Laboratory diagnosis of Pneumocystis carinii infections by PCR directed to genes encoding for mitochondrial 5S and 28S ribosomal RNA

Molecular diagnosis of Pneumocystis pneumonia in immunocompromised patients

PURPOSE OF REVIEW

Pneumocystis pneumonia (PCP) is a frequent opportunistic infection associated with a high mortality rate. PCP is of increasing importance in non-HIV immunocompromised patients, who present with severe respiratory distress with low fungal loads. Molecular detection of Pneumocystis in broncho-alveolar lavage (BAL) has become an important diagnostic tool, but quantitative PCR (qPCR) needs standardization.

RECENT FINDINGS

Despite a high negative predictive value, the positive predictive value of qPCR is moderate, as it also detects colonized patients. Attempts are made to set a cut-off value of qPCR to discriminate between PCP and colonization, or to use noninvasive samples or combined strategies to increase specificity.

SUMMARY

It is easy to set a qPCR cut-off for HIV-infected patients. In non-HIV IC patients, a gain in specificity could be obtained by combining strategies, that is, qPCR on BAL and a noninvasive sample, or qPCR and serum beta-1,3-D-glucan dosage.

Finding your way through Pneumocystis sequences in the NCBI gene database

Pneumocystis sequences can be downloaded from GenBank for purposes as primer/probe design or phylogenetic studies. Due to changes in nomenclature and assignment, available sequences are presented with a variety of inhomogeneous information, which renders practical utilization difficult. The aim of this study was the descriptive evaluation of different parameters of 532 Pneumocystis sequences of mitochondrial and ribosomal origin downloaded from GenBank with regard to completeness and information content. Pneumocystis sequences were characterized by up to four different names. Official changes in nomenclature have only been partly implemented and the usage of the "forma specialis", a special feature of Pneumocystis, has only been established fragmentary in the database. Hints for a mitochondrial or ribosomal genomic origin could be found, but can easily be overlooked, which renders the download of wrong reference material possible. The specification of the host was either not available or variable regarding the used language and the localization of this information in the title or several subtitles, which limits their applicability in phylogenetic studies. Declaration of products and geographic origin was incomplete. The print version of this manuscript is completed by an online database which contains detailed information to every accession number included in the meta-analysis.

Degree and frequency of inhibition in a routine real-time PCR detecting Pneumocystis jirovecii for the diagnosis of Pneumocystis pneumonia in Turkey

Routine laboratory diagnosis of Pneumocystis jirovecii is currently achieved by PCR in almost all laboratories with sufficient equipment due to its high sensitivity and specificity compared to staining methods. A current issue that limits the reliability and sensitivity of PCR is the degree of inhibition caused by inhibitory substances in respiratory samples. The present study aimed to analyse the degree and frequency of inhibition in real-time PCR detecting P. jirovecii in respiratory specimens submitted to a Pneumocystis pneumonia (PcP) diagnosis laboratory in Ege University Medical School, Turkey. Between July 2009 and December 2010, 76 respiratory specimens [63 bronchoalveolar lavage (BAL) fluid, 10 sputum samples, two tracheal aspiration fluid and one thoracentesis fluid] obtained from 69 PcP-suspected patients were investigated for the presence of P. jirovecii using real-time PCR targeting the cdc2 gene. Of these samples, 42 of the specimens were stained and examined by microscopy according to the request of the clinicians. PCR was positive in 15 specimens in the initial run. Of the remaining 61 samples, 41 of them were negative with positive internal inhibition controls (i.e. true-negative group). The frequency of inhibition in the initial run was 26.31 % (20/76) as determined by spiked negative controls. All of the inhibited samples were resolved after 1 : 2, 1 : 5, 1 : 10 and 1 : 20 dilutions. P. jirovecii was detected by PCR in two inhibited specimens after retesting with diluted samples which were also positive by microscopy. The incidence of P. jirovecii in respiratory specimens was 22.36 % (17/76) as determined by real-time PCR and 7.14 % (3/42) by microscopy. Overall, the incidence of P. jirovecii in respiratory samples was 23.68 % (18/76) as detected by both methods. In conclusion, inclusion of spiked positive controls in each sample and retesting with diluted samples to resolve inhibition increased the reliability of the real-time PCR assay in terms of determining false-negative results and influencing the treatment of the patient. Furthermore, results of the present study determined for the first time the frequency and degree of inhibition in a real-time PCR detecting P. jirovecii in respiratory specimens during routine diagnosis of PcP.

