Application of DNA amplification to pneumocystosis: presence of serum Pneumocystis carinii DNA during human and experimentally induced Pneumocystis carinii pneumonia

Non-invasive diagnosis of Pneumocystis jirovecii pneumonia: a systematic review and meta-analysis

BACKGROUND

Pneumocystis jirovecii pneumonia (PCP) is an opportunistic infection commonly affecting immunocompromised people. Diagnosis usually requires invasive techniques to obtain respiratory specimens. Minimally invasive detection tests have been proposed, but their operating characteristics are poorly described.

OBJECTIVES

To systematically review and meta-analyse the performance of minimally invasive PCP detection tests to inform diagnostic algorithms.

DATA SOURCES

Medline, Embase, Cochrane Library (inception to 15 October 2020).

STUDY ELIGIBILITY CRITERIA

Studies of minimally invasive PCP detection tests were included if they contained a minimum of ten PCP cases.

PARTICIPANTS

Adults at risk of PCP.

TESTS

Non-invasive PCP detection tests.

REFERENCE STANDARD

Diagnosis using the combination of clinical and radiographical features with invasive sampling.

ASSESSMENT OF RISK BIAS

Using the QUADAS-2 tool.

METHODS

We used bivariate and, when necessary, univariate analysis models to estimate diagnostic test sensitivity and specificity.

RESULTS

Fifty-two studies were included; most studies (40) comprised exclusively human immunodeficiency virus (HIV) -infected individuals; nine were mixed (HIV and non-HIV), two were non-HIV and one study did not report HIV status. Sampling sites included induced sputum, nasopharyngeal aspirate, oral wash and blood. The four testing modalities evaluated were cytological staining, fluorescent antibody, PCR and lactate dehydrogenase. Induced sputum had the most data available; this modality was both highly sensitive at 99% (95% CI 51%-100%) and specific at 96% (95% CI 88%-99%). Induced sputum cytological staining had moderate sensitivity at 50% (95% CI 39%-61%) and high specificity at 100% (95% CI 100%-100%), as did fluorescent antibody testing with sensitivity 74% (95% CI 62%-87%) and specificity 100% (95% CI 91%-100%).

CONCLUSION

There are several promising minimally invasive PCP diagnostic tests available, some of which may reduce the need for invasive respiratory sampling. Understanding the operating characteristics of these tests can augment current diagnostic strategies and help establish a more confident clinical diagnosis of PCP. Further studies in non-HIV infected populations are needed.

Diagnosing Pneumocystis jirovecii pneumonia: A review of current methods and novel approaches

Pneumocystis jirovecii can cause life-threatening pneumonia in immunocompromised patients. Traditional diagnostic testing has relied on staining and direct visualization of the life-forms in bronchoalveolar lavage fluid. This method has proven insensitive, and invasive procedures may be needed to obtain adequate samples. Molecular methods of detection such as polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and antibody-antigen assays have been developed in an effort to solve these problems. These techniques are very sensitive and have the potential to detect Pneumocystis life-forms in noninvasive samples such as sputum, oral washes, nasopharyngeal aspirates, and serum. This review evaluates 100 studies that compare use of various diagnostic tests for Pneumocystis jirovecii pneumonia (PCP) in patient samples. Novel diagnostic methods have been widely used in the research setting but have faced barriers to clinical implementation including: interpretation of low fungal burdens, standardization of techniques, integration into resource-poor settings, poor understanding of the impact of host factors, geographic variations in the organism, heterogeneity of studies, and limited clinician recognition of PCP. Addressing these barriers will require identification of phenotypes that progress to PCP and diagnostic cut-offs for colonization, generation of life-form specific markers, comparison of commercial PCR assays, investigation of cost-effective point of care options, evaluation of host factors such as HIV status that may impact diagnosis, and identification of markers of genetic diversity that may be useful in diagnostic panels. Performing high-quality studies and educating physicians will be crucial to improve the rates of diagnosis of PCP and ultimately to improve patient outcomes.

