Pneumocystis pneumonia in HIV patients: a diagnostic challenge till date

Outcome of Pneumocystis pneumonia in transplant and non-transplant HIV-negative immunocompromised patients

BACKGROUND

Previous studies showed HIV-negative immunocompromised patients are susceptible to Pneumocystis pneumonia (PCP). However, the PCP outcome has not been compared among HIV-negative immunocompromised patients.

METHODS

In this retrospective cohort study at the University Health Network, we included all HIV-negative immunocompromised patients who fulfilled the European Organization for Research and Treatment of Cancer (EORTC) PCP diagnosis criteria from December 2018 to December 2019. We compared the demographics, comorbidities, course of illness, and PCP outcome (28-day mortality and composite outcome [i.e., death or intensive care unit (ICU) admission]) between solid organ transplant (SOT) and non-SOT patients.

RESULTS

Of 160 non-HIV patients with PCP diagnoses, 118 patients fulfilled EORTC criteria (76 males [64.4%], median [range] age: 65.5 [21-87] years). PCP presentation in SOT recipients (n = 14) was more severe than non-SOT patients (n = 104): acute presentation (onset <7 days before admission: 11/14 [78.6%] vs. 51/104 [56%], p = .037), shortness of breath (100% vs. 75/104 [74.3%], p = .037), median [range] O2 saturation (88% [75%, 99%] vs. 92%[70%, 99%], p = .040), and supplemental O2 requirement (12/14 [85.7%] vs. 59/104 [56.7%], p = .044). The mortality [4/14, (28.6%) vs. 15/104 (14.4%), p = .176], ICU admission (10/14 [71.4%] vs. 18/104 [17.3%], p < .0001), and mechanical ventilation (8/14 [57.1%] vs. 18/104 [17.3%], p = .0007) in SOT patients was different from non-SOT patients. In multivariable analysis, SOT recipients were at greater risk of composite outcome than non-SOT patients (aOR [CI95%]: 12.25 [3.08-48.62], p < .001).

CONCLUSION

PCP presentation and outcomes in SOT recipients are more severe than in non-SOT patients. Further studies are required to explore the biological reasons for this difference.

Pneumocystis jirovecii Pneumonia in HIV-Negative, Non-transplant Patients: Epidemiology, Clinical Manifestations, Diagnosis, Treatment, and Prevention

Purpose of Review

Pneumocystis jirovecii pneumonia (PJP) is an opportunistic fungal infection that is increasingly seen in HIV-negative patients with immune compromise due to other etiologies. We lack comprehensive clinical recommendations for this population.

Recent Findings

In non-HIV cases, PJP has a mortality rate of up to 50%, which is unacceptable despite the presence of safe and effective prophylaxis and therapy. Steroid use is one of the most common risk factors for disease development. New data suggests that lower doses of the preferred treatment regimen, TMP-SMX, may be equally effective for treatment while limiting side effects. While commonly used, the benefit of corticosteroids for the treatment of PJP has recently been called into question, with a recent multicenter cohort demonstrating no benefit among solid organ transplant recipients.

Summary

A high suspicion of PJP in individuals with pneumonia during immunosuppressant use is crucial. Therapeutic options are evolving to decrease potential side effects while maintaining efficacy in this highly morbid disease.

Pneumocystis pneumonia in HIV-positive and non-HIV patients: a retrospective comparative study from a lower-middle income country

In this study, we compared the predisposing factors, key demographic and clinical characteristics, clinical outcomes, and factors associated with poor prognosis in pneumocystis pneumonia (PCP) infection among the human immunodeficiency virus (HIV)-positive and non-HIV patient populations. This retrospective analysis was conducted at the Aga Khan University Hospital, Karachi, via the collection and analysis of patient records with a diagnosis of "pneumocystosis" between January 2015 and October 2020. Additionally, the laboratory database was evaluated, and patients with a laboratory-confirmed diagnosis of PCP were included. During the study period, 52 laboratory-confirmed hospitalized PCP patients were identified. Of these, 23 and 29 patients were diagnosed using microscopy and polymerase chain reaction, respectively. 34.6% of our patients were HIV positive, with a median CD4 count of 20.5 cells/mm3 (range: 10.7-50.5). Other conditions identified were corticosteroid use, autoimmune diseases, malignancy, radiation, and chemotherapy. On chest imaging, consolidation was found in 30%, ground-glass opacities in 24%, and nodular infiltrates in 20% of the cases. HIV-positive patients had a lower hemoglobin level and a higher level of β-D-glucan at the time of admission, whereas non-HIV patients were found to have more co-morbid conditions than HIV patients. We observed no difference in clinical outcomes between the two populations. Factors associated with a poor prognosis among our patients included concomitant infections at the time of diagnosis, the need for invasive mechanical ventilation, and a longer duration of stay in the hospital as well as the intensive care unit.

