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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T12","span":{"begin":459,"end":464},"obj":"Body_part"},{"id":"T13","span":{"begin":908,"end":913},"obj":"Body_part"},{"id":"T14","span":{"begin":937,"end":943},"obj":"Body_part"},{"id":"T15","span":{"begin":1233,"end":1238},"obj":"Body_part"}],"attributes":[{"id":"A12","pred":"fma_id","subj":"T12","obj":"http://purl.org/sig/ont/fma/fma63083"},{"id":"A13","pred":"fma_id","subj":"T13","obj":"http://purl.org/sig/ont/fma/fma63083"},{"id":"A14","pred":"fma_id","subj":"T14","obj":"http://purl.org/sig/ont/fma/fma312401"},{"id":"A15","pred":"fma_id","subj":"T15","obj":"http://purl.org/sig/ont/fma/fma9576"}],"text":"Clinical presentation and diagnosis of IAPA\nA retrospective Belgian study of influenza patients admitted to ICU between September 2009 and March 2011 showed that 9 of 40 (23%) patients had IAPA. Four cases (44%) were proven despite not being immunocompromised according to the EORTC/MSGERC consensus definitions [7]. The median time between influenza diagnosis and IAPA was 2 days (range 0–4 days). All IAPA patients had positive BAL GM, and 78% had positive serum GM, despite not being neutropenic. Eighty-nine percent of patients had Aspergillus growth in BAL culture (almost exclusively Aspergillus fumigatus), and 55% of patients had endobronchial lesions observed during bronchoscopy, possibly indicating invasive tracheobronchitis [7]. Similar performance characteristics of BAL GM and culture were reported in two other cohort studies [8, 9]. BAL sampling is thus an important diagnostic procedure as serum GM can be negative and sputum/tracheal aspirate cultures can remain sterile.\nLesions that are suggestive of invasive mold disease on imaging in neutropenic patients, such as the halo sign, are often absent in critically ill patients. However, in some IAPA patients with autopsy-confirmed Aspergillus tracheobronchitis, chest CT demonstrated peribronchial infiltrates. The main diagnostic clue for airway-invasive Aspergillus tracheobronchitis is epithelial plaques, pseudomembranes or ulcers that can be visualized via bronchoscopy, as radiological features may be subtle [31]. Worsening of radiographic pulmonary infiltrates in patients with influenza is often attributed to progression of ARDS or bacterial infection, leading to a change of antimicrobial therapy without performing diagnostic procedures [32]. Patients who survived IAPA received antifungal therapy much earlier than those who did not (2 days after diagnosis of influenza among survivors versus 9 days among non-survivors) [8], suggesting that early diagnosis and administration of antifungal therapy may be important. Lateral flow tests have recently become available as an alternative for diagnosing IPA (AspLFD, OLM Diagnostics and the sōna Aspergillus GM, IMMY) showing overall good performance in hematology patients [33]. The very quick assessment, with results available within 30–45 min, makes this type of test very attractive for the management of IAPA and use in clinical trials. However, lateral flow tests have not yet been validated in the ICU population.\nIAPA needs to be considered in patients admitted to the ICU with influenza and where indicated these patients should undergo early BAL for Aspergillus antigen testing, culture and microscopy. Patients who test positive require anti-Aspergillus therapy, and the BAL fluid sample should be fast-tracked for azole resistance testing by PCR (and culture when positive) in regions with high (\u003e 5%) azole resistance rates [34]. This would enable diagnostic assessment and initiation of adequate antifungal therapy within 24–48 h of ICU admission. Diagnostic workup for IAPA may be repeated in patients deteriorating while on antivirals and/or appropriate antibiotics or when initiating corticosteroid treatment is unavoidable."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T10","span":{"begin":459,"end":464},"obj":"Body_part"},{"id":"T11","span":{"begin":908,"end":913},"obj":"Body_part"},{"id":"T12","span":{"begin":937,"end":943},"obj":"Body_part"},{"id":"T13","span":{"begin":1233,"end":1238},"obj":"Body_part"}],"attributes":[{"id":"A10","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"A11","pred":"uberon_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"A12","pred":"uberon_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/UBERON_0007311"},{"id":"A13","pred":"uberon_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"}],"text":"Clinical presentation and diagnosis of IAPA\nA retrospective Belgian study of influenza patients admitted to ICU between September 2009 and March 2011 showed that 9 of 40 (23%) patients had IAPA. Four cases (44%) were proven despite not being