Next-generation sequencing technology for the diagnosis of Pneumocystis pneumonia in an immunocompetent female:A case report

BACKGROUND Pneumocystis pneumonia(PCP)is a serious fungal infection usually seen in patients with human immunodeficiency virus,and it is more frequently found and has a high fatality rate in immunocompromised people.Surprisingly,it rarely occurs in immunocompetent patients.However,the clinical diagnosis of this pathogen is made more difficult by the difficulty of obtaining accurate microbiological evidence with routine tests.This case reports a PCP patient with normal immune function who was diagnosed through next-generation sequencing(NGS).CASE SUMMARY A 23-year-old female who had no special disease in the past was admitted to the hospital with a persistent fever and cough.Based on the initial examination results,the patient was diagnosed with bipulmonary pneumonia,and empirical broad-spectrum antibiotic therapy was administered.However,due to the undetermined etiology,the patient's condition continued to worsen.She was transferred to the intensive care unit because of acute respiratory failure.After the diagnosis of Pneumocystis jirovecii infection through NGS in bronchoalveolar lavage fluid and treatment with trimethoprim/sulfamethoxazole and caspofungin,the patient gradually recovered and had a good prognosis.CONCLUSION This case emphasizes that,for patients with normal immune function the possibility of PCP infection,although rare,cannot be ignored.NGS plays an important role in the diagnosis of refractory interstitial pneumonia and acute respiratory failure.

Relationship between Radiological Stages and Prognoses of Pneumocystis Pneumonia in Non-AIDS Immunocompromised Patients

Background： Although radiological features ofpneumocystis pneumonia （PCP） in non-Acquired Immune Deficiency Syndrome （AIDS） immunocompromised patients have been reported by other authors, there were no studies on the radiological stages of PCP previously. This study aimed to elucidate the radiological stages and prognoses of PCP in non-AIDS immunocompromised patients. Methods： Retrospective analysis ofradiological manifestations and prognoses of 105 non-AIDS PCP immunocompromised patients from August 2009 to April 2016 was conducted. Chest radiograph was divided into three stages： early stage （normal or nearly normal chest radiograph）, mid stage （bilateral pulmonary infiltrates）, and late stage （bilateral pulmonary consolidations）; chest high-resolution computed tomography （HRCT） was also divided into three stages： early stage （bilateral diffuse ground-glass opacity [GGO]）, mid stage （bilateral diffuse GGO and patchy consolidations）, and late stage （bilateral diffuse consolidations）. Results： The case fatality rate （CFR） of all patients was 34.3% （36/105）, all of them took routine chest X-ray （CXR）, and 84 underwent chest CT examinations. According to the CXR most near the beginning ofanti-PCP therapy, 18 cases were at early stage and CFR was 0 （0/18, P 〈 0.01）, 50 cases were at mid stage and CFR was 28.0% （14/50, P〉 0.05）, and 37 cases were at late stage and CFR was 59.5% （22/37, P 〈 0.01）. According to the chest HRCT most near the beginning ofanti-PCP therapy, 40 cases were at early stage and CFR was 20.0% （8/40, P 〉 0.05）, 34 cases were at mid stage and CFR was 47.1% （l 6/34, P 〉 0.05）, and 10 cases were at late stage and CFR was 80.0% （8/10, P 〈 0.05）; barotrauma, including pneumothorax, pneumomediastinum, and pneumohypoderma, was found in 18 cases and the CFR was 77.8% （14/18, P 〈 0.01）. Conclusions： Based on the radiological manifestations, the course of PCP in non-A1DS immunocompromised patients can be divided into three stages： early stage, mid stage, and late stage. The prognoses of patients treated at early stage are good, and those at late stage are poor. Furthermore, the CFR of patients with barotrauma is high.

