Typing of Pneumocystis carinii strains that infect humans based on nucleotide sequence variations of internal transcribed spacers of rRNA genes

Abstract

Small portions of the 18S and the 26S rRNA genes, the entire 5.8S rRNA gene, and internal transcribed spacers ITS1 and ITS2 (located between the 18S and 5.8S rRNA genes and between the 5.8S and 26S rRNA genes, respectively) of Pneumocystis carinii that infect humans were cloned and sequenced. The nucleotide sequences of the 18S, 5.8S, and 26S rRNA genes determined in the study were approximately 90% homologous to those of P. carinii that infect rats, while the sequences of ITS1 and ITS2 of P. carinii from the two different hosts were only 60% homologous. The 18S, 5.8S, and 26S rRNA gene sequences of P. carinii from 15 patient specimens were determined and were found to be identical to each other, whereas the ITS sequences were found to be variable. With the observed sequence variation, it was possible to classify the ITS1 sequences into two types and the ITS2 sequences into three types. P. carinii strains that had the same type of ITS1 sequence could have a different type of ITS2 sequence. On the basis of the sequence types of the two ITS regions, P. carinii from the 15 patients were classified into four groups. P. carinii from three patient specimens were found to contain two different ITS sequence patterns. More surprisingly, one additional specimen was found to have one ITS sequence typical of P. carinii isolates that infect humans and another typical of P. carinii isolates that infect rats. The studies indicate that it is possible to type P. carinii strains on the basis of their ITS sequences and that more than one ITS sequence pattern may be demonstrated in P. carinii from one patient, suggesting that coinfection with more than one strain of P. carinii may occur in the same patient.

Pneumocystis jirovecii multilocus genotyping profiles in patients from Portugal and Spain

“…With respect to ITS types, the present results revealed a significant diversity in both populations because of the high sequence variability in these genomic regions [17,25,27]. The data suggest a probable dominance of ITS type Eg in the Portuguese population, as reported previously [17], but the second most common ITS type in the Portuguese population was Cg, followed by Gg, which is in contrast to previous findings [17].…”

“…Several polymorphic loci have been studied in order to clarify the epidemiological profile of P. jirovecii, with particular respect to its virulence, drug resistance and modes of transmission. The mitochondrial large-subunit rRNA (mtLSU rRNA), the dihydropteroate synthase (DHPS) gene and the internal transcribed spacer regions 1 and 2 (ITS1 and ITS2) of the nuclear rRNA operon are among these loci [12][13][14][15][16][17][19][20][21][22][23][24][25][26][27][28].…”

“…ITS1 and ITS2 show the highest level of sequence variation in P. jirovecii and are considered to be the most discriminatory DNA regions for genotyping studies. According to the nomenclature of Lee et al [27], 16 different DNA ITS1 sequences and 15 different ITS2 sequences have been described, with a total of 60 different combined types being reported from among a theoretical total of 240 [24,25,27].…”

Comparison of Coding and Spacer Region Sequences of Chromosomal rRNA‐Coding Genes of Two Sequevars of Pneumocystis carinii

“…The data presented here and in previous reports indicate that three distinct sequevars ofP. carinii exist based on chromosomal rRNA gene sequence and organization: Pcl and Pc2 have been identified in immunosuppressed rats [3,19,201 and Pc3 in multiple human infections [19,21, also see 321. Pcl and Pc2 differ by the absence of a group I intron in the 16s rRNA gene of Pc2 and have distinct sequences for their 26s rRNA introns and 16S, 5.8s and 26s rRNA genes [3,19,20 and Results].…”

I. Genetic heterogeneity in Pneumocystis carinii: an introduction

“…The comparison of the introns in the sequence revealed that the rat-derived Pneumocystis rRNA operon contained two group I self-splicing introns, one in the 18S rRNA gene and the other in the 26S rRNA gene, whereas the human-derived organisms only had an intron in the 26S rRNA gene [35]. The internal transcribed spacer (ITS) regions of the nuclear rRNA operon have been used in the analysis of genetic heterogeneity, primarily in isolates of humanderived Pneumocystis [36,37] (see Chapter VI, this volume).…”