Biodiversity of Pneumocystis carinii hominis: typing with different DNA regions

Genetic heterogeneity in human-derived Pneumocystis carinii

Genetic heterogeneity has been observed among isolates of human-derived Pneumocystis carinii (P. carinii sp. f. hominis). DNA sequence analysis has been shown to be informative in distinguishing between isolates of P. carinii sp. f. hominis. Single base polymorphisms have been observed in the genes encoding the mitochondrial large subunit ribosomal RNA, the mitochondrial small subunit ribosomal RNA and the AROM protein. The highest level of genetic variation has been found at the internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA operon. Typing of isolates of P. carinii sp. f. hominis has enabled the examination of the frequency of different types of P. carinii sp. f. hominis in distinct populations. It has also facilitated studies on the acquisition and transmission of P. carinii sp. f. hominis infection.

Determination of copy number of rRNA genes in Pneumocystis carinii f. sp. hominis

Differential PCR was performed to determine the copy number of rRNA genes in Pneumocystis carinii f. sp. hominis. Two different reference genes, thymidylate synthase (TS) and beta-tubulin (BTU) genes, were used. Primers for the internal transcribed spacer (ITS) region of nuclear rRNA genes and either the TS or BTU gene were mixed together to perform PCR on seven different bronchoalveolar lavage specimens from patients with P. carinii pneumonia. The radioactivity derived from the incorporated radioactive nucleotides of each PCR product band was then used to calculate the copy number of the ITS relative to that of the TS or BTU gene. The copy number ratio between the ITS and the TS gene was determined to be 0.8, and that between the ITS and the BTU gene was also 0.8. These results suggest that the ITS has the same copy number as the TS or BTU gene. Since the copy number of the TS or BTU gene is presumed to be 1, the results also suggest that P. carinii f. sp. hominis has only one copy of the ITS and thus one copy of the nuclear rRNA genes. Therefore, two types of ITS sequences derived from a specimen would indicate that the patient is infected by two types of P. carinii f. sp. hominis.

Typing methods to approach Pneumocystis carinii genetic heterogeneity

The study of the genetic heterogeneity of P. carinii is complicated by the lack of an in vitro culture system, as well as by the likely occurrence of co-infections with several special forms or types in a single host. Karyotyping and multilocus enzyme electrophoresis are useful for studies at the evolutionary level. However, these methods require a large number of cells, which prevents their use for the special form infecting humans. DNA sequence analysis of genomic regions is useful to study P. carinii diversity, both at the evolutionary and epidemiological levels. To type the special form specific to humans, several methods are currently used to detect polymorphism in PCR products of polymorphic regions of the genome: DNA sequencing, type-specific hybridisations, and single-strand conformation polymorphism. All these methods still need evaluation. The frequency of potential co-infections in humans determined by these various methods is different. The differences could be due to methodological problems or to real variations between patient populations, geographical locations and/or prophylaxis regimens. In the future, elucidating the population structure of P. carinii and the frequency of potential co-infections is going to be crucial for a better understanding of its epidemiology, and thus for a better prevention of P. carinii pneumonia in humans.

Identification of Pneumocystis carinii f. sp. hominis gene sequences in filtered air in hospital environments

To evaluate the risk of a nosocomial spread of Pneumocystis carinii f. sp. hominis (P. carinii hominis), air filter samples from rooms of P. carinii pneumonia (PCP) patients, adjacent corridors, and other hospital environments have been investigated for the presence of P. carinii hominis. Amplified DNA from air filters and sputum or bronchoalveolar lavage samples from the PCP patients have been genotyped with the P. carinii hominis genes of the mitochondrial large-subunit (mtLSU) rRNA and the internal transcribed spacers (ITS1 and ITS2) of the rRNA. Genotypes of the two loci were identified by direct sequencing, and for site 85 of the mtLSU locus, three allele-specific PCR assays were used. P. carinii hominis DNA was identified in the air of five of seven PCP patient rooms and in the air of two of four air filtrations from the ward corridors. The P. carinii hominis genotypes were the same in four of the five room air samples as those in the corresponding patients, suggesting a risk of person-to-person transmission of P. carinii hominis from PCP patients. Three of 16 air samples collected in infectious disease wards without the presence of PCP patients and one sample from a cardiology unit in a separate hospital building were also positive, which further strengthens the possibility of acquisition of P. carinii hominis from the environment.

