scholarly journals Application of Metagenomic Next-Generation Sequencing in The Diagnosis and Treatment Guidance of Pneumocystis Jirovecii Pneumonia in Renal Transplant Recipients

2021 ◽  
Author(s):  
Feng Zhang ◽  
Jia Chen ◽  
He Huang ◽  
Rangjiao Liu ◽  
Xiaomei Ren ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Univariate Analysis ◽  
Clinical Decision ◽  
Torque Teno Virus ◽  
Pneumocystis Jirovecii ◽  
Control Group ◽  
Pneumocystis Jirovecii Pneumonia ◽  
Renal Transplant Recipients ◽  
Next Generation ◽  
Generation Sequencing

Abstract Purpose: Pneumocystis jirovecii pneumonia (PJP) is difficult to be diagnosed, so this study explored if PJP could be diagnosed by metagenomic next-generation sequencing (mNGS) and if mNGS could guide the therapy of PJP. Methods: mNGS successfully diagnosed 13 out of 14 PJP recipients with 11 through peripheral blood samples, verified by PCR. Ten non-PJP recipients were enrolled as the control group. Results: Blood tests revealed a high β-Dglucan (BDG) level in all recipients with PJP during the hospitalization. Four (28.6%) of 14 PJP patients were infected with cytomegalovirus simultaneously, while 8 (57.1%) suffered from a combined infection caused by Torque teno virus. Five (35.7%) of 14 cases died of PJP or the subsequent bacteremias/bacterial pneumonia with a longer interval between the onset and diagnosis of/the available therapy against PJP than survival cases. Univariate analysis of Characteristics between PJP and non-PJP recipients revealed that BDG assays was higher at the admission in PJP group ( P =0.011). Conclusions: This present study supports the value of mNGS detection of blood sample in diagnosing PJP, which could assist clinical decision for therapy against PJ and improve outcome of PJP. The study also highlights the sensitivity of BDG assays. Cytomegalovirus and Torque teno virus infections often occur at the same time of PJP, thus can be alerts of PJP.

scholarly journals Application of Metagenomic Next-Generation Sequencing in the Diagnosis and Treatment Guidance of Pneumocystis jirovecii Pneumonia in Renal Transplant Recipients

2021 ◽  
Author(s):  
Feng Zhang ◽  
Jia Chen ◽  
He Huang ◽  
Rangjiao Liu ◽  
Xiaomei Ren ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Univariate Analysis ◽  
Clinical Decision ◽  
Torque Teno Virus ◽  
Pneumocystis Jirovecii ◽  
Control Group ◽  
Pneumocystis Jirovecii Pneumonia ◽  
Renal Transplant Recipients ◽  
Next Generation ◽  
Generation Sequencing

Abstract Background Pneumocystis jirovecii pneumonia (PJP) is difficult to be diagnosed, so this study explored if PJP could be diagnosed by metagenomic next-generation sequencing (mNGS) and if mNGS could guide the therapy of PJP. Methods mNGS successfully diagnosed 13 out of 14 PJP recipients with 11 through peripheral blood samples, verified by PCR. Ten non-PJP recipients were enrolled as the control group. Results Blood tests revealed a high β-Dglucan (BDG) level in all recipients with PJP during the hospitalization. Four (28.6%) of 14 PJP patients were infected with cytomegalovirus simultaneously, while 8 (57.1%) suffered from a combined infection caused by Torque teno virus. Five (35.7%) of 14 cases died of PJP or the subsequent bacteremias/bacterial pneumonia with a longer interval between the onset and diagnosis of/the available therapy against PJP than survival cases. Univariate analysis of Characteristics between PJP and non-PJP recipients revealed that BDG assays was higher at the admission in PJP group ( P = 0.011). Conclusion This present study supports the value of mNGS detection of blood sample in diagnosing PJP, which could assist clinical decision for therapy against PJ and improve outcome of PJP. The study also highlights the sensitivity of BDG assays. Cytomegalovirus and Torque teno virus infections often occur at the same time of PJP, thus can be alerts of PJP.