Improved detection of Pneumocystis jirovecii infection in a tertiary care reference hospital in India

We prospectively examined 143 clinical samples from 115 patients including both HIV infected (n=53) and HIV uninfected immunocompromized (n=62) patients, with lung infiltrates and with clinical features suggestive of Pneumocystis carinii pneumonia/ PneumoCystis Pneumonia (PcP), using both microscopic techniques as well as PCR assay. Clinical samples in the present study consisted of bronchoalveolar lavage (BAL), tracheal aspirate (TA), nasopharyngeal aspirate (NPA), sputum and gastric aspirate (GA). Another group of 21 individuals with other respiratory diseases not compatible with PcP served as control during the study period of 15 months. Overall, P. jirovecii positivity rate by PCR was 12.17% (14/115 patients) compared to 3.4% (4/115) by microscopy. None of the specimens in the control group was positive by any of the techniques used. All PCR negative patients including cases and controls showed no evidence of PcP. After resolution of the discrepant results upon review of the clinical data, the sensitivity and specificity were 100% and 99%, respectively, for PCR and 30.7% and 100%, respectively, for microscopy by GMS staining. Thus, our data support the significance of PCR assay for confirming and improving the diagnosis of PcP in high-risk patients.

Polymerase chain reaction detection of Pneumocystis jiroveci: evaluation of 9 assays

Various polymerase chain reaction (PCR) amplification strategies have been described for detecting Pneumocystis jiroveci in clinical specimens. Different combinations of primer/target and platforms have been reported to yield varying PCR detection rates. PCR was evaluated on clinical specimens using internal transcribed spacer regions of the rRNA nested, dihydropteroate synthase single and nested, dihydrofolate reductase nested, major surface glycoprotein heminested, mitochondrial large subunit rRNA (mtLSUrRNA) single and nested, 18S rRNA 1-tube nested, and real-time 5S rRNA PCR. The most sensitive PCR was subsequently compared with routine diagnostic immunofluorescence (IF) microscopy. Discrepant PCR and IF results were resolved after review of clinical and histology/cytology records. Major discrepancies were observed among the methods investigated. mtLSUrRNA nested PCR was the most sensitive, produced less false-negative results, and displayed the highest degree of concordance with histology. Direct comparison of mtLSUrRNA nested PCR versus IF yielded low sensitivity and specificity, which were improved for PCR and lowered for IF on review of clinical and laboratory records.

Molecular diagnosis ofPneumocystispneumonia

The detection of Pneumocystis DNA in clinical specimens by using PCR assays is leading to important advances in Pneumocystis pneumonia (PcP) clinical diagnosis, therapy and epidemiology. Highly sensitive and specific PCR tools improved the clinical diagnosis of PcP allowing an accurate, early diagnosis of Pneumocystis infection, which should lead to a decreased duration from onset of symptoms to treatment, a period with recognized impact on prognosis. This aspect has marked importance in HIV-negative immunocompromised patients, who develop often PcP with lower parasite rates than AIDS patients. The specific amplification of selected polymorphous sequences of Pneumocystis jirovecii genome, especially of internal transcribed spacer regions of the nuclear rRNA operon, has led to the identification of specific parasite genotypes which might be associated with PcP severity. Moreover, multi-locus genotyping revealed to be a useful tool to explore person-to-person transmission. Furthermore, PCR was recently used for detecting P. jirovecii dihydropteroate synthase gene mutations, which are apparently associated with sulfa drug resistance. PCR assays detected Pneumocystis-DNA in bronchoalveolar lavage fluid or biopsy specimens, but also in oropharyngeal washings obtained by rinsing of the mouth. This non-invasive procedure may reach 90%-sensitivity and has been used for monitoring the response to treatment in AIDS patients and for typing Pneumocystis isolates.

