Antibiotic resistance genes

The discovery and use of antibiotics are two of the most significant breakthroughs in twentieth-century medicine—leading to dramatic reductions in human morbidity and mortality. Antibiotics and other antimicrobial agents are also used extensively in agriculture. Typically, livestock are given antibiotics to encourage growth and prevent illness, thereby increasing the amount of food produced. There are multiple classes of antibiotics, categorized based on their mechanism of action. Antibiotics can damage the cell wall of a bacterium, block DNA, RNA, or protein synthesis, or even inhibit the metabolic growth of bacteria. Some antibiotics are specific to certain species of bacteria (narrow-spectrum), whereas others can affect a wide range of bacteria (broad-spectrum).

One emerging problem with antibiotics is the development of antibiotic-resistant bacteria. Bacteria can acquire antibiotic resistance genes (ARGs) over time due to selective pressure. Excessive antibiotic use can lead to the development of spontaneous ARGs in certain strains. As these strains grow and expand, different antibiotics have to be developed to combat them. Ultimately, the current strategy is to prevent overuse of antibiotics, thereby limiting the exposure of bacteria to these agents and minimizing selective pressures. For human patients, overuse can result from incorrect dosing, over- or mis-prescribing, or improper disposal. Critically, antibiotic use in agriculture can also contribute to bacteria developing ARGs. Not only can antibiotic-resistant bacteria develop in livestock, but manure can act as a vector to transmit antibiotic-resistant strains into the environment via soil, water, and produce. Thus, antibiotic-resistant bacteria can be spread widely, and recent efforts have focused on identifying ARGs and tracking their prevalence in a variety of environments and sample types.

There are currently over 1,000 types of ARGs that have been identified to confer resistance to the hundreds of available antibiotics. Consequently, monitoring human and environmental samples for ARGs requires the ability to perform high-throughput real-time PCR (qPCR) screens for many different target sequences in numerous sample types. Further, because bacteria are constantly developing new ARGs, it is critical to be able to modify and add new targets to the screen. Thus, ARG research requires a flexible, high-throughput qPCR system to monitor gene expression in a wide range of sample types.

The SmartChip Real-Time PCR System has been used in numerous studies for profiling and tracking ARGs in a variety of samples. Initially, high-throughput screens were performed using panels of 296 targets, which supported the ability to screen up to 16 soil samples per chip. In recent years, the panels have evolved to contain 384 targets (see Table I), as well as being run on soil, water, sediment, manure, lettuce, fish, and sludge sample types. The flexibility and throughput of the SmartChip system have been instrumental in enabling these and future studies of the antibiotic resistome. In fact, the SmartChip system has been utilized in 75% of the publications using high-throughput qPCR for antibiotic resistance research (Waseem et al. 2019).

Citations

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