The SSS revolution in fungal diagnostics: speed, simplicity and sensitivity

INTRODUCTION

Fungal disease has historically presented a diagnostic challenge due to its often non-specific clinical presentations, relative infrequency and reliance on insensitive and time-intensive fungal culture.

SOURCES OF DATA

We present the recent developments in fungal diagnostics in the fields of serological and molecular diagnosis for the most clinically relevant pathogens; developments that have the potential to revolutionize fungal diagnosis through improvements in speed, simplicity and sensitivity. We have drawn on a body of evidence including recent studies and reviews demonstrating the effectiveness of antigen and antibody detection and polymerase chain reaction (PCR) in patients with and without concurrent human immunodeficiency virus infection.

AREAS OF AGREEMENT

This includes recently developed fungal lateral flow assays, which have a low cost and operator skill requirement that give them great applicability to low-resource settings. Antigen detection for Cryptococcus, Histoplasma and Aspergillus spp. are much more sensitive than culture. PCR for Candida spp., Aspergillus spp., Mucorales and Pneumocystis jirovecii is more sensitive than culture and usually faster.

AREAS OF CONTROVERSY

Effort must be made to utilize recent developments in fungal diagnostics in clinical settings outside of specialist centres and integrate their use into standard medical practice. Given the clinical similarities of the conditions and frequent co-infection, further study is required into the use of serological and molecular fungal tests, particularly in patients being treated for tuberculosis.

GROWING POINTS

Further study is needed to clarify the utility of these tests in low-resource settings confounded by a high prevalence of tuberculosis.

AREAS TIMELY FOR DEVELOPING RESEARCH

The diagnostic utility of these tests may require revision of laboratory work flows, care pathways and clinical and lab coordination, especially for any facility caring for the immunosuppressed, critically ill or those with chronic chest conditions, in whom fungal disease is common and underappreciated.

Microscopic Imaging and Labeling Dataset for the Detection of Pneumocystis jirovecii Using Methenamine Silver Staining Method

Pneumocystis jirovecii pneumonia is one of the diseases that most affects immunocompromised patients today, and under certain circumstances, it can be fatal. On the other hand, more and more automatic tools based on artificial intelligence are required every day to help diagnose diseases and thus optimize the resources of the healthcare system. It is therefore important to develop techniques and mechanisms that enable early diagnosis. One of the most widely used techniques in diagnostic laboratories for the detection of its etiological agent, Pneumocystis jirovecii, is optical microscopy. Therefore, an image dataset of 29 different patients is presented in this work, which can be used to detect whether a patient is positive or negative for this fungi. These images were taken in at least four random positions on the specimen holder. The dataset consists of a total of 137 RGB images. Likewise, it contains realistic, annotated, and high-quality microscope images. In addition, we provide image segmentation and labeling that can also be used in numerous studies based on artificial intelligence implementation. The labeling was also validated by an expert, allowing it to be used as a reference in the training of automatic algorithms with supervised learning methods and thus to develop diagnostic assistance systems. Therefore, the dataset will open new opportunities for researchers working in image segmentation, detection, and classification problems related to Pneumocystis jirovecii pneumonia diagnosis.

Performance of a Real Time PCR for Pneumocystis jirovecii Identification in Induced Sputum of AIDS Patients: Differentiation between Pneumonia and Colonization

Pneumocystis jirovecii pneumonia (PcP) remains an important cause of morbimortality worldwide and a diagnostic challenge. Conventional methods have low accuracy, hardly discriminating colonization from infection, while some new high-cost or broncho-alveolar lavage-based methods have limited usefulness in developing countries. Quantitative PCR (qPCR) tests may overcome these limitations due to their high accuracy, possibility of automation, and decreasing cost. We evaluated an in-house qPCR targeting the fungus mtSSU gene using induced sputum. Sensitivity of the assay (ten target gene copies/assay) was determined using recombinant plasmids. We prospectively studied 86 AIDS patients with subacute respiratory symptoms in whom PcP was suspected. qPCR results were determined as quantification cycles (Cq) and compared with a qualitative PCR performed in the same IS, serum 1,3-β-D-Glucan assay, and a clinical/laboratory/radiology index for PcP. The qPCR clustered the patients in three groups: 32 with Cq ≤ 31 (qPCR+), 45 with Cq ≥ 33 (qPCR-), and nine with Cq between 31-33 (intermediary), which, combined with the other three analyses, enabled us to classify the groups as having PcP, not P. jirovecii-infected, and P. jirovecii-colonized, respectively. This molecular assay may contribute to improve PcP management, avoiding unnecessary treatments, and our knowledge of the natural history of this infection.