Serum-based diagnosis of Pneumocystis pneumonia by detection of Pneumocystis jirovecii DNA and 1,3-β-D-glucan in HIV-infected patients: a retrospective case control study

BACKGROUND

Pneumocystis jirovecii pneumonia (PCP) is one of the most common HIV-related opportunistic infections. The diagnosis of PCP is based on analyses from respiratory tract specimens which may require the invasive procedure of a diagnostic bronchoscopy. The objective of this study was to evaluate the diagnostic potential of Pneumocystis jirovecii PCR in serum combined with the 1,3-β-D-glucan (betaglucan) test for the diagnosis of PCP in HIV-infected patients.

METHODS

This was a retrospective case-control study including serum samples from 26 HIV-infected patients with PCP collected within 5 days prior to the start of PCP treatment, 21 HIV-infected control subjects matched by blood CD4⁺ cell counts, and 18 blood donors. The serum samples were analyzed for Pneumocystis jirovecii PCR and betaglucan. The reference standard for PCP was based on previously described microbiological and clinical criteria.

RESULTS

All patients with PCP had detectabe Pneumocystis jirovecii DNA in serum yielding a sensitivity for the Pneumocystis jirovecii PCR assay in serum of 100%. All blood donors had negative Pneumocystis PCR in serum. The specificity when testing HIV-infected patients was 71%, but with a PCR Cycle threshold (Ct) value of 34 as cut-off the specificity was 90%. At a putative pretest probaility of 20%, the negative and positive predictive value for the Pneumocystis PCR assay in serum was 0.99 and 0.71, respectively. Betaglucan with cut-off level 200 pg/ml combined with a positive Pneumocystis jirovecii PCR result had sensitivity and specificity of 92 and 90%, respectively. The concentration of Pneumocystis jirovecii DNA in serum samples, expressed by the PCR Ct values, correlated inversely to the betaglucan levels in serum.

CONCLUSION

In this case-control study including 70% of all HIV-infected patients with PCP treated at Sahlgrenska University Hospital during a time period of 13 years, Pneumocystis PCR analysis on serum samples had a very high sensitivity and negative predictive value for the diagnosis of PCP in HIV-infected patients. A serum-based diagnostic procedure either based on Pneumocystis jirovecii PCR alone or in combination with betaglucan analysis may thus be feasible and would facilitate the care of HIV-infected patients with suspected PCP.

Diagnosis of Pneumocystis jirovecii pneumonia with serum cell-free DNA in non-HIV-infected immunocompromised patients

Conventional respiratory tract specimens, such as bronchoalveolar lavage (BAL) fluid and induced sputum for diagnosing Pneumocystis jirovecii pneumonia (PCP) in immunocompromised patients are difficult to obtain. Besides, bronchoscopy is an invasive procedure that carries the risk of causing rapidly progressive respiratory insufficiency. By contrast, serum cell-free DNA (cfDNA) is easy to obtain and has been proven useful in diagnosing cancer, pregnancy associated complications, parasite infection and sepsis. In this study, we performed quantitative polymerase chain reaction (qPCR) to assess the diagnostic efficiency of using serum cfDNA, BAL fluid, and sputum DNA for PCP. Seventy-one patients (35 PCP patients and 36 non-PCP patients) were enrolled according to the clinical PCP diagnostic criteria. The sensitivity, specificity, positive predictive value, and negative predictive value of PCR using serum cfDNA were 68.6% (95% CI, 50.7–83.1), 97.2% (95% CI, 85.5–99.9), 96.0%, and 76.1%, respectively. PCR using BAL fluid and sputum had a high sensitivity (97.1% and 91.4%, respectively) but relatively low specificity (86.1% and 86.1%, respectively). The combination of the sputum PCR OR serum cfDNA PCR yielded a sensitivity of 97.1%.These results indicated that serum cfDNA might be a valuable method in PCP diagnosis.

