Harnessing aptamers for rapid detection of bacteria and antibiotics in our food.

Bacterial Genetics and Genomics book Discussion Topic: Chapter 4, question 14

The specificity of antibody binding has been exploited for many years in a variety of technologies. Although perhaps less famous, aptamers also have high binding specificity for their targets and, being made of RNA or DNA rather than protein, are much smaller in size, can be modified more easily, can be more easily reproduced, and can be stored and delivered more easily than antibodies.

Figure 4.14 from Bacterial Genetics and Genomics. In the top panel, an Aptamer is depicted as a bent green line. In the bottom panel, the Aptamer has bound a target and changed conformation; the green line has changed in shape around a purple sphere representing a Ligand.
Figure 4.14 from Bacterial Genetics and Genomics. In the top panel, an Aptamer is depicted as a bent green line. In the bottom panel, the Aptamer has bound a target and changed conformation; the green line has changed in shape around a purple sphere representing a Ligand.

It is by virtue of these properties that aptamers have been explored for a range of biotechnology applications, including as tools for detection of bacterial contamination of foods for human consumption.

The food-borne pathogen Vibrio parahaemolyticus is the leading cause of seafood-associated bacterial gastroenteritis. All of the traditional methods of detection rely on bulky laboratory equipment and are time-consuming. In a paper by Jiang et al., 2021, the goal was to create an electrochemical aptasensor. This combined microfluidic technology with the specificity of binding in an aptamer to enable detection of the V. parahaemalyticus outside of a laboratory within 30 minutes. The paper demonstrates the sensitivity and specificity of their device and suggests that it could be adapted to detect other bacterial pathogens.

Photograph of raw seafood, a common source of transmission of V. parahaemolyticus to humans. Photograph from Photographer Sergy from Thailand.
Photograph of raw seafood, a common source of transmission of V. parahaemolyticus to humans. Photograph from Photographer Sergy from Thailand.

Although we tend to think of Staphylococcus aureus perhaps in other contexts, it is also an important food-borne pathogen, particularly in the USA. To overcome time delays associated with traditional methods of detection of S. aureus using culturing, Yang and colleagues developed an aptamer-based technology that makes use of established portable detection platforms available in personal glucose meters. These hand-held devices are already readily available and reliable, so they made an ideal starting point for development of a portable bacterial detection device. The sensitivity of the aptamer biosensors were able to selectively detect S. aureus in food samples, demonstrating the usefulness of the portable technology.

Portable glucose meter icon image by By Laymik, UA. An icon drawing of a glucose meter, which has been used as part of an aptamer-based detection technology by Yang et al., 2021.
Portable glucose meter icon image by By Laymik, UA. An icon drawing of a glucose meter, which has been used as part of an aptamer-based detection technology by Yang et al., 2021.

There is a study published in Analyst, a journal from the Royal Society of Chemistry, which investigated the contamination of powdered infant formula by the food-borne pathogen Cronobacter sakazakii. These bacteria cause meningitis, sepsis, and necrotizing enterocolitis in premature and immune-compromised infants. It is therefore vitally important that these bacteria do not end up in products for babies, like powdered infant formula. This particular study by Hye Ri Kim and colleagues, published in 2021, did not use the standard SELEX technique to develop its aptamers for detection of these pathogens. SELEX is ‘systematic evolution of ligands by exponential enrichment’ and has been used since 1990 to produce aptamers. Instead of SELEX, Kim et al. used a centrifugation-based partitioning method (CBPM), which produces target-specific aptamers in a shorter time-frame. Using this CBPM method, these researchers were able to isolate two aptamers against C. sakazakii and demonstrated that these could be used to efficiently detect the pathogen in powdered infant formula.

An icon drawing of a baby bottle beside a can of powdered infant formula with a scoop measure above it. Infant formula icon image by Chiara Rossi, IT.
An icon drawing of a baby bottle beside a can of powdered infant formula with a scoop measure above it. Infant formula icon image by Chiara Rossi, IT

Sometimes the issue isn’t the bacteria, but rather the antibiotics we have been using to combat the bacteria. For example, an aptamer was developed by Komal Birader and colleagues that specifically detects the antibiotic oxytetracycline in milk. This antibiotic was used in veterinary practice, however it was banned due to potential side effects. This meant that it was necessary to develop a way to detect oxytetracycline in milk that was destined for human consumption. The detection method needed to be both affordable and one that could be used in the field. This team was able to modify the aptamer that they developed so that the presence of the antibiotic would result in a visual detection, making it ideally suitable for use in the field.

A glass of milk. Photograph by H. Zell.
A glass of milk. Photograph by H. Zell.

Much like antibodies have been used in a variety of ways that are well outside of their original purpose inside our bodies to fight off foreign invaders, aptamers are therefore being used in a range of ways that are beyond their original purpose. As explored in Chapter 4 of Bacterial Genetics and Genomics, aptamers can have a role in bacterial gene expression, but outside of the bacterial cell, scientists have found a whole range of uses for them, including detecting bacteria and antibiotics in our food.

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