TABLE 2.
Comparison of three examined phenotyping methods in this studya
| Assessment indicator | Serotyping | AMR profile | MIC profile |
|---|---|---|---|
| Repeatability | Good | Moderate | Moderate |
| Reproducibility | Moderateb | Moderate | Poor |
| Discriminatory power (DI)c | 0.7820 | 0.9940 | 1 |
| Discriminated types | 9 | 51 | 61 |
| Scheme standardized or notd | Yes | No | No |
| Ease of interpretation of data generatede | Good | Excellent | Excellent |
| Ease of use | Poor to moderatef | Good to moderateg | Poor to moderateh |
| Throughput | No | Yes | Yes |
| Cost | Moderate to highi | Moderate to highj | High |
| Time required (days)k | 2~17# (usually > 5 days for expt) (13) | 3 | 3 |
Ranking: 1. DI in order (good to poor): MIC profile = wgMLST > CoreSNP > AMR profile > CRISPR-MVLST > VF gene profile > AMR gene profile > plasmid profile > cgMLST > CRISPR > MLST > serotyping. 2. Ease of use (good to poor): CRISPR > CRISPR-MVLST > MLST > cgMLST = wgMLST > plasmid profile = AMR gene profile = VF gene profile = CoreSNP > AMR profile = MIC profile = serotyping. 3. Cost (low to high): CRISPR < CRISPR-MVLST < MLST = VF gene profile = AMR gene profile = plasmid profile < wgMLST = cgMLST = coreSNP < AMR profile < serotyping < MIC profile. 4. Time required (short to long): MLST < CRISPR < CRISPR-MVLST < AMR profile = MIC profile < plasmid profile = VF gene profile = AMR gene profile < wgMLST < CoreSNP = cgMLST < serotyping.
We summarized three phenotyping methods in a similar manner of a previous study (28).
Using the Discriminatory index (DI) for a description of discriminatory power.
If there is 1~2 universally acknowledged standard for this typing or not.
Intended as unequivocal interpretation.
Using in silico prediction will be easier and faster.
Using disc agar diffusion test will be easier.
Become easier if the lab is doing antimicrobial resistance-related research.
Using in silico prediction will be cheaper.
Using disc agar diffusion test will be more affordable.
The approximate number of days to get typing results is estimated by excluding the interval of time to obtain a single pure colony suitable to be handled by the method.