Pneumocystis jiroveci Pneumonia

Pneumocystis pneumonia (PCP) is one of the most common pulmonary infections in persons with impaired cell-mediated immunity, and particularly those infected with human immunodeficiency virus (HIV).1–7 Pneumocystis was first described in the lungs of guinea pigs, during experiments on American trypanosomiasis by Carlos Chagas8 in 1909 and by Antonio Carinii9 in 1910. Both considered the cysts of Pneumocystis as part of the trypanosome’s life cycle. Shortly afterward the Delanoes10 found identical forms in the lungs of rats that had not been infected with trypanosomes and recognized the organism as a separate species. The name Pneumocystis carinii, was given to this organism as a generic name (Greek:pneumon, “lung”; kystis, “cyst”), honoring Carinii.11

Pneumocystis: newer knowledge about the biology of this group of organisms in laboratory rats and mice

This review is an update on some of the remarkable advances that have led to greater understanding of Pneumocystis, an important group of rodent pathogens. The author outlines the life cycle of these pulmonic fungi, their taxonomic position, and their nomenclature. He discusses how infections begin and spread in laboratory rodent colonies, and how those infections are inadvertently maintained in barriered breeding colonies. He also addresses the diagnosis of Pneumocystis infection and provides suggestions for the establishment of Pneumocystis-free animal colonies.

Molecular detection and typing of fungal pathogens

A major goal of molecular testing is to develop a cost-effective as well as sensitive and specific assay that can detect microbial DNA in clinical samples early in the course of disease. Additionally, the ability to analyze the genetic relatedness of fungi on a timelier basis using molecular methods will have a positive impact on epidemiologic investigating. As technology advances, it seems apparent that commercially available molecular assays will become available in the near future for the management of patients with suspected fungal infections.

Development of a rapid real-time PCR assay for quantitation of Pneumocystis carinii f. sp. carinii

A method for reliable quantification of Pneumocystis carinii in research models of P. carinii pneumonia (PCP) that is more convenient and reproducible than microscopic enumeration of organisms would greatly facilitate investigations of this organism. We developed a rapid quantitative touchdown (QTD) PCR assay for detecting P. carinii f. sp. carinii, the subspecies of P. carinii commonly used in research models of PCP. The assay was based on the single-copy dihydrofolate reductase gene and was able to detect <5 copies of a plasmid standard per tube. It was reproducibly quantitative (r = 0.99) over 6 log values for standards containing > or =5 copies/tube. Application of the assay to a series of 10-fold dilutions of P. carinii organisms isolated from rat lung demonstrated that it was reproducibly quantitative over 5 log values (r = 0.99). The assay was applied to a recently reported in vitro axenic cultivation system for P. carinii and confirmed our microscopy findings that no organism multiplication had occurred during culture. For all cultures analyzed, QTD PCR assays showed a decrease in P. carinii DNA that exceeded the expected decrease due to dilution of the inoculum upon transfer. In conclusion, a rapid, sensitive, and reproducible quantitative PCR assay for P. carinii f. sp. carinii has been developed and is applicable to in vivo as well as in vitro systems. The assay should prove useful for conducting studies in which quantification of organism burden or growth assessment is critical, such as in vitro antimicrobic susceptibility testing or in vivo immunopathological experiments.

Pneumocystis carinii diagnosis: an update

From 1994 to date we have been using the internal transcribed spacers (ITSs) nested polymerase chain reaction (PCR) to investigate the possibility of diagnosing Pneumocystis carinii pneumonia on non-invasive samples collected from HIV-positive patients with pulmonary involvement. The objectives were: (1) to test the sensitivity, specificity and prognostic value of PCR in diagnosis and follow up of PCP; (2) to investigate the eventual occurrence and role of asymptomatic carriers of P. carinii; (3) to evaluate the prognostic significance of blood PCR positivity versus respiratory samples; (4) to verify the occurrence of exogenous infections or endogenous reactivations in cases of recurrent P. carinii pneumonia; and (5) to study the possible correlation between P. carinii genotype identified and capability of blood dissemination, prior prophylactic treatments, clinical parameters and outcome of the patients.