Use of real-time polymerase chain reaction for the diagnosis of Pneumocystis pneumonia in immunocompromised patients： a meta-analysis

Background The diagnosis of Pneumocystis pneumonia （PCP） in immunocompromised patients is still challenging today due to the absence of an in vitro culture system and the low diagnostic accuracy of microscopic examinations. Herein, we performed a meta-analysis to evaluate the accuracy of real-time polymerase chain reaction （PCR） in the diagnosis of PCP. Methods We searched Web of Knowledge and Medline from 1990 to May 2010 for studies reporting diagnostic accuracy data regarding the use of real-time PCR in the diagnosis of PCP in immunocompromised patients. Results Ten individual studies were included. Overall, the sensitivity of real-time PCR was 97% （95% CI： 93%-99%）; the specificity was 94% （95% CI： 90%-96%）. The area under the HSROC curve （95% CO for real-time PCR was 0.99 （0.97-0.99）. In a subgroup analysis regarding studies involving HIV patients among the study population, the sensitivity and specificity were 97% （95% CI： 93%-99%） and 93% （95% CI： 89%-96%）, respectively. Regarding studies using Bronchoalveolar lavage （BAL） samples only： sensitivity =98% （95% CI： 94%-99%）; specificity =93% （95% CI： 89%- 96%）, respectively. Regarding studies using microscopy as a reference standard： sensitivity =97% （95% CI： 92%-99%）; specificity =93% （95% CI： 88%-96%）. However, high between-study statistical heterogeneity was observed in all analyses. Conclusions Real-time PCR has a good diagnostic accuracy and may provide a useful adjunctive tool for the diagnosis of PCP in immunocompromised patients. Further studies are needed in order to identify any differences in the diagnostic performance of real-time PCR in HIV and non-HIV immunocompromised patients.

Diferences and similarities of high-resolution computed tomography features between pneumocystis pneumonia and cytomegalovirus pneumonia in AIDS patients

Background:Accurately diferentiating pneumocystis from cytomegalovirus pneumonia is crucial for correct therapy selection in AIDS patients.Hence,the goal of this study was to compare the computerized tomography(CT)features of pneumocystis pneumonia and cytomegalovirus pneumonia in AIDS patients and identify clinical hallmarks to accurately distinguish these two pathologies.Methods:A total of 112 AIDS patients(78 with pneumocystis pneumonia and 34 cytomegalovirus pneumonia)at Beijing Ditan Hospital from January 2017 to May 2019 were included in this study.Two experienced chest radiologists retrospectively reviewed CT images for 17 features including ground-glass opacity,consolidation,nodules,and halo sign.Binary logistic regression analyses were conducted to identify the signifcant parameters that distinguished pneumocystis pneumonia from cytomegalovirus pneumonia.Correlations were analyzed by Pearson or Spearman correlation analyses.Result were considered signifcant if P<0.05.Results:The presence of consolidation,halo signs,and nodules(all P<0.05)were signifcantly more frequent in patients with cytomegalovirus pneumonia than in those with pneumocystis pneumonia.Small nodules(32.5%in cytomegalovirus pneumonia,6.41%in pneumocystis pneumonia,P<0.001)without perilymphatic distribution were particularly common in patients with cytomegalovirus pneumonia.Large nodules were not found in any of patients with cytomegalovirus pneumonia.The presence of ground-glass opacity,reticulation,and bronchial wall thickening(all P>0.05)were common in both groups.Conclusions:Analysis of consolidation,nodules,and halo signs may contribute to the diferential diagnosis of pneumocystis pneumonia or cytomegalovirus pneumonia.However,some CT features considered typical in one or other diseases appear with similar frequency in both cohorts of AIDS patients.CT features are potentially useful for the diferential diagnosis of pneumocystis pneumonia and cytomegalovirus pneumonia in AIDS patients.

Caspofungin in salvage treatment of severe pneumocystis pneumonia： case report and literature review

Pneumocystis pneumonia （PCP） is one of the most critical and life-threatening infections in immunocompromised patients with AIDS （especially CD4^＋ T cell less than 0.2×10^9/L）, hematological malignancies, organ transplantation or connective tissue diseases. It is caused by a fungus called Pneumocystis jiroveci （P. jiroveci, formerly called P carinii）.

