Diagnostic value of direct fluorescence antibody staining for detecting Pneumocystis jirovecii in expectorated sputum from patients with HIV infection

Comparing Polymerase Chain Reaction Testing of Nasopharyngeal Swab and Lower Respiratory Tract Specimens for the Diagnosis of Pneumocystis jirovecii Pneumonia

Using nasopharyngeal (NP) swab samples instead of lower respiratory tract specimens for polymerase chain reaction (PCR) to diagnose Pneumocystis jirovecii pneumonia (PJP) may be better tolerated and improve diagnostic accessibility. In this 2-year Australian retrospective cohort study of patients with clinically suspected PJP, P jirovecii PCR on NP swab samples had perfect specificity but low sensitivity (0.66).

Molecular diagnostics of infectious disease: Detection and characterization of microbial agents in cytology samples

BACKGROUND

Cytology samples are widely used to diagnose various infectious diseases by detection and identification of causative infectious agents, including bacteria, fungi, and viruses. The role of cytopathology in infectious disease has expanded tremendously in the past decades with the advances in molecular techniques. Molecular diagnostic methods, compared to conventional methods, have shown improved patient outcome, reduction in cost, and shortened hospital stay times. The aim of this article is to review molecular testing in cytology samples for diagnosis of infectious diseases.

METHODS

The literature search for molecular testing in common cytology samples for diagnosis of infectious diseases was performed. The findings of the studies were summarized. The common cytology samples included in this article were gynecologic specimens, cerebrospinal fluid, bronchoalveolar lavage, and urine samples.

CONCLUSIONS

There are a number of molecular diagnostic tests that are available to be used in common cytology samples to detect infectious agents. Each test has its own advantages and limitations. It is our hope that upon reading this review article, the readers will have better understanding of molecular diagnostic testing of infectious diseases utilizing commonly sampled cytology specimens in daily practice.

Clinical Characteristics and Prognosis of the Modified Probable Pneumocystis jirovecii Pneumonia in Korean Children, 2001-2021

There are few data about Pneumocystis jirovecii pneumonia (PCP) in children, particularly in developed countries. This study investigated the clinical characteristics and prognosis of the clinical PCP in non-HIV-infected Korean children. Children with positive results for the staining and/or polymerase chain reaction (PCR) for P. jirovecii between 2001 and 2021 were identified. Patients were grouped into clinical PCP, which comprised proven and modified probable cases, and non-PCP groups. Modified probable PCP (mp-PCP) indicate the case which P. jirovecii was detected by conventional PCR rather than real-time PCR test. The differences in demographic and clinical characteristics were analyzed between the groups. A total of 110 pneumonia cases with positive results for P. jirovecii PCR and/or stain were identified from 107 children. Of these, 28.2% were classified as non-PCP, 12.7% of proven PCP, and 59.1% of mp-PCP. Compared with the non-PCP group, the mp-PCP group had a significantly higher rate of solid organ transplantation (3.2% vs. 24.6%), fever (58.1% vs. 76.9%), tachypnea (25.8% vs. 66.2%), dyspnea (48.4% vs. 83.1%), desaturation (48.4% vs. 80.0%), and bilateral ground-glass opacity on chest radiograph (19.4% vs. 73.8%). However, when the mp-PCP group was compared with the proven PCP group, there was no statistically significant difference. For children with clinical PCP, age under 5 years of age (odds ratio [OR] 10.7), hospital-onset (OR 6.9), and desaturation as initial symptom (OR 63.5) were significant risk factors for death in multivariable analysis. Modified probable PCP might reliably reflect true PCP in terms of patient's demographic, clinical features, treatment response, and prognosis. Immunocompromised children with hospital-onset pneumonia who are younger than 5 years of age and have desaturation would be more cautiously and aggressively managed for survival through the screening for P. jirovecii by conventional PCR on appropriate lower respiratory specimens.