Development of a PCR assay for diagnosis of Pneumocystis carinii pneumonia based on amplification of the multicopy major surface glycoprotein gene family

We have evaluated a PCR technique using primers based on Pneumocystis carinii major surface glycoprotein (MSG) genes, a multicopy gene family, for utility in detection of P. carinii in BAL and oropharyngeal samples obtained from immunosuppressed patients. These primers were able to detect P. carinii DNA in as little as 16 fg of genomic DNA. PCR using MSG primers detected P. carinii DNA in 7 smear-positive BAL samples (100% sensitivity), and found no P. carinii DNA in 12 smear-negative BAL samples (100% specificity). Mitochondrial ribosomal RNA (mrRNA) primers, commonly used in PCR studies of PCP, detected P. carinii in six of seven positive samples (85.7% sensitivity) and none of 12 were negative samples (100% specificity). Diagnosis of PCP by amplification of 81 oropharyngeal samples using MSG primers had a 50% sensitivity (4/8) and 96% specificity (70/73). PCR with mrRNA primers was 37.5% sensitive (3/8) and 100% specific (73/73). All three false-positive MSG results showed a very low intensity on Southern hybridization. PCR using MSG gene primers should prove valuable in the diagnosis of PCP.

Detection of Pneumocystis carinii DNA in blood specimens from human immunodeficiency virus-infected patients by nested PCR

The detection of Pneumocystis carinii DNA in blood by PCR could be useful for studying the natural history of pneumocystosis and could also be a noninvasive diagnostic method. The results of previous studies are nevertheless conflicting. In our study, we compared three commercially available DNA extraction kits (GeneReleaser, QIAamp Tissue Kit, and ReadyAmp Genomic DNA Purification System) and proteinase K and proteinase K-phenol-chloroform treatments for the extraction of P. carinii DNA from dilutions of a P. carinii f. sp. hominis cyst suspension mixed with human whole blood. A rapid and simple nested PCR protocol which amplifies a portion of the mitochondrial large-subunit rRNA gene was applied to all the extraction products. The QIAmp Tissue Kit was the most effective kit for the isolation of amplification-ready P. carinii DNA and was used with nested PCR for the testing of whole-blood specimens from 35 immunocompetent control patients and 84 human immunodeficiency virus (HIV)-infected patients investigated for pulmonary disease and/or fever. In HIV-infected patients, P. carinii DNA was detected by nested PCR in blood samples from 3 of 14 patients with microscopically proven P. carinii pneumonia, 7 of 22 patients who were considered to be colonized with P. carinii, and 9 of 48 patients who were neither infected nor colonized with P. carinii. P. carinii DNA was not detected in blood specimens from the 35 immunocompetent patients. P. carinii DNA in blood might represent viable P. carinii organisms or DNA complexes released from pulmonary phagocytes. In conclusion, P. carinii DNA may be detected in whole blood from HIV-infected patients, but the nature and the meaning of the circulating form of P. carinii remain to be established.

Potential impact of Pneumocystis genetic diversity on the molecular detection of the parasite in human host

Our aim was to evaluate if genetic diversity of Pneumocystis carinii could influence the detection by molecular techniques in bronchoalveolar lavage (BAL) fluids and in non-invasive specimens (induced sputum, oropharyngeal washing and serum/blood). P. carinii is morphologically similar in different hosts although several strains have been identified by biomolecular techniques. Variations of mt-LSU and ITSs sequences could determine a lack of hybridization of some clinical samples and could have diagnostic consequences with loss in sensitivity and specificity of available molecular tests, but at the moment no data support a significant impact of genetic diversity in these sequences on molecular detection of P. carinii for clinical purposes.

PCR for detecting Pneumocystis carinii in clinical or environmental samples

Since Pneumocystis carinii cannot be cultured in vitro, the introduction of polymerase chain reaction (PCR) has been an enormous advantage for research purposes. It is now possible to detect P. carinii in specimens containing low numbers of organisms where conventional detection methods using microscopic examination of histochemical stains has been insufficient. PCR has been used to detect P. carinii in bronchoalveolar lavage, induced sputum, spontaneous expectorates, oropharyngeal gargles, nasopharyngeal aspirates, serum, blood and in environmental samples. The use of PCR will enable the study of the epidemiology of P. carinii infection by detecting the organism in environmental samples, permitting molecular typing and thereby the study of the transmission of the organism. Furthermore PCR will facilitate studies on the response to therapy, studies monitoring for the emergence of drug resistant strains of P. carinii and in the diagnosis of P. carinii pneumonia in noninvasive specimens, in patients unable to undergo more invasive diagnostic procedures.