A clinical comparative study of polymerase chain reaction assay for diagnosis of pneumocystis pneumonia in non-AIDS patients

Background Pneumocystis jirovecii pneumonia （PCP） is one of the most common and fatal infections in non-AIDS immunocompromised patients, which is difficult to diagnose by traditional morphologic methods. This study evaluated polymerase chain reaction （PCR） assays of Pneumocystis jirovecii mitochondrial large subunits ribosomal RNA in sputum and bronchioalveolar lavage fluid （BALF） for diagnosing PCP. Methods Sputum and BALF specimens from two groups were collected： one group （PCP group） included 20 patients definitely diagnosed of PCP by Gomori methenamine silver （GMS） stains of BALF; the other group （non-PCP group） included 40 patients. Each specimen was examined by GMS stains and PCR assays. Results GMS stains of BALF in PCP group were 100% positive （20/20）, GMS stains of sputum in PCP group were 35% positive （7/20）; GMS stains of BALF in non-PCP group were 100% negative （40/40）, GMS stains of sputum in non-PCP group were 100% negative （40/40）. PCR assays of BALF in PCP group were 100% positive （20/20）, PCR assays of sputum in PCP group were 100% positive （20/20）; PCR assays of BALF in non-PCP group were 100% negative （40/40）, PCR assays of sputum in non-PCP group were 100% negative （40/40）. Sensitivity and specificity of PCR assays of sputum and BALF were both 100%; positive and negative predictive values were also both 100%. Conclusion The diagnostic value of PCR assays of Pneumocystisjirovecii mitochondrial large subunits ribosomal RNA on sputum and BALF for pneumocystis pneumonia are both high and equivalent.

Treatment of Pneumocystis jirovecii pneumonia in non-human immunodeficiency virus-infected patients using a combination of trimethoprim-sulfamethoxazole and caspofungin

BACKGROUND Pneumocystis jirovecii pneumonia(PJP)is an infectious disease common in immunocompromised hosts.However,the currently,the clinical characteristics of non-HIV patients with PJP infection have not been fully elucidated.AIM To explore efficacy of trimethoprim–sulfamethoxazole(TMP-SMX)and caspofungin for treatment of non-human immunodeficiency virus(HIV)-infected PJP patients.METHODS A retrospective study enrolled 22 patients with non-HIV-infected PJP treated with TMP-SMX and caspofungin from 2019 to 2021.Clinical manifestations,treatment and prognosis of the patients were analyzed.RESULTS Five patients presented with comorbidity of autoimmune diseases,seven with lung cancer,four with lymphoma,two with organ transplantation and four with membranous nephropathy associated with use of immunosuppressive agents.The main clinical manifestations of patients were fever,dry cough,and progressive dyspnea.All patients presented with acute onset and respiratory failure.The most common imaging manifestation was ground glass opacity around the hilar,mainly in the upper lobe.All patients were diagnosed using next-generation sequencing,and were treated with a combination of TMP-SMX and caspofungin.Among them,17 patients received short-term adjuvant glucocorticoid therapy.All patients recovered well and were discharged from hospital.CONCLUSION Non-HIV-infected PJP have rapid disease progression,high risk of respiratory failure,and high mortality.Combination of TMP-SMX and caspofungin can effectively treat severe non-HIVinfected PJP patients with respiratory failure.

