Identification of<i>Listeria</i>Species by Microarray-Based Assay

Volokhov, Dmitriy V.; Rasooly, Avraham; Chumakov, Konstantin; Chizhikov, Vladimir

doi:10.1128/jcm.40.12.4720-4728.2002

Cited by 205 publications

(122 citation statements)

References 41 publications

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“…During a single hybridization, arrays can integrate probes that provide microbial identification but also enclose large sets of discriminative epidemiological markers [31,31,70,182,183,198], or contain probes to detect virulence or antimicrobial resistance determinants [17,36,38,91,176]. The high parallelism of microarray systems appears particularity adapted provided their design includes the following: (1) targeted universal gene(s), (2) simplified coupling and labeling protocols, (3) exquisite sensitivity, and (4) adapted analysis strategy.…”

Section: Discussionmentioning

confidence: 99%

“…Reports have already shown that oligonucleotide microarrays can enable bacterial detection utilizing conserved bacterial genes [158], species identification [189] as well as genotyping of bacterial pathogens, by using large sets of discriminative epidemiological markers [32,36,70,183,198]. Detection of genetically encoded virulence or antimicrobial resistance determinants [17,36,112,176] may also afford a major benefit for selection of an adequate chemotherapy.…”

Section: Introduction To Microarray Technologymentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

Section: Introduction To Microarray Technologymentioning

confidence: 99%

Introduction to Microarray‐Based Detection Methods

Schrenzel

Kostić²,

Bodrossy

et al. 2009

Detection of Highly Dangerous Pathogens

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“…However, some authors chose genes that are more strongly related to virulence, hence considered more pathogen specific. For instance, Volokhov and colleagues [60] developed a Listeria diagnostic microarray-based on genes essential for the bacteria virulence but found in all Listeria strains, such as the invasion associated protein (iap), and in pathogenic strain-specific genes, such as hly.…”

Section: Choice Of the Target Genementioning

confidence: 99%

Potentials and limitations of molecular diagnostic methods in food safety

Lauri

Mariani

2008

Genes Nutr

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Molecular methods allow the detection of pathogen nucleic acids (DNA and RNA) and, therefore, the detection of contamination in food is carried out with high selectivity and rapidity. In the last 2 decades molecular methods have accompanied traditional diagnostic methods in routine pathogen detection, and might replace them in the upcoming future. In this review the implementation in diagnostics of four of the most used molecular techniques (PCR, NASBA, microarray, LDR) are described and compared, highlighting advantages and limitations of each of them. Drawbacks of molecular methods with regard to traditional ones and the difficulties encountered in pathogen detection from food or clinical specimen are also discussed. Moreover, criteria for the choice of the target sequence for a secure detection and classification of pathogens and possible developments in molecular diagnostics are also proposed.

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“…It also may allow for the detection of those mutations even when they occur at relatively low levels (up to 1%) as in the case of mixtures of quasispecies that cannot be detected by traditional direct sequencing methods (Cherkasova et al, 2003;Leberre at al., 2007). The efficiency of microarrays for identification and discrimination of closely related bacteria and viruses has been previously demonstrated Hsia et al, 2007;Laassri et al, 2003;Nordström et al, 2005;Volokhov et al, 2002;Wade et al, 2004). The use of oligonucleotide microchips for screening of random mutations is based on the ability of microarrays to identify the presence of singlenucleotide mutations in the hybridization template (Hacia et al, 1999;Urakawa et al, 2003).…”

Section: Optimization Of the Wnv Microarray Assaymentioning

confidence: 99%

“…The microarrays consisting of multiple individual short oligoprobes were shown to be an efficient and sensitive genetic method for detection of single point mutations in viral and bacterial genomes Grinev et al, 2008b;Laassri et al, 2003Laassri et al, , 2005Laassri et al, , 2007Volokhov et al, 2002). Microarray assays can also help simultaneously detect and identify the genotype and strain of common food-borne viruses without using PCR (Chen et al, 2011).…”

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confidence: 99%