Diagnostic use of PCR for detection of Pneumocystis carinii in oral wash samples

There is a need to develop noninvasive methods for the diagnosis of Pneumocystis carinii pneumonia in patients unable to undergo bronchoscopy or induction sputum. Oral wash specimens are easily obtained, and P. carinii nucleic acid can be amplified and demonstrated by PCR. In routine clinical use, easy sample processing and single-round PCR are needed to ensure rapid analysis and to reduce the risk of contamination. We developed a single-round Touchdown PCR (TD-PCR) protocol with the ability to detect PCR inhibition in the specimen. The TD-PCR was evaluated in a routine diagnostic laboratory and was compared to a previously described PCR protocol (mitochondrial RNA) run in a research laboratory. Both PCR methods amplified a sequence of the mitochondrial rRNA gene of P. carinii. Paired bronchoalveolar lavage (BAL) and oral wash specimens from 76 consecutive human immunodeficiency virus type 1-infected persons undergoing a diagnostic bronchoscopy were included. The TD-PCR procedure was quicker than the mitochondrial PCR procedure (<24 versus 48 h) and, compared to microscopy, had sensitivity, specificity, and positive and negative predictive values of 89, 94, 93, and 91%, respectively, for oral wash specimens and 100, 91, 90, and 100%, respectively, for BAL specimens. Our results suggest that oral wash specimens are a potential noninvasive method to obtain a diagnostic specimen during P. carinii pneumonia infection and that it can be applied in a routine diagnostic laboratory.

Rapid detection of Pneumocystis carinii in bronchoalveolar lavage specimens from human immunodeficiency virus-infected patients: use of a simple DNA extraction procedure and nested PCR

We report on the development of a rapid nested PCR protocol for the detection of Pneumocystis carinii DNA in bronchoalveolar lavage (BAL) specimens in which the protocol included the use of a commercially available DNA extraction kit (GeneReleaser). GeneReleaser enabled us to obtain amplification-ready DNA within 20 min without requiring the purification of the DNA. The nested PCR was performed with the primers pAZ102-E, pAZ102-H, and pAZ102-L2 (A. E. Wakefield, F. J. Pixley, S. Banerji, K. Sinclair, R. F. Miller, E. R. Moxon, and J. M. Hopkin, Lancet 336:451-453, 1990.). Results were obtained in about 4 h with the adoption of denaturation, annealing, and extension steps shortened to 20 seconds. The sensitivity of the nested PCR was tested with a P. carinii cyst suspension and was found to be less than one cyst (one to eight nuclei). The detection limit was the same with the use of GeneReleaser or proteinase K-phenol chloroform for DNA extraction. The nested PCR assay was prospectively compared with staining with Giemsa and methenamine silver stains for the detection of P. carinii in 127 BAL samples from 105 human immunodeficiency virus-infected patients investigated for acute respiratory illness. Twenty-five BAL specimens (20%) were positive by staining and the nested PCR and 25 (20%) were negative by staining and positive by the nested PCR. These 25 BAL specimens with conflicting results were obtained from 23 patients, 82% of whom were receiving prophylactic therapy against P. carinii pneumonia (PCP). Only two patients were diagnosed with possible PCP. The final diagnosis was not PCP for 20 patients who were considered to be colonized or to have a low level of infection. This colonization is not of clinical importance but is of epidemiological importance. Our rapid, simple, and sensitive amplification protocol may be performed in clinical laboratories for the routine diagnosis of PCP with BAL specimens.

Electroretinographic and psychophysical findings during early and late stages of human immunodeficiency virus infection and cytomegalovirus retinitis

PURPOSE

The authors examined electrophysiologic and psychophysical measures of retinal function in patients infected with human immunodeficiency virus (HIV) at different stages of infection, including patients with cytomegalovirus retinitis (CMVR).

METHODS

All patients had complete ophthalmologic examinations. Rod-mediated psychophysical thresholds were measured using a modified two-color dark-adapted perimetry technique. Rod-dominated full field flash electroretinograms (ERGs) were obtained as a function of flash intensity, followed by cone-dominated ERGs. The 26 patients infected with HIV (26 eyes) were categorized into three groups. Six patients were infected with HIV but had not progressed to acquired immunodeficiency syndrome (AIDS), and 14 had AIDS. Six patients had CMVR with less than 10% of the retina involved. The data were compared with results from age-similar control subjects.

