Non-invasive diagnosis of Pneumocystis carinii pneumonia in haematological patients using PCR on oral washes

Use of Oropharyngeal Washes to Diagnose and Genotype Pneumocystis jirovecii

Pneumocystis jirovecii is a symbiotic respiratory fungus that presents in 2 clinical forms: pneumonia in immunocompromised patients or colonization, defined by the presence of the organism without associated clinical symptoms. Currently, diagnosis requires invasive bronchoscopy, which may not be available in some settings and is inappropriate for detecting colonization in healthy individuals. Noninvasive diagnostic techniques and molecular strain typing tools that can be used on these samples are critical for conducting studies to better understand transmission. We evaluated 2 real-time polymerase chain reaction (PCR) assays targeting dihydropteroate synthase and the major surface glycoprotein for detection in 77 oropharyngeal washes (OPWs) from 43 symptomatic human immunodeficiency virus-infected patients who underwent bronchoscopy. We also evaluated the ability of a new microsatellite (MS) genotyping panel to strain type infections from these samples. Each PCR used individually provided a high sensitivity (>80%) for detection of pneumonia but a modest specificity (<70%). When used in combination, specificity was increased to 100% with a drop in sensitivity (74%). Concentration of organisms by PCR in the OPW tended to be lower in colonized individuals compared with those with pneumonia, but differences in concentration could not clearly define colonization in symptomatic individuals. Oropharyngeal wash samples were genotyped using 6 MSs with ≥4 alleles successfully genotyped in the majority of colonized patients and ≥5 alleles in patients with pneumonia. The MS profile was consistent over time within patients with serial OPWs analyzed. Microsatellite genotyping on noninvasive samples may aid in studying the molecular epidemiology of this pathogen without requiring invasive diagnostic techniques.

Cost-effectiveness analysis of diagnostic options for pneumocystis pneumonia (PCP)

Background

Diagnosis of Pneumocystis jirovecii pneumonia (PCP) is challenging, particularly in developing countries. Highly sensitive diagnostic methods are costly, while less expensive methods often lack sensitivity or specificity. Cost-effectiveness comparisons of the various diagnostic options have not been presented.

Methods and Findings

We compared cost-effectiveness, as measured by cost per life-years gained and proportion of patients successfully diagnosed and treated, of 33 PCP diagnostic options, involving combinations of specimen collection methods [oral washes, induced and expectorated sputum, and bronchoalveolar lavage (BAL)] and laboratory diagnostic procedures [various staining procedures or polymerase chain reactions (PCR)], or clinical diagnosis with chest x-ray alone. Our analyses were conducted from the perspective of the government payer among ambulatory, HIV-infected patients with symptoms of pneumonia presenting to HIV clinics and hospitals in South Africa. Costing data were obtained from the National Institutes of Communicable Diseases in South Africa. At 50% disease prevalence, diagnostic procedures involving expectorated sputum with any PCR method, or induced sputum with nested or real-time PCR, were all highly cost-effective, successfully treating 77–90% of patients at $26–51 per life-year gained. Procedures using BAL specimens were significantly more expensive without added benefit, successfully treating 68–90% of patients at costs of $189–232 per life-year gained. A relatively cost-effective diagnostic procedure that did not require PCR was Toluidine Blue O staining of induced sputum ($25 per life-year gained, successfully treating 68% of patients). Diagnosis using chest x-rays alone resulted in successful treatment of 77% of patients, though cost-effectiveness was reduced ($109 per life-year gained) compared with several molecular diagnostic options.

Conclusions

For diagnosis of PCP, use of PCR technologies, when combined with less-invasive patient specimens such as expectorated or induced sputum, represent more cost-effective options than any diagnostic procedure using BAL, or chest x-ray alone.

Few but severe viral infections in children with cancer: a prospective RT-PCR and PCR-based 12-month study

BACKGROUND

Treatment of low-risk febrile episodes with oral administered antibiotics at home is a new approach in pediatric oncology and protective isolation is loosened in more centers. The impact of viral respiratory infections in febrile diseases in this population is still unclear in terms of occurrence and morbidity.

PROCEDURE

A prospective follow-up study of all febrile episodes during 12 months in a pediatric oncology department with a high level of protective isolation was set-up with expanded molecular viral examinations. Reverse transcriptase polymerase chain reaction (RT-PCR) and PCR diagnostics of ten viruses, two atypical bacteria, and one fungus were performed and clinical information on all infections was registered.

RESULTS

A total of 250 febrile episodes in 66 patients were registered. In all, 198 respiratory secretions, predominantly oral washes, and 165 anal swabs were analyzed. Twenty-two infections were diagnosed: 7 rhinovirus infections, 4 respiratory syncytial virus (RSV) infections, 2 herpes simplex virus (HSV) infections, 2 varicella-zoster-virus (VZV) infections, 1 influenza B virus infection, 1 parainfluenza virus type 3 infection (PIV3), 1 human metapneumovirus (HMPV) infection, 1 enterovirus infection, 0 adenovirus infections, 0 influenza A virus infections, and 3 non-viral pneumonias: 1 M. Pneumonia, 1 C. Pneumonia, and 1 P. Carinii. The detected pathogens correlated well to the clinical disease. Patients with viral infections were as affected as patients with bacteria in the blood. One of 19 viral infections was lethal, a RSV pneumonia. C-reactive protein concentrations were not able to distinguish viral infections from bacteremias.

CONCLUSIONS

The applied sampling method was acceptable and molecular diagnosis of viruses, atypical bacteria and P. Carinii increased the microbiological verification of infections by 35%. Viral infections were few in our protected population but caused severe infectious complications in these patients.

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.

DNA amplification of nasopharyngeal aspirates in rats: a procedure to detect Pneumocystis carinii

The diagnosis of Pneumocystis carinii pneumonia (PCP) requires invasive methods of bronchoalveolar lavage and lung biopsy. In this study, we examined efficacy of polymerase chain reaction (PCR) compared to Giemsa and silver ammoniacal staining to detect P. carinii in easily accessible extrapulmonary sites as well as lung. Samples were collected from lung, nasal and pharyngeal aspirates, gastric contents, urine and blood from dexamethasone treated or untreated virus-free Sprague-Dawley rats. All immunosuppressed lung samples were P. carinii positive by PCR analysis and both stains. Respectively DNA fragments of P. carinii were found in 93%, of nasal and 75% of pharyngeal aspirates, and 0% of sera, urine or gastric aspirates from immunosuppressed rats. However, no P. carinii cysts or trophozoites were found in nasal and pharyngeal aspirates (extrapulmonary sites) by silver ammoniacal or Giemsa staining. In comparison, none of the specimens from immunocompetent rats were PCR positive at any sites tested including the lungs. Therefore, PCR amplification products of nasal and pharyngeal aspirates showed that immunosuppressed rats with PCP can carry P. carinii DNA fragments in their upper respiratory tracts, but immunocompetent animals without PCP, are free of the organism and this suggests an approach to be investigated in humans with PCP.

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.

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.