Epidemiology of fungal diseases in Africa: A review of diagnostic drivers

Background and Purpose:

There has been a significant increase in the burden of fungal diseases in the last few decades which has imposed a global threat to the health of humans, animals, and plants. Epidemiology of fungal diseases is not completely understood in Africa. Most of these diseases are under-reported or not reported at all mainly due to the challenges related to the availability of and access to fungal diagnostics and the lack of human resources in clinical and diagnostic mycology across the continent. Therefore, it is imperative to highlight the epidemiology of the endemic and epidemic of emerging and re-emerging fungal diseases as well as their diagnostic challenges in Africa based on the available data. Moreover, it is important to underline the existing gaps in this regard as well.

Materials and Methods:

For the purposes of the study, Medline and Google Scholar were searched to retrieve articles on these prominent fungal diseases, as well as their etiologies and available diagnostics.

Results:

It was found that histoplasmosis and other AIDS-associated mycoses have been reported in Africa, including blastomycosis, coccidioidomycosis, and paracocci-dioidomycosis. Other reported infections were fungal neglected tropical diseases, especially sporotrichosis, dermatophytosis, mycetoma, and chromoblastomycosis as well as emerging fungal diseases, such as Emergomyces africanus, Candida auris, and Blastomyces emzantsi. In Africa, the major drivers of fungal diseases include human immunodeficiency infection, tuberculosis, and poverty.

Conclusion:

Serious fungal diseases are common in Africa; however, the true burden remains unknown.

The diagnostic challenge of pneumocystis pneumonia and COVID-19 co-infection in HIV

Coronavirus disease 2019 (COVID-19) and pneumocystis pneumonia (PCP) share many overlapping features and may be clinically indistinguishable on initial presentation in people living with HIV. We present the case of co-infection with COVID-19 and PCP in a patient with progressive respiratory failure admitted to our intensive care unit where the dominant disease was uncertain. This case highlights the difficulty in differentiating between the two diseases, especially in a high HIV prevalence setting where PCP is frequently diagnosed using case definitions and clinical experience due to limited access to bronchoscopy, appropriate laboratory testing, and computed tomography scans. In addition, diagnostic testing may yield false-negative results in both diseases, and clinician awareness to the overlap and pitfalls is essential if COVID-19 becomes endemic in such settings.

Diagnosis of Pneumocystis jirovecii Pneumonia in Pediatric Patients in Serbia, Greece, and Romania. Current Status and Challenges for Collaboration

Pneumocystis jirovecii can cause fatal Pneumocystis pneumonia (PcP). Many children have been exposed to the fungus and are colonized in early age, while some individuals at high risk for fungal infections may develop PcP, a disease that is difficult to diagnose. Insufficient laboratory availability, lack of knowledge, and local epidemiology gaps make the problem more serious. Traditionally, the diagnosis is based on microscopic visualization of Pneumocystis in respiratory specimens. The molecular diagnosis is important but not widely used. The aim of this study was to collect initial indicative data from Serbia, Greece, and Romania concerning pediatric patients with suspected PcP in order to: find the key underlying diseases, determine current clinical and laboratory practices, and try to propose an integrative future molecular perspective based on regional collaboration. Data were collected by the search of literature and the use of an online questionnaire, filled by relevant scientists specialized in the field. All three countries presented similar clinical practices in terms of PcP prophylaxis and clinical suspicion. In Serbia and Greece the hematology/oncology diseases are the main risks, while in Romania HIV infection is an additional risk. Molecular diagnosis is available only in Greece. PcP seems to be under-diagnosed and regional collaboration in the field of laboratory diagnosis with an emphasis on molecular approaches may help to cover the gaps and improve the practices.

Evaluation of a PCR-electrospray ionization mass spectrometry platform for detection and identification of fungal pathogens directly from prospectively collected bronchoalveolar lavage specimens

The incidence of invasive fungal infections is on the rise worldwide due to the growth of the immunocompromised population. We report here the use of a diagnostic assay that utilizes a universal extraction method, broad spectrum PCR amplification and analysis via electrospray ionization mass spectrometry (PCR/ESI-MS) to detect and identify more than 200 pathogenic fungi directly from bronchoalveolar lavage (BAL) specimens in less than 8 hours. In this study, we describe both analytical and clinical performance of the assay, when run with prospectively collected clinical BAL specimens. In 146 patients with probable and possible fungal infections defined by EORTC/MSG (European Organization for Research and Treatment of Cancer/Mycoses Study Group) criteria, the PCR/ESI-MS assay demonstrated a sensitivity of 90.9% (95% CI: 76.4–96.9%) and a specificity of 82.3% (95% CI: 74.2–88.2%). This data demonstrates the utility of a non-culture based broad fungal targets molecular diagnostic tool for rapid and accurate diagnosis of invasive fungal infections in patients at risk of developing fungal diseases.