Pneumocystis jiroveci pneumonia after total hip arthroplasty in a dermatomyositis patient:A case report

BACKGROUND Pneumocystis jiroveci pneumonia(PJP)is a serious opportunistic infection that occurs mostly in patients with immunodeficiency and long-term immunosuppressive therapy.In non-human immunodeficiency virus-infected patients,the most important risk factor for PJP is the use of glucocorticoids in combination with other immunosuppressive treatments.The management of glucocorticoids during the perioperative period in patients with dermatomyositis requires special care.CASE SUMMARY We report a case of PJP in the perioperative period.A 61-year-old woman with a history of anti-melanoma differentiation-associated gene 5(MDA5)-positive dermatomyositis and interstitial pneumonia was administered with long-term oral methylprednisolone and cyclosporine.The patient underwent right total hip arthroplasty in the orthopaedic department for bilateral osteonecrosis of the femoral head.She was given intravenous drip hydrocortisone before anesthesia and on the first day after surgery and resumed oral methylprednisolone on the second postoperative day.On the fifth day after surgery,the patient suddenly developed dyspnea.The computed tomography scan showed diffuse grid shadows and ground glass shadows in both lungs.Polymerase chain reaction testing of bronchoalveolar lavage fluid was positive for Pneumocystis jiroveci.The patient was eventually diagnosed with PJP and was administered with oral trimethoprim-sulfamethoxazole.At the 6-mo review,there was no recurrence or progression.CONCLUSION Continued perioperative glucocorticoid use in patients with anti-MDA5-positive dermatomyositis may increase the risk of PJP.

Analysis of 8 chronic kidney disease patients complicated with Pneumocystis carinii pneumonia

Objective To study the clinical characteristics and outcome of Pneumocystis carinii pneumonia(PCP) in patients with chronic kidney diseases.Methods Clinical data of 8 cases of chronic kidney diseases complicated with PCP(excluding renal transplant patients) were examined retrospectively.Results The most common presenting symptoms at admission were fever(100%),cough without or with a little sputum(87.5%),and exertional dyspnea(75%).Beside these,they complained of chest tightness,fatigue,sweating and chills.Six patients(75%) presented with hypoxemia were diagnosed with type 1 respiratory failure during the course of illness.The most common CT feature was bilateral patchy areas of ground-glass opacities.Five patients had peripheral blood lymphocyte count less than 1 ×109/L.Four patients had CD4 cell count less than 200/mm3.Serum LDH level was elevated in 5 patients(582±222.55).Among the 8 patients,2 patients died within 20 days of PCP diagnosis.Conclusion Pneumocystis carinii pneumonia is an opportunistic and serious complication in chronic kidney disease patients treated with immunosuppressants.The disease progression is fast and patients with respiratory failure have a high mortality rate.Early diagnosis and appropriate treatment are important for better prognosis.

Pneumocystis jirovecii diagnosed by next-generation sequencing of bronchoscopic alveolar lavage fluid: A case report and review of literature

BACKGROUND The advent of molecular targeted agents and immune checkpoint inhibitors has greatly improved the treatment of advanced renal cell carcinoma(RCC), thus significantly improving patient survival. The incidence of rare drug-related adverse events has gained increased attention.CASE SUMMARY We report a patient with advanced RCC treated with multiple lines of molecular targeted agents and immune checkpoint inhibitors, who developed a pulmonary infection after treatment with everolimus in combination with lenvatinib. Determining the pathogenic organism was difficult, but it was eventually identified as Pneumocystis jirovecii by next-generation sequencing(NGS) of bronchoscopic alveolar lavage fluid(BALF) and successfully treated with trimethoprim-sulfamethoxazole.CONCLUSION Rare pulmonary infections caused by molecular targeted agents are not uncommon in clinical practice, but their diagnosis is difficult. Evaluating BALF with NGS is a good method for rapid diagnosis of such infections.