scholarly journals Rare Presentation of Toxoplasma Pneumonitis in the Absence of Neurological Symptoms in an AIDS Patient and Use of Next-Generation Sequencing for Diagnosis

2020 ◽  
Author(s):  
Moni Roy ◽  
Nikhut Siddique ◽  
Bindu Bathina ◽  
Sharjeel Ahmad
Keyword(s):  
Next Generation Sequencing ◽  
Opportunistic Infections ◽  
Miliary Tuberculosis ◽  
Neurological Symptoms ◽  
Pneumocystis Jirovecii Pneumonia ◽  
Next Generation ◽  
Rare Presentation ◽  
Immunodeficiency Syndrome ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Toxoplasma gondii is a known cause of encephalitis in human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) patients. Toxoplasma pneumonitis is a manifestation of extracerebral toxoplasmosis and can be clinically indistinguishable from other opportunistic infections including Pneumocystis jirovecii pneumonia (PJP) and miliary tuberculosis. In this case report, Toxoplasma pneumonitis and disseminated toxoplasmosis was diagnosed using next-generation sequencing (NGS) and polymerase chain reaction (PCR) assessment. NGS can detect microbial cell-free DNA (cfDNA) circulating in the plasma of over 1,000 pathogens. This case is a rare presentation of Toxoplasma pneumonitis in the absence of neurological symptoms and we discuss the use of NGS of microbial cfDNA and PCR tests that may be utilized for the timely diagnosis of such challenging cases.

scholarly journals Comparison of three commercial decision support platforms for matching of next-generation sequencing results with therapies in patients with cancer

ESMO Open ◽  
2020 ◽  
Vol 5 (5) ◽  
pp. e000872
Author(s):  
Samantha O Perakis ◽  
Sabrina Weber ◽  
Qing Zhou ◽  
Ricarda Graf ◽  
Sabine Hojas ◽  
...  
Keyword(s):  
Decision Support ◽  
Next Generation Sequencing ◽  
Metastatic Breast ◽  
Clinical Decision ◽  
Molecular Data ◽  
Current Status ◽  
Precision Oncology ◽  
Next Generation ◽  
Generation Sequencing ◽  
Tier I

ObjectivePrecision oncology depends on translating molecular data into therapy recommendations. However, with the growing complexity of next-generation sequencing-based tests, clinical interpretation of somatic genomic mutations has evolved into a formidable task. Here, we compared the performance of three commercial clinical decision support tools, that is, NAVIFY Mutation Profiler (NAVIFY; Roche), QIAGEN Clinical Insight (QCI) Interpret (QIAGEN) and CureMatch Bionov (CureMatch).MethodsIn order to obtain the current status of the respective tumour genome, we analysed cell-free DNA from patients with metastatic breast, colorectal or non-small cell lung cancer. We evaluated somatic copy number alterations and in parallel applied a 77-gene panel (AVENIO ctDNA Expanded Panel). We then assessed the concordance of tier classification approaches between NAVIFY and QCI and compared the strategies to determine actionability among all three platforms. Finally, we quantified the alignment of treatment suggestions across all decision tools.ResultsEach platform varied in its mode of variant classification and strategy for identifying druggable targets and clinical trials, which resulted in major discrepancies. Even the frequency of concordant actionable events for tier I-A or tier I-B classifications was only 4.3%, 9.5% and 28.4% when comparing NAVIFY with QCI, NAVIFY with CureMatch and CureMatch with QCI, respectively, and the obtained treatment recommendations differed drastically.ConclusionsTreatment decisions based on molecular markers appear at present to be arbitrary and dependent on the chosen strategy. As a consequence, tumours with identical molecular profiles would be differently treated, which challenges the promising concepts of genome-informed medicine.

scholarly journals Severe pulmonary co-infection with varicella-zoster virus, Pneumocystis jirovecii and Cytomegalovirus: a case report

