TABLE 1.
Genotypic and phenotypic identification of 147 isolates not belonging to the ACB complex
| Genomic speciesa (species) as determined by:
|
No. of isolates | |||
|---|---|---|---|---|
| ARDRA | Phenotypic identificationb using probability matrices of:
|
Consensus identificationc | ||
| Gerner-Smidt et al. (14) | Bouvet and Grimont (15) | |||
| 4 or 13BJ/14TUd | 4 | 4 | 4 (A. haemolyticus) | 4 |
| 4 or 13BJ/14TUd | 4 | Unidentified | 4 (A. haemolyticus) | 2 |
| 5 | 5 | 5 | 5 (A. junii) | 5 |
| 7 | 7 | 7 | 7 (A. johnsonii) | 4 |
| 8/9 | 8 | 8/9 | 8/9 (A. lwoffii) | 29 |
| 8/9 | 8 or 15TUe | 8/9 | 8/9 (A. lwoffii) | 25 |
| 8/9 | Unidentified | 8/9 | 8/9 (A. lwoffii) | 1 |
| 8/9 | 8 | Unidentified | 8/9 (A. lwoffii) | 1 |
| 10 | 10 | 10 | 10 | 3 |
| 11 | 11 | 11 | 11 | 1 |
| 11 | 11 | Unidentified | 11 | 1 |
| 12 | 12 | Unidentified | 12 (A. radioresistens) | 4 |
| 13BJ/14TU | 14TU | 13BJ | 13BJ/14TU | 6 |
| 4 or 13BJ/14TUd | Unidentifiedf | 13BJ | 13BJ/14TU | 1 |
| 15TU | 15TU | Unidentified | 15TU | 1 |
| 16 | Unidentified | 16 | 16 | 1 |
| 6 | Unidentifiedg | Unidentifiedg | 6 | 1 |
| 4 or 7 or 13BJ/14TUh | 7 | 7 | 7 (A. johnsonii) | 2 |
| 4 or 7 or 13BJ/14TUh | Unidentified | 7 | 7 (A. johnsonii) | 1 |
| 8/9i | 8 | 8/9 | 8/9 (A. lwoffii) | 4 |
| 8/9i | 8 or 15TUe | 8/9 | 8/9 (A. lwoffii) | 2 |
| 8/9i | 8 or 15TUe | Unidentified | 8/9 (A. lwoffii) | 1 |
| 4 or 13BJ/14TUd | Unidentifiedf | Unidentified | 13BJ/14TU | 1 |
| 4 or 13BJ/14TUd | 6 | 13BJ | 13BJ/14TU | 1 |
| 5 | 4 | 4 | Unidentified | 1 |
| 13BJ/14TU | 4 | 4 | Unidentified | 1 |
| 13BJ/14TU | 4 | Unidentified | Unidentified | 1 |
| Unidentified | 8 or 15TUe | 8/9 | Unidentified | 1 |
| Unidentified | 8 or 15TUe | Unidentified | Unidentified | 3 |
| Unidentified | 15TU | Unidentified | Unidentified | 2 |
| Unidentified | Unidentified | Unidentified | Unidentified | 36 |
Genomic species are numbered according to Bouvet and Grimont (5) (no suffix), Bouvet and Jeanjean (7) (suffix BJ), or Tjernberg and Ursing (25) (suffix TU).
For an explanation of phenotypic identification and numerical probabilistic identification, see Materials and Methods.
Criteria for consensus identification are given in Results. According to these criteria, 89 isolates were unambiguously identified, 13 isolates were presumptively identified, and 45 isolates remained unidentified. These three groups appear, respectively, in the three major blocks in the table [i.e., results of consensus identification 4 (A. haemolyticus) to 16, 6 to 13BJ/14TU, and unidentified].
Genomic species 4 and 13BJ/14TU cannot be differentiated; CfoI, AluI, MboI, RsaI, MspI, and BfaI patterns are common to both these genomic species (10).
Genomic species 8 and 15TU cannot be differentiated (14); the sum of their ISs is ≥0.95.
Identified as genomic species 14TU (0.95 > IS ≥0.90).
Biochemical properties intermediate between those of A. haemolyticus and genomic species 6.
CfoI, AluI, MboI, RsaI, and MspI patterns as in genomic species 4, 7, and 13BJ/14TU, but BfaI pattern is aberrant (10).
CfoI, AluI, MboI, RsaI, and MspI patterns specific for A. lwoffii, except for one additional fragment in AluI pattern 3.