Table 2.
Biochemical and molecular methods used for reference identification
| Final identification | No. of isolates | Initial identification method |
Final reference identification method |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Conventional biochemical | Automated system | API 20 NE | 16S rRNA gene sequencing | PCR | Conventional biochemical | Automated system | API 20 NE | 16S rRNA gene sequencing | PCR | ||
| Achromobacter spp. | 12 | 4a | 7 | 1 | 12 | ||||||
| Achromobacter xylosoxidans | 3 | 3 | 3 | ||||||||
| Burkholderia cepacia complex (BCC) | |||||||||||
| B. cenocepacia | 4 | 4 | 4 | ||||||||
| B. multivorans | 10 | 10 | 10 | ||||||||
| Species indeterminate | 2 | 1 | 1 | 1 | 1 | ||||||
| Burkholderia gladioli | 2 | 2 | 2 | ||||||||
| Burkholderia sp. | 1 | 1b | 1 | ||||||||
| Bordetella petrii | 1 | 1 | 1 | ||||||||
| Bordetella bronchiseptica | 2 | 2 | 2 | ||||||||
| Capnocytophaga gingivalis | 1 | 1c | 1 | ||||||||
| Capnocytophaga sputigena | 1 | 1c | 1 | ||||||||
| Cellulomonas hominis | 1 | 1d | 1 | ||||||||
| Chryseobacterium indologenes | 2 | 1 | 1 | 1 | 1 | ||||||
| Chryseobacterium sp. | 1 | 1e | 1 | ||||||||
| Elizabethkingia meningoseptica | 1 | 1 | 1 | ||||||||
| Herbaspirillum seropedicae | 1 | 1 | 1 | ||||||||
| Pandoraea sp. | 1 | 1 | 1 | ||||||||
| Pantoea agglomerans | 1 | 1f | 1 | ||||||||
| Pseudomonas aeruginosa | 73 | 51 | 4g | 5h | 13 | 51 | 2 | 20 | |||
| Pseudomonas aeruginosa, mucoid | 16 | 14 | 2 | 14 | 2 | ||||||
| Pseudomonas pseudoalcaligenes | 1 | 1i | 1 | ||||||||
| Pseudomonas spp. | 3 | 1j | 2 | 3 | |||||||
| Ralstonia mannitolilytica | 1 | 1 | 1 | ||||||||
| Ralstonia spp. | 2 | 2 | 2 | ||||||||
| Roseomonas sp. | 1 | 1k | 1 | ||||||||
| Sphingomonas roseiflava | 1 | 1l | 1 | ||||||||
| Stenotrophomonas maltophilia | 55 | 51 | 1m | 3 | 39 | 16 | |||||
| Total | 200 | 67 | 59 | 25 | 31 | 18 | 65 | 41 | 11 | 66 | 17 |
API identifications of A. xylosoxidans (“excellent”; n = 2), Alcaligenes (Achromobacter) spp. (faecalis 59%/denitrificans 31%; n = 1), and Burkholderia (Ralstonia) pickettii (“good”; n = 1).
API “acceptable” identification as Ralstonia pickettii.
RapID ANA identification as Capnocytophaga species.
API “very good” identification as Sphingomonas paucimobilis.
API “good” identification as Chryseobacterium indologenes.
API “very good” identification as Pseudomonas luteola.
Four isolates with Vitek 2 identification as Pseudomonas fluorescens.
Three isolates with API “good” identifications as Psychrobacter phenylpyruvicus (n = 2) and Ralstonia pickettii (n = 1).
Vitek 2 identification as Pseudomonas stutzeri.
API “good” identification as Alcaligenes faecalis.
Vitek 2 identification as Bordetella bronchiseptica.
API “good” identification as Sphingomonas paucimobilis.
API “acceptable” identification as Brevundimonas vesicularis.