EPIDEMIOLOGY, ECOLOGY, AND MOLECULAR GENETICS OF ANTIMICROBIAL RESISTANCE IN PATHOGENIC AND COMMENSAL BACTERIA FROM FOOD ANIMALS
Location: Bacterial Epidemiology and Antimicrobial Resistance
Title: Application of microarray technology for microbial source tracking
Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: July 22, 2011
Publication Date: July 1, 2012
Citation: Frye, J.G. 2012. Application of microarray technology for microbial source tracking. In: Foley, S.L., Nayak, R., Johnson, T.J., Shukla, S.K., editors. Molecular Typing Methods for Tracking Foodborne Microorganisms. New York, NY: Nova Science Publishers. p. 319-340.
Interpretive Summary: Detection, typing, and tracing microbes to their sources are major food safety goals. Typing of foodborne organisms has been improved with the use of molecular techniques to detect different genetic lineages of these microbes. Detection of different genotypes of an organism can potentially be used to trace it to a specific source. DNA microarrays have been designed to do this, and offer several advantages over other molecular methods. Microarrays can detect multiple DNA sequences in an organism in one assay. Because of the large amount of genetic information that can be collected with microarrays, they can be used for typing microbes at sufficient detail to be used for source tracking. However, there are many different types of microarrays used to type foodborne organisms, each with their own characteristics and capabilities. Additionally, these microarrays may have very different abilities to type organisms, making it difficult to compare data collected by different microarrays. This chapter explains the basic concepts of DNA microarray methods; introduces some commonly used types of microarrays, and presents examples of microarray typing of foodborne microorganisms. The understanding of microarray methods provided by this knowledge will allow scientists, clinicians, and food safety/public health administrators to comprehend how microarrays are used for source tracking and will provide them with the ability to evaluate the data collected with these assays.
Typing of foodborne microorganisms for source tracking was radically improved with the implementation of molecular techniques. These assays were designed to detect genetic differences in lineages of foodborne organisms. Molecular techniques can detect the natural variability in the genome of a microbe and use this information to identify genotypes of the organism that can be traced to a specific food source. DNA microarrays have been recently employed in this effort, and offer several advantages over genomic analyses with other molecular methods. Microarrays are usually constructed of DNA probes immobilized on a solid surface, with each probe complementary to a specific sequence in the organism’s genome. The microbe’s labeled DNA is applied to the microarray where sequences that match the array’s probes hybridize to them and are detected. The microarray probes are often arrayed at a very high density, enabling a single assay to detect from hundreds to millions of sequences. Because of this, DNA microarrays can determine enough genetic characteristics to be used for typing microbes at sufficient detail to be used for source tracking. However, methods in microarray design, construction, and utilization are complex, resulting in many different microarray platforms being used by investigators or manufactured by commercial companies. Additionally, the data collected by each microarray platform may not yield the same level of discrimination, making it difficult to compare data across microarray platforms. This chapter will explain the basic concepts of DNA microarrays, introduce commonly used platforms, and present examples of microarray typing of foodborne microorganisms.