PMC:7558333 / 5758-7832 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T17","span":{"begin":1242,"end":1245},"obj":"Body_part"},{"id":"T18","span":{"begin":1572,"end":1577},"obj":"Body_part"},{"id":"T19","span":{"begin":1714,"end":1722},"obj":"Body_part"},{"id":"T20","span":{"begin":1742,"end":1745},"obj":"Body_part"},{"id":"T21","span":{"begin":1853,"end":1858},"obj":"Body_part"},{"id":"T22","span":{"begin":2038,"end":2041},"obj":"Body_part"}],"attributes":[{"id":"A17","pred":"fma_id","subj":"T17","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma63083"},{"id":"A19","pred":"fma_id","subj":"T19","obj":"http://purl.org/sig/ont/fma/fma62871"},{"id":"A20","pred":"fma_id","subj":"T20","obj":"http://purl.org/sig/ont/fma/fma62872"},{"id":"A21","pred":"fma_id","subj":"T21","obj":"http://purl.org/sig/ont/fma/fma63083"},{"id":"A22","pred":"fma_id","subj":"T22","obj":"http://purl.org/sig/ont/fma/fma74412"}],"text":"2.2. Aspergillus Detection\nRespiratory samples, either bronchial or endotracheal aspirates or bronchoalveolar lavages, were systematic twice weekly and Aspergillus detection was performed using culture and real-time quantitative PCR, but GM was not performed to avoid any risk of lab contamination.\nBriefly, respiratory samples were first digested using v/v digestEUR (Eurobio) for 30 min under shaking. Mycological culture were performed after centrifugation of fluidified samples by inoculation of 100–200 µL of pellet on Sabouraud-Chloramphenicol dextrose Agar plates, and incubated for 7 days at 30 °C and 37 °C. Mold identification at genus or species complex level was performed microscopically, and confirmed at species level using MALDI-ToF mass spectrometry (MALDI Biotyper, Bruker France, Marne-la-Vallée, France), after fungal material extraction [9]. Spectrum profiles were then submitted to the Mass Spectrometry Identification (MSI) online database for definitive identification (https://msi.happy-dev.fr/ [10]).\nFor molecular detection, 200 µL of plain fluidified respiratory sample underwent immediate SARS-CoV-2 inactivation by heating at 56 °C overnight in ATL Lysis buffer (Qiagen, Saint-Quentin Fallavier, France), before DNA extraction using the EZ1 DSP virus kit (Qiagen) on a EZ1 Advanced XL device (Qiagen). Molecular detection of A. fumigatus was done using a 28S rDNA Aspergillus-targeted PCR, as previously published [11,12].\nIn case of Aspergillus positive culture and/or positive PCR in respiratory samples, additional tests were performed on serum, i.e., detection of GM (Platelia GM Aspergillus, Biorad, Marnes-la-Coquette, France), Aspergillus PCR and detection of anti-Aspergillus antibody by ELISA (Platelia IgG Aspergillus, Biorad) and in-house immunoelectrophoresis. Briefly, Aspergillus PCR was performed on 1 mL of serum extracted using MagNA Pure 24 Total NA Isolation kit (Roche diagnostics, Meylan, France) on a MagNA Pure 24 device (Roche diagnostics), according to manufacturer recommendations. DNA was eluted in a volume of 50 µL."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T13","span":{"begin":1572,"end":1577},"obj":"Body_part"},{"id":"T14","span":{"begin":1853,"end":1858},"obj":"Body_part"}],"attributes":[{"id":"A13","pred":"uberon_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"A14","pred":"uberon_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"}],"text":"2.2. Aspergillus Detection\nRespiratory samples, either bronchial or endotracheal aspirates or bronchoalveolar lavages, were systematic twice weekly and Aspergillus detection was performed using culture and real-time quantitative PCR, but GM was not performed to avoid any risk of lab contamination.\nBriefly, respiratory samples were first digested using v/v digestEUR (Eurobio) for 30 min under shaking. Mycological culture were performed after centrifugation of fluidified samples by inoculation of 100–200 µL of pellet on Sabouraud-Chloramphenicol dextrose Agar plates, and incubated for 7 days at 30 °C and 37 °C. Mold identification at genus or species complex level was performed microscopically, and confirmed at species level using MALDI-ToF mass spectrometry (MALDI Biotyper, Bruker France, Marne-la-Vallée, France), after fungal material extraction [9]. Spectrum profiles were then submitted to the Mass Spectrometry Identification (MSI) online database for definitive identification (https://msi.happy-dev.fr/ [10]).