Table 3.
Description of genotypes for phylogroup assignment.1
| Phylogroup | Quadruplex genotype |
|||
|---|---|---|---|---|
| arpA | chuA | yjaA | TspE4.C2 | |
| A | + | − | − | − |
| B1 | + | − | − | + |
| F | − | + | − | − |
| B2 | − | + | + | − |
| B2 | − | + | + | + |
| B2 | − | + | − | + |
| A or C | + | − | + | − |
| D or E | + | + | − | − |
| D or E | + | + | − | + |
| E or clade I | + | + | + | − |
| Clade I or II | − | − | + | − |
| Clade III, IV or V | − | 4762 | − | − |
| Unknown3 | − | − | − | + |
| Unknown | − | − | + | + |
| Unknown | + | − | + | + |
| Unknown | + | + | + | + |
1
Reference (Clermont et al., 2013).
2
The quadruplex PCR reaction can result in strains belonging to cryptic clade III, IV or V yielding a 476 bp PCR product. If this is the case, such strains should be screened using the cryptic clade detection primers (Clermont et al., 2011b).
3
These unassignable strains represent phylogroups that are very rare or are the results of large-scale recombinations and therefore untypable unless multilocus sequence typing (MLST) is performed.