2022 ◽  
Vol 50 (1) ◽  
pp. 030006052110707
Author(s):  
Zhijiang Qi ◽  
Yanting Sun ◽  
Jun Li ◽  
Yingjie Wang ◽  
Haining Lu ◽  
...  
Keyword(s):  
Case Report ◽  
Next Generation Sequencing ◽  
Varicella Zoster Virus ◽  
Pneumocystis Jirovecii ◽  
Imaging Features ◽  
Severe Respiratory Failure ◽  
Next Generation ◽  
Varicella Zoster ◽  
Immunosuppressed Patients ◽  
Generation Sequencing

Pneumocystis jirovecii, Cytomegalovirus and varicella-zoster virus are all opportunistically infective pathogens, but pulmonary co-infection with these pathogens is rare. Herein, this case report describes a patient with autoimmune haemolytic anaemia treated with methylprednisolone and cyclosporine that presented with rapidly progressive severe respiratory failure. Analysis of microbial nucleic acid sequences in both blood and sputum using next-generation sequencing revealed pulmonary co-infection with Pneumocystis jirovecii, varicella-zoster virus, and possibly Cytomegalovirus. After timely targeted and supportive treatments, the patient recovered. This case report highlights the imaging features of co-infection with these pathogens, the importance of next-generation sequencing for early diagnosis in immunosuppressed patients, and the effects of corticosteroid therapy.

scholarly journals Subacute Thyroiditis is Associated with HLA-B*18:01, -DRB1*01 and -C*04:01—The Significance of the New Molecular Background

2020 ◽  
Vol 9 (2) ◽  
pp. 534
Author(s):  
Magdalena Stasiak ◽  
Bogusław Tymoniuk ◽  
Renata Michalak ◽  
Bartłomiej Stasiak ◽  
Marek L. Kowalski ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Human Leukocyte ◽  
Subacute Thyroiditis ◽  
Control Group ◽  
Next Generation ◽  
Sequencing Method ◽  
Triggering Factor ◽  
Almost All ◽  
Generation Sequencing ◽  
Next Generation Sequencing Method

Subacute thyroiditis (SAT) is a thyroid inflammatory disease whose pathogenesis is still not completely defined. Previous viral infection is considered to be a triggering factor in genetically predisposed individuals. In about 70% of patients, susceptibility to SAT is associated with the HLA-B*35 allele. The correlation between SAT and other human leukocyte antigens (HLA) has not yet been unequivocally demonstrated and the genetic background is still unknown in about 30% of patients. The purpose of our study was to perform HLA genotyping using a next-generation sequencing method, to find out whether alleles other than HLA-B*35 are correlated with SAT morbidity. HLA-A, -B, -C, -DQB1, -DRB1 were genotyped using a next-generation sequencing method in 1083 subjects, including 60 SAT patients and 1023 healthy controls. Among 60 patients diagnosed with SAT, 81.7% of subjects were identified as having allele HLA-B*35, 23.3% had HLA-B*18:01, 28.3% had HLA-DRB1*01 and 75.5% had HLA-C*04:01. These alleles occurred in the control group at frequencies of 10.2%, 7.2%, 12.9% and 12.5%, respectively. The differences were statistically significant, with p < 0.05. In addition to its previously described relationship with HLA-B*35, genetic susceptibility to SAT was associated with the presence of HLA-B*18:01, DRB1*01 and C*04:01. The alleles HLA-B*18:01 and DRB1*01 were independent SAT risk factors. The assessment of these four alleles allows the confirmation of genetic predisposition in almost all patients with SAT.

scholarly journals Next Generation Sequencing (NGS) and patient pathways: What is the impact on clinical decision?

2018 ◽  
Vol 29 ◽  
pp. vi14-vi15
Author(s):  
S. Coquerelle ◽  
M. Darlington ◽  
M. Michel ◽  
M. Durand ◽  
J. Gutton ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Decision ◽  
Next Generation ◽  
Patient Pathways ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Generation Sequencing
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