- SmartChip real-time PCR system overview
- SmartChip Real-Time PCR System technical specifications
- SmartChip Real-Time PCR System applications
- SmartChip Real-Time PCR System video resources
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 is 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 (wide-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 over-use of antibiotics, thereby limiting the exposure of bacteria to these agents and minimizing selective pressures. For human patients, over-use can result from incorrect dosing, over- or misprescribing, 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 nearly 400 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, 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. Read below to see examples of antibiotic resistance research enabled by the SmartChip system.
Chen, Q. et al. Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil. Environ. Int. 92-93, 1–10 (2016).
Chen, Q.-L. et al. Application of Struvite Alters the Antibiotic Resistome in Soil, Rhizosphere, and Phyllosphere. Environ. Sci. Technol. 51, 8149–8157 (2017).
Karkman, A. et al. High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant. FEMS Microbiol. Ecol. 92, fiw014 (2016).
Lin, W., Zhang, M., Zhang, S. & Yu, X. Can chlorination co-select antibiotic-resistance genes? Chemosphere 156, 412–419 (2016).
Lu, X.-M., Li, W.-F. & Li, C.-B. Characterization and quantification of antibiotic resistance genes in manure of piglets and adult pigs fed on different diets. Environ. Pollut. 229, 102–110 (2017).
Muurinen, J. et al. Influence of Manure Application on the Environmental Resistome under Finnish Agricultural Practice with Restricted Antibiotic Use. Environ. Sci. Technol. 51, 5989–5999 (2017).
Muziasari, W. I. et al. Aquaculture changes the profile of antibiotic resistance and mobile genetic element associated genes in Baltic Sea sediments. FEMS Microbiol. Ecol. 92, fiw052 (2016).
Muziasari, W. I. et al. The Resistome of Farmed Fish Feces Contributes to the Enrichment of Antibiotic Resistance Genes in Sediments below Baltic Sea Fish Farms. Front. Microbiol. 7, 2137 (2017).
Ouyang, W.-Y., Huang, F.-Y., Zhao, Y., Li, H. & Su, J.-Q. Increased levels of antibiotic resistance in urban stream of Jiulongjiang River, China. Appl. Microbiol. Biotechnol. 99, 5697–707 (2015).
Stedtfeld, R. D., Stedtfeld, T. M., Fader, K. A., et al. TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome. FEMS Microbiol. Ecol. 93, (2017).
Stedtfeld, R. D., Stedtfeld, T. M., Waseem, H., et al. Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers. J. Environ. Manage. 198, 213–220 (2017).
Su, J.-Q. et al. Antibiotic resistome and its association with bacterial communities during sewage sludge composting. Environ. Sci. Technol. 49, 7356–63 (2015).
Tang, M. et al. Abundance and distribution of antibiotic resistance genes in a full-scale anaerobic-aerobic system alternately treating ribostamycin, spiramycin and paromomycin production wastewater. Environ. Geochem. Health (2017).
Wang, F. et al. Influence of Soil Characteristics and Proximity to Antarctic Research Stations on Abundance of Antibiotic Resistance Genes in Soils. Environ. Sci. Technol. 50, 12621–12629 (2016).
Wang, F.-H. et al. High throughput profiling of antibiotic resistance genes in urban park soils with reclaimed water irrigation. Environ. Sci. Technol. 48, 9079–85 (2014).
Wang, H. et al. The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome. ISME J. 11, 100–111 (2017).
Xie, W.-Y., McGrath, S. P., et al. Long-Term Impact of Field Applications of Sewage Sludge on Soil Antibiotic Resistome. Environ. Sci. Technol. 50, 12602–12611 (2016).
Xie, W.-Y., Yang, X.-P., et al. Changes in antibiotic concentrations and antibiotic resistome during commercial composting of animal manures. Environ. Pollut. 219, 182–190 (2016).
Zheng, J. et al. High-throughput profiling and analysis of antibiotic resistance genes in East Tiaoxi River, China. Environ. Pollut. 230, 648–654 (2017).
Zhu, B., Chen, Q., Chen, S. & Zhu, Y.-G. Does organically produced lettuce harbor higher abundance of antibiotic resistance genes than conventionally produced? Environ. Int. 98, 152–159 (2017).
Zhu, Y.-G. et al. Continental-scale pollution of estuaries with antibiotic resistance genes. Nat. Microbiol. 2, 16270 (2017).
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