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

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.

Pre-AIDS era isolates of Pneumocystis carinii f. sp. hominis: high genotype similarity with contemporary isolates

Isolates of Pneumocystis carinii f. sp. hominis were examined from six individuals who died of P. carinii pneumonia between 1968 and 1981 and who had underlying immunodeficiencies which were not due to human immunodeficiency virus infection. DNA sequence variation was analyzed in the genes encoding the mitochondrial large subunit rRNA (mt LSU rRNA), the internal transcribed spacer (ITS) regions of the nuclear rRNA, the arom locus, and the mitochondrial small subunit rRNA. No major variations were observed when these isolates were compared to isolates from HIV-infected individuals. A small number of minor differences were detected. A new position at which variation occurred in the mt LSU rRNA was observed in one sample. Three new ITS sequence types were identified. A total of nine different ITS sequence types were found in the six samples. Mixed infection with different ITS sequence types of P. carinii f. sp. hominis was observed in four of the six samples. The ITS locus was the most informative of the four loci for distinguishing among the isolates of P. carinii f. sp. hominis. The data suggest that isolates of P. carinii f. sp. hominis from before the AIDS pandemic are genetically very similar to those currently found in HIV-infected individuals.

Typing of Pneumocystis carinii f. sp. hominis by single-strand conformation polymorphism of four genomic regions

To better investigate Pneumocystis carinii f. sp. hominis epidemiology, we have developed a molecular typing method. Because of the limited genetic variability of the P. carinii hominis genome, a multitarget approach was used. Four variable regions of the genome were amplified by PCR, polymorphism in each region was assessed by the single-strand conformation polymorphism (SSCP) technique, and the results for the four regions of each patient were combined. Bronchoalveolar lavage specimens collected from 11 patients were examined. Four patients were probably infected by a single strain, since their specimens yielded simple SSCP patterns (two bands corresponding to one allele). The combinations of these patterns were unique, suggesting that the strains which infected these patients were different. For the other seven patients, complex patterns were found (three or four bands corresponding to two alleles). The presence of more than one allele of a region in a patient is likely to be due to coinfection. Polymorphism was also assessed by sequencing, which revealed variations at nucleotide positions previously reported to vary. About half of the observed alleles had already been reported by laboratories in different countries. Multitarget typing of P. carinii hominis by PCR-SSCP should allow investigation of strain diversity and thus be useful for future epidemiological studies.

Typing with ITS regions of P.carinii from AIDS patients with recurrent pneumonia

To understand the way of reinfection of Pneumocystis carinii we have analyzed the genetic variation at the internal transcribed spacer (ITS) in DNA samples from bronchoalveolar lavage fluid of Italian HIV patients who had multiple episodes of P.carinii pneumonia. The presence of the same and/or a new type in both episodes suggest the possible occurrence of both reactivation of a previously acquired infection and reinfection from an exogenous source. Furthermore the occurrence of two different types in the same episode indicate that a mixed infection is common.

Study of internal transcribed spacer and mitochondrial large-subunit genes of Pneumocystis carinii hominis isolated by repeated bronchoalveolar lavage from human immunodeficiency virus-infected patients during one or several episodes of pneumonia

The objective of this study was to type, analyze, and compare Pneumocystis carinii hominis strains obtained from different samples during a given or recurrent episodes of P. carinii pneumonia (PCP) for epidemiologic purposes. We studied 36 bronchoalveolar lavage (BAL) or induced sputum (IS) samples from 16 human immunodeficiency virus-infected patients with one or several episodes of PCP. PCR amplification and direct sequencing were performed on the two internal transcribed spacers (ITS1 and ITS2) of P. carinii hominis rRNA genes by using DNA extracted from BAL or IS samples, and the sequences were compared to the mitochondrial large-subunit (mt LSU) gene sequence determined in a previous study in our laboratory. The studies of the mt LSU and ITS sequences showed that some patients (n = 10) were infected with the same strains of P. carinii hominis during a given episode of PCP. In one patient infected with strains with identical sequences in several episodes, the recurrence could have been due to reactivation of organisms not eliminated by treatment during the first episode or to de novo infection by an identical strain. In five patients infected with strains with different sequences in each episode, recurrence was due to de novo infection. Sequence analysis of these two P. carinii hominis gene regions showed that de novo infection can occur in AIDS patients with recurrent PCP.