\nFor molecular detection, 200 µL of plain fluidified respiratory sample underwent immediate SARS-CoV-2 inactivation by heating at 56 °C overnight in ATL Lysis buffer (Qiagen, Saint-Quentin Fallavier, France), before DNA extraction using the EZ1 DSP virus kit (Qiagen) on a EZ1 Advanced XL device (Qiagen). Molecular detection of A. fumigatus was done using a 28S rDNA Aspergillus-targeted PCR, as previously published [11,12].\nIn case of Aspergillus positive culture and/or positive PCR in respiratory samples, additional tests were performed on serum, i.e., detection of GM (Platelia GM Aspergillus, Biorad, Marnes-la-Coquette, France), Aspergillus PCR and detection of anti-Aspergillus antibody by ELISA (Platelia IgG Aspergillus, Biorad) and in-house immunoelectrophoresis. Briefly, Aspergillus PCR was performed on 1 mL of serum extracted using MagNA Pure 24 Total NA Isolation kit (Roche diagnostics, Meylan, France) on a MagNA Pure 24 device (Roche diagnostics), according to manufacturer recommendations. DNA was eluted in a volume of 50 µL."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T45","span":{"begin":1118,"end":1126},"obj":"Disease"}],"attributes":[{"id":"A45","pred":"mondo_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"2.2. Aspergillus Detection\nRespiratory samples, either bronchial or endotracheal aspirates or bronchoalveolar lavages, were systematic twice weekly and Aspergillus detection was performed using culture and real-time quantitative PCR, but GM was not performed to avoid any risk of lab contamination.\nBriefly, respiratory samples were first digested using v/v digestEUR (Eurobio) for 30 min under shaking. Mycological culture were performed after centrifugation of fluidified samples by inoculation of 100–200 µL of pellet on Sabouraud-Chloramphenicol dextrose Agar plates, and incubated for 7 days at 30 °C and 37 °C. Mold identification at genus or species complex level was performed microscopically, and confirmed at species level using MALDI-ToF mass spectrometry (MALDI Biotyper, Bruker France, Marne-la-Vallée, France), after fungal material extraction [9]. Spectrum profiles were then submitted to the Mass Spectrometry Identification (MSI) online database for definitive identification (https://msi.happy-dev.fr/ [10]).\nFor molecular detection, 200 µL of plain fluidified respiratory sample underwent immediate SARS-CoV-2 inactivation by heating at 56 °C overnight in ATL Lysis buffer (Qiagen, Saint-Quentin Fallavier, France), before DNA extraction using the EZ1 DSP virus kit (Qiagen) on a EZ1 Advanced XL device (Qiagen). Molecular detection of A. fumigatus was done using a 28S rDNA Aspergillus-targeted PCR, as previously published [11,12].\nIn case of Aspergillus positive culture and/or positive PCR in respiratory samples, additional tests were performed on serum, i.e., detection of GM (Platelia GM Aspergillus, Biorad, Marnes-la-Coquette, France), Aspergillus PCR and detection of anti-Aspergillus antibody by ELISA (Platelia IgG Aspergillus, Biorad) and in-house immunoelectrophoresis. Briefly, Aspergillus PCR was performed on 1 mL of serum extracted using MagNA Pure 24 Total NA Isolation kit (Roche diagnostics, Meylan, France) on a MagNA Pure 24 device (Roche diagnostics), according to manufacturer recommendations. DNA was eluted in a volume of 50 µL."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T40","span":{"begin":1275,"end":1280},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T41","span":{"begin":1297,"end":1298},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T42","span":{"begin":1315,"end":1321},"obj":"http://purl.obolibrary.org/obo/OBI_0000968"},{"id":"T43","span":{"begin":1355,"end":1356},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T44","span":{"begin":1383,"end":1384},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T45","span":{"begin":1548,"end":1553},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T46","span":{"begin":1951,"end":1952},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T47","span":{"begin":1967,"end":1973},"obj":"http://purl.obolibrary.org/obo/OBI_0000968"},{"id":"T48","span":{"begin":2056,"end":2057},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"2.2. Aspergillus Detection\nRespiratory samples, either bronchial or endotracheal aspirates or bronchoalveolar lavages, were systematic twice weekly and Aspergillus detection was performed using culture and real-time quantitative PCR, but GM was not performed to avoid any risk of lab contamination.