Multipathogen oligonucleotide microarray for environmental and biodefense applications

Sergeev, N. V.; Distler, Margaret G.; Courtney, Shannon; Al-Khaldi, Sufian F.; Volokhov, Dmitriy V.; Chizhikov, Vladimir; Rasooly, Avraham

doi:10.1016/j.bios.2004.04.030

Cited by 121 publications

(68 citation statements)

References 20 publications

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“…Recently, various reports have demonstrated the efficacy of this approach in the detection of waterborne pathogens (21), marine fish pathogens (11), and other food-borne pathogens (7,10,19,28,30). To our knowledge, this study describes for the first time the application of DNA microarray technology for the rapid and reliable detection of pathogens associated with PIF contamination.…”

Section: Discussionmentioning

confidence: 96%

Detection of Enterobacter sakazakii and Other Pathogens Associated with Infant Formula Powder by Use of a DNA Microarray

et al. 2009

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Pathogen detection is critical to the process of generating and testing powdered infant formula (PIF).An obstacle associated with PIF microbial surveillance is that most current procedures are time-consuming and labor-intensive. We have developed a rapid, DNA microarray-based detection technique to identify 10 different pathogenic bacteria associated with PIF contamination based on the 16S-23S rRNA gene internal transcribed spacer (ITS) sequences and wzy (O antigen polymerase) gene. Using this procedure, Enterobacter sakazakii, Salmonella enterica, Klebsiella pneumoniae, Klebsiella oxytoca, Serratia marcescens, Acinetobacter baumannii, Bacillus cereus, Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli O157 were identified. One hundred eighty-five strains were used to validate the microarray assay (including 134 target pathogen strains and 51 closely related bacteria). Twenty-seven probes reproducibly detected multiple pathogens with high specificity and sensitivity (0.100 ng genomic DNA or 10 4 CFU/ml). Twenty-one real PIF samples were tested by the microarray with 100% accuracy. The data presented reveal that the designed oligonucleotide microarray is a promising method for basic microbiology, clinical diagnosis, food safety, and epidemiological surveillance.

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Section: Discussionmentioning

confidence: 96%

Detection of Enterobacter sakazakii and Other Pathogens Associated with Infant Formula Powder by Use of a DNA Microarray

et al. 2009

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“…For example the hypothetical lipoproteins on genomic island uSaa2 were not returned by the genome browser using the keyword 'lipoprotein'. Sergeev et al (2004) have described a microarray consisting of oligonucleotide probes for an assembly of enterotoxin genes. The array was shown to be able to analyse multiple enterotoxin genes of test strains.…”

Section: Discussionmentioning

confidence: 99%

A virulence-associated gene microarray: a tool for investigation of the evolution and pathogenic potential of Staphylococcus aureus

