Multicenter, prospective clinical evaluation of respiratory samples from subjects at risk for Pneumocystis jirovecii infection by use of a commercial real-time PCR assay

Enhancing molecular approaches for diagnosis of fungal infections

Molecular tests can improve the diagnosis of fungal infections. Despite the increasing application for fungal detection, molecular tests are still not accepted as a diagnostic criterion to define invasive fungal diseases. This limitation is largely due to a lack of a standardized method. Method standardization can be achieved by following a consensus protocol developed by a working group, by performing a molecular test in a centralized laboratory or by using a commercial assay that provides a standardized method and quality-controlled reagents. Forming a consortium or a working group consisting of large-scale diagnostic mycology laboratories can accelerate the process of validating and implementing a commercial molecular assay for clinical use through a joint effort between industry partners and clinicians. Development of molecular tests not only for the detection of fungi but also for the identification of antifungal drug resistance directly in blood, bronchoalveolar lavage fluid, cerebrospinal fluid, and formalin-fixed and paraffin-embedded tissues greatly enhances fungal diagnostic capacities. Advances of developing quantitative assays and RNA detection platforms may provide another avenue to further improve fungal diagnostics.

Frequency, diagnosis and management of fungal respiratory infections

PURPOSE OF REVIEW

This review highlights key recent advances in fungal respiratory infections, encompassing developments in epidemiology, diagnostics and management, focussing on Aspergillus, Pneumocystis and Cryptococcus as key pathogens.

RECENT FINDINGS

Chronic pulmonary aspergillosis complicates existing lung diseases, particularly those associated with cavities or bullae, with a high global disease burden (prevalence estimate >1.1 million following tuberculosis) and significant under diagnosis (using Aspergillus IgG antibody). Several new treatment studies have been published (using caspofungin and voriconazole). Pneumocystis jirovecii demonstrates airborne transmission between infected and noninfected individuals necessitating isolation, and possibly identifying colonized patients. Early detection of serum cryptococcal antigenaemia in HIV may prevent development of meningitis, reducing morbidity and mortality, and routine testing of serum in community-acquired pneumonia cases in high endemicity areas may be helpful. Respiratory Aspergillus antigen and PCR testing is more sensitive than culture or serum testing. A new lateral flow antigen testing device may provide rapid bedside diagnosis of aspergillosis. Azole resistance to Aspergillus fumigatus is increasing across Europe.

SUMMARY

The field of fungal respiratory infection continues to evolve and develop, with many recent key advances. Patients, and possibly colonized patients, with Pneumocystis require isolation in hospitals and preferably segregation in outpatients. Challenges remain in almost all areas, with further work needed to identify the true burden of Aspergillus disease and address the increasing problem of azole resistance.

Clinical review: Respiratory failure in HIV-infected patients--a changing picture

Respiratory failure in HIV-infected patients is a relatively common presentation to ICU. The debate on ICU treatment of HIV-infected patients goes on despite an overall decline in mortality amongst these patients since the AIDS epidemic. Many intensive care physicians feel that ICU treatment of critically ill HIV patients is likely to be futile. This is mainly due to the unfavourable outcome of HIV patients with Pneumocystis jirovecii pneumonia who need mechanical ventilation. However, the changing spectrum of respiratory illness in HIV-infected patients and improved outcome from critical illness remain under-recognised. Also, the awareness of certain factors that can affect their outcome remains low. As there are important ethical and practical implications for intensive care clinicians while making decisions to provide ICU support to HIV-infected patients, a review of literature was undertaken. It is notable that the respiratory illnesses that are not directly related to underlying HIV disease are now commonly encountered in the highly active antiretroviral therapy (HAART) era. The overall incidence of P. jirovecii as a cause of respiratory failure has declined since the AIDS epidemic and sepsis including bacterial pneumonia has emerged as a frequent cause of hospital and ICU admission amongst HIV patients. The improved overall outcome of HIV patients needing ICU admission is related to advancement in general ICU care, including adoption of improved ventilation strategies. An awareness of respiratory illnesses in HIV-infected patients along with an appropriate diagnostic and treatment strategy may obviate the need for invasive ventilation and improve outcome further. HIV-infected patients presenting with respiratory failure will benefit from early admission to critical care for treatment and support. There is evidence to suggest that continuing or starting HAART in critically ill HIV patients is beneficial and hence should be considered after multidisciplinary discussion. As a very high percentage (up to 40%) of HIV patients are not known to be HIV infected at the time of ICU admission, the clinicians should keep a low threshold for requesting HIV testing for patients with recurrent pneumonia.

