Pneumocystis jirovecii Infections Among COVID-19 Patients: A Case Series and Literature Review

Epidemiology, Clinical Significance, and Diagnosis of Respiratory Viruses and Their Co-Infections in the Post-COVID Era

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel human coronavirus, emerged in late 2019 and rapidly evolved into a pandemic around the world. The coronavirus disease (COVID-19) pandemic has dramatically changed the epidemiology and seasonality of other traditional respiratory viruses, e.g., influenza, respiratory syncytial virus, enterovirus, etc. These traditional respiratory viruses have transmission mode and clinical symptoms similar to SARS-CoV-2 but may differ in clinical outcomes and management. Co-infection between SARS-CoV-2 and one or more traditional respiratory viruses have been reported in the literature but have shown mixed evidence in clinical outcomes. With SARS-CoV-2 evolving into mild Omicron variants, it is believed that SARS-CoV-2 co-circulates with other respiratory viruses, which in turn affect the epidemiology and clinical course of respiratory viral infections. In response to these changes, multiplex molecular tests for SARS-CoV-2 and one or more traditional respiratory viruses are attracting more attention in the field and have been developed into a variety of testing modalities. In this review, we describe the seasonality (i.e., in the Northern Hemisphere), epidemiology, and clinical significance of traditional respiratory viruses and their co-infection with SARS-CoV-2 in the post-COVID era. Furthermore, we review commonly used multiplex molecular tests and their applications for the detection of respiratory viruses and their co-infections. Altogether, this review not only sheds light on the epidemiology and clinical significance of respiratory viral infections and co-infections in the post-COVID era, and but also provides insights into the laboratory-based diagnoses of respiratory viral infections using multiplex molecular testing.

Epidemiology of Coronavirus Disease 2019-Associated Fungal Infections in the Intensive Care Unit: A Single-Center Retrospective Study

INTRODUCTION

Invasive fungal disease (IFD) is a morbid superinfection that can arise in critically ill patients with COVID-19 infection. Studies evaluating the full spectrum of COVID-19-associated fungal infections remain limited.

METHODS

Single-center retrospective study assessing IFD in patients with COVID-19, hospitalized for ≥ 72 h in the intensive care unit (ICU) between 02/25/20 and 02/28/22 (n = 1410). IFD was assessed using consensus criteria (EORTC/MSGERC or ISHAM/ECMM criteria). T- and chi-square tests compared demographic/clinical characteristics between IFD and non-IFD patients. Cox proportional hazards regression estimated risk factors for in-hospital mortality.

RESULTS

Of 1410 patients with severe COVID-19, 70 (5%) had a diagnosis of COVID-19-associated fungal infection with invasive candidiasis occurring in 3%, and invasive aspergillosis in 2%. Other fungal infections were rare. Patients with IFD had longer ICU stays (26 vs. 13 days; p < 0.001); increased rates of mechanical ventilation (99% vs. 70%; p < 0.001); and a higher risk of in-hospital death (69% vs. 36%; p < 0.001). On multivariable analysis, COVID-associated fungal infections were associated with an increased risk of in-hospital mortality.

CONCLUSIONS

This real-world study of critically ill patients with COVID-19 demonstrated a low incidence of COVID-19-associated fungal infections with invasive candidiasis occurring most frequently. Fungal infections were associated with an increased risk of in-hospital mortality in this population.

Strengths and limitations of molecular diagnostics for Pneumocystis jirovecii pneumonia

INTRODUCTION

While Pneumocystis pneumonia (PcP) remains a major AIDS-defining disease, the majority of cases of PcP now present in the HIV-negative cohort, causing significant mortality. PcP PCR diagnosis is not novel, and the optimal route of diagnosis remains unclear, with an imperfect reference method and complexity in result interpretation for alternative tests.

AREAS COVERED

This extensive review utilizing a literature search underpinning a recent systematic review/meta-analysis discusses the technical and clinical performance of PcP PCR, the added benefits of PCR testing, future aspects/considerations, and how PCR may be best used in clinical algorithms to provide a probability of PcP.

EXPERT OPINION

Given the current imperfect reference test for PcP, an alternative would be beneficial. Concerns over PcP PCR generating false positive results are valid but can be resolved by using positivity thresholds that drive specificity. Unfortunately, the extensive range of PCR assays complicates the provision of a PCR reference method. Combination testing incorporating PCR and B-D-Glucan, along with clinical and host risk factors, is key to understanding the individual probability of PcP. It is critical that access to PcP PCR testing is improved through technical and logistical development. Conversely, syndromic approaches including PcP need to be fully evaluated.

Pneumocystis jirovecii pneumonia in non-HIV patients: need for a more extended prophylaxis

Background

Pneumocystis jirovecii pneumonia (PCP) has a significant mortality rate for non-HIV immunocompromised patients. Prevention is primarily based on combined trimethoprim and sulfamethoxazole (TMP-SMX) but guidelines on pneumocystosis prophylaxis are scattered and not consensual.

Objectives

This study aims to describe PCP in non-HIV patients and to review case by case the prior indication of prophylaxis according to specific guidelines.We included patients with confirmed diagnosis of PCP admitted to one university hospital from 2007 to 2020. Prior indication for pneumocystis prophylaxis was assessed according to the specific guidelines for the underlying pathology or treatment.

