7 Genotypic versus phenotypic methods
Activity 8 Advantages and disadvantages of each approach
Complete Table 4 below then compare with the example answer.
| Comparator | Phenotypic tests | Genotypic tests |
|---|---|---|
| Speed | ||
| Equipment | ||
| Cost | ||
| Can be used for | ||
| Suitable for laboratory type | ||
| Other Advantages |
Discussion
| Comparator | Phenotypic tests | Genotypic tests |
|---|---|---|
| Speed | Culture-based tests take 24 hours Some tests, e.g. lateral flow testing, nitrocefin testing, may take only 10-15 minutes. |
Variable: PCR gives results within hours but WGS can take days to read and interpret results. |
| Equipment | Only simple requirements. | Complex – require maintenance. |
| Cost | Low – though still more than basic AST. | High – expensive equipment and maintenance. Reagents are also expensive. |
| Can be used for | Detection of mechanisms in routine clinical and veterinary practice. | Rapid PCR can detect known genes WGS can characterise new ones, but still needs to be carried out in conjunction with phenotypic testing. |
| Suitable for laboratory type | Standard clinical or veterinary diagnostic microbiology laboratory (first line). | Rapid PCR suitable for some diagnostic laboratories. Other tests done in research or reference laboratories (second line). |
| Other Advantages | Clinically useful in real time to guide antimicrobial use, infection control etc.. Does not require prior knowledge of the precise resistance genes. Can perform more tests at one time. |
Use in Epidemiology and Public health: e.g. can distinguish between mechanisms which are likely to spread and those that are not. Use of rapid PCR for hospital infection control to enable measures to be taken quickly e.g. isolating a patient with a carbapenemase-producing organism. |
6.2 Genome sequencing techniques