Diagnosing Pneumocystis jirovecii pneumonia: A review of current methods and novel approaches

Pneumocystis jirovecii can cause life-threatening pneumonia in immunocompromised patients. Traditional diagnostic testing has relied on staining and direct visualization of the life-forms in bronchoalveolar lavage fluid. This method has proven insensitive, and invasive procedures may be needed to obtain adequate samples. Molecular methods of detection such as polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and antibody-antigen assays have been developed in an effort to solve these problems. These techniques are very sensitive and have the potential to detect Pneumocystis life-forms in noninvasive samples such as sputum, oral washes, nasopharyngeal aspirates, and serum. This review evaluates 100 studies that compare use of various diagnostic tests for Pneumocystis jirovecii pneumonia (PCP) in patient samples. Novel diagnostic methods have been widely used in the research setting but have faced barriers to clinical implementation including: interpretation of low fungal burdens, standardization of techniques, integration into resource-poor settings, poor understanding of the impact of host factors, geographic variations in the organism, heterogeneity of studies, and limited clinician recognition of PCP. Addressing these barriers will require identification of phenotypes that progress to PCP and diagnostic cut-offs for colonization, generation of life-form specific markers, comparison of commercial PCR assays, investigation of cost-effective point of care options, evaluation of host factors such as HIV status that may impact diagnosis, and identification of markers of genetic diversity that may be useful in diagnostic panels. Performing high-quality studies and educating physicians will be crucial to improve the rates of diagnosis of PCP and ultimately to improve patient outcomes.

Pneumocystis Jirovecii detection and comparison of multiple diagnostic methods with quantitative real-time PCR in patients with respiratory symptoms

Pneumocystis jirovecii (PCP) remains a significant cause of mortality and morbidity in patients with respiratory infections. Accurate diagnosis of PCP is still a diagnostic challenge. Hence, the main objectives were to study the incidence of Pneumocystis Jirovecii pneumonia infection among respiratory problems patients and to compare the real-time quantitative PCR technique with various diagnostic methodologies. Patients who have respiratory symptoms of PCP like breathlessness, cough, and fever were enrolled. Bronchoalveolar lavage (BAL) samples were collected and homogenized, and then smears were prepared for examination by Gomorimethanamine silver staining (GMSS), Immunofluorescent staining (IFAT), Toludine blue O (TBO), and Giemsa staining. Further, RT-PCR was also performed for the detection of PCP. The mean patients’ age was 52 (SD ± 16) years. 41% were female, and 59% of the patients were male. Weight loss (80%), fever (92%), cough (100%), and dyspnea (76%) were the most common complaints. Twenty-eight patients have been diagnosed with pulmonary infiltrates using chest X-ray. Out of 100 patients, 35% were positive for PCP. The organism was detected using IFAT in all the 35 specimens, 15 of 35 (42.86%) by GMSS, 8 of 35 (17.6%) by Giemsa stain, and 1 of 35 (2.8%) was detected by TBO stains. RT-PCR showed that 39 patients was found to be positive for PCP. Thirty-five of these 39 patients had a positive IFAT (89.74%); the IFAT was negative or undefined in 4 samples. All 39 patients (100%) had signs and symptoms for PCP. Our results suggest that RT-PCR is still the most highly sensitive method for Pneumocystis Jirovecii detection. In poor resource settings where RT-PCR and IFAT is not available, diagnosis of Pneumocystis jirovecii pneumonia remains a complicated issue. In settings where RT-PCR & IFAT are not available, GMSS staining may be the next best choice to detect PCP.

PCR methodology and applications for the detection of human fungal pathogens

INTRODUCTION

Polymerase chain reaction (PCR) has emerged as a promising technology for the rapid and reliable detection and identification of medical mycoses. Recent technological advancements - including microarray, multiplex PCR with magnetic resonance, and beacon probes - have mitigated the technical difficulties of performing nucleic amplification in fungi, thereby improving the sensitivity and specificity of PCR-based assays. In this paper, we examine current applications of PCR in the diagnosis of human fungal infections and look ahead to emerging techniques that may play a larger role in molecular diagnostics in the future.

AREAS COVERED

This review includes a brief overview of the advantages and disadvantages of PCR using various clinical specimens, manual versus automated DNA extraction procedures, panfungal versus specific targets, and spectrum of pathogens detected. This is followed by a brief synopsis of species-specific PCR approaches and a more in-depth look at the obstacles to widespread implementation. Expert commentary: The review concludes with a short perspective for the next five years, including the hurdles to standardization and validation, as well as the role of PCR coupled with electrospray-ionization mass spectrometry (PCR/ESI-MS) or nuclear magnetic resonance for the diagnosis of medical mycoses.