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. 1998 Mar;36(3):734-41.
doi: 10.1128/JCM.36.3.734-741.1998.

Update on Pneumocystis carinii f. sp. hominis typing based on nucleotide sequence variations in internal transcribed spacer regions of rRNA genes

C H Lee  1 , J Helweg-Larsen, X Tang, S Jin, B Li, M S Bartlett, J J Lu, B Lundgren, J D Lundgren, M Olsson, S B Lucas, P Roux, A Cargnel, C Atzori, O Matos, J W Smith
Affiliations

Update on Pneumocystis carinii f. sp. hominis typing based on nucleotide sequence variations in internal transcribed spacer regions of rRNA genes

C H Lee et al. J Clin Microbiol. 1998 Mar.

Abstract

Pneumocystis carinii f. sp. hominis isolates from 207 clinical specimens from nine countries were typed based on nucleotide sequence variations in the internal transcribed spacer regions I and II (ITS1 and ITS2, respectively) of rRNA genes. The number of ITS1 nucleotides has been revised from the previously reported 157 bp to 161 bp. Likewise, the number of ITS2 nucleotides has been changed from 177 to 192 bp. The number of ITS1 sequence types has increased from 2 to 15, and that of ITS2 has increased from 3 to 14. The 15 ITS1 sequence types are designated types A through O, and the 14 ITS2 types are named types a through n. A total of 59 types of P. carinii f. sp. hominis were found in this study.

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Figures

FIG. 1
FIG. 1
Revised nucleotide sequences of ITS1 and ITS2. The number of nucleotides has been changed from the previously reported 157 bp to 161 bp for ITS1 and from 177 to 192 bp for ITS2. The sequences shown are consensus sequences; they are not the sequences of a certain type of P. carinii f. sp. hominis.
FIG. 2
FIG. 2
Nucleotide sequences of various types of ITS1 of P. carinii f. sp. hominis. A sequence which is found in two or more specimens is considered a distinct type. A total of 15 ITS1 types, designated A through O, have been found. Two sequences representing each type are aligned. Bases that are identical to those of the consensus sequence are indicated by periods, missing bases are indicated by hyphens, and bases that are different from those of the consensus sequence are given. The sequences at positions 61 to 70 and 91 to 110 are not shown, because no sequence variations are found in these areas.
FIG. 3
FIG. 3
Nucleotide sequences of various types of ITS2 of P. carinii f. sp. hominis. A sequence which is found in two or more specimens is considered a distinct type, and 14 sequences (designated a through n) met this requirement. Two sequences representing each type are aligned. Bases that are identical to those of the consensus sequence are indicated by periods, missing bases are indicated by hyphens, and bases that are different from those of the consensus sequence are given. The sequences at positions 1 to 40, 81 to 120, and 131 to 150, are not shown, because no sequence variations are found in these areas. Six sequences from specimens (IT007, FR004, DK029, DK594, DK323, and DK313) are also listed but are not considered distinct types, because they are found in only one specimen each.
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