2.3 How WGS compares with standard approaches
Molecular testing refers to techniques such as PCR (polymerase chain reaction) that detect specific resistance genes or mutations at the genetic level. PCR is a method used to amplify small segments of DNA, allowing the detection of even low levels of a resistance gene in a sample. Unlike phenotypic AST, which tests whether bacteria can grow when exposed to antibiotics, molecular methods look for specific resistance genes in the bacteria’s DNA. This means they can detect resistance even if it’s not currently causing a problem.
Molecular tests are often used to confirm the presence of specific resistance genes; for example, following phenotypic detection of AMR. However they can only detect what they are designed to target, so may miss novel or unexpected resistance mechanisms.
To better appreciate the pros and cons of the three main different approaches to AMR screening, Table 2 shows a comparison between AST, molecular testing and WGS.
| Feature | Phenotypic tests (AST) | Molecular tests | WGS analysis |
|---|---|---|---|
| What is measured? | Bacterial growth in the presence of antibiotics | Whether specific resistance genes are present | All the genetic information, including all resistance genes |
| Main methods | Sequencing machines and bioinformatic software | ||
| Main outcomes | Shows which antibiotics the bacteria are resistant to | Shows known resistance genes | Lists all resistance genes, mutations and other information such as plasmid types and |
| Detects actual resistance? | Yes | No, only predicts based on genes | No, only predicts based on genes |
| Identifies specific resistance genes? | No | Yes, but only the ones you look for | Yes, all known genes in the genome |
| Identifies resistance mutations? | No | Sometimes | Yes, all known ones |
| Detects plasmids? | Sometimes, limited to methods | Sometimes, limited to methods | Yes |
| Identifies strain typing and epidemiology? | Yes, with some laboratory methods | Yes, if specific tools are used | Yes, very detailed and automated |
| Identifies serotypes and pathotypes? | Yes, via specific laboratory tests | Yes, via PCR | Yes |
| Detects unknown mechanisms? | Sometimes | No | Not without extensive analysis; without it, it only finds known resistance gene/mutations |
| Detects virulence? | Yes, with laboratory tests | Yes | Yes |
| Turnaround time | 1–3 days | 1–2 days | 1–5+ days (depending on sequencing technology) |
| Infrastructure needed? | Microbiology lab: incubator, media, antibiotic disks or strips, and tools for measuring growth (e.g. spectrophotometer or visual reading) | Molecular biology lab: PCR machine (thermocycler), gel electrophoresis equipment and reagents for extracting and amplifying DNA; Sanger sequencing | Sequencing machine and software, bioinformatic tools; requires a DNA extraction set-up, a sequencing machine (e.g. Illumina or Oxford Nanopore) and computers with specialised software for genome analysis; also needs trained staff for both laboratory and data analysis |
| Scalability | Low to moderate | Moderate | High |
| Use in surveillance | Mostly used in clinical settings; provides baseline resistance trends and prevalence data | Used in some labs; detects known genes in targeted surveillance | Widely used for AMR and outbreak surveillance; offers high-resolution data for source-tracking and resistance mechanisms |
Activity 3: Reflecting on your experience
Use the space below to spend a few minutes noting which approaches and tests shown in Table 2 you are familiar with and are used in your area; these might be in local hospitals or other regional surveillance centres.
How many of these involve molecular-based tests? You will see later why this can be an important factor when considering the introduction of WGS approaches to surveillance.
Discussion
The approaches and tests that you have noted will depend upon your setting and context. If you’re not sure what types of tests are used in your area, you might like to discuss this with colleagues.
2.2 How can WGS surveillance supplement phenotypic surveillance?