Combination of β-(1, 3)-D-glucan testing in serum and qPCR in nasopharyngeal aspirate for facilitated diagnosis of Pneumocystis jirovecii pneumonia

BACKGROUND

Currently, the biological diagnosis of Pneumocystis jirovecii pneumonia (PjP infection) usually relies on microbiological investigations in bronchial-alveolar lavage fluid (BALF) by conventional staining methods and/or molecular biology. However, bronchial-alveolar lavage is sometimes complicated to manage, especially in weakened patients. Therefore, alternative clinical samples-easier to collect-are warranted in such specific contexts.

OBJECTIVE

Over a four-year period, diagnostic performance of an original method based on combination of quantitative real-time polymerase chain reaction (qPCR) in nasopharyngeal aspirate (NPA) with measurement of β-(1, 3)-D-glucan antigen (BDG) in serum was prospectively assessed in a single centre.

PATIENTS/METHODS

Results were compared with those obtained in BALF through direct staining methods and qPCR. True positives were defined by an independent committee based on clinical, radiological and biological data. Overall, 48 individuals with a definitive diagnosis of PjP infection were included, and 48 controls were selected upon matching for age, sex and underlying disease(s).

RESULTS

qPCR results were strongly correlated between BALF and NPA (P < .0001). Altogether, greater diagnostic performance was achieved when establishing the positive cut-off of BDG antigen at 143 pg/mL. In such conditions, sensitivity of the testing based on either positive BDG measurement or positive qPCR in NPA was then calculated at 93.75%, _95% CI [82.37%-98.40%], and specificity at 97.87%, _95% CI [87.66%-100.00%].

CONCLUSIONS

Further validation through multicentre studies is now required, especially for establishing clear cut-offs. However, one could already state that combination of qPCR in the NPA with BDG measurement in serum may be a valuable substitute for BALF examination.

Minimizing fungal disease deaths will allow the UNAIDS target of reducing annual AIDS deaths below 500 000 by 2020 to be realized

Deaths from AIDS (1 500 000 in 2013) have been falling more slowly than anticipated with improved access to antiretroviral therapy. Opportunistic infections account for most AIDS-related mortality, with a median age of death in the mid-30s. About 360 000 (24%) of AIDS deaths are attributed to tuberculosis. Fungal infections deaths in AIDS were estimated at more than 700 000 deaths (47%) annually. Rapid diagnostic tools and antifungal agents are available for these diseases and would likely have a major impact in reducing deaths. Scenarios for reduction of avoidable deaths were constructed based on published outcomes of the real-life impact of diagnostics and generic antifungal drugs to 2020. Annual deaths could fall for cryptococcal disease by 70 000, Pneumocystis pneumonia by 162 500, disseminated histoplasmosis by 48 000 and chronic pulmonary aspergillosis by 33 500, with approximately 60% coverage of diagnostics and antifungal agents; a total of >1 000 000 lives saved over 5 years. If factored in with the 90–90–90 campaign rollout and its effect, AIDS deaths could fall to 426 000 annually by 2020, with further reductions possible with increased coverage. Action could and should be taken by donors, national and international public health agencies, NGOs and governments to achieve the UNAIDS mortality reduction target, by scaling up capability to detect and treat fungal disease in AIDS.

This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.

Pneumocystis jirovecii immunostain versus Gomori/Grocott methenamine silver stain of bronchoalveolar lavage in cell blocks: an institutional experience

INTRODUCTION

Current approaches to Pneumocystis jirovecii (PCJ) screening on bronchioalveolar lavage samples (BAL) include Gomori/Grocott methenamine silver stain (GMS), toluidine blue O stain, Wright-Giemsa stain, immunofluorescent antibody stain, and polymerase chain reaction. Another method available is PCJ immunohistochemistry stain (PCJ IHC). There are no published series evaluating the efficacy of PCJ IHC in cell block preparation of BAL, we sought to compare GMS versus PCJ IHC at our institution.

