Early Identification of Fungal and Mycobacterium Infections in Pulmonary Granulomas Using Metagenomic Next-Generation Sequencing on Formalin fixation and paraffin embedding tissue

References

• Chopra A, Avadhani V, Tiwari A, et al. Granulomatous lung disease: clinical aspects. Expert Rev Respir Med. 2020;14(10):1045–1063.
   PubMed Web of Science ®Google Scholar
• Nazarullah A, Nilson R, Maselli DJ, et al. Incidence and aetiologies of pulmonary granulomatous inflammation: a decade of experience. Respirology. 2015;20:115–121.
   PubMed Web of Science ®Google Scholar
• Mukhopadhyay S. Role of histology in the diagnosis of infectious causes of granulomatous lung disease. Curr Opin Pulm Med. 2011;17:189–196.
   PubMed Web of Science ®Google Scholar
• Ohshimo S, Guzman J, Costabel U, et al. Differential diagnosis of granulomatous lung disease: clues and pitfalls: number 4 in the series “Pathology for the clinician” Edited by Peter Dorfmüller and Alberto Cavazza. Eur Respir Rev. 2017;26(145):170012.
   PubMed Web of Science ®Google Scholar
• Mukhopadhyay S, Wilcox BE, Myers JL, et al. Pulmonary necrotizing granulomas of unknown cause: clinical and pathologic analysis of 131 patients with completely resected nodules. Chest. 2013;144(3):813–824.
   PubMed Web of Science ®Google Scholar
• Klopfleisch R, Weiss AT, Gruber AD. Excavation of a buried treasure – DNA, mRNA, miRNA and protein analysis in formalin fixed paraffin embedded tissues. Histol Histopathol. 2011;26:797–810.
   PubMed Web of Science ®Google Scholar
• Ai J-W, Li Y, Cheng Q, et al. Diagnosis of local hepatic tuberculosis through next-generation sequencing: smarter, faster and better. Clin Res Hepatol Gastroenterol. 2018;42:178–181.
   PubMed Web of Science ®Google Scholar
• Miao Q, Ma Y, Wang Q, et al. Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice. Clin Infect Dis. 2018;67:S231–S240.
   PubMed Web of Science ®Google Scholar
• Chen Y, Wang D, Wu Y, et al. The feasibility of metagenomic next-generation sequencing to identify pathogens causing tuberculous meningitis in cerebrospinal fluid. Front Microbiol. 2019;10:1993.
   PubMed Web of Science ®Google Scholar
• Zhang HC, Ai JW, Cui P, et al. Incremental value of metagenomic next generation sequencing for the diagnosis of suspected focal infection in adults. J Infect. 2019;79(5):419–425.
   PubMed Web of Science ®Google Scholar
• Henan L, Hua G, Han M, et al. Detection of pulmonary infectious pathogens from lung biopsy tissues by metagenomic next-generation sequencing. Front Cell Infect Microbiol. 2018;8:205.
   PubMed Web of Science ®Google Scholar
• Frickmann H, Künne C, Hagen RM, et al. Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples- a proof-of-principle assessment. BMC Microbiol. 2019;19(1):75.
   PubMedGoogle Scholar
• Forbes JD, Knox NC, Ronholm J, et al. Metagenomics: the next culture-independent game changer. Front Microbiol. 2017;8:1069.
   PubMed Web of Science ®Google Scholar
• Schlaberg R, Chiu CY, Miller S, et al. Professional practice committee and committee on laboratory practices of the American Society for Microbiology; microbiology resource committee of the college of American pathologists. Validation of metagenomic next-generation sequencing tests for universal pathogen detection. Arch Pathol Lab Med . 2017;141:776–786.
   PubMed Web of Science ®Google Scholar
• Simner PJ, Miller S, Carroll KC. Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases. Clin Infect Dis. 2018;66:778–788.
   PubMed Web of Science ®Google Scholar
• Li N, Cai Q, Miao Q, et al. High-Throughput metagenomics for identification of pathogens in the clinical settings. Small Methods. 2021;5:2000792.
   PubMed Web of Science ®Google Scholar
• Sun WW, Lu ZH, Yan LP. Clinical efficacy of metagenomic next-generation sequencing for rapid detection of Mycobacterium tuberculosis in smear-negative extrapulmonary specimens in a high tuberculosis burden area. Int J Infect Dis. 2020;103:91–96.
   PubMed Web of Science ®Google Scholar
• Daley Charles L, Iaccarino Jonathan M, Lange C, et al. Treatment of nontuberculous mycobacterial pulmonary disease: an official ATS/ERS/ESCMID/IDSA clinical practice guideline. Clin Infect Dis. 2020;71:905–913.
   PubMed Web of Science ®Google Scholar
• Perfect JR, Hachem R, Wingard JR. Update on epidemiology of and preventive strategies for invasive fungal infections in cancer patients. Clin Infect Dis. 2014;59(suppl 5):S352–355.
   PubMedGoogle Scholar
• Salian NV, Rish JA, Eisenach KD, et al. Polymerase chain reaction to detect mycobacterium tuberculosis in histologic specimens. Am J Respir Crit Care Med. 1998;158:1150–1155.
   PubMed Web of Science ®Google Scholar
• World Health Organisation. Global tuberculosis report 2018. France: World Health Organization; 2018. [cited 16 May 2019]. https://apps.who.int/iris/handle/10665/274453
   Google Scholar
• Yan L, Sun W, Lu Z, et al. Metagenomic Next-Generation Sequencing (mNGS) in cerebrospinal fluid for rapid diagnosis of Tuberculosis meningitis in HIV-negative population. Int J Infect Dis. 2020;96:270–275.
   PubMed Web of Science ®Google Scholar
• Chen P, Sun W, He Y. Comparison of metagenomic next-generation sequencing technology, culture and GeneXpert MTB/RIF assay in the diagnosis of tuberculosis. J Thorac Dis. 2020;12:4014–4024.
   PubMed Web of Science ®Google Scholar
• Lee S, Yun NR, Kim KH, et al. Discrepancy between histology and culture in filamentous fungal infections. Med Mycol. 2010;48:886–888.
   PubMed Web of Science ®Google Scholar
• Salehi E, Hedayati Mohammad T, Zoll J, et al. Discrimination of aspergillosis, mucormycosis, fusariosis, and scedosporiosis in formalin-fixed paraffin-embedded tissue specimens by use of multiple real-time quantitative PCR assays. J Clin Microbiol. 2016;54:2798–2803.
   PubMed Web of Science ®Google Scholar
• Higuchi H, Yamakawa N, Imadome KI, et al. Role of exosomes as a proinflammatory mediator in the development of EBV-associated lymphoma. Blood. 2018;2017(7): 794–529.
   Google Scholar
• Stämmler F, Gläsner J, Hiergeist A, et al. Adjusting microbiome profiles for differences in microbial load by spike-in bacteria. Microbiome. 2016;4:28.
   PubMed Web of Science ®Google Scholar