\nBriefly, respiratory samples were first digested using v/v digestEUR (Eurobio) for 30 min under shaking. Mycological culture were performed after centrifugation of fluidified samples by inoculation of 100–200 µL of pellet on Sabouraud-Chloramphenicol dextrose Agar plates, and incubated for 7 days at 30 °C and 37 °C. Mold identification at genus or species complex level was performed microscopically, and confirmed at species level using MALDI-ToF mass spectrometry (MALDI Biotyper, Bruker France, Marne-la-Vallée, France), after fungal material extraction [9]. Spectrum profiles were then submitted to the Mass Spectrometry Identification (MSI) online database for definitive identification (https://msi.happy-dev.fr/ [10]).\nFor molecular detection, 200 µL of plain fluidified respiratory sample underwent immediate SARS-CoV-2 inactivation by heating at 56 °C overnight in ATL Lysis buffer (Qiagen, Saint-Quentin Fallavier, France), before DNA extraction using the EZ1 DSP virus kit (Qiagen) on a EZ1 Advanced XL device (Qiagen). Molecular detection of A. fumigatus was done using a 28S rDNA Aspergillus-targeted PCR, as previously published [11,12].\nIn case of Aspergillus positive culture and/or positive PCR in respiratory samples, additional tests were performed on serum, i.e., detection of GM (Platelia GM Aspergillus, Biorad, Marnes-la-Coquette, France), Aspergillus PCR and detection of anti-Aspergillus antibody by ELISA (Platelia IgG Aspergillus, Biorad) and in-house immunoelectrophoresis. Briefly, Aspergillus PCR was performed on 1 mL of serum extracted using MagNA Pure 24 Total NA Isolation kit (Roche diagnostics, Meylan, France) on a MagNA Pure 24 device (Roche diagnostics), according to manufacturer recommendations. DNA was eluted in a volume of 50 µL."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T4","span":{"begin":1179,"end":1184},"obj":"http://purl.obolibrary.org/obo/GO_0019835"}],"text":"2.2. Aspergillus Detection\nRespiratory samples, either bronchial or endotracheal aspirates or bronchoalveolar lavages, were systematic twice weekly and Aspergillus detection was performed using culture and real-time quantitative PCR, but GM was not performed to avoid any risk of lab contamination.\nBriefly, respiratory samples were first digested using v/v digestEUR (Eurobio) for 30 min under shaking. Mycological culture were performed after centrifugation of fluidified samples by inoculation of 100–200 µL of pellet on Sabouraud-Chloramphenicol dextrose Agar plates, and incubated for 7 days at 30 °C and 37 °C. Mold identification at genus or species complex level was performed microscopically, and confirmed at species level using MALDI-ToF mass spectrometry (MALDI Biotyper, Bruker France, Marne-la-Vallée, France), after fungal material extraction [9]. Spectrum profiles were then submitted to the Mass Spectrometry Identification (MSI) online database for definitive identification (https://msi.happy-dev.fr/ [10]).\nFor molecular detection, 200 µL of plain fluidified respiratory sample underwent immediate SARS-CoV-2 inactivation by heating at 56 °C overnight in ATL Lysis buffer (Qiagen, Saint-Quentin Fallavier, France), before DNA extraction using the EZ1 DSP virus kit (Qiagen) on a EZ1 Advanced XL device (Qiagen). Molecular detection of A. fumigatus was done using a 28S rDNA Aspergillus-targeted PCR, as previously published [11,12].