Genotyping and Coalescent Phylogenetic Analysis of Pneumocystis jiroveci from South Africa

DOI: 10.1128/JCM.42.4.1505-1510.2004

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FIG. 1.
Alignment of new ITS1 sequences. GenBank accession numbers are AY328043 to AY328053 for sequences I to XI, respectively.
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FIG. 2.
Alignment of new ITS2 sequences. The GenBank accession number for type u is AY328054 ; the GenBank accession numbers for sequences 1 to 12 are AY328055 to AY328066 , respectively.
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FIG. 3.
Resultant ITS haplotype network derived from Table 2 by coalescent theory (15). Lines connecting haplotypes are equivalent to one mutational difference, with empty nodes representing haplotypes not found in the population. Haplotype subdivisions incorporating insertion-deletion (indel) information (one indel is depicted by a connecting line) are shown in boxed haplotypes Eg and Ge.
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FIG. 4.
ITS haplotype network focusing on samples from twins who presented concurrently with PCP. Lines connecting haplotypes are equivalent to one mutational difference, with empty nodes representing haplotypes not found in the population.
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FIG. 5.
Alignment of new 5.8S rDNA sequences. The GenBank accession numbers are as follows: A to M, AY328067 to AY328078 and AY330724 , respectively; P. ratti, L27658 ; P. macaca, AF288848 ; P. jiroveci (P. carinii f. sp. hominis), AF013954 .

TABLE 1.

ITS types demonstrated from 20 specimens^a

Specimen	ITS type(s) obtained from each specimen
1	Eg, Eu
2^b^,^c	Je, Ne, Ig, Eo, Eg, IIg
3^b^,^c	Eg, IIIg, IV1, Ng
4^c	Eg, Ge, No
5	Gb, Eb, Eg
6	E2, Eg
7	V3, Eg, E4
8	Gg, Gh, VIg
9	E5, Eg
10	VII6, E7, Gh, G6
11	Eg
12	E8, Eg, E9, G8
13	Eg, Gg
14	Eg
15	VIII10, Gg, IXg
16	Eg, Eu, Xg
17	Ea
18	Eu
19	Eg, XI11, E12
20	Eg, Gg

↵ a A total of 83 clones were obtained. A novel ITS2 type was demonstrated from three patients and was designated type u. New ITS1 and ITS2 sequences that were only detected once are indicated by Roman and Arabic numerals, respectively.
↵ b Specimens 2 and 3 (a tracheal aspirate and a biopsy specimen, respectively) were from the same patient.
↵ c Specimens from twins (twin 1, specimens 2 and 3; twin 2, specimen 4).

TABLE 2.

Real distance matrix analysis with the 33 different ITS1 and ITS2 sequences obtained^a

↵ a The distances were determined with the TCS program (version 1.13; Clement et al., Brigham Young University). ITS1 and ITS2 sequences were concatenated. Gaps were treated as missing data. The parsimony limit was 95%.