Microbiome, AMR, Antimicrobial resistance, campaign visual for AMR 2023
Feb 2023 | Genomics

Battling known and unknown threats with NGS-based AMR detection

Antimicrobial resistance – the silent pandemic?

Antimicrobials have transformed modern medicine. However, the overuse and misuse of antimicrobials are leading to alarming levels of antimicrobial resistance (AMR). Resistant microbes or ‘superbugs’ are harder to treat and increase morbidity, mortality and healthcare costs. AMR is associated with 2.8 million infections and 35,000 deaths annually in the USA (1) and €1.5 billion in extra healthcare costs and productivity losses in the EU (2). Worryingly, experts predict that by 2050, deaths due to antimicrobial-resistant infections will surpass those of cancer (3). AMR research is, therefore, of vital importance to help tackle this looming global public health crisis.

Unraveling the ‘resistome’

What is the ‘resistome’? The term has been used to describe all the AMR genes in an organism. AMR genes constitute a small percentage of the complete genome. Therefore, choosing the right AMR detection technology is critical. While 16s rRNA sequencing allows the identification of bacteria down to the genus and species level, it doesn’t provide the resolution needed to detect mutations or AMR regions. 

Did you know that each year in the US, there are 223,900 cases and 12,800 deaths caused by Clostridioides difficile?*

Hybrid capture vs. whole genome metagenomics shotgun sequencing

The highly diverse nature of microbial genomes and genes, particularly bacterial antimicrobial resistance genes, makes sequencing more complex. The only options for examining AMR are whole genome metagenomics or a targeted sequencing approach. A key challenge is that low-abundance AMR genes are difficult to detect if looking at the full profile. When using shotgun sequencing, a large portion of the sequenced samples is not relevant for AMR studies. This means shotgun sequencing is not as cost-effective. Another obstacle is the data analysis of key genes of interest, which can be overly complicated. 

While deep sequencing can detect diverse antimicrobial signatures, it lacks the sensitivity of targeted sequencing approaches. Hybrid capture approaches can provide an edge when it comes to the sensitive detection of low-abundance AMR genes.

Hybrid capture-based panels provide the following benefits over shotgun sequencing:

Higher sensitivity

  • Detect lower-abundance AMR genes with high-level enrichment
  • Guaranteed to capture your region of interest

Lower sequencing cost

  • Multiplex over 10x samples in a single sequencing run

Faster data analysis

  • Targeted sequencing allows for streamlined bioinformatic analysis

Harness the power of hybrid capture technology to detect bacterial AMR genes 

If you’re looking to detect and sequence AMR targets with confidence, ease and efficiency, our hybrid capture-based QIAseq xHYB AMR Panel can be a game changer. Delivering high sensitivity, the panel provides targeted enrichment, sequencing and detection of over 2700 separate AMR gene targets with over 6200 unique AMR alleles. 
After you’ve gathered your NGS data, you need to analyze your results. Data analysis remains an infamous bottleneck for many researchers. That’s why we’ve included access to the GeneGlobe platform with the QIAseq xHYB AMR Panel allowing you to seamlessly transition from generating data to figuring out what it all means. GeneGlobe offers a simplified overview of the sequencing results, so you can quickly determine if any antimicrobial resistance genes are detected in your samples.

Absolute quantification of low-abundance AMR genes 

Antibiotic resistance is a major component of antimicrobial resistance. Targeting antibiotic-resistance genes (ARGs) can be tricky when there are a small subset of antibiotic-resistant organisms present within a large population. Sensitivity and accuracy are prerequisites in such scenarios. This is where digital PCR (dPCR) can help. Explore the benefits of dPCR with our dPCR Microbial DNA Detection Assays, which are designed to simultaneously quantify up to five known AMR target genes on the QIAcuity dPCR platform.

Accelerating antimicrobial resistance research

The importance of AMR research is undisputed. However, optimizing your workflow is critical, from sample prep to detection and analysis. We can help you navigate the complexity of AMR detection workflows with our Sample to Insight solutions. From nucleic acid extraction from the most challenging samples to hybrid capture-based NGS and dPCR technologies for AMR detection and intuitive tools for data analysis, we’ve got you covered.

* Source: CDC webpage www.cdc.gov/drugresistance/biggest-threats.html 

  1. Centers for Disease Control and Prevention Antibiotic / Antimicrobial Resistance (AR / AMR) https://www.cdc.gov/drugresistance/about.html
  2. Wellcome Trust (2016) Four Diagnostic Strategies for Better-Targeted Antibiotic Use. London: Wellcome Trust. https://wellcome.org/sites/default/files/diagnostic-strategies-for-better-targeted-antibiotic-use-wellcome-jul15.pdf
  3. WHO. New report calls for urgent action to avert antimicrobial resistance crisis. https://www.who.int/news/item/29-04-2019-new-report-calls-for-urgent-action-to-avert-antimicrobial-resistance-crisis (Accessed June 16, 2022)