Update on Diagnosis of Pneumocystis Pulmonary Infections

Pneumocystis pneumonia in COVID-19 patients: A comprehensive review

The admitted patients of intensive care units with coronavirus disease 2019 (COVID-19) meet the challenges of subsequent infections. Opportunistic fungal infections such as Pneumocystis pneumonia (PCP) are among the important factors in the context of COVID-19 patients affecting illness severity and mortality. We reviewed the literature on COVID-19 patients with PCP to identify features of this infection. Although studies confirmed at least the presence of one immunosuppressive condition in half of PCP patients, this disease can also occur in immunocompetent patients who developed the immunosuppressive condition during Covid-19 treatment. The major risk factors associated with COVID-19 patients with PCP can be considered low lymphocyte counts and corticosteroid therapy. Diagnostic and treatment options are complicated by the overlapping clinical and radiologic characteristics of PCP and COVID-19 pneumonia. Therefore, physicians should comprehensively evaluate high-risk patients for PCP prophylaxis.

Comparison of PneumID real-time PCR assay with Amplex eazyplex LAMP assay for laboratory diagnosis of Pneumocystis jirovecii Pneumonia

We compared PneumID PCR with Amplex eazyplex LAMP assay for the diagnosis of Pneumocystis jirovecii pneumonia (PJP). Both assays enable accurate diagnosis of definite PJP. Cut-off cycle threshold of the PneumID assay was < 26.68 while the cut-off time-to-positivity of the eazyplex assay was 16:02 (minutes:seconds). The positive and negative percentage agreement of eazyplex assay with PneumID assay was 75.0% and 100.0% respectively, while the overall agreement was substantial with kappa = 0.80. For both assays, establishment of cut-off values to differentiate probable PJP from colonization was not feasible as results overlapped.

Comparison of the PneumoGenius® and RealStar® Pneumocystis jirovecii PCR CE-IVD assays with a lab developed test for the detection of Pneumocystis jirovecii

Pneumocystis jirovecii (Pj) is a fungal pathogen that can cause severe and potential fatal pneumonia (Pneumocystis pneumonia, PCP) in immunocompromised patients. Microbiological diagnosis is necessary to confirm PCP, for which mainly real-time PCR assays are used by detecting Pj from bronchoalveolar lavage (BAL) specimens. In this study, we evaluate the performance of the CE-IVD PneumoGenius® assay and CE-IVD RealStar® Pneumocystis jirovecii PCR assay in comparison to the lab developed test (LDT) that is used in routine diagnostics. Comparison was done by including 100 BAL specimens: 25 retrospective specimens, selected based on results obtained with LDT (15 positive/10 negative), and 75 prospectively collected specimens. LDT (targeting MSG) was performed according to local procedures and the PneumoGenius® (targeting mtLSU and DHPS fas) and RealStar® assays (targeting mtLSU) according to manufacturer's instructions. Combining results of retrospective and prospective analysis, sensitivity was 69.7%, 100% and 100% for the LDT, PneumoGenius® and RealStar®, respectively. Specificity was 100% for LDT and Pneumogenius®, whereas RealStar® showed a specificity of 97%. Correlation of fungal loads found with the PneumoGenius® and RealStar® assays was high (R2: 0.98). The PneumoGenius® and RealStar® assays performed comparable, and both showed high sensitivity in comparison to the LDT. For optimal diagnosis of PCP, the LDT has to be replaced by another, more sensitive assay.

Is It Possible to Differentiate Pneumocystis jirovecii Pneumonia and Colonization in the Immunocompromised Patients with Pneumonia?

Respiratory sample staining is a standard tool used to diagnose Pneumocystis jirovecii pneumonia (PjP). Although molecular tests are more sensitive, their interpretation can be difficult due to the potential of colonization. We aimed to validate a Pneumocystis jirovecii (Pj) real-time PCR (qPCR) assay in bronchoscopic bronchoalveolar lavage (BAL) and oropharyngeal washes (OW). We included 158 immunosuppressed patients with pneumonia, 35 lung cancer patients who underwent BAL, and 20 healthy individuals. We used a SYBR green qPCR assay to look for a 103 bp fragment of the Pj mtLSU rRNA gene in BAL and OW. We calculated the qPCR cut-off as well as the analytical and diagnostic characteristics. The qPCR was positive in 67.8% of BAL samples from the immunocompromised patients. The established cut-off for discriminating between disease and colonization was Ct 24.53 for BAL samples. In the immunosuppressed group, qPCR detected all 25 microscopy-positive PjP cases, plus three additional cases. Pj colonization in the immunocompromised group was 66.2%, while in the cancer group, colonization rates were 48%. qPCR was ineffective at diagnosing PjP in the OW samples. This new qPCR allowed for reliable diagnosis of PjP, and differentiation between PjP disease and colonization in BAL of immunocompromised patients with pneumonia.

