TABLE 3.
PAduplex PCR, API 20NE, ARDRA, and partial 16S rRNA gene sequencing results for the 58 isolates that were discordant or negative by the PAduplex PCR assay
| Group | No. of isolates | No. of patients | Result
|
Final identification | |||||
|---|---|---|---|---|---|---|---|---|---|
| PAduplex PCR
|
Oxidasea | API 20NE | ARDRA | Partial 16S rRNA gene sequencing | |||||
| gyrB | ecfX | ||||||||
| 1 | 3 | 1 | − | − | + | Alcaligenes faecalis (59.3%); low discrimination level | A. xylosoxidans | Not performed | Achromobacter xylosoxidans |
| 13 | 8 | − | − | + | Achromobacter xylosoxidans (94.5%); excellent or good identification | A. xylosoxidans | Not performed | Achromobacter xylosoxidans | |
| 1 | 1 | − | − | + | Burkholderia pseudomallei (81.7%); very good identification to the genus level | A. xylosoxidans | Not performed | Achromobacter xylosoxidans | |
| 1 | 1 | − | − | + | Mannheimia hemolytica/Pastuerella trehalosi (92.9%); good identification | A. xylosoxidans | Not performed | Achromobacter xylosoxidans | |
| 1 | 1 | − | − | + | Pseudomonas stutzeri (76.0%); doubtful profile | A. xylosoxidans | Not performed | Achromobacter xylosoxidans | |
| 1 | 1 | − | − | + | Unacceptable profile | A. xylosoxidans | Not performed | Achromobacter xylosoxidans | |
| 1 | 1 | − | − | + | Comamonas testosteroni/Pseudomonas alcaligenes (57.4%); low discrimination level | A. xylosoxidans | Not performed | Achromobacter xylosoxidans | |
| Total | 21 | 14 | |||||||
| 2 | 5 | 3 | − | − | − | Stenotrophomonas maltophilia (99.9%); excellent or very good identification | S. maltophilia | Not performed | Stenotrophomonas maltophilia |
| 6 | 2 | − | − | − | Stenotrophomonas maltophilia (99.9%); doubtful profile | S. maltophilia | Not performed | Stenotrophomonas maltophilia | |
| 1 | 1 | − | − | − | Unacceptable profile | S. maltophilia | Not performed | Stenotrophomonas maltophilia | |
| 1 | 1 | − | − | − | Weeksella virosa/Empedobacter brevis (64.0%); low discrimination level | S. maltophilia | Not performed | Stenotrophomonas maltophilia | |
| 2 | 1 | − | − | − | Stenotrophomonas maltophilia (99.9%); excellent identification | Indeterminate | Stenotrophomonas maltophilia (100%); 815 bp | Stenotrophomonas maltophilia | |
| Total | 15 | 8 | |||||||
| 3 | 1 | 1 | + | − | + | Burkholderia cepacia (99.9%); good identification, possibility of B. gladioli | P. aeruginosa | Pseudomonas aeruginosa (100%); 723 bp | Pseudomonas aeruginosa |
| 2 | 1 | + | − | + | Pseudomonas aeruginosa (97.9%); acceptable identification | P. aeruginosa | Pseudomonas aeruginosa (100%); 787 bp | Pseudomonas aeruginosa | |
| 1 | 1 | + | − | + | Unacceptable profile | P. aeruginosa | Pseudomonas aeruginosa (100%); 782 bp | Pseudomonas aeruginosa | |
| 1 | 1 | − | + | + | Pseudomonas aeruginosa (99.9%); very good identification | P. aeruginosa | Pseudomonas aeruginosa (100%); 870 bp | Pseudomonas aeruginosa | |
| 2 | 1 | − | − | + | Pseudomonas fluorescens (99.9%); very good identification | Indeterminate | Pseudomonas fluorescens/synxantha/reactans (100%); 827bp | Pseudomonas spp. | |
| 1 | 1 | − | − | + | Pseudomonas stutzeri (99.2%); very good identification | Indeterminate | Pseudomonas mendocina (100%); 793 bp | Pseudomonas mendocina | |
| Total | 8 | 6 | |||||||
| 4 | 1 | 1 | − | − | − | Pseudomonas luteola (92.0%); acceptable identification | Indeterminate | Pantoea agglomerans (100%); 867 bp | Pantoea agglomerans |
| 4 | 2 | − | − | + | Sphingomonas paucimobilis (96.8%); good identification | I. limosus | Not performed | Inquilinus limosus | |
| 3 | 1 | − | − | + | Rhizobium radiobacter (99.9%); very good identification | Indeterminate | Rhizobium radiobacter (100%); 864 bp | Rhizobium radiobacter | |
| 2 | 1 | − | − | + | Watersia paucula (47.6%); low discrimination level | Indeterminate | Cupriavidus respiraculi (100%); 824 bp | Cupriavidus respiraculi | |
| 2 | 2 | − | − | − | Unacceptable profile | Indeterminate | Serrata marcescens (100%); 751 bp | Serrata marcescens | |
| 1 | 1 | − | − | − | Burkholderia cepacia (99.9%); excellent identification, possibility of B. gladioli | B. gladioli | Not performed | Burkholderia gladioli | |
| 1 | 1 | − | − | + | Methylobacterium mesophilicum (84.5%); acceptable identification, possibility of Ochrobactrum anthropi | Indeterminate | Ralstonia mannitolilytica (100%); 803 bp | Ralstonia mannitolilytica | |
| Total | 14 | 9 | |||||||
a
A positive oxidase test was recorded only if an isolate produced a violet to purple pigment within 10 to 15 s.