Table 2.

Results of genotyping of P. jirovecii at the eight loci^a

Patient no.	Sample typeb	Genotype determined in each locus
		ITS1	CYB	mt26S	SOD	26S	β-TUB	DHFR	DHPS	Multilocus genotype
1	BAL	B	CYB 1	8	SOD 2	5	β-TUB 3	WTd	WT	A
2	BAL	B1	CYB 2	7	SOD 1	1	β-TUB 3	WT	WT	B
3	BAL	B5	CYB 1	8	SOD 2	1	β-TUB 3	WT	WT	C
4	BAL	B	CYB 9	7	SOD 2	8	β-TUB 3	DHFR 312	WT	D
5f	BAL	A5	CYB 1	8	SOD 2+ SOD 1	5	β-TUB 1	DHFR 312	WT	Mixede
6	BAL	B	CYB 1	2	SOD 2	5	β-TUB 3	DHFR 201	WT	E
7	BAL	B2	CYB 1	7	SOD 1	1	β-TUB 1	WT	WT	F
8	BAL	B1	CYB 2	3	SOD 1	NDc	β-TUB 1	DHFR 312	WT	G
9	BAL	ND	CYB 7	8	SOD 2	5	β-TUB 3	DHFR 312	WT	H
10	BAL	B	CYB 2	7	SOD 1	5	β-TUB 1	WT	WT	I
11	BAL	ND	CYB 2 + CYB 8	7 + 3	SOD 2	ND	β-TUB 1 + β-TUB 3	DHFR 312	WT	Mixed
12	BAL	B2	CYB 5	7	SOD 1	1	β-TUB 1	WT	WT	J
13	BAL	A3	CYB 8	8	SOD 2	5	β-TUB 3	WT	WT	K
14	BAL	A3	CYB 2	3	SOD 1	5	β-TUB 3	WT	WT	L
15	BAL	A4	CYB 2	8	SOD 1	5	β-TUB 3	WT	WT	M
16	BAL	B3	CYB 1	2	SOD 1	9	β-TUB 1	WT	WT	N
17	BAL	A4	CYB 6	8	SOD 2	10	β-TUB 3	WT	WT	O
18	BAL	A3	CYB 1 + CYB 2	3	SOD 1	5	β-TUB 1	WT	WT	Mixed
19	TRA	A3	CYB 1	3	SOD 1	5	β-TUB 1	DHFR 312	ND	P
20	BAL	A4	CYB 6	2	SOD 2	ND	β-TUB 1 + β-TUB 3	ND	WT	Mixed
21	BAL	B1	CYB 1	8	SOD 5	5	β-TUB 3	WT	WT	Q
22	BAL	B1	CYB 8	7	SOD 1	5	β-TUB 1 + β-TUB 3	WT	WT	Mixed
23	BAL	B	CYB 8	2	SOD 2	5	β-TUB 1	WT	WT	R
24	BAL	A3	CYB 2	3	ND	5	β-TUB 3	ND	WT	L
25	BAL	B	CYB 2	8	SOD 5	6	β-TUB 3	WT	WT	S
26	BAL	B	CYB 1 + CYB 6	2	SOD 1	1 + 5	β-TUB 1	WT	WT	Mixed
27	BAL	B	CYB 8	8	SOD 1	5	β-TUB 1	ND	WT	T
28	BAL	B	CYB 7	7	SOD 1	5	β-TUB 1	WT	WT	U
29	BAL	ND	CYB 1 + CYB 7	7	SOD 1	1 + 5	β-TUB 3	WT	WT	Mixed
30	SPU	ND	CYB 1	7 + 8 + 2	SOD 2	5	β-TUB 1 + β-TUB 3	DHFR WT + DHFR312	WT	Mixed
31	BAL	B6	CYB 1	7	SOD 2	7	β-TUB 1	WT	WT	V
32	BAL	B	CYB 3 + CYB 1	7 + 8	SOD 4 + SOD 3	5	β-TUB 1	WT	WT	Mixed
33	BAL	ND	CYB 8	7 + 3	SOD 1	ND	β-TUB 1	WT	WT	Mixed

^aNew genotypes are underlined.

^bBAL, bronchoalveolar lavage fluid; TRA, tracheal aspiration; SPU, sputum.

^cND, not determined.

^dWT, wild type.

^eMixed, more than one P. jirovecii genotype. For each sample or patient displaying a mixed genotype, the putative combination of genotypes is given.

^fThe ITS1 genotype observed for patient 5 (T/2, TT/8–10, A/11, T/17, T/22, TC/46–47, 10 × T/54–62, GG/70–71, TTA/111–113) that has been previously reported but never designated was therefore named A5.