RESULTS

Psychophysical thresholds as a function of retinal eccentricity were elevated for each of the three stages of HIV infection. The group of patients with CMVR had the greatest amount of threshold elevation and threshold elevation increased with retinal eccentricity. In addition, all three patient groups had abnormal electroretinographic findings. Patients with CMVR were affected more severely on all measures than were the other HIV-infected groups.

CONCLUSIONS

Results reveal that a diffuse functional retinal pathology exists in eyes with the funduscopic appearance of localized peripheral CMVR. Additionally, patients infected with HIV, including those without cotton wool spots, may have abnormal retinal function.

Serum PCR of Pneumocystis carinii DNA in immunocompromised patients

The detection of Pneumocystis carinii DNA in serum, a potentially useful and attractive tool for the diagnosis of P. carinii infection and for monitoring the success of therapeutic interventions, remains a controversial issue. In a prospective study of 29 immunocompromised patients, including 16 with HIV infection undergoing bronchoscopy and bronchoalveolar lavage, we examined 32 bronchoalveolar lavage fluids and multiple serum samples for the presence of P. carinii DNA by using mitochondrial rRNA gene fragments pAZ102-E as pAZ102-H as primers. Samples from 7 immunocompetent patients were analysed as a control. 13/32 bronchoalveolar lavage fluids of immunocompromised patients (41%), but none of the controls, had both microscopic evidence of P. carinii cysts as well as P. carinii DNA detection. In none of these patients were serum samples obtained before therapy positive for P. carinii DNA, while in 1 patient (8%), P. carinii DNA was detected in 2/5 serum samples obtained during therapy. Interestingly, PCR detected P. carinii DNA in sera of 3/15 immunocompromised patients without detection of P. carinii DNA or organisms in BAL. Two of these 3 patients were taking secondary prophylactics for P. carinii pneumonia. In conclusion, PCR for P. carinii DNA in serum, at least in certain circumstances, may be of little value for the diagnosis of P. carinii pneumonia.

Pneumocystis carinii

Improved understanding of Pneumocystis carinii, in particular the widespread use of chemoprophylaxis, has resulted in a declining incidence of infection in patients infected with HIV since the late 1980s. Despite these advances, P. carinii pneumonia continues to represent an important cause of pulmonary disease in HIV-seropositive individuals who do not receive chemoprophylaxis or when breakthrough episodes occur. This article reviews the history, biology, clinical manifestations, prognostic markers, therapy, and chemoprophylaxis of P. carinii pneumonia in HIV-seropositive patients.

P.carinii DNA detected by ITSs nested PCR in serum and PBMC of AIDS patients with PCP

Pneumocystis carinii pneumonia (PCP) is usually diagnosed by examination of BAL, a sample often unpleasant to be collected from immunocompromised host affected by acute respiratory disease. We studied by the Internal Transcribed Spacers (ITSs) nested PCR the presence of P.carinii DNA in serum and Peripheral Blood Mononuclear Cells (PBMC) during acute episodes of PCP to test blood as a possible noninvasive diagnostic tool.

Identification of extrapulmonary Pneumocystis carinii in immunocompromised rats by PCR

Pneumocystis carinii has been shown to cause extra-alveolar infections in humans, but the lack of a reproducible animal model has hindered the elucidation of mechanisms of P. carinii dissemination. In the present study, PCR and the immunosuppressed rat model were used to gain further insight into the dissemination of P. carinii organisms in extrapulmonary (EP) tissues. Primer sequences specific to major surface glycoprotein (MSG) and dihydrofolate reductase (DHFR) were used to detect P. carinii in lungs and EP tissues. Sprague-Dawley rats were grouped into two classes: one group included rats that had primary episodes of pneumocystosis and the other group included rats that had undergone treatment for P. carinii infection and that had second episodes of pneumocystosis. PCR analysis with MSG primers with tissues obtained from both groups of rats showed the presence of P. carinii DNA in adrenal tissue, bone marrow, blood, and heart, kidney, liver, lymph node, spleen, and thyroid tissues. Reverse transcriptase-PCR (RT-PCR) analysis was carried out with DHFR primers with lung, spleen, heart, kidney, and liver tissues from both groups of rats. Only those tissues that showed a positive PCR result and hybridization signal for the MSG gene were used for the RT-PCR experiments. RT-PCR analysis showed that the P. carinii DHFR gene is actively transcribed in these tissues, thereby indicating the presence of viable P. carinii organisms in EP tissues. Our observations suggest that P. carinii dissemination is influenced by factors other than P. carinii chemotherapy and that heavy organism load and destruction of lung tissue may contribute to the dissemination of P. carinii. The study provides an animal model that can be used for further investigations of the causes of EP pneumocystosis.