\nIn case of Aspergillus positive culture and/or positive PCR in respiratory samples, additional tests were performed on serum, i.e., detection of GM (Platelia GM Aspergillus, Biorad, Marnes-la-Coquette, France), Aspergillus PCR and detection of anti-Aspergillus antibody by ELISA (Platelia IgG Aspergillus, Biorad) and in-house immunoelectrophoresis. Briefly, Aspergillus PCR was performed on 1 mL of serum extracted using MagNA Pure 24 Total NA Isolation kit (Roche diagnostics, Meylan, France) on a MagNA Pure 24 device (Roche diagnostics), according to manufacturer recommendations. DNA was eluted in a volume of 50 µL."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T8","span":{"begin":238,"end":240},"obj":"GlycoEpitope"},{"id":"T9","span":{"begin":1598,"end":1600},"obj":"GlycoEpitope"},{"id":"T10","span":{"begin":1611,"end":1613},"obj":"GlycoEpitope"}],"attributes":[{"id":"A8","pred":"glyco_epitope_db_id","subj":"T8","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A9","pred":"glyco_epitope_db_id","subj":"T9","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A10","pred":"glyco_epitope_db_id","subj":"T10","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"2.2. Aspergillus Detection\nRespiratory samples, either bronchial or endotracheal aspirates or bronchoalveolar lavages, were systematic twice weekly and Aspergillus detection was performed using culture and real-time quantitative PCR, but GM was not performed to avoid any risk of lab contamination.\nBriefly, respiratory samples were first digested using v/v digestEUR (Eurobio) for 30 min under shaking. Mycological culture were performed after centrifugation of fluidified samples by inoculation of 100–200 µL of pellet on Sabouraud-Chloramphenicol dextrose Agar plates, and incubated for 7 days at 30 °C and 37 °C. Mold identification at genus or species complex level was performed microscopically, and confirmed at species level using MALDI-ToF mass spectrometry (MALDI Biotyper, Bruker France, Marne-la-Vallée, France), after fungal material extraction [9]. Spectrum profiles were then submitted to the Mass Spectrometry Identification (MSI) online database for definitive identification (https://msi.happy-dev.fr/ [10]).\nFor molecular detection, 200 µL of plain fluidified respiratory sample underwent immediate SARS-CoV-2 inactivation by heating at 56 °C overnight in ATL Lysis buffer (Qiagen, Saint-Quentin Fallavier, France), before DNA extraction using the EZ1 DSP virus kit (Qiagen) on a EZ1 Advanced XL device (Qiagen). Molecular detection of A. fumigatus was done using a 28S rDNA Aspergillus-targeted PCR, as previously published [11,12].\nIn case of Aspergillus positive culture and/or positive PCR in respiratory samples, additional tests were performed on serum, i.e., detection of GM (Platelia GM Aspergillus, Biorad, Marnes-la-Coquette, France), Aspergillus PCR and detection of anti-Aspergillus antibody by ELISA (Platelia IgG Aspergillus, Biorad) and in-house immunoelectrophoresis. Briefly, Aspergillus PCR was performed on 1 mL of serum extracted using MagNA Pure 24 Total NA Isolation kit (Roche diagnostics, Meylan, France) on a MagNA Pure 24 device (Roche diagnostics), according to manufacturer recommendations. DNA was eluted in a volume of 50 µL."}

{"project":"LitCovid-sentences","denotations":[{"id":"T45","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T46","span":{"begin":5,"end":26},"obj":"Sentence"},{"id":"T47","span":{"begin":27,"end":298},"obj":"Sentence"},{"id":"T48","span":{"begin":299,"end":403},"obj":"Sentence"},{"id":"T49","span":{"begin":404,"end":616},"obj":"Sentence"},{"id":"T50","span":{"begin":617,"end":862},"obj":"Sentence"},{"id":"T51","span":{"begin":863,"end":1026},"obj":"Sentence"},{"id":"T52","span":{"begin":1027,"end":1331},"obj":"Sentence"},{"id":"T53","span":{"begin":1332,"end":1452},"obj":"Sentence"},{"id":"T54","span":{"begin":1453,"end":1802},"obj":"Sentence"},{"id":"T55","span":{"begin":1803,"end":2037},"obj":"Sentence"},{"id":"T56","span":{"begin":2038,"end":2074},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.2. Aspergillus Detection\nRespiratory samples, either bronchial or endotracheal aspirates or bronchoalveolar lavages, were systematic twice weekly and Aspergillus detection was performed using culture and real-time quantitative PCR, but GM was not performed to avoid any risk of lab contamination.