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Invasive Pulmonary Aspergillosis Diagnosis via Peripheral Blood Metagenomic Next Generation Sequencing

ABSTRACT: Invasive Pulmonary Aspergillosis Diagnosis via Peripheral Blood Metagenomic Next Generation Sequencing

PROVIDER: PRJEB43573 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR6929510.fastq.gz	Fastqsanger.gz
	ERR6929511.fastq.gz	Fastqsanger.gz
	ERR6929506.fastq.gz	Fastqsanger.gz
	ERR6929507.fastq.gz	Fastqsanger.gz
	ERR6929508.fastq.gz	Fastqsanger.gz

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Spatial transcriptomics of in vivo invasive trancheobronchitis biopsies obtained from patients with influenza-associated pulmonary aspergillosis or COVID-19-associated pulmonary aspergillosis

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Project description:Despite available diagnostic tests and recent advances, diagnosis of pulmonary invasive aspergillosis (IPA) remains challenging. By undertaking a longitudinal case-control study, we explored the possibility to identify novel non-invasive human biomarkers candidates for IPA in patients post allogeneic stem cell transplantation (alloSCT). Using both RNA-sequencing and immunoassays, we investigated 66 blood samples of 3 probable IPA cases and 3 matched controls without Aspergillus infection. Selected potential biomarker candidates were evaluated further in additional alloSCT (n=23) and patients suffering from COVID-19-associated pulmonary aspergillosis (CAPA) and their appropriate control patients (n=65). Profiling analysis suggested LGALS2, MMP1 and caspase-3 as potential biomarker candidates indicating IPA in investigated alloSCT patients. Significant differences in IL-8 and caspase-3 levels were observed among CAPA patients compared to control patients. Given our conceptual work we demonstrate the value of seeking human IPA indicating biomarkers, which together with already established fungal biomarkers potentially improve the accuracy of IPA diagnostic.

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Project description:Abstract From manuscript: Incidences of invasive pulmonary aspergillosis, an infection caused predominantly by Aspergillus fumigatus, have increased due to the growing number of immunocompromised individuals. While A. fumigatus is reliant upon deficiencies in the host to facilitate invasive disease, the distinct mechanisms that govern the host-pathogen interaction remain enigmatic, particularly in the context of distinct immune modulating therapies. To gain insights into these mechanisms, RNA-Seq technology was utilized to sequence RNA derived from lungs of 2 clinically relevant, but immunologically distinct murine models of IPA on days 2 and 3 post inoculation when infection is established and active disease present. Our findings identify notable differences in host gene expression between the chemotherapeutic and steroid models at the interface of immunity and metabolism. RT-qPCR verified model specific and nonspecific expression of 23 immune-associated genes. Deep sequencing facilitated identification of highly expressed fungal genes. We utilized sequence similarity and gene expression to categorize the A. fumigatus putative in vivo secretome. RT-qPCR suggests model specific gene expression for nine putative fungal secreted proteins. Our analysis identifies contrasting responses by the host and fungus from day 2 to 3 between the two models. These differences may help tailor the identification, development, and deployment of host- and/or fungal-targeted therapeutics.

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Project description:Invasive pulmonary aspergillosis (IPA) is one of the major causes of morbidity and mortality in immunocompromised patients such as hematological malignancies, hematopoietic stem cell transplantation, and solid organ transplantation. The diagnosis of IPA in these patients is still difficult because it has no obvious specificity in clinical symptoms, signs and imaging, and test sensitivity of blood 1,3-β-d-glucan test, galactomannan are low. Therefore, we still need to explore more diagnostic methods. In our study, via peripheral blood metagenomic next-generation sequencing (mNGS), five patients were tested positive for Aspergillus DNA and then quickly diagnosed as IPA. Out of the 5 cases, 1 was proven and 4 were probable IPA. The underlying diseases of the 5 patients were myelodysplastic syndrome (2 cases), acute myeloid leukemia (2 cases), and renal transplantation (1 case). Then they were diagnosed as IPA using other methods such as lung histopathology, bronchoalveolar lavage fluid (BALF) mNGS, and sputum culture or sputum mNGS. In case 1, sputum culture suggested Aspergillus flavus. In case 2, both Grocott methenamine silver (GMS) stain of lung histopathology and lung tissue mNGS suggested Aspergillus infection. In cases 3 and 4, BALF-mNGS suggested Aspergillus infection. In case 5, sputum mNGS suggested Aspergillus infection. In conclusion, detecting the cfDNA of Aspergillus via peripheral blood mNGS can be used to diagnose IPA and is a rapid and non-invasive diagnosis method.

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