Metagenomic next-generation sequencing for pneumocystis jirovecii pneumonia in patients with connective tissue disease

Background:Accurate diagnosis of Pneumocystis jirovecii pneumonia(PJP)is challenging,and the delayed diagnosis of PJP is associated with high mortality in patients with connective tissue disease(CTD).Metagenomic next-generation sequencing(mNGS)technology facilitates etiological diagnosis of various infectious diseases,with promising application in diagnosing PJP.This study aimed to investigate the value of mNGS using bronchoalveolar lavage fluid(BALF)for diagnosing PJP infection.Methods:Data from 55 patients with CTD and suspected pulmonary infection was retrospectively collected and analysed.A PJP group and non-PJP group were formed.The clinical manifestations,laboratory test results,treatment methods,and outcomes were summarized.BALF mNGS results were compared with traditional pathogen tests(TPT)and serum 1,3-beta-D-glucan(BDG)testing.Results:The mean age of PJP patients was 54 years,and 59%(10/17)of the patients were female.A significant difference was found between the average daily dose of prednisone administered to the PJP group and non-PJP group(25 mg vs.16 mg,P<0.001).The PJP group had a significantly higher incidence of dyspnoea(88%[15/17]vs.16%[6/38],P<0.001)and elevated serum BDG level(167.73 vs.30.67 pg/mL,P<0.001).BALF mNGS was more sensitive than both TPT(100%[95%confidence interval{CI}:77.1%-100%]vs.11.8%[95%CI:2.1%-37.7%],P<0.001)and serum BDG(100%[95%CI:77.1%-100%]vs.85.7%[95%CI:42%-99.2%],P<0.001).BALF mNGS was more specific than serum BDG(89.5%[95%CI:74.3%-96.6%]vs.46.7%[95%CI:22.3%-72.6%],P=0.493).Co-infection with cytomegalovirus(CMV)was more common in the PJP patients than in the non-PJP patients(59%[10/17]vs.11%[4/38],respectively,P<0.001).Conclusion:BALF mNGS technology is highly effective for diagnosing PJP in patients with CTD and identifying co-infections.

Adrenocorticotropic hormone-secreting pancreatic neuroendocrine carcinoma with multiple organ infections and widespread thrombosis:A case report

BACKGROUND Ectopic adrenocorticotropic hormone(ACTH)-secreting neuroendocrine tumors are rare diseases.Patients with ACTH-secreting pancreatic neuroendocrine carcinomas have a poor prognosis.Infections and coagulopathies have been reported as the cause of death.However,detailed clinical descriptions of the morbid complications of ACTH-secreting neuroendocrine carcinomas have not been reported.CASE SUMMARY A 78-year-old Japanese woman consulted a medical center due to systemic edema and epigastric discomfort.Laboratory analysis revealed hypercortisolemia with increased ACTH secretion without diurnal variation in serum cortisol level.An enhanced computed tomography(CT)scan revealed a 3-cm tumor in the pancreatic head.The cytological material from endoscopic ultrasound-guided fine-needle aspiration was compatible with ACTHsecreting pancreatic neuroendocrine carcinoma.The Ki-67 index was 40%.She was transferred to Mie University Hospital for surgical treatment.The patient was diagnosed with urinary tract infection,cytomegalovirus hepatitis,esophageal candidiasis,pulmonary infiltrates suspicious for Pneumocystis carinii pneumonia,peripheral deep vein thrombosis,pulmonary embolism,and disseminated intravascular coagulation.The multiple organ infections and thromboses responded well to antimicrobial and anticoagulant therapy.Radioisotope studies disclosed a pancreatic tumor and a metastatic lesion in the liver,whereas somatostatin receptor scintigraphy showed negative findings,suggesting the primary and metastatic tumors were poorly differentiated.A CT scan before admission showed no metastatic liver lesion,suggesting that the pancreatic tumor was rapidly progressing.Instead of surgery,antitumor chemotherapy was indicated.The patient was transferred to another hospital to initiate chemotherapy.However,she died four months later due to the rapidly progressive tumor.CONCLUSION ACTH-secreting pancreatic neuroendocrine neoplasm is a rare disease with a very poor prognosis.The clinical course and acute complications of the tumor remain unreported.Here we report the clinical course of a rapidly progressive case of ACTH-secreting pancreatic neuroendocrine tumor that developed infectious complications due to many types of pathogens in multiple organs,widespread thromboses,pulmonary embolism,and disseminated intravascular coagulation.