Results

Of 150 patients with a medical diagnosis of PCP, 78 were included. Four groups of underlying pathologies were identified: hematological pathologies (42%), autoimmune diseases (27%), organ transplantation (17%), and other pathologies at risk of PCP (14%). A small subgroup of 14 patients (18%) had received a prior prescription of pneumocystis prophylaxis but none at the time of the episode. Transfer to intensive care was necessary for 33 (42%) patients, and the mortality rate at 3 months was 20%. According to international disease society guidelines, 52 patients (59%) should have been on prophylaxis at the time of the pneumocystis episode. Lowest compliance with guidelines was observed in the hematological disease group for 24 patients (72%) without prescription of indicated prophylaxis.

Conclusion

Infectious disease specialists should draw up specific prophylactic guidelines against pneumocystis to promote a better prevention of the disease and include additional criteria in their recommendations according to individual characteristics to prevent fatal cases.

Candent issues in pneumonia. Reflections from the Fifth Annual Meeting of Spanish Experts 2023

Pneumonia is a multifaceted illness with a wide range of clinical manifestations, degree of severity and multiple potential causing microorganisms. Despite the intensive research of recent decades, community-acquired pneumonia remains the third-highest cause of mortality in developed countries and the first due to infections; and hospital-acquired pneumonia is the main cause of death from nosocomial infection in critically ill patients. Guidelines for management of this disease are available world wide, but there are questions which generate controversy, and the latest advances make it difficult to stay them up to date. A multidisciplinary approach can overcome these limitations and can also aid to improve clinical results. Spanish medical societies involved in diagnosis and treatment of pneumonia have made a collaborative effort to actualize and integrate last expertise about this infection. The aim of this paper is to reflect this knowledge, communicated in Fifth Pneumonia Day in Spain. It reviews the most important questions about this disorder, such as microbiological diagnosis, advances in antibiotic and sequential therapy, management of beta-lactam allergic patient, preventive measures, management of unusual or multi-resistant microorganisms and adjuvant or advanced therapies in Intensive Care Unit.

Persistent fever after coronavirus disease 2019 in liver/kidney transplant recipient

In this case, a 64-year-old male with a history of simultaneous orthotopic liver transplant and cadaveric renal transplant presented five years prior presented with persistent fevers two days after a positive SARS-CoV-2 nasal PCR. A CT scan of the chest on hospital day nine revealed innumerable 1-2 mm nodules in a miliary pattern throughout the lung. (1,3)-β-D-glucan on hospital day 11 was 133 pg/mL. In this article, the approach, diagnostic and management strategies for patients with persistent fevers after diagnosis of COVID-19 in a transplant recipient are discussed.

Prevalence of Pneumocystis jirovecii Colonization in Non-Critical Immunocompetent COVID-19 Patients: A Single-Center Prospective Study (JiroCOVID Study)

BACKGROUND

Pneumocystis jirovecii pneumonia (PJP) is an invasive fungal infection (IFI) that occurs mainly in immunocompromised hosts. After observing a high prevalence of PJP as a complication of COVID-19 in immunocompetent patients, we conducted a study to evaluate the prevalence of P. jirovecii colonization with PCR on oral washing samples (OWS) among non-immunocompromised and non-critical patients admitted with COVID-19 pneumonia at our university hospital.

METHODS

All patients over 18 years of age admitted to the Infectious Diseases Unit for SARS-CoV-2 pneumonia between July 2021 and December 2022 were included. Patients undergoing invasive mechanical ventilation or ECMO, those with risk factors for developing PJP, and those receiving prophylaxis for P. jirovecii were excluded. Samples were collected by gargling with 10 mL of 0.9% NaCl on day 14 of the hospital stay or at discharge.

RESULTS

Of 290 screened patients, 59 (20%) met the inclusion criteria and were enrolled. Only 1 of 59 patients (1.7%) tested positive for P. jirovecii detection with PCR, and the same patient was the only one to develop PJP in the follow-up period.

CONCLUSIONS

Our results are in line with the previous findings of other studies that confirmed a very low prevalence of P. jirovecii colonization on OWS in the immunocompetent population. Despite the limitations of the study, the fact that the only patient who tested positive for P. jirovecii was the only one in our cohort to develop PJP leads us to reflect on the role of this non-invasive sample in predicting the risk of PJP in patients with COVID-19.

Risk Factors for Pneumocystis jirovecii Pneumonia in Non-HIV Patients Hospitalized for COVID-19: A Case-Control Study

BACKGROUND

Very few cases of Pneumocystis jirovecii pneumonia (PJP) have been reported in COVID-19 so far, and mostly in patients with concomitant HIV infection or in solid-organ transplant recipients. Despite COVID-19 being associated with lymphopenia and the use of steroids, there are no studies specifically aimed at investigating the risk factors for PJP in COVID-19.

METHODS

A retrospective case-control study was performed. We matched PJP cases with controls with a 1:2 ratio, based on age ± 10 years, solid-organ transplantation (SOT), hematological malignancies, and in the setting of PJP development (ICU vs. non-ICU). A direct immunofluorescence assay on bronchoalveolar lavage fluid was used to diagnose PJP.

RESULTS

We enrolled 54 patients. Among 18 cases of PJP, 16 were diagnosed as "proven". Seven of the eighteen cases were immunocompromised, while the other patients had no previous immunological impairment. Patients with PJP had significantly lower median lymphocyte values (p = 0.033), longer COVID-19 duration (p = 0.014), a higher dose of steroid received (p = 0.026), higher CRP values (p = 0.005), and a lower SARS-CoV-2 vaccination rate than the controls (p = 0.029). Cumulative steroid dose is the independent risk factor for PJP development (OR = 1.004, 95%CI = 1-1.008, p = 0.042).

CONCLUSIONS

PJP develops in COVID-19 patients regardless of immunosuppressive conditions and the severity of disease, and it is correlated to the corticosteroid dose received.