immunocompromised according to the EORTC/MSGERC consensus definitions [7]. The median time between influenza diagnosis and IAPA was 2 days (range 0–4 days). All IAPA patients had positive BAL GM, and 78% had positive serum GM, despite not being neutropenic. Eighty-nine percent of patients had Aspergillus growth in BAL culture (almost exclusively Aspergillus fumigatus), and 55% of patients had endobronchial lesions observed during bronchoscopy, possibly indicating invasive tracheobronchitis [7]. Similar performance characteristics of BAL GM and culture were reported in two other cohort studies [8, 9]. BAL sampling is thus an important diagnostic procedure as serum GM can be negative and sputum/tracheal aspirate cultures can remain sterile.\nLesions that are suggestive of invasive mold disease on imaging in neutropenic patients, such as the halo sign, are often absent in critically ill patients. However, in some IAPA patients with autopsy-confirmed Aspergillus tracheobronchitis, chest CT demonstrated peribronchial infiltrates. The main diagnostic clue for airway-invasive Aspergillus tracheobronchitis is epithelial plaques, pseudomembranes or ulcers that can be visualized via bronchoscopy, as radiological features may be subtle [31]. Worsening of radiographic pulmonary infiltrates in patients with influenza is often attributed to progression of ARDS or bacterial infection, leading to a change of antimicrobial therapy without performing diagnostic procedures [32]. Patients who survived IAPA received antifungal therapy much earlier than those who did not (2 days after diagnosis of influenza among survivors versus 9 days among non-survivors) [8], suggesting that early diagnosis and administration of antifungal therapy may be important. Lateral flow tests have recently become available as an alternative for diagnosing IPA (AspLFD, OLM Diagnostics and the sōna Aspergillus GM, IMMY) showing overall good performance in hematology patients [33]. The very quick assessment, with results available within 30–45 min, makes this type of test very attractive for the management of IAPA and use in clinical trials. However, lateral flow tests have not yet been validated in the ICU population.\nIAPA needs to be considered in patients admitted to the ICU with influenza and where indicated these patients should undergo early BAL for Aspergillus antigen testing, culture and microscopy. Patients who test positive require anti-Aspergillus therapy, and the BAL fluid sample should be fast-tracked for azole resistance testing by PCR (and culture when positive) in regions with high (\u003e 5%) azole resistance rates [34]. This would enable diagnostic assessment and initiation of adequate antifungal therapy within 24–48 h of ICU admission. Diagnostic workup for IAPA may be repeated in patients deteriorating while on antivirals and/or appropriate antibiotics or when initiating corticosteroid treatment is unavoidable."}

LitCovid-PubTator

LitCovid-PD-MONDO

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T67","span":{"begin":44,"end":45},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T68","span":{"begin":1233,"end":1238},"obj":"http://www.ebi.ac.uk/efo/EFO_0000965"},{"id":"T69","span":{"begin":1311,"end":1317},"obj":"http://purl.obolibrary.org/obo/UBERON_0001005"},{"id":"T70","span":{"begin":1360,"end":1370},"obj":"http://purl.obolibrary.org/obo/CL_0000066"},{"id":"T71","span":{"begin":1645,"end":1646},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T72","span":{"begin":2014,"end":2019},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T73","span":{"begin":2270,"end":2272},"obj":"http://purl.obolibrary.org/obo/CLO_0053799"},{"id":"T74","span":{"begin":2297,"end":2301},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T75","span":{"begin":2395,"end":2400},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T76","span":{"begin":2611,"end":2618},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T77","span":{"begin":2657,"end":2661},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T78","span":{"begin":2774,"end":2781},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T79","span":{"begin":2869,"end":2871},"obj":"http://purl.obolibrary.org/obo/CLO_0001302"},{"id":"T80","span":{"begin":2970,"end":2972},"obj":"http://purl.obolibrary.org/obo/CLO_0001382"}],"text":"Clinical presentation and diagnosis of IAPA\nA retrospective Belgian study of influenza patients admitted to ICU between September 2009 and March 2011 showed that 9 of 40 (23%) patients had IAPA. Four cases (44%) were proven despite not being immunocompromised according to the EORTC/MSGERC consensus definitions [7]. The median time between influenza diagnosis and IAPA was 2 days (range 0–4 days). All IAPA patients had positive BAL GM, and 78% had positive serum GM, despite not being neutropenic. Eighty-nine percent of patients had Aspergillus growth in BAL culture (almost exclusively Aspergillus fumigatus), and 55% of patients had endobronchial lesions observed during bronchoscopy, possibly indicating invasive tracheobronchitis [7]. Similar performance characteristics of BAL GM and culture were reported in two other cohort studies [8, 9]. BAL sampling is thus an important diagnostic procedure as serum GM can be negative and sputum/tracheal aspirate cultures can remain sterile.