Global prevalence,mortality,and main risk factors for COVID-19 associated pneumocystosis:A systematic review and meta-analysis

Objective:Pneumocystis pneumonia(PcP)is a life-threatening infection caused by the opportunistic fungi Pneumocystis jirovecii.The emergence of the COVID-19 pandemic forced the focus of attention of health policymakers on these two infections due to their clinical and paraclinical similarities,which cause diagnostic dilemmas.This study was undertaken to evaluate and estimate the global prevalence and main leading risk factors of coronavirus-associated pneumocystosis(CAP).Methods:We searched related databases between December 2019 and May 2022 for studies reporting CAP.Meta-analysis was performed using StatsDirect software(version 2.7.9)according to the DerSimonian and Laird method applying the random-effects model.We evaluated heterogeneity using theχ2-based Q statistic(significant for P<0.05)and the I2 statistic(>75%indicative of“notable”heterogeneity).Moreover,an odds ratio(OR)analysis was performed for eligible data.Results:Our meta-analysis included eight studies with 923 patients hospitalized with COVID-19;among them,92 were PcP cases.The overall pooled prevalence of CAP was estimated at 11.5%.The mortality among CAP patients was lower than that of non-PcP patients(OR 1.93;95%CI 0.86-4.31).Long-term corticosteroid therapy(OR 28.22;95%CI 0.54-1480.84)was the most predisposing factor for PcP among COVID-19 patients,followed by pulmonary diseases(OR 1.46;95%CI 0.43-4.98),kidney diseases(OR 1.26;95%CI 0.21-7.49),and acute respiratory destruction syndrome(OR 1.22;95%CI 0.05-29.28).Conclusions:The prevalence of PcP among the COVID-19 population is almost similar to the pre-COVID era.However,PcP-related mortality was decreased by the emergence of the COVID-19 pandemic.Women with COVID-19 are more susceptible to PcP than men.Acute respiratory distress syndrome,kidney diseases,pulmonary diseases,and long-term corticosteroid therapy increased the risk of PcP;however,transplantation and malignancy decreased the risk for PcP among COVID-19 patients.Further retrospective,case-control,prospective,and more precisely systematic review and meta-analysis studies are needed in this field.

Clinical parameters and outcomes of Pneumocystis jiroveci pneumonia in non-HIV/AIDS patients

Pneumocystis jiroveci pneumonia （PCP） is one of the most serious and potentially fatal infectionsencountered in immonosuppressed patients. It remains the most common cause of pulmonary morbidity and mortality in patients infected with human immunodeficiency virus （HIV）.

Spontaneous remission of Pneumocystisjiroveci pneumonia in 2 non-AIDS immunocompromised patients

Pneumocystis jiroveci （P. jiroveci） pneumonia （PCP） in non-AIDS immunocompromised patients ismuch more critical than that in AIDS patients,1 Without treatment, mortality of PCP in immunocompromised patients approaches 100 percent, and there were no reports of spontaneous remissions of PCP without anti-PCP therapy.2 Here we report 2 non-AIDS immunocompromised patients in whom PCP developed and remitted without treatment.

Diffuse lung involvement in rheumatoid arthritis:a respiratory physician’s perspective

The lungs are one of the most common extra-articular organs involved in rheumatoid arthritis(RA),which is reported to occur in up to 60%to 80%of RA patients.Respiratory complications are the second leading cause of death due to RA.Although there is a wide spectrum of RA-associated respiratory diseases,interstitial lung disease is the most common manifestation and it impacts the prognosis of RA.There has been progress in understanding the management and progression of rheumatoid arthritis-associated interstitial lung disease(RA-ILD)and RA-associated respiratory diseases recently,for example,opportunistic pulmonary infectious diseases and toxicity from RA therapies.From a chest physicians’perspective,we will update the diagnosis and treatment of RA-associated ILD,methotrexate-associated lung disease,and the complication of Pneumocystis jiroveci pneumonia in RA in this review.