Development and evaluation of a real-time PCR assay for detection of Pneumocystis jirovecii on the fully automated BD MAX platform

Pneumocystis jirovecii is an opportunistic pathogen in immunocompromised and AIDS patients. Detection by quantitative PCR is faster and more sensitive than microscopic diagnosis yet requires specific infrastructure. We adapted a real-time PCR amplifying the major surface glycoprotein (MSG) target from Pneumocystis jirovecii for use on the new BD MAX platform. The assay allowed fully automated DNA extraction and multiplex real-time PCR. The BD MAX assay was evaluated against manual DNA extraction and conventional real-time PCR. The BD MAX was used in the research mode running a multiplex PCR (MSG, internal control, and sample process control). The assay had a detection limit of 10 copies of an MSG-encoding plasmid per PCR that equated to 500 copies/ml in respiratory specimens. We observed accurate quantification of MSG targets over a 7- to 8-log range. Prealiquoting and sealing of the complete PCR reagents in conical tubes allowed easy and convenient handling of the BD MAX PCR. In a retrospective analysis of 54 positive samples, the BD MAX assay showed good quantitative correlation with the reference PCR method (R(2) = 0.82). Cross-contamination was not observed. Prospectively, 278 respiratory samples were analyzed by both molecular assays. The positivity rate overall was 18.3%. The BD MAX assay identified 46 positive samples, compared to 40 by the reference PCR. The BD MAX assay required liquefaction of highly viscous samples with dithiothreitol as the only manual step, thus offering advantages for timely availability of molecular-based detection assays.

Fungal diagnostics: review of commercially available methods

Fungi and yeasts are critical causes of acute infection. As such, the detection and identification of these organisms are crucial in the diagnosis of affected patient populations. There is a vast array of commercial tests currently available for diagnostic purposes. These vary from traditional culture and biochemical methods to advanced multiparameter molecular tests. Recent technological advances have driven the development of rapid tests which are complementing and in some cases replacing the more traditional methods of detection. Irrespective of the method used the ultimate goal is timely detection of the infectious agent allowing appropriate treatment and improved outcome for the patient.

Emerging invasive fungal diseases in transplantation

Invasive fungal infections continue to be a major cause of morbidity and mortality in severely immunocompromised transplant patients. Although Candida spp. and Aspergillus spp. represent the majority of identified pathogens, other fungi have become increasingly prevalent among this patient population. Diagnosis and treatment of invasive fungal infections remain a challenge in transplant medicine despite recent major advances. In this review, we will emphasize emerging topics in invasive fungal infections in transplantations that occurred in 2011-2012. The current literature was reviewed to synthesize new trends in epidemiology, recent outbreaks, clinical findings, and advances in diagnostic and therapeutic resources.

The role of the clinical microbiology laboratory in solid organ transplantation programs

Infections remain a major complication of solid organ transplantation. For this reason, the clinical microbiology laboratory plays a key role in the success of transplant programs, which must have the support of a qualified laboratory, both technically and professionally. Transplant programs strongly condition the structure and functionality of microbiology laboratories, but at the same time, benefit greatly from the knowledge generated from these programs. The laboratory must make a special effort to implement rapid methods that can respond to the broad spectrum of potential pathogens in solid organ transplant patients. The integration of microbiologists in multidisciplinary teams is highly recommended, as only then can they obtain the highest quality and efficiency in the diagnostic process. This article provides an updated review of the techniques to be used once transplantation has occurred. The role of the microbiologist is also crucial in the pretransplant period, as good microbiological candidate evaluation at this time strongly conditions the success of the transplantation program.

Outcome of human immunodeficiency virus-exposed and -infected children admitted to a pediatric intensive care unit for respiratory failure

OBJECTIVE

Acute severe pneumonia with respiratory failure in human immunodeficiency virus-infected and -exposed infants carries a high mortality. Pneumocystis jiroveci is one cause, but other organisms have been suggested to play a role. Our objective is to describe the coinfections and treatment strategies in a cohort of human immunodeficiency virus-infected and -exposed infants with respiratory failure and acute respiratory distress syndrome, in an attempt to improve survival.

DESIGN

Prospective intervention study.

SETTING

Steve Biko Academic Hospital, Pretoria, South Africa.

PATIENTS

Human immunodeficiency virus-exposed infants with respiratory failure and acute respiratory distress syndrome were recruited into the study.

