Antimicrobial resistance (AMR) occurs when bacteria and other pathogenic microorganisms evolve to survive the antibiotics designed to kill them. These microorganisms develop AMR primarily by acquiring antibiotic resistance genes (ARGs) that enable them to thrive even upon antibiotic exposure. Limiting the spread of antibiotic-resistant bacteria has rapidly become a pressing global public health challenge, particularly as AMR-related infection rates have increased 20% since 2020 (CDC 2024).
AMR surveillance is a critical tool to assess the burden of resistant pathogens and subsequently develop policies to prevent and control infections (WHO 2024; National Academies of Sciences, Palmer, and Buckley 2021). Effective surveillance requires accurate, sensitive monitoring of numerous pathogen-related targets like ARGs across a wide range of crops, livestock, wastewater, and other environmental samples. Currently, over 1,000 types of ARGs have been identified that confer resistance to the hundreds of available antibiotics. As new ARGs continue to be identified, comprehensive AMR surveillance grows both increasingly essential and more challenging.
Though there are numerous methods of ARG detection, qPCR has gained popularity for its speed, ease, and sensitive quantification of environmental samples (Abramova, Berendonk, and Bengtsson-Palme 2023; Takara Bio Blog Team 2024). However, scientists using qPCR for AMR surveillance struggle with its limitations, including low throughput, intensive labor demands, and high scale-up costs. In response to the growing need for routine quantification of large numbers of ARGs, many AMR surveillance organizations have turned to high-throughput qPCR technology like the SmartChip ND Real-Time PCR System.
Figure 1. Limitations for different methods of AMR pathogen detection. PCR/qPCR stands out, offering an easy and cost-effective AMR surveillance method primarily limited by its difficulty to scale up.
The SmartChip system has long been an established mainstay of AMR surveillance. The SmartChip system was utilized in 75% of antibiotic resistance research publications in the first decade after its launch (Waseem et al. 2019), and is still recognized as one of the most popular, scalable, and affordable technologies for high-throughput PCR (Delannoy et al. 2022). With a proven record of quantifying ARGs across multiple target gene categories and sample types—including soil, water, sediment, manure, lettuce, fish, and sludge (Antibiotic Resistance Genes 2020), the SmartChip system has recently expanded to enabling environmental surveillance on a national scale, as AMR researchers monitored wastewater treatment plant effluents across Wales (Knight et al. 2024). The SmartChip system is currently the only high-throughput PCR technology of its kind that combines a decade of dependable performance with the flexible assay formats that AMR surveillance requires. Resistomap, a leader in antibiotic resistance monitoring, regularly employs the SmartChip system in a variety of AMR-related projects, from tracking antibiotics impact on dairy farms to wastewater management consulting (Somers 2022).
With features ideally suited for high-throughput monitoring (Table 1), the SmartChip ND Real-Time PCR System offers a time-tested, trusted solution for large-scale AMR surveillance.
| Essentials for effective AMR surveillance | Features of SmartChip ND Real-Time PCR System |
|---|---|
| High-throughput capacity to process thousands of samples |
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| Low cost for wide-scale monitoring |
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| Fast assay turnaround time |
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| Minimal labor for large-scale processing |
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| Flexible accommodation of new ARG targets |
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| Simple data analysis |
|
Table 1. Overview of SmartChip ND Real-Time PCR System features addressing essential needs for effective AMR surveillance.
ARG detection workflow
ARG detection assays for AMR surveillance using the SmartChip ND Real-Time PCR System follow a simple workflow with ~30 min of hands-on time and less than 3 hr of total processing time per 5,184 reactions.
Samples are first collected and processed to extract and purify sample DNA. The DNA is then combined with assay mix and dispensed into 5,184-well SmartChip MyDesign Chips. Once the chips are loaded into the SmartChip ND Real-Time PCR Cycler, the instrument amplifies sample, detects target genes, and prepares data for analysis (Figure 2).
Sample collection
DNA extraction & purification
Chip preparation
Target detection by qPCR
Data analysis
Figure 2. Workflow for ARG detection using the SmartChip ND Real-Time PCR System. This streamlined workflow takes less than 3 hr from DNA extraction & purification to data analysis, with only ~30 min of hands-on time.
