TABLE 2.
Species identifications of 94 clinical Nocardia isolates by secA1 gene sequencing where species assignment was concordant with partial 16S rRNA gene sequencing
| Species identification (606-bp 16S rRNA gene) | No. of isolates | Sequence similarity to reference sequences |
||
|---|---|---|---|---|
| secA1 gene [bp (%)] | SecA1 amino acid [bp (%)] | 606-bp 16S rRNA gene (%) | ||
| N. abscessus | 1 | 469/470 (99.8) | 156/156 (100) | 100 |
| N. arthritidis | 1 | 463/470 (98.5) | 156/156 (100) | 604/606 (99.7) |
| N. asteroides | 1 | 470/470 (100) | 156/156 (100) | 100 |
| 1 | 458/470 (97.4) | 156/156 (100) | 600/606 (99.0) | |
| N. beijingensis | 1 | 469/470 (99.8) | 156/156 (100) | 100 |
| N. brasiliensis | 2 | 466/470 (99.1) | 155/156 (99.4) | 604/606 (99.7) |
| 2 | 465/470 (98.9) | 155/156 (99.4) | 604/606 (99.7) | |
| 1 | 464/470 (98.7) | 155/156 (99.4) | 604/606 (99.7) | |
| 1 | 459/470 (97.6) | 154/156 (98.7) | 603/606 (99.5) | |
| 1 | 460/470 (97.9) | 154/156 (98.7) | 602/606 (99.3) | |
| N. cyriacigeorgica | 3 | 470/470 (100) | 156/156 (100) | 100 |
| 2a | 467/470 (99.4) | 156/156 (100) | 100 | |
| 1 | 465/470 (98.9) | 156/156 (100) | 100 | |
| 1 | 463/470 (98.5) | 153/156 (98.1) | 100 | |
| 1 | 461/470 (98.1) | 155/156 (99.4) | 100 | |
| 10a | 459/470 (97.6) | 156/156 (100) | 100 | |
| 7a | 458/470 (97.4) | 155/156 (99.4) | 100 | |
| 1 | 457/470 (97.2) | 155/156 (99.4) | 100 | |
| 1 | 456/470 (97.0) | 154/156 (98.7) | 100 | |
| 1 | 454/470 (96.6) | 154/156 (98.7) | 100 | |
| 1 | 459/470 (97.6) | 156/156 (100) | 605/606 (99.8) | |
| 5a | 458/470 (97.4) | 155/156 (98.7) | 605/606 (99.8) | |
| N. farcinica | 7a | 469/470 (99.8) | 156/156 (100) | 100 |
| 5a | 468/470 (99.6) | 156/156 (100) | 100 | |
| 1 | 467/470 (99.4) | 156/156 (100) | 100 | |
| 1 | 468/470 (99.6) | 156/156 (100) | 605/606 (99.8) | |
| 1 | 468/470 (99.6) | 156/156 (100) | 604/606 (99.7) | |
| N. nova | 4 | 470/470 (100) | 156/156 (100) | 100 |
| 2 | 469/470 (99.8) | 156/156 (100) | 100 | |
| 1 | 470/470 (100) | 156/156 (100) | 605/606 (99.8) | |
| 1 | 467/470 (99.4) | 156/156 (100) | 604/606 (99.7) | |
| 1 | 466/470 (99.1) | 156/156 (100) | 604/606 (99.7) | |
| 1 | 470/470 (100) | 156/156 (100) | 602/606 (99.3) | |
| N. otitidiscaviarum | 2 | 470/470 (100) | 156/156 (100) | 100 |
| 1 | 469/470 (99.8) | 156/156 (100) | 100 | |
| 1 | 467/470 (99.4) | 156/156 (100) | 100 | |
| N. paucivorans | 7 | 469/470 (99.8) | 156/156 (100) | 606/608 (99.7) |
| N. thailandica | 1 | 467/468 (99.8) | 155/156 (98.7) | 100 |
| N. veterana | 2 | 469/470 (99.8) | 156/156 (100) | 100 |
| 2 | 468/470 (99.6) | 156/156 (100) | 100 | |
| 2 | 467/470 (99.4) | 156/156 (100) | 100 | |
| 1 | 465/470 (98.9) | 156/156 (100) | 100 | |
| 1 | 437/470 (93.0) | 154/156 (98.7) | 100 | |
| 1b | 430/470 (91.5) | 155/156 (99.4) | 599/606 (98.8) | |
| 1c | 437/470 (93.0) | 155/156 (99.4) | 596/606 (98.3) | |
| N. vinacea | 1 | 466/470 (99.1) | 156/156 (100) | 100 |
a
Strains with the same percentage sequence similarity but with one or more strains yielding nucleotide heterogeneity and hence representing a different sequence type of the secA1 gene(see Table S1 in the supplemental material).
b
The 16S rRNA gene sequence was 98.8% similar to archived N. veterana 16S rRNA gene sequences in the GenBank database. SecA1 amino acid analysis identified the isolate as N. veterana.
c
The 16S rRNA gene sequence was 98.3% similar to archived N. veterana 16S rRNA gene sequences in the GenBank database. SecA1 amino acid analysis identified the isolate as N. veterana.