Application of microarray analysis of foodborne Salmonella in poultry production: A review

Abstract

Salmonellosis in the United States is one of the most costly foodborne diseases. Given that Salmonella can originate from a wide variety of environments, reduction of this organism at all stages of poultry production is critical. Salmonella species can encounter various environmental stress conditions that can dramatically influence their survival and virulence. Previous knowledge of Salmonella species genomic regulation of metabolism and physiology in relation to poultry is based on limited information of a few well-characterized genes. Consequently, although there is some information about environmental signals that control Salmonella growth and pathogenesis, much still remains unknown. Advancements in DNA sequencing technologies revolutionized the way bacteria were studied and molecular tools such as microarrays have subsequently been used for comprehensive transcriptomic analysis of Salmonella. With microarray analysis, the expression levels of each single gene in the Salmonella genome can be directly assessed and previously unknown genetic systems that are required for Salmonella growth and survival in the poultry production cycle can be elucidated. This represents an opportunity for development of novel approaches for limiting Salmonella establishment in all phases of poultry production. In this review, recent advances in transcriptome-microarray technologies that are facilitating a better understanding of Salmonella biology in poultry production and processing are discussed.

An Efficient Multiplex PCR-Based Assay as a Novel Tool for Accurate Inter-Serovar Discrimination of Salmonella Enteritidis, S. Pullorum/Gallinarum and S. Dublin

“…Thus, a simple method to detect and monitor Salmonella serovars in farms is urgently required. Several approaches based on antigens and DNA analysis have been developed to detect Salmonella in foodstuffs, including enzyme-linked immunosorbent assay, PCR analysis, and next generation sequencing (Ricke et al, 2013; Park et al, 2014). …”

Application of Molecular Methods for Traceability of Foodborne Pathogens in Food Safety Systems

“…Wang et al (2013) has suggested that polymorphisms of the CRISPR regions in pathogenic E. coli may also prove to be unique targets for PCR. (Dowd et al, 2007;Milillo et al, 2011;Sirsat et al, 2011a;Chalova et al, 2012;Ricke et al, 2013). (Dowd et al, 2007;Milillo et al, 2011;Sirsat et al, 2011a;Chalova et al, 2012;Ricke et al, 2013).…”

“…As more becomes known about CRISPR systems and more regions are identified for additional foodborne pathogens, there appear to be opportunities to fully develop subtyping approaches that combine these sequences with other typing methodologies and/or in some cases use them alone (Barco et al, 2013). The advantage of using microarrays for these types of questions was not just in the ability to assess entire genomes but also in the capacity to determine gene relatedness via quantitation of individual gene level responses and subsequent generation of Venn diagrams to identify shared gene responses to seemingly different environmental conditions (Sirsat et al, 2010;Ricke et al, 2013). The advantage of using microarrays for these types of questions was not just in the ability to assess entire genomes but also in the capacity to determine gene relatedness via quantitation of individual gene level responses and subsequent generation of Venn diagrams to identify shared gene responses to seemingly different environmental conditions (Sirsat et al, 2010;Ricke et al, 2013).…”

“…DNA MICROARRAYSIn the early 2000s, as more genomes were sequenced, efforts were undertaken to use the resulting genomic information to develop methods for simultaneously screening an entire genome of a particular organism. As would be expected, the potential for quantitation of gene expression in a presentation of the entire genome for a particular foodborne organism was highly attractive for assessing responses to environmental cues commonly encountered(Kuipers et al, 1999;Ricke et al, 2013). As would be expected, the potential for quantitation of gene expression in a presentation of the entire genome for a particular foodborne organism was highly attractive for assessing responses to environmental cues commonly encountered(Kuipers et al, 1999;Ricke et al, 2013).…”

“…This led to the generation of glass DNA microarray slides, which essentially consist either of cross-linked oligonucleotides or PCR products representing individual genes, the detection of which is essentially based on the level of hybridization between the single-stranded DNA probes attached to the surface versus the target DNA(Lucchini et al, 2001;Sirsat et al, 2010;Douglas et al, 2013;Ricke et al, 2013). This led to the generation of glass DNA microarray slides, which essentially consist either of cross-linked oligonucleotides or PCR products representing individual genes, the detection of which is essentially based on the level of hybridization between the single-stranded DNA probes attached to the surface versus the target DNA(Lucchini et al, 2001;Sirsat et al, 2010;Douglas et al, 2013;Ricke et al, 2013).…”