Detection of Pneumocystis carinii DNA in blood by PCR is not of value for diagnosis of P. carinii pneumonia

A nested PCR which amplified a portion of the mitochondrial large-subunit rRNA gene of Pneumocystis carinii was used to detect P. carinii DNA in blood from patients with P. carinii pneumonia. P. carinii DNA was not detected in serum and was detected at low levels of blood cells.

Detection of Pneumocystis carinii sequences in serum by polymerase chain reaction

The clinical significance of the detection of Pneumocystis carinii DNA was evaluated, as well as the detection of circulating P. carinii antigen from serum using previously collected samples. Fourteen serum samples from 13 patients were diagnosed positively for P. carinii DNA by polymerase chain reaction (PCR). Ten of 14 episodes (71.4%) of pulmonary complications were compatible with P. carinii pneumonia. Two patients were definitely diagnosed as having had P. carinii pneumonia at autopsy. All patients positive for circulating antigens were also positive for P. carinii DNA, suggesting that the detection of P. carinii DNA by PCR is more sensitive compared to the detection of circulating antigens by the Ouchterlony method. It is concluded that the detection of P. carinii DNA in serum by PCR provides useful information for identifying P. carinii pneumonia.

Variable efficiency of three primer pairs for the diagnosis of Pneumocystis carinii pneumonia by the polymerase chain reaction

The efficiency of three different primer pairs, complementary to different Pneumocystis carinii DNA regions, was compared in the polymerase chain reaction (PCR) for the diagnosis of Pneumocystis carinii pneumonia (PCP) on bronchoalveolar fluid (BALF) from patients with AIDS. PCR coupled with dot-blot hybridization (BLOT) using primers and probe from the mitochondrial 23SrDNA region showed the highest sensitivity, with a lower detection limit of 0.5-1 organisms microliter-1. When testing 47 BALF, PCR plus BLOT of the mitochondrial 23SrDNA region showed also the best diagnostic efficiency (97% sensitivity, 100% specificity). Sensitivity was significantly higher than with PCR and BLOT of the 5SrDNA region (81.5% sensitivity; P = 0.025, McNemar test); and of the dehydrofolate reductase (DHFR) gene region (75.6% sensitivity; P = 0.019). Sensitivity was also significantly higher than indirect immunofluorescence (75.8% sensitivity; P = 0.008). Using DHFR primers and probe, specificity was also reduced. The diagnostic sensitivity in clinical specimens paralleled the detection limit in the standard dilutions. The use of repeated DNA sequences of proven specificity as target of PCR amplification favourably influences sensitivity and specificity. This comparative study demonstrates that primer selection plays a significant role in the diagnosis of PCP by PCR.

Use of semiquantitative PCR to assess onset and treatment of Pneumocystis carinii infection in rat model

The use of semiquantitative PCR (SQPCR) to assess Pneumocystis carinii pneumonia (PCP) infection and its response to treatment was studied with rats. Groups of eight rats were immunosuppressed with steroids for 3 to 12 weeks. Untreated controls were maintained for the same periods. Three groups of rats were treated with pentamidine, three groups were treated with trimethoprim-sulfamethoxazole, and three groups of rats were tapered from steroids. At various times during suppression, rats from the different groups were sacrificed. At necropsy, lungs were lavaged to obtain bronchoalveolar fluids and then homogenized. Bronchoalveolar fluids and homogenates were assayed by cyst counting and SQPCR. An increase in the SQPCR signal was seen throughout immunosuppression, with a slow decrease upon the withdrawal of steroids and a faster decrease with drug treatment. SQPCR results with lung homogenates and bronchoalveolar fluids strongly correlated with each other and with cyst counts. These results warrant investigation of SQPCR for assessing treatment results of human P. carinii pneumonia infection.

