Fingerprinting for Detecting Contaminants in Food

K. Bohme1, J. Barros-Veiazquez2 and P. Calo-Mata2

1Agrifood Technological Centre of Lugo (CETAL), Lugo, Spain, 2University of Santiago de Compostela, Lugo, Spain


Food quality and safety are increasingly important public health issues. Every year, about 600 million persons fall ill after consuming contaminated food or water and 420,000 of them die. Diseases caused by unsafe food can cause severe diarrhea, life-threatening intoxications, and cancer (WHO, 2015). Consumers need to purchase safe products that do not involve any kind of health risk. The aim of “food safety” is to avoid health hazards for the consumer, such as microbiological and chemical contaminants, as well as adulteration.

Chemical food contaminants are veterinary drugs, feed additives, growth promoters, dioxins, heavy metals, and pesticides that are known or suspected to be carcinogenic, causing cardiovascular disease, kidney and liver dysfunction, etc., when humans are exposed by ingestion of the contaminated food or water. Thus, food products are under stringent laboratory control to assure they comply with the regulatory limits for residues and contaminants. The progress made in analytical chemistry in the last decades toward significantly higher sensitivity and specificity now allows the detection of chemical contaminants in complex food matrices, down to parts per billion. Routine analytical methods for the detection of single or multiple chemical contaminants include rapid screening tests, such as enzyme-linked immunosorbent assays and microbial inhibition tests, as well as complex multitarget instrumental analysis based on chromatography, mass spectrometry, and vibrational and atomic spectroscopy.

The contamination of food products with microorganisms presents a problem of global concern, since the growth and metabolism of microorganisms can cause serious foodborne intoxications. Thus, the safety of a food product depends in great part on the presence and nature of the microorganisms.

Food Protection and Security. DOI:

© 2017 Elsevier Ltd. All rights reserved.

Besides molds and yeasts, bacteria are the principal microorganisms responsible for various types of food spoilage and foodborne intoxications. It should be mentioned that a food product naturally contains an indigenous microbiota that can include pathogenic bacterial species; however, most bacterial contamination occurs during processing and manipulation of the food products. The global incidence of foodborne disease is difficult to estimate, but it has been reported that every year 230,000 people die due to diarrheal diseases after consuming contaminated food or water. In industrialized countries, the percentage of the population suffering from foodborne diseases each year has been reported to be up to 30% (WHO, 2015). In order to control and minimize the microbial hazard, pathogenic bacteria need to be identified in a rapid and unequivocal way. Traditionally, bacterial species have been identified by classic tools relying on culturing processes coupled to morphological, physiological, and biochemical characterization. In the last few decades, the field of microbiological identification has turned to more rapid and sensitive methods, including antibody-based assays and DNA-based methods, together with important advances in bioinformatics tools. Thus, some methodologies such as ELISA or PCR have already become classics. Recently, the development of rapid and highly sensitive techniques, such as real-time PCR, DNA microarrays, and biosensors, has provoked the replacement of traditional culturing methods in the field of bacterial identification in clinical diagnostics, as well as in the food sector. Furthermore, Fourier transform infrared spectroscopy (FT-IR) has been described as a new method for rapid and reliable bacterial identification (Sandt et al., 2006). At the same time, proteomic tools such as mass spectrometry have been introduced for the identification of microorganisms (Klaenhammer et al., 2007).

This chapter aims to review the detection of food contaminants by fingerprinting techniques. The term fingerprinting has its origin in forensics, where specific DNA profiles are used to differentiate individuals. DNA fingerprinting is the most common approach for species differentiation and identification, with many applications in the food sector, as much for food authentication purposes as for microbial pathogen identification. The different techniques, such as amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), repetitive sequence-based PCR (rep-PCR), multiple-locus variable number tandem repeat analysis (MLVA), multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE), create sets of characteristic DNA profiles, specific for every individual. All these techniques have been extensively studied with the aim of determining plant varieties, animal species, and the source and/or geographic origin of a food or food ingredient. Besides food authenticity, DNA fingerprinting is a common tool for bacterial species differentiation at the genus, species, and strain levels (Mandal et al., 2011). On the one hand, identification of the microbiota of a food product allows shelf life to be determined and any necessary measures to be taken to assure quality. On the other hand, the detection of certain microbial contaminants with a foodborne pathogenic character is crucial to avoid a microbial health risk for consumers. Furthermore, DNA typing of bacterial strains at the subspecies level is carried out to classify the strains in relation to their origin, antibiotic resistance and virulence, being crucial for microbial source tracking (MST), and epidemiological studies.

Nowadays, molecular fingerprinting is not restricted to DNA-based methods, but describes a variety of analytical methods that can measure the composition of a sample in a nonselective way, such as by collecting a spectrum. In following sections, molecular fingerprinting techniques, different from DNA fingerprinting, and their applications for detecting food contaminants are described. Analytical methods, such as spectroscopy and spectrometry generate spectral profiles that represent fingerprints of the analyzed target. As with DNA fingerprints, the information obtained may be used to differentiate and identify individuals for food authenticity and microbial identification purposes. This chapter focuses especially on (1) the detection of bacterial contaminants and (2) bacterial discrimination at the species and subspecies levels. Closely related species are sometimes difficult to distinguish by traditional and DNA-based methods, but the pathogenic character may differ significantly. This is even more important in those cases where different strains of the same species exhibit different virulent potentials. That is why identification at the species level is not always sufficient and bacterial typing methods that give information about virulence factors and antibiotic resistance are key aspects of ongoing research. Table 2.1 gives an overview of the main foodborne pathogenic bacterial species studied by molecular fingerprinting techniques and the corresponding references are listed. Spectral approaches are also being applied to the detection of mycotoxins and food contaminants different from those of microbial origin. In this chapter, the use of spectral fingerprinting techniques to detect chemical contaminants is summarized, including detection of antibiotics, drugs, hormones, melamine, pesticides, and some further banned food ingredients.

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