INTERVENTIONS

All infants were treated with routine therapy for Pneumocystis jiroveci and bacterial coinfection. However, in addition, all infants received ganciclovir from admission until the cytomegalovirus viral load result was demonstrated to be <log 4.

MEASUREMENTS

Routine investigations included human immunodeficiency virus polymerase chain reaction, cytomegalovirus viral load, blood culture, C-reactive protein, and white cell count. Tracheal aspirates for Pneumocystis jiroveci detection, bacterial culture, tuberculosis culture, and viral identification were performed.

MAIN RESULTS

Sixty-three patients met the recruitment criteria. The mortality rate was 30%. Pneumocystis jiroveci was positive in 33% of infants, while 38% had cytomegalovirus viral load ≥log 4. Only 7.9% of infants had a positive tuberculosis culture. Nineteen deaths occurred, 13 of which had a cytomegalovirus viral load ≥log 4. Bacterial coinfection and CD4 count were not predictors of mortality.

CONCLUSIONS

A case fatality rate of 30% is achievable if severe pneumonia with respiratory failure and acute respiratory distress syndrome is managed with a combination of antibiotics and ventilation strategies. Cytomegalovirus infection appears to be associated with an increased risk of death in this syndrome. This may, however, be a marker of as yet undefined pathology.

Colonization by Pneumocystis jirovecii and its role in disease

Although the incidence of Pneumocystis pneumonia (PCP) has decreased since the introduction of combination antiretroviral therapy, it remains an important cause of disease in both HIV-infected and non-HIV-infected immunosuppressed populations. The epidemiology of PCP has shifted over the course of the HIV epidemic both from changes in HIV and PCP treatment and prevention and from changes in critical care medicine. Although less common in non-HIV-infected immunosuppressed patients, PCP is now more frequently seen due to the increasing numbers of organ transplants and development of novel immunotherapies. New diagnostic and treatment modalities are under investigation. The immune response is critical in preventing this disease but also results in lung damage, and future work may offer potential areas for vaccine development or immunomodulatory therapy. Colonization with Pneumocystis is an area of increasing clinical and research interest and may be important in development of lung diseases such as chronic obstructive pulmonary disease. In this review, we discuss current clinical and research topics in the study of Pneumocystis and highlight areas for future research.

Validation of the MycAssay Pneumocystis kit for detection of Pneumocystis jirovecii in bronchoalveolar lavage specimens by comparison to a laboratory standard of direct immunofluorescence microscopy, real-time PCR, or conventional PCR

Pneumocystis jirovecii pneumonia is a significant cause of morbidity and mortality in AIDS patients as well as those with non-HIV immunosuppressive diseases. To aid diagnosis, the commercial MycAssay Pneumocystis real-time PCR assay (Myconostica, Ltd., Manchester, United Kingdom) targeting the mitochondrial ribosomal large subunit (mtLSU) has been developed to detect P. jirovecii in bronchoalveolar lavage (BAL) specimens. Here, we validated this assay against a laboratory standard of direct immunofluorescence microscopy, a cdc2 real-time PCR assay, or conventional PCR and sequencing of mtLSU. While more sensitive than any of these three assays analyzed individually, the MycAssay Pneumocystis assay demonstrated 100% sensitivity, 100% specificity, a 100% negative predictive value, and a 100% positive predictive value for detecting the presence of P. jirovecii in BAL specimens compared to the laboratory standard. Of note, two samples with positive cycle threshold (C(T)) values according to the MycAssay Pneumocystis assay lacked exponential amplification curves and thus were deemed negative. Also negative according to the laboratory standard, these samples highlight the importance of examining the amplification curves, in addition to noting the C(T) values, when interpreting positive results. Comparison of the MycAssay Pneumocystis assay to a laboratory standard establishes this assay to be a highly sensitive and specific method for the detection of P. jirovecii in bronchoalveolar lavage specimens. The approach may also be useful for the clinical laboratory validation of other sensitive real-time PCR assays.

Updating our understanding of pulmonary disease associated with HIV infection

The introduction of highly active antiretroviral therapy (HAART) has resulted in a reduction of opportunistic infections associated with cellular and humoral immunosuppression. However, what is still unclear is the impact of HAART on the development of other diseases not associated with AIDS, such as lung cancer and COPD. The aim of this paper is to review the most innovative and relevant aspects of lung pathology in patients infected with HIV.