\nBriefly, respiratory samples were first digested using v/v digestEUR (Eurobio) for 30 min under shaking. Mycological culture were performed after centrifugation of fluidified samples by inoculation of 100–200 µL of pellet on Sabouraud-Chloramphenicol dextrose Agar plates, and incubated for 7 days at 30 °C and 37 °C. Mold identification at genus or species complex level was performed microscopically, and confirmed at species level using MALDI-ToF mass spectrometry (MALDI Biotyper, Bruker France, Marne-la-Vallée, France), after fungal material extraction [9]. Spectrum profiles were then submitted to the Mass Spectrometry Identification (MSI) online database for definitive identification (https://msi.happy-dev.fr/ [10]).\nFor molecular detection, 200 µL of plain fluidified respiratory sample underwent immediate SARS-CoV-2 inactivation by heating at 56 °C overnight in ATL Lysis buffer (Qiagen, Saint-Quentin Fallavier, France), before DNA extraction using the EZ1 DSP virus kit (Qiagen) on a EZ1 Advanced XL device (Qiagen). Molecular detection of A. fumigatus was done using a 28S rDNA Aspergillus-targeted PCR, as previously published [11,12].\nIn case of Aspergillus positive culture and/or positive PCR in respiratory samples, additional tests were performed on serum, i.e., detection of GM (Platelia GM Aspergillus, Biorad, Marnes-la-Coquette, France), Aspergillus PCR and detection of anti-Aspergillus antibody by ELISA (Platelia IgG Aspergillus, Biorad) and in-house immunoelectrophoresis. Briefly, Aspergillus PCR was performed on 1 mL of serum extracted using MagNA Pure 24 Total NA Isolation kit (Roche diagnostics, Meylan, France) on a MagNA Pure 24 device (Roche diagnostics), according to manufacturer recommendations. DNA was eluted in a volume of 50 µL."}

{"project":"LitCovid-PubTator","denotations":[{"id":"143","span":{"begin":5,"end":16},"obj":"Species"},{"id":"146","span":{"begin":152,"end":163},"obj":"Species"},{"id":"147","span":{"begin":238,"end":240},"obj":"Chemical"},{"id":"149","span":{"begin":524,"end":563},"obj":"Chemical"},{"id":"154","span":{"begin":1118,"end":1128},"obj":"Species"},{"id":"155","span":{"begin":1355,"end":1367},"obj":"Species"},{"id":"156","span":{"begin":1394,"end":1405},"obj":"Species"},{"id":"157","span":{"begin":1175,"end":1184},"obj":"Disease"},{"id":"165","span":{"begin":1464,"end":1475},"obj":"Species"},{"id":"166","span":{"begin":1664,"end":1675},"obj":"Species"},{"id":"167","span":{"begin":1702,"end":1713},"obj":"Species"},{"id":"168","span":{"begin":1812,"end":1823},"obj":"Species"},{"id":"169","span":{"begin":1598,"end":1600},"obj":"Chemical"},{"id":"170","span":{"begin":1602,"end":1625},"obj":"Disease"},{"id":"171","span":{"begin":1733,"end":1757},"obj":"Disease"}],"attributes":[{"id":"A143","pred":"tao:has_database_id","subj":"143","obj":"Tax:746128"},{"id":"A146","pred":"tao:has_database_id","subj":"146","obj":"Tax:746128"},{"id":"A147","pred":"tao:has_database_id","subj":"147","obj":"MESH:C012990"},{"id":"A154","pred":"tao:has_database_id","subj":"154","obj":"Tax:2697049"},{"id":"A155","pred":"tao:has_database_id","subj":"155","obj":"Tax:746128"},{"id":"A156","pred":"tao:has_database_id","subj":"156","obj":"Tax:746128"},{"id":"A157","pred":"tao:has_database_id","subj":"157","obj":"MESH:D015275"},{"id":"A165","pred":"tao:has_database_id","subj":"165","obj":"Tax:746128"},{"id":"A166","pred":"tao:has_database_id","subj":"166","obj":"Tax:746128"},{"id":"A167","pred":"tao:has_database_id","subj":"167","obj":"Tax:746128"},{"id":"A168","pred":"tao:has_database_id","subj":"168","obj":"Tax:746128"},{"id":"A169","pred":"tao:has_database_id","subj":"169","obj":"MESH:C012990"},{"id":"A170","pred":"tao:has_database_id","subj":"170","obj":"MESH:C562602"},{"id":"A171","pred":"tao:has_database_id","subj":"171","obj":"MESH:D017099"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"2.2. Aspergillus Detection\nRespiratory samples, either bronchial or endotracheal aspirates or bronchoalveolar lavages, were systematic twice weekly and Aspergillus detection was performed using culture and real-time quantitative PCR, but GM was not performed to avoid any risk of lab contamination.