), complementary to the unique sequences of each toxin gene, were designed and immobilized on a surface of aldehyde-coated glass slides. Multiplex PCR was used to simultaneously amplify DNA target regions of all six genes. Single-stranded DNA (ssDNA) samples for microarray analysis were prepared by following a primer extension of amplicons in the presence of one primer. Fluorescent moieties (Cy3) were incorporated into the ssDNA by chemical modification of guanine bases. The presence of toxin genes in C. perfringens was established by hybridization of the fluorescently labeled ssDNA representing different samples to the microarray gene-specific oligoprobes. Results of the study showed sensitivity and specificity of genotyping C. perfringens using multiple microarray-based assays.
    Preview · Article · Jan 2005 · Molecular and Cellular Probes
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    ABSTRACT: The potential applications of microarray technology used for high-throughput printing of bacterial samples were discussed. The microarray printing technology was also used to enhance the utility of Focal-plane-array (FPA) and Fourier transform infrared spectroscopy (FTIR) bacteria identification. The microarray deposition required small amount of sample and allowed reduction in growth times. The microarray deposition technique was more precise which could be achieved by the manual deposition techniques and allowed samples to be spaced on the order of 20-50μm apart.
    No preview · Article · Dec 2004 · Applied Spectroscopy
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    ABSTRACT: Food-borne pathogens are a major health problem. The large and diverse number of microbial pathogens and their virulence factors has fueled interest in technologies capable of detecting multiple pathogens and multiple virulence factors simultaneously. Some of these pathogens and their toxins have potential use as bioweapons. DNA microarray technology allows the simultaneous analysis of thousands of sequences of DNA in a relatively short time, making it appropriate for biodefense and for public health uses. This paper describes methods for using DNA microarrays to detect and analyze microbial pathogens. The FDA-1 microarray was developed for the simultaneous detection of several food-borne pathogens and their virulence factors including Listeria spp., Campylobacter spp., Staphylococcus aureus enterotoxin genes and Clostridium perfringens toxin genes. Three elements were incorporated to increase confidence in the microarray detection system: redundancy of genes, redundancy of oligonucleotide probes (oligoprobes) for a specific gene, and quality control oligoprobes to monitor array spotting and target DNA hybridization. These elements enhance the reliability of detection and reduce the chance of erroneous results due to the genetic variability of microbes or technical problems with the microarray. The results presented demonstrate the potential of oligonucleotide microarrays for detection of environmental and biodefense relevant microbial pathogens.
    Preview · Article · Dec 2004 · Biosensors & Bioelectronics
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    Sufian F Al-Khaldi · Doralis Villanueva · Vladimir Chizhikov
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    ABSTRACT: A DNA microarray method was developed to identify the presence of toxin genes: encoding beta toxin (cpb), epsilon toxin (etx), enterotoxin (cpe), alpha toxin (cpa), and iota toxin (iA) in Clostridium perfringens. To build the DNA chip, each gene sequence was represented by one approximately 22-bp amino-modified oligonucleotide printed twice on aldehyde-coated slides. Multiplex PCR with Cy3 and Cy5-dCTP derivatized fluorescent nucleotides was used to label five genes and fluorescent probes were prepared. The PCR probes were denatured and single-strand-labeled DNAs were separated and purified using magnetic beads. The presence of toxin genes in C. perfringens was detected by hybridization of amplified ssDNA probes to oligonucleotides on the chip representing one target sequence of each toxin gene. The DNA chip was able to identify eight strains of C. perfringens.
    Preview · Article · Apr 2004 · International Journal of Food Microbiology
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    Sufian F Al-Khaldi · Magdi M Mossoba · Ashraf A Ismail · Fred S Fry
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    ABSTRACT: A microarray method for the deposition of bacteria onto an agar slide was developed to accelerate the formation of microcolonies. Representative microarrays each consisting of 40 micro-spots of five replicates of eight foodborne bacteria (Yersinia enterocolitica, Staphylococcus aureus, Salmonella typhimurium, Listeria monocytogenes, Enterobacter cloacae, Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli) were printed on a Brain Heart Infusion (BHI) agar slide using a contact micro-spotting robotic system. Within 3 h, sufficient bacterial cells were obtained to allow accurate identification of the microorganism by infrared spectroscopy. This approach allows a "complete-in-a-single-day" analysis of a large array of samples.
    Preview · Article · Feb 2004 · Foodborne Pathogens and Disease

Publication Stats

526 Citations
63.37 Total Impact Points


  • 2002-2009
    • U.S. Food and Drug Administration
      • • Division of Microbiology
      • • Center for Food Safety and Applied Nutrition
      Washington, Washington, D.C., United States
  • 1999-2002
    • University of Georgia
      • Department of Animal and Dairy Science
      Атина, Georgia, United States
  • 2000
    • Oklahoma State University - Stillwater
      • Department of Microbiology and Molecular Genetics
      Stillwater, Oklahoma, United States