\nLesions that are suggestive of invasive mold disease on imaging in neutropenic patients, such as the halo sign, are often absent in critically ill patients. However, in some IAPA patients with autopsy-confirmed Aspergillus tracheobronchitis, chest CT demonstrated peribronchial infiltrates. The main diagnostic clue for airway-invasive Aspergillus tracheobronchitis is epithelial plaques, pseudomembranes or ulcers that can be visualized via bronchoscopy, as radiological features may be subtle [31]. Worsening of radiographic pulmonary infiltrates in patients with influenza is often attributed to progression of ARDS or bacterial infection, leading to a change of antimicrobial therapy without performing diagnostic procedures [32]. Patients who survived IAPA received antifungal therapy much earlier than those who did not (2 days after diagnosis of influenza among survivors versus 9 days among non-survivors) [8], suggesting that early diagnosis and administration of antifungal therapy may be important. Lateral flow tests have recently become available as an alternative for diagnosing IPA (AspLFD, OLM Diagnostics and the sōna Aspergillus GM, IMMY) showing overall good performance in hematology patients [33]. The very quick assessment, with results available within 30–45 min, makes this type of test very attractive for the management of IAPA and use in clinical trials. However, lateral flow tests have not yet been validated in the ICU population.\nIAPA needs to be considered in patients admitted to the ICU with influenza and where indicated these patients should undergo early BAL for Aspergillus antigen testing, culture and microscopy. Patients who test positive require anti-Aspergillus therapy, and the BAL fluid sample should be fast-tracked for azole resistance testing by PCR (and culture when positive) in regions with high (\u003e 5%) azole resistance rates [34]. This would enable diagnostic assessment and initiation of adequate antifungal therapy within 24–48 h of ICU admission. Diagnostic workup for IAPA may be repeated in patients deteriorating while on antivirals and/or appropriate antibiotics or when initiating corticosteroid treatment is unavoidable."}

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T11","span":{"begin":548,"end":554},"obj":"http://purl.obolibrary.org/obo/GO_0040007"}],"text":"Clinical presentation and diagnosis of IAPA\nA retrospective Belgian study of influenza patients admitted to ICU between September 2009 and March 2011 showed that 9 of 40 (23%) patients had IAPA. Four cases (44%) were proven despite not being immunocompromised according to the EORTC/MSGERC consensus definitions [7]. The median time between influenza diagnosis and IAPA was 2 days (range 0–4 days). All IAPA patients had positive BAL GM, and 78% had positive serum GM, despite not being neutropenic. Eighty-nine percent of patients had Aspergillus growth in BAL culture (almost exclusively Aspergillus fumigatus), and 55% of patients had endobronchial lesions observed during bronchoscopy, possibly indicating invasive tracheobronchitis [7]. Similar performance characteristics of BAL GM and culture were reported in two other cohort studies [8, 9]. BAL sampling is thus an important diagnostic procedure as serum GM can be negative and sputum/tracheal aspirate cultures can remain sterile.\nLesions that are suggestive of invasive mold disease on imaging in neutropenic patients, such as the halo sign, are often absent in critically ill patients. However, in some IAPA patients with autopsy-confirmed Aspergillus tracheobronchitis, chest CT demonstrated peribronchial infiltrates. The main diagnostic clue for airway-invasive Aspergillus tracheobronchitis is epithelial plaques, pseudomembranes or ulcers that can be visualized via bronchoscopy, as radiological features may be subtle [31]. Worsening of radiographic pulmonary infiltrates in patients with influenza is often attributed to progression of ARDS or bacterial infection, leading to a change of antimicrobial therapy without performing diagnostic procedures [32]. Patients who survived IAPA received antifungal therapy much earlier than those who did not (2 days after diagnosis of influenza among survivors versus 9 days among non-survivors) [8], suggesting that early diagnosis and administration of antifungal therapy may be important. Lateral flow tests have recently become available as an alternative for diagnosing IPA (AspLFD, OLM Diagnostics and the sōna Aspergillus GM, IMMY) showing overall good performance in hematology patients [33]. The very quick assessment, with results available within 30–45 min, makes this type of test very attractive for the management of IAPA and use in clinical trials. However, lateral flow tests have not yet been validated in the ICU population.