\nBriefly, respiratory samples were first digested using v/v digestEUR (Eurobio) for 30 min under shaking. Mycological culture were performed after centrifugation of fluidified samples by inoculation of 100–200 µL of pellet on Sabouraud-Chloramphenicol dextrose Agar plates, and incubated for 7 days at 30 °C and 37 °C. Mold identification at genus or species complex level was performed microscopically, and confirmed at species level using MALDI-ToF mass spectrometry (MALDI Biotyper, Bruker France, Marne-la-Vallée, France), after fungal material extraction [9]. Spectrum profiles were then submitted to the Mass Spectrometry Identification (MSI) online database for definitive identification (https://msi.happy-dev.fr/ [10]).\nFor molecular detection, 200 µL of plain fluidified respiratory sample underwent immediate SARS-CoV-2 inactivation by heating at 56 °C overnight in ATL Lysis buffer (Qiagen, Saint-Quentin Fallavier, France), before DNA extraction using the EZ1 DSP virus kit (Qiagen) on a EZ1 Advanced XL device (Qiagen). Molecular detection of A. fumigatus was done using a 28S rDNA Aspergillus-targeted PCR, as previously published [11,12].\nIn case of Aspergillus positive culture and/or positive PCR in respiratory samples, additional tests were performed on serum, i.e., detection of GM (Platelia GM Aspergillus, Biorad, Marnes-la-Coquette, France), Aspergillus PCR and detection of anti-Aspergillus antibody by ELISA (Platelia IgG Aspergillus, Biorad) and in-house immunoelectrophoresis. Briefly, Aspergillus PCR was performed on 1 mL of serum extracted using MagNA Pure 24 Total NA Isolation kit (Roche diagnostics, Meylan, France) on a MagNA Pure 24 device (Roche diagnostics), according to manufacturer recommendations. DNA was eluted in a volume of 50 µL."}

{"project":"2_test","denotations":[{"id":"32664423-28637907-60101697","span":{"begin":1021,"end":1023},"obj":"28637907"},{"id":"32664423-29248586-60101698","span":{"begin":1445,"end":1447},"obj":"29248586"},{"id":"32664423-14766869-60101699","span":{"begin":1448,"end":1450},"obj":"14766869"}],"text":"2.2. Aspergillus Detection\nRespiratory samples, either bronchial or endotracheal aspirates or bronchoalveolar lavages, were systematic twice weekly and Aspergillus detection was performed using culture and real-time quantitative PCR, but GM was not performed to avoid any risk of lab contamination.\nBriefly, respiratory samples were first digested using v/v digestEUR (Eurobio) for 30 min under shaking. Mycological culture were performed after centrifugation of fluidified samples by inoculation of 100–200 µL of pellet on Sabouraud-Chloramphenicol dextrose Agar plates, and incubated for 7 days at 30 °C and 37 °C. Mold identification at genus or species complex level was performed microscopically, and confirmed at species level using MALDI-ToF mass spectrometry (MALDI Biotyper, Bruker France, Marne-la-Vallée, France), after fungal material extraction [9]. Spectrum profiles were then submitted to the Mass Spectrometry Identification (MSI) online database for definitive identification (https://msi.happy-dev.fr/ [10]).\nFor molecular detection, 200 µL of plain fluidified respiratory sample underwent immediate SARS-CoV-2 inactivation by heating at 56 °C overnight in ATL Lysis buffer (Qiagen, Saint-Quentin Fallavier, France), before DNA extraction using the EZ1 DSP virus kit (Qiagen) on a EZ1 Advanced XL device (Qiagen). Molecular detection of A. fumigatus was done using a 28S rDNA Aspergillus-targeted PCR, as previously published [11,12].\nIn case of Aspergillus positive culture and/or positive PCR in respiratory samples, additional tests were performed on serum, i.e., detection of GM (Platelia GM Aspergillus, Biorad, Marnes-la-Coquette, France), Aspergillus PCR and detection of anti-Aspergillus antibody by ELISA (Platelia IgG Aspergillus, Biorad) and in-house immunoelectrophoresis. Briefly, Aspergillus PCR was performed on 1 mL of serum extracted using MagNA Pure 24 Total NA Isolation kit (Roche diagnostics, Meylan, France) on a MagNA Pure 24 device (Roche diagnostics), according to manufacturer recommendations. DNA was eluted in a volume of 50 µL."}