Outbreak of Pneumocystis carinii pneumonia in a renal transplant unit

The charts for seven renal transplant recipients who developed Pneumocystis carinii pneumonia were reviewed. They included six men and one woman transplanted a mean of 150 days before the diagnosis of this infection. Six presented at least one episode of acute graft rejection. Cytomegalovirus pneumonia was diagnosed in six of the patients. All patients were treated with cotrimoxazole. Global mortality was 43%. In additional to the classic hypothesis of latent Pneumocystis carinii reactivation in immunocompromised hosts, this and previous reports of outbreaks strongly suggest either a person-to-person transmission or acquisition from the environment. Molecular typing of isolates could be of value in identifying the source of such outbreaks. Chemoprophylaxis should be more systematically administered to renal transplant patients, co-trimoxazole being the drug of choice.

Comparison of coding and spacer region sequences of chromosomal rRNA-coding genes of two sequevars of Pneumocystis carinii

Two distinct sequevars, denoted Pc1 and Pc2, of the opportunistic pathogen Pneumocystis carinii have been previously identified based on the sequence of their 26S rRNA genes, the location of group I self-splicing introns and pulsed field electrophoretic patterns of chromosomal DNA. This study shows that the sequences of 16S and 5.8S rRNA genes also vary between these sequevars, and that greater variation was seen in the internal transcribed spacer regions. Polymerase chain reaction and restriction analysis can distinguish between these sequevars.

Clinical utility of the polymerase chain reaction in the diagnosis of infections due to Mycobacterium tuberculosis

OBJECTIVE

To evaluate the clinical utility of the polymerase chain reaction (PCR) in the diagnosis of infections due to Mycobacterium tuberculosis.

DESIGN

Clinical specimens were assayed by PCR for the presence of the insertion element IS6110, a DNA sequence unique to the M tuberculosis complex of organisms. The PCR results were then correlated with acid-fast bacilli (AFB) smears, cultures, pathology, and clinical histories.

SETTING

Bellevue Hospital, a large municipal teaching hospital.

PATIENTS

Inpatients on the Bellevue Chest Service.

MEASUREMENTS AND RESULTS

Sixty-five patients were evaluated. The PCR for M tuberculosis was positive in 37 patients and negative in 28. When correlated with smears, cultures, pathology, and clinical history, the sensitivity of PCR for a diagnosis of active tuberculosis (TB) was 100 percent. However, the specificity for a diagnosis of active TB was only 70 percent, as the PCR assay was positive in a number of patients with only prior, treated TB, or asymptomatic tuberculous infection. For a diagnosis of any TB infection (active, treated, or asymptomatic), sensitivity of PCR was 87.5 percent and specificity was 90 percent.

CONCLUSIONS

The PCR assay for TB is extremely sensitive, but it lacks specificity for a diagnosis of active TB. Its role in clinical practice will likely be limited to well-defined situations, such as HIV-positive patients with intrathoracic adenopathy, and it may be most useful in excluding active TB from consideration in selected patients. Given the cost of the assay and the labor intensity it requires, it should not be part of the routine initial evaluation of patients with suspected pulmonary TB.

Latency is not an inevitable outcome of infection with Pneumocystis carinii

Severe combined immunodeficiency (SCID) mice resolve naturally acquired Pneumocystis carinii pneumonia after reconstitution with immunocompetent spleen cells and can therefore be used as a model to study latent P. carinii infection. Neither P. carinii nor amplified P. carinii DNA was detected in the lungs of SCID mice killed 21 days after spleen cell reconstitution. Furthermore, SCID mice that recovered from P. carinii infection failed to reactivate the infection after they were either depleted of CD4+ cells for up to 84 days or depleted of CD4+ cells and treated with corticosteroid for 35 days. These results indicate that an immune response to P. carinii can completely clear the organism from the host. This supports the hypothesis that P. carinii pneumonia that develops in immunocompromised patients may be a new infection resulting from exposure to an exogenous source of P. carinii and not necessarily from reactivation of latent infection.