Saunders

Underwood

Kearns³

et al. 2004

Microbiology

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An oligonucleotide probe microarray for investigation of the evolution of epidemic Staphylococcus aureus strains has been constructed. The array comprises 383 probes based on virulence-associated genes present in four key strains. Twelve strains including seven for which the complete chromosomal nucleotide sequence was available were tested on the array. Twenty-six per cent of the probes were able to differentiate between strains to give a minimum of two gene differences between pairs. A gene difference distance tree based on the array data had approximately the same topology as one prepared using concatenated MLST sequences. Differences in the topologies of these trees were found to indicate that large-scale recombination events had occurred during the evolution of the species. One such occurrence appears to have been a key event in the genesis of the EMRSA-15 clone (ST22) that currently represents the most prevalent methicillin-resistant S. aureus (MRSA) in the UK. INTRODUCTIONStaphylococcus aureus is an important human pathogen responsible for bacterial infections seen both in the community and in hospitals. Over the last decades the emergence of multi-drug resistant strains has greatly increased the economic and health importance of staphylococcal infection (Chambers, 2001;Stefani & Varaldo, 2003;Wenzel, 1982). S. aureus is a highly adapted and extremely successful colonizer of the human nasopharynx, other mucosal surfaces and skin (Kluytmans et al., 1997;Williams, 1963). Colonization is generally asymptomatic but occasionally results in disease with a wide variety of signs and symptoms. These range from mild self-limiting infections of the skin to fulminating septicaemia (Lowy, 1998;Projan & Novick, 1997). Staphylococcal disease appears to result from an imbalance between the bacterium and the immune system and is associated with tissue invasion or unchecked growth. S. aureus is able to maintain its colonist status by producing a variety of proteins that interact with host-cell components (Baba et al., 2002;Kuroda et al., 2001). These proteins are described as virulence-associated and have functions such as extracellular matrix binding and host cell lysis. Expression of the S. aureus virulence-associated proteins is very carefully controlled by means of a network of regulatory genes including the agr and sar operons (Chien & Cheung, 1998;Sabersheikh & Saunders, 2004). Strain variation in these regulatory mechanisms may be an important factor influencing the switch from colonization to disease. Such variations may also contribute towards the success of the species by helping to minimize the emergence of immunity to essential S. aureus-specific antigens.Genome sequencing has shown that the species maintains a large number of virulence-associated genes but that not all are carried by each individual strain (Baba et al., 2002;Holden et al., 2004;Kuroda et al., 2001). Pairwise comparisons show as much as 20 % variation in the gene inventory of different S. aureus with most of the difference contributed by virule...

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“…Reversible hybridization kinetics and lower target binding capacity (in comparison to long oligonucleotides) are responsible for somewhat limited detection sensitivity (Figure 1.2). Short oligonucleotide are widely used for both environmental and diagnostic microbial diagnostic microarrays (MDMs) [21,78,110,155]. …”

Section: Oligonucleotide Probesmentioning

confidence: 99%

Introduction to Microarray‐Based Detection Methods

Schrenzel

Kostić²,

Bodrossy

et al. 2009

Detection of Highly Dangerous Pathogens

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Microarrays consist of an orderly arrangement of probes (oligonucleotides, DNA fragments, proteins, sugars or lectins) attached to a solid surface. The main advantages of microarray technology are high throughput, parallelism, miniaturization, speed and automation. Despite the fact that microarray analysis is a relatively novel technology, with the publication of the first microarray studies in 1995 [101,152], it is now broadly applied and the milestone of nearly 5000 published microarray papers was recorded in 2004 [80]. The scientific and technological background discussed here will be limited to DNA microarrays, excluding the new evolving fields of protein microarrays and glycomics [140].Analogous to antigen-antibody interactions on immunoarrays, DNA microarrays rely on sequence complementarity of the two strands. They put in practice the fundamentals of complementary base-pairing (hybridization) that were first described by Ed Southern [162]. In general, the strategy of microarray hybridization is reversed to that of a standard dot-blot, leading to recurring confusion in the nomenclature. Therefore, it has been suggested to describe tethered nucleic acid as the probe and free nucleic acid as the target [134].Earlier studies on duplex melting and reformation, carried out on DNA solutions, have provided the basic knowledge about the reaction kinetics. Furthermore, a method for computational determination of the melting point as a function of nucleic acid composition and salt concentration was established [6,148,149]. Much of the pioneering work can be linked to the use of nitrocellulose membranes [69], dot-blots [84] and Southern blots [162]. Development of cDNA or oligonucleotide arrays was possible by combined innovations in micro-engineering, molecular biology [33,120,123,156,163,164] and bioinformatics [59]. The real breakthrough in microarray technology was initiated by two key innovations: the use of non-porous solid supports (such as glass and silicon) and the development of methods for highdensity synthesis of oligonucleotides directly onto the microarray surface [59].

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Multipathogen oligonucleotide microarray for environmental and biodefense applications

Cited by 121 publications

References 20 publications

Detection of Enterobacter sakazakii and Other Pathogens Associated with Infant Formula Powder by Use of a DNA Microarray

Detection of Enterobacter sakazakii and Other Pathogens Associated with Infant Formula Powder by Use of a DNA Microarray

A virulence-associated gene microarray: a tool for investigation of the evolution and pathogenic potential of Staphylococcus aureus

Introduction to Microarray‐Based Detection Methods

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