PCR diagnosis of Pneumocystis carinii on sputum and bronchoalveolar lavage samples in immuno-compromised patients

The polymerase chain reaction (PCR) technique was compared with Wright-Giemsa (WG), Gomori methenamine silver (GMS) stains and an immunofluorescence assay (IFA) for detection of Pneumocystis carinii in immuno-compromised patients. Specimens of 21 bronchoalveolar lavages (BAL) and 139 sputum samples, were obtained from 157 patients (38 with AIDS and 119 with HIV) from four hospitals in Khon Kaen, Thailand. A true positive required at least two positives by techniques considered gold standard tests. Eleven (52.38%) BAL and 13 (9.35%) sputum specimens were positive. PCR produced the highest sensitivity and negative predictive values for the BAL (100% for each) vs. sputum samples at 84.62 and 98.41 percent, respectively. The specificity of PCR was 90% and 98.41% for BAL and sputum samples, respectively. We suggest PCR is an important tool for the epidemiological study of P. carinii in high-risk individuals.

Pulmonary blastomycosis: an appraisal of diagnostic techniques

OBJECTIVES

Pulmonary blastomycosis often mimics bacterial pneumonia or bronchogenic carcinoma, which may result in delayed therapy or the performance of unnecessary diagnostic procedures. We have reviewed the utilization of diagnostic techniques in the workup of patients with pulmonary blastomycosis, defined their diagnostic yields, and proposed an optimal diagnostic approach for the patient in whom pulmonary blastomycosis is considered.

DESIGN

Retrospective chart review of all patients with the diagnosis of blastomycosis at a major academic medical center.

RESULTS

Of the 119 patients with blastomycosis, 56 (47%) had pulmonary involvement. A total of 92 specimens were obtained by noninvasive means (sputa, 72 specimens; tracheal secretions, 5 specimens; and gastric washings, 15 specimens) in 35 patients. KOH smears were prepared from 22 of those specimens (24%). The diagnostic yield from these culture specimens obtained by noninvasive means was 86% per patient, and 75% per single sample. The diagnostic yields from KOH smears were 46% and 36%, respectively. Flexible bronchoscopy was performed in 24 patients and yielded a diagnosis in 22 (92%). Cultures of bronchial secretions (19 patients) and BAL fluid (6 patients) were positive in 100% and 67% of patients, respectively. The corresponding yields of KOH preparations were 17% (1 of 6 preparations) and 50% (3 of 6 preparations), respectively. Pathology specimens including those from bronchoscopic lung biopsies (nine patients), bronchial brushings (two patients), and bronchoscopic needle aspiration (one patient) were positive in 22%, 50%, and 0% of cases, respectively. Cytology was usually performed to exclude malignancy and was positive for Blastomyces dermatitidis in five patients (sputum, three patients; bronchial washings, two patients). Thoracotomy was performed in 11 cases, and in all patients the procedure yielded a diagnosis. Serology results were available in 25 patients. Immunodiffusion was positive in 10 patients (40%), and complement fixation in 4 patients (16%).

CONCLUSIONS

In patients with pulmonary blastomycosis, the positive yield from respiratory specimen cultures is high, but the confirmation of a diagnosis may take up to 5 weeks. Wet smears and cytology examinations of respiratory specimens provide quicker diagnoses but are underutilized. Their routine use is recommended in endemic areas. Commonly used serologic assays are insensitive and are not useful for diagnostic screening.