Diagnóstico microscópico de neumonía por Pneumocystis jirovecii en muestras de lavado broncoalveolar y lavado orofaríngeo de pacientes inmunocomprometidos con neumonía

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.

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 y SARS-CoV-2; COVID-19

Pneumocystis jirovecii, es un agente fúngico oportunista causante de neumonía (pneumocistosis) que puede ser mortal en personas con condición de inmunocompromiso, incluyendo pacientes VIH con recuento de linfocitos T CD4+ < 200 céls/mm3 y en pacientes inmunocomprometidos por otras etiologías como trasplantes de órgano sólido y cáncer, entre otras. Muchas personas pueden ser portadoras sanas de este agente etiológico y actuar como reservorio y fuente de infección. Artículos relacionados con coinfección entre SARS-CoV-2 y los de carácter oportunistas como P. jirovecii y Aspergillus fumigatus empiezan a publicarse, donde se argumenta que esta infección viral tiene un alto riesgo de coinfección y se manifiesta la importancia de no excluir los patógenos respiratorios, como P. jirovecii, entre otros. La coinfección con P. jirovecii puede no ser detectada en pacientes con infección grave por SARS-CoV-2, dado que pueden compartir características clínicas comunes como infiltrados multifocales bilaterales e hipoxemia profunda entre otras. Por lo tanto, es necesario realizar pruebas diagnósticas adicionales para P. jirovecii en pacientes con infección por SARS-CoV-2, especialmente cuando se presenten otras características clínicas que pueden apoyar la coinfección, como hallazgos quísticos en la TC torácica y niveles elevados en sangre de 1,3-D-glucano, incluso en ausencia de factores de riesgo clásicos para P. jirovecii, para el diagnóstico de neumonía por Pneumocystis en pacientes con sospecha de infección por SARS-CoV-2.

Prevalence of Pneumocystis jirovecii among immunocompromised patients in hospitals of Tehran city, Iran

Pneumocystis jirovecii is an opportunistic organism that can cause extreme complications such as Pneumocystis pneumonia in immunocompromised individuals. There is no comprehensive study was conducted Iran to determine the prevalence of this infection in susceptible individuals. In the present study, 160 sera samples were collected from immunocompromised patients, including acquired immunodeficiency syndrome (AIDS) patients, diabetic patients, Hodgkin lymphoma patients and non-Hodgkin lymphoma patients. The specimens were collected from Imam Khomeini and army's 501 hospitals. The specimens were examined using indirect fluorescent antibody test. The results of the study showed that 39.30% specimens were found positive, with different rates in different groups, including 20, 22.50, 37.50, and 77.50% of diabetic patients, non-Hodgkin patients, Hodgkin lymphoma patients, and AIDS patients, respectively. This occurrence is relatively high and can be a potential life-threatening hazard to infected patients in studied groups, on the other hand the organism can be transmitted from infected people to other susceptible individuals.

Low incidence of Pneumocystis jirovecii pneumonia in an unprophylaxed liver transplant cohort

BACKGROUND

Liver transplant recipients are managed with a range of immunosuppressive regimens that place them at heightened risk of life-threatening opportunistic infections such as Pneumocystis jirovecii pneumonia (PJP). No routine PJP prophylaxis is used at out institution. We reviewed the incidence of PJP in this cohort of unprophylaxed liver transplant recipients.

METHODS

We examined all liver transplants performed between January 2000 and January 2012 in Ireland's National Liver Transplant Centre, St. Vincent's University Hospital, Dublin. Cases were identified through a computerized database and through the histopathology and microbiology registration system. The diagnosis of PJP was confirmed by identification of Pneumocystis cysts in bronchoalveolar lavage (BAL) fluid or on autopsy specimens using Grocott-Gomori methenamine-silver nitrate or modified Wright-Giemsa staining methods.

RESULTS

During the study period, 687 liver transplants were performed. We found 7 cases of PJP with an incidence rate of 0.84 per 1000 person transplant years. Five cases occurred within 12 months of transplant with 2 cases occurring at 56 and 60 months, respectively. Two cases were diagnosed at postmortem; 1 previously had negative cytology from BAL, while the other could not be bronchoscoped because of rapid deterioration in the clinical condition. Three of the 5 treated patients died.

CONCLUSIONS

The incidence of PJP in this cohort was very low, but the case fatality rate was high. Two cases occurred well after the usual recommended period of prophylaxis. In institutions with a very low risk of infection, targeted rather than universal prophylaxis may be reasonable.