\nIAPA needs to be considered in patients admitted to the ICU with influenza and where indicated these patients should undergo early BAL for Aspergillus antigen testing, culture and microscopy. Patients who test positive require anti-Aspergillus therapy, and the BAL fluid sample should be fast-tracked for azole resistance testing by PCR (and culture when positive) in regions with high (\u003e 5%) azole resistance rates [34]. This would enable diagnostic assessment and initiation of adequate antifungal therapy within 24–48 h of ICU admission. Diagnostic workup for IAPA may be repeated in patients deteriorating while on antivirals and/or appropriate antibiotics or when initiating corticosteroid treatment is unavoidable."}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T4","span":{"begin":434,"end":436},"obj":"GlycoEpitope"},{"id":"T5","span":{"begin":465,"end":467},"obj":"GlycoEpitope"},{"id":"T6","span":{"begin":785,"end":787},"obj":"GlycoEpitope"},{"id":"T7","span":{"begin":914,"end":916},"obj":"GlycoEpitope"},{"id":"T8","span":{"begin":2138,"end":2140},"obj":"GlycoEpitope"}],"attributes":[{"id":"A4","pred":"glyco_epitope_db_id","subj":"T4","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A5","pred":"glyco_epitope_db_id","subj":"T5","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A6","pred":"glyco_epitope_db_id","subj":"T6","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A7","pred":"glyco_epitope_db_id","subj":"T7","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A8","pred":"glyco_epitope_db_id","subj":"T8","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"Clinical presentation and diagnosis of IAPA\nA retrospective Belgian study of influenza patients admitted to ICU between September 2009 and March 2011 showed that 9 of 40 (23%) patients had IAPA. Four cases (44%) were proven despite not being immunocompromised according to the EORTC/MSGERC consensus definitions [7]. The median time between influenza diagnosis and IAPA was 2 days (range 0–4 days). All IAPA patients had positive BAL GM, and 78% had positive serum GM, despite not being neutropenic. Eighty-nine percent of patients had Aspergillus growth in BAL culture (almost exclusively Aspergillus fumigatus), and 55% of patients had endobronchial lesions observed during bronchoscopy, possibly indicating invasive tracheobronchitis [7]. Similar performance characteristics of BAL GM and culture were reported in two other cohort studies [8, 9]. BAL sampling is thus an important diagnostic procedure as serum GM can be negative and sputum/tracheal aspirate cultures can remain sterile.\nLesions that are suggestive of invasive mold disease on imaging in neutropenic patients, such as the halo sign, are often absent in critically ill patients. However, in some IAPA patients with autopsy-confirmed Aspergillus tracheobronchitis, chest CT demonstrated peribronchial infiltrates. The main diagnostic clue for airway-invasive Aspergillus tracheobronchitis is epithelial plaques, pseudomembranes or ulcers that can be visualized via bronchoscopy, as radiological features may be subtle [31]. Worsening of radiographic pulmonary infiltrates in patients with influenza is often attributed to progression of ARDS or bacterial infection, leading to a change of antimicrobial therapy without performing diagnostic procedures [32]. Patients who survived IAPA received antifungal therapy much earlier than those who did not (2 days after diagnosis of influenza among survivors versus 9 days among non-survivors) [8], suggesting that early diagnosis and administration of antifungal therapy may be important. Lateral flow tests have recently become available as an alternative for diagnosing IPA (AspLFD, OLM Diagnostics and the sōna Aspergillus GM, IMMY) showing overall good performance in hematology patients [33]. The very quick assessment, with results available within 30–45 min, makes this type of test very attractive for the management of IAPA and use in clinical trials. However, lateral flow tests have not yet been validated in the ICU population.\nIAPA needs to be considered in patients admitted to the ICU with influenza and where indicated these patients should undergo early BAL for