MATERIALS AND METHODS

We performed a retrospective analysis at our institution of all BAL with cell blocks where PCJ IHC and GMS were done simultaneously since March 2015.

RESULTS

982 BAL samples were identified from 640 patients (median age: 54 years; range: 1-84 years). For 895 cases, GMS and PCJ IHC were performed simultaneously. PCJ was identified in 14 samples, from 13 patients (2.2% of patients) using PCJ IHC. GMS stains were read as positive in only 6 of these 14 cases (42.8%); in two of those cases, PCJ was easily identified on routine Papanicolaou stains. We repeated GMS staining on those 14 cases following before-schedule maintenance in our Ventana Benchmark Autostainer, identifying 12 cases positive. In addition, a significantly higher number of organisms was seen on repeat GMS (median: 58) than the original GMS (median: 8.7). Nevertheless, a statistically significant higher number of organisms was detected by PCJ IHC (median: 474).

CONCLUSIONS

PCJ IHC performed in cell block is more sensitive and specific than GMS and is a reliable marker when a low number of PCJ organisms are present.

Delivering on Antimicrobial Resistance Agenda Not Possible without Improving Fungal Diagnostic Capabilities

Antimicrobial resistance, a major public health concern, largely arises from excess use of antibiotic and antifungal drugs. Lack of routine diagnostic testing for fungal diseases exacerbates the problem of antimicrobial drug empiricism, both antibiotic and antifungal. In support of this contention, we cite 4 common clinical situations that illustrate this problem: 1) inaccurate diagnosis of fungal sepsis in hospitals and intensive care units, resulting in inappropriate use of broad-spectrum antibacterial drugs in patients with invasive candidiasis; 2) failure to diagnose chronic pulmonary aspergillosis in patients with smear-negative pulmonary tuberculosis; 3) misdiagnosis of fungal asthma, resulting in unnecessary treatment with antibacterial drugs instead of antifungal drugs and missed diagnoses of life-threatening invasive aspergillosis in patients with chronic obstructive pulmonary disease; and 4) overtreatment and undertreatment of Pneumocystis pneumonia in HIV-positive patients. All communities should have access to nonculture fungal diagnostics, which can substantially benefit clinical outcome, antimicrobial stewardship, and control of antimicrobial resistance.

Profile of pneumocystis infection in a tertiary care institute in North India

CONTEXT

Pneumocystis jirovecii pneumonia (PcP) is still remains a common opportunistic disease in human immunodeficiency virus (HIV) infected individuals. Study on PcP in developing countries are scarce.

AIMS

To study the occurrence of P. jirovecii infection in clinically suspected individuals in a tertiary care institute.

SETTINGS AND DESIGN

Retrospective study conducted in a tertiary care hospital.

MATERIALS AND METHODS

Two years data regarding respiratory sample analysis, HIV status, and cluster of differentiation 4 (CD4) cell count of clinically suspected pneumocystis infection patients with known/unknown HIV status were analyzed.

RESULTS

Data of 45 eligible patients were analyzed. The majority of the patients were male (between 21 and 50 years of age). Total 26 (57.7%) patients were HIV reactive, of which 14 had CD4 count of <200 cells/mm³. 20 patients (9 HIV reactive and 11 unknown HIV status) were confirmed with pneumocystosis by direct fluorescent antibody (DFA) staining. Four of 14 HIV reactive individuals who had CD4 count of <200 cells/mm³ and 5 of 12 HIV reactive individuals who had CD4 count of >200 cells/mm³ were positive for pneumocystosis.

CONCLUSIONS

Pneumocystis pneumonia is still prevalent in North India and is mainly affecting patients in economically productive and sexually active age group. To diagnose pneumocystosis, DFA is an easily available method in resource-limited settings. Appreciating the actual HIV or immunodeficiency status and the CD4 profile of an individual with symptoms of pneumocystis infection will help the clinicians in early diagnosis and initiation appropriate therapy in individuals living with the disease.