Pneumocystis jirovecii Disease: Basis for the Revised EORTC/MSGERC Invasive Fungal Disease Definitions in Individuals Without Human Immunodeficiency Virus

BACKGROUND

Pneumocystis jirovecii pneumonia (PCP) causes substantive morbidity in immunocompromised patients. The EORTC/MSGERC convened an expert group to elaborate consensus definitions for Pneumocystis disease for the purpose of interventional clinical trials and epidemiological studies and evaluation of diagnostic tests.

METHODS

Definitions were based on the triad of host factors, clinical-radiologic features, and mycologic tests with categorization into probable and proven Pneumocystis disease, and to be applicable to immunocompromised adults and children without human immunodeficiency virus (HIV). Definitions were formulated and their criteria debated and adjusted after public consultation. The definitions were published within the 2019 update of the EORTC/MSGERC Consensus Definitions of Invasive Fungal Disease. Here we detail the scientific rationale behind the disease definitions.

RESULTS

The diagnosis of proven PCP is based on clinical and radiologic criteria plus demonstration of P. jirovecii by microscopy using conventional or immunofluorescence staining in tissue or respiratory tract specimens. Probable PCP is defined by the presence of appropriate host factors and clinical-radiologic criteria, plus amplification of P. jirovecii DNA by quantitative real-time polymerase chain reaction (PCR) in respiratory specimens and/or detection of β-d-glucan in serum provided that another invasive fungal disease and a false-positive result can be ruled out. Extrapulmonary Pneumocystis disease requires demonstration of the organism in affected tissue by microscopy and, preferably, PCR.

CONCLUSIONS

These updated definitions of Pneumocystis diseases should prove applicable in clinical, diagnostic, and epidemiologic research in a broad range of immunocompromised patients without HIV.

Evaluation of a commercial Loop-mediated Isothermal Amplification (LAMP) assay for rapid detection of Pneumocystis jirovecii

BACKGROUND

Various tools are obtainable for the detection of Pneumocystis jirovecii, among them qPCR promising highest sensitivity. A novel molecular method is commercially available, the loop-mediated isothermal amplification (LAMP) assay.

OBJECTIVES

We compared the performance of the LAMP eazyplex^® Pneumocystis jirovecii with the RealStar Pneumocystis jirovecii PCR 1.0 qPCR.

MATERIAL/METHODS

Overall, 162 lower respiratory tract specimens from 146 critically ill patients were investigated. LAMP assay and qPCR were carried out according to the manufacturer's recommendations. Positive results of the LAMP were described as time to positivity (TTP). The limit of detection (LOD) of the LAMP was analysed using 10-fold serial dilutions of a high positive P jirovecii respiratory sample. For each serial dilution, TTP of the LAMP was plotted against cycle threshold (Ct) values of the qPCR.

RESULTS

The LOD of the LAMP was determined to be approximately 4 × 10³ copies/mL. While the LAMP revealed 28 (17%) positive signals from 20 patients, by using qPCR 41 (25%) positive samples from 28 patients were identified. Overall agreement with qPCR was 92%. Five false-negative, one false-positive and nine invalid results were detected by the LAMP. Positive and negative predictive values were 96% each, and sensitivity and specificity were 84% and 99%, respectively. There was a low correlation between the TTP and the fungal load.

CONCLUSION

The LAMP is a time-saving and easy-to-perform method. It can be used as an alternative diagnostic method. However, for quantification purposes the qPCR is still the gold standard.

The changing trends and profile of pneumocystosis mortality in the United States, 1999-2014

Pneumocystosis (PCP) mortality in the U.S. has received less attention in recent years. This study describes recent trends in mortality and the estimated burden of PCP in the U.S., using the national multiple cause of death data during 1999-2014. PCP mortality rates were calculated for age, sex, race and year. Demographic differences were presented for decedents with and without a human immunodeficiency virus (HIV) co-diagnosis. Matched odds ratios (MOR) were generated to describe associations between non-HIV conditions and PCP mortality. In total, 11 512 PCP deaths occurred during 1999-2014. Annual age-adjusted PCP mortality decreased over this time period, from 0.479 to 0.154 per 100 000 population (1999 vs 2014 respectively). Over two-thirds of decedents were male and Blacks had the highest mortality as compared to Whites. HIV co-diagnosis accounted for 48% of all PCP deaths in 2014 vs 71% in 1999. Comorbid conditions such as connective tissue disorders (MOR=12.29; 95% confidence interval=[10.26, 14.71]) were associated with a PCP diagnosis. Productivity losses amounted to >$12 billion during the study period. Although widespread use of antiretroviral therapy and PCP prophylaxis for HIV infection likely contributed to the overall decline in PCP deaths during 1999-2014, a continual need exists to prevent and treat this fungal disease in immune-compromised populations that are not infected with HIV.