Pneumocystis jiroveci Internal Transcribed Spacer Types in Patients Colonized by the Fungus and in Patients with Pneumocystosis from the Same French Geographic Region

Gilles Nevez; Anne Totet; Vincent Jounieaux; Jean-Luc Schmit; Eduardo Dei-Cas; Christian Raccurt

doi:10.1128/JCM.41.1.181-186.2003

DOI: 10.1128/JCM.41.1.181-186.2003

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Tables

TABLE 1.

Characteristics of 6 patients colonized by P. jiroveci and 11 patients who developed PCP, for all of whom the fungus detected in BAL fluids was typed

Patient no.	Age	Sex^a	Date of BAL (mo-day-yr)	Underlying condition(s)	T-cell count^b		Clinical presentation of P. jiroveci infection (alternative diagnosis of PCP, duration of follow-up without PCP)
Patient no.	Age	Sex^a	Date of BAL (mo-day-yr)	Underlying condition(s)	CD4⁺/CD8⁺	CD4⁺ (10⁶/liter)
A.6	64	F	03-06-96	Myeloma	0.97	185	Pulmonary colonization (bacterial pneumonia, 3 months)
A.9^c	44	M	03-08-96	Panhypopituitarism	0.46	389	Pulmonary colonization (sarcoidosis, 12 months)
A.10	44	F	03-13-96	Renal transplantation	ND	ND	Pulmonary colonization (bacterial pneumonia, 12 months)
A.20	44	F	04-17-96	HIV infection	0.08	6	PCP
A.36	35	M	05-22-96	HIV infection	0.18	31	PCP
A.64	33	M	08-30-96	HIV infection	0.06	108	PCP
A.93	50	M	02-06-97	HIV infection	0.19	59	PCP
N.20^d	85	F	05-30-97	Chronic obstructive pulmonary disease	1.8	968	Pulmonary colonization (exacerbation of chronic bronchitis, 6 months)
N.24	52	F	07-09-97	Systemic lupus erythematosus	0.60	569	Pulmonary colonization (pulmonary lymphoma, 32 months)
N.28	67	M	07-17-97	HIV infection	0.20	68	PCP
N.60	29	F	10-03-97	Systemic lupus erythematosus, long-term corticosteroid treatment	0.97	332	PCP
N.61	34	M	01-26-98	HIV infection	0.04	7	PCP
N.51	41	F	03-26-98	Chronic lymphoid leukemia	1.64	71	Pulmonary colonization (bacterial pneumonia, 16 months)
N.50	60	M	05-20-98	Pemphigus vulgaris, long-term cortico- steroid treatment	0.92	638	PCP
N.69	33	M	11-27-98	HIV infection	0.09	17	PCP
N.70	35	M	02-18-99	Hepatic granulomatosis, long-term corticosteroid treatment	ND	ND	PCP
N.71	40	F	03-03-99	HIV infection	0.09	22	PCP

↵ a F, female; M, male.
↵ b The normal values were as follows: for CD4⁺/CD8⁺ T cells, >1; for CD4⁺ T cells, >600. ND, not done.
↵ c The case of patient A.9 was previously reported in reference 29.
↵ d Patient N.20 was the only immunocompetent colonized patient.

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 locus^a:										Type(s)	C^b 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’a₃^c	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.
↵ c The ITS1 allele designated ‘A’ differs from the A₂ and A₃ previously described (37, 38) by having T residues at positions 2 and 16.
↵ d The ITS2 allele designated ‘b’ (GenBank accession number AF498265 ) differs from the b₁ previously described (38) by having an A residue at position 176.