TABLE 2.
Identification of P. jiroveci ITS types in 6 patients colonized by the fungus and in 11 patients who developed PCP in the University Hospital, Amiens, France
| Patient no. | Clone no. | Nucleotide(s) at indicated position(s) in locusa:
|
Type(s) | Cb or PCP | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ITS1
|
ITS2
|
||||||||||||
| 2 | 16 | 74-75 | 111-113 | 54-56 | 63 | 67-71 | 122 | 169-172 | 176 | ||||
| A.6 | A6.4 | T | A | AG | TTA | TAA | - | AATAT | - | ---- | G | B2a1 | C |
| A.9 | A9.1 | T | T | -- | TTA | TAA | - | AATAA | - | ---- | A | ‘A’a3c | C |
| A9.2 | T | T | -- | TTA | TAA | - | AATAA | - | ---- | A | ‘A’a3 | ||
| A9.3 | T | T | -- | TTA | TAA | - | AATAA | - | ---- | A | ‘A’a3 | ||
| A.10 | A10.1 | T | T | AG | TTA | TAA | - | AATAA | - | ---- | A | B1a3 | C |
| A10.3 | T | T | AG | TTA | TAA | - | AATAA | - | ---- | A | B1a3 | ||
| A10.5 | T | T | AG | TTA | TAA | - | AATAA | - | ---- | A | B1a3 | ||
| A.20 | A20.1 | T | T | -- | TTA | TAA | - | AATAA | - | ---- | A | ‘A’3 | PCP |
| A20.2 | T | T | AG | TTA | TAA | - | AATAA | - | ---- | A | B1a3 | ||
| A.36 | A36.2 | T | A | AG | TTA | TAA | - | AATAT | - | ---- | G | B2a1 | PCP |
| A36.3 | T | A | AG | TTA | TAA | - | AATAT | - | ---- | G | B2a1 | ||
| A36.7 | T | A | AG | TTA | TAA | - | AATAT | - | ---- | G | B2a1 | ||
| A.64 | A64.1 | C | T | -- | TTA | TAA | - | AATAT | - | ---- | A | A2a4 | PCP |
| A64.2 | T | A | -- | TTA | TAA | - | AATAT | - | ---- | A | A3a4 | ||
| A64.3 | C | T | -- | TTA | --- | A | ----- | - | ---- | A | A2c1 | ||
| A.93 | A93.2 | T | A | AG | TTA | TAA | - | AATAT | - | ---- | G | B2a1 | PCP |
| A93.3 | T | A | AG | TTA | TAA | - | AATAT | - | ---- | G | B2a1 | ||
| A93.6 | T | A | AG | TTA | TAA | - | AATAA | - | ---- | A | B2a3 | ||
| A93.8 | T | A | AG | TTA | TAA | - | AATAT | - | ---- | G | B2a1 | ||
| N.20 | N20.2 | T | A | AG | TTA | TAA | - | AATAT | - | ---- | G | B2a1 | C |
| N20.7 | T | A | AG | TTA | TAA | - | AATAT | - | ---- | G | B2a1 | ||
| N.24 | N24.1 | T | T | AG | TTA | TAA | - | AATAA | - | ---- | A | B1a3 | C |
| N24.2 | T | T | AG | TTA | TAA | - | AATAA | - | ---- | A | B1a3 | ||
| N24.4 | T | A | -- | TTA | TAA | - | AATAA | - | ---- | A | A3a3 | ||
| N.28 | N28.1 | T | T | AG | TTA | TAA | - | AATAT | C | --AT | G | B1b2 | PCP |
| N28.9 | T | T | AG | TTA | TAA | - | AATAT | C | --AT | G | B1b2 | ||
| N28.10 | T | T | AG | TTA | TAA | - | AATAT | C | --AT | G | B1b2 | ||
| N.60 | N60.3 | T | T | AG | TTA | TAA | - | AATAA | - | ---- | A | B1a3 | PCP |
| N60.6 | T | T | AG | TTA | TAA | - | AATAA | - | ---- | A | B1a3 | ||
| N60.9 | T | T | AG | TTA | TAA | - | AATAA | - | ---- | A | B1a3 | ||
| N.61 | N61.6 | C | T | -- | TTA | --- | A | ----- | - | ---- | A | A2c1 | PCP |
| N61.7 | C | T | -- | TTA | --- | A | ----- | - | ---- | A | A2c1 | ||
| N61.10 | C | T | -- | TTA | --- | A | ----- | - | ---- | A | A2c1 | ||
| N.51 | N51.1 | T | T | AG | TTA | TAA | - | AATAA | - | ---- | A | B1a3 | C |
| N51.6 | T | T | AG | TTA | TAA | - | AATAA | - | ---- | A | B1a3 | ||
| N51.7 | T | A | -- | TTA | TAA | - | AATAA | - | ---- | A | A3a3 | ||
| N.50 | N50.2 | T | A | AG | TTA | TAA | - | AATAT | - | ---- | G | B2a1 | PCP |
| N50.5 | T | A | AG | TTA | TAA | - | AATAT | - | ---- | G | B2a1 | ||
| N.69 | N69.1 | C | T | -- | TTA | --- | A | ----- | - | ---- | A | A2c1 | PCP |
| N69.2 | C | T | -- | TTA | TAA | - | AATAT | - | ---- | A | A2a4 | ||
| N69.4 | C | T | -- | TTA | TAA | - | AATAT | - | --AT | A | A2‘b’d | ||
| N.70 | N70.2 | T | A | AG | TTA | TAA | - | AATAA | - | ---- | A | B2a3 | PCP |
| N70.3 | T | T | AG | TTA | TAA | - | AATAT | - | --AT | G | B1b1 | ||
| N70.4 | T | A | AG | TTA | TAA | - | AATAT | - | --AT | G | B2b1 | ||
| N.71 | N71.1 | T | A | -- | TTA | TAA | - | AATAA | - | ---- | G | A3a2 | PCP |
| N71.2 | T | T | -- | TTA | TAA | - | AATAA | - | ---- | A | ‘A’a3 | ||
| N71.3 | T | T | -- | TTA | TAA | - | AATAA | - | ---- | A | ‘A'a3 | ||
| N71.4 | T | T | -- | TTA | TAA | - | AATAA | - | ---- | G | ‘A'a2 | ||
| N71.5 | T | A | AG | TTA | TAA | - | AATAT | - | ---- | G | B2a1 | ||
a
Scoring positions are described in references 37 and 38; complete sequence data are available upon request from the authors. Each dash represents one position for which the nucleotide is not specified.
b
C, colonized.