Pneumocystis jirovecii pneumonia in non-HIV-infected patients: new risks and diagnostic tools

PURPOSE OF REVIEW

Non-HIV-infected populations are increasingly identified as being at risk for developing Pneumocystis jirovecii pneumonia (PJP). These patients typically present with severe disease and poorly tolerate invasive diagnostic procedures. This review examines recently reported risks for PJP in non-HIV populations and summarizes new diagnostic techniques.

RECENT FINDINGS

PJP is associated with immunomodulatory drug therapies, including monoclonal antibody therapies such as tumour necrosis factor α antagonists, and calcineurin inhibitors. Underlying disease states include solid-organ transplantation, connective tissue and rheumatologic disorders, inflammatory bowel disease, haematological malignancies, and solid tumours. Modern diagnostic techniques [conventional PCR, quantitative PCR, (1→3)-β-D-glucan assays, and PET] are reviewed with respect to predictive value and clinical utility. In particular, current literature regarding validation and specificity of molecular diagnostic techniques is summarized, including application to minimally invasive specimens.

SUMMARY

HIV-negative populations at risk for PJP can be identified. Conventional PCR increases diagnostic sensitivity but may detect asymptomatic colonization. Quantitative PCR demonstrates potential for distinguishing colonization from infection, but clinical validation is required. Serum (1→3)-β-D-glucan may be elevated in PJP, although standardized cut-off values for clinical infection have not been determined. Further validation of serum markers and molecular diagnostic methods is necessary for early and accurate diagnosis in non-HIV populations.

Fungal diagnostics in pneumonia

Fungal pneumonia is increasingly common, particularly in highly immunosuppressed patients, such as solid organ or hematopoietic stem cell transplant recipients, and the diagnosis is evolving. Although standard techniques such as microscopy and culture remain the mainstays of diagnosis, relatively recent advances in serological and molecular testing are important additions to the field. This article reviews the laboratory tools used to diagnose fungal respiratory disease.

Clinical significance of quantifying Pneumocystis jirovecii DNA by using real-time PCR in bronchoalveolar lavage fluid from immunocompromised patients

Quantitative PCR (qPCR) is more sensitive than microscopy for detecting Pneumocystis jirovecii in bronchoalveolar lavage (BAL) fluid. We therefore developed a qPCR assay and compared the results with those of a routine immunofluorescence assay (IFA) and clinical data. The assay included automated DNA extraction, amplification of the mitochondrial large-subunit rRNA gene and an internal control, and quantification of copy numbers with the help of a plasmid clone. We studied 353 consecutive BAL fluids obtained for investigation of unexplained fever and/or pneumonia in 287 immunocompromised patients. No qPCR inhibition was observed. Seventeen (5%) samples were both IFA and qPCR positive, 63 (18%) were IFA negative and qPCR positive, and 273 (77%) were both IFA and qPCR negative. The copy number was significantly higher for IFA-positive/qPCR-positive samples than for IFA-negative/qPCR-positive samples (4.2 ± 1.2 versus 1.1 ± 1.1 log(10) copies/μl; P < 10(-4)). With IFA as the standard, the qPCR assay sensitivity was 100% for ≥2.6 log(10) copies/μl and the specificity was 100% for ≥4 log(10) copies/μl. Since qPCR results were not available at the time of decision-making, these findings did not trigger cotrimoxazole therapy. Patients with systemic inflammatory diseases and IFA-negative/qPCR-positive BAL fluid had a worse 1-year survival rate than those with IFA-negative/qPCR-negative results (P < 10(-3)), in contrast with solid-organ transplant recipients (P = 0.88) and patients with hematological malignancy (P = 0.26). Quantifying P. jirovecii DNA in BAL fluids independently of IFA positivity should be incorporated into the investigation of pneumonia in immunocompromised patients. The relevant threshold remains to be determined and may vary according to the underlying disease.

PCR diagnosis of Pneumocystis pneumonia: a bivariate meta-analysis

We undertook a bivariate meta-analysis to assess the overall accuracy of respiratory specimen PCR assays for diagnosing Pneumocystis pneumonia. The summary sensitivity and specificity were 0.99 (95% confidence interval, 0.96 to 1.00) and 0.90 (0.87 to 0.93). Subgroup analyses showed that quantitative PCR analysis and the major surface glycoprotein gene target had the highest specificity value (0.93). Respiratory specimen PCR results are sufficient to confirm or exclude the disease for at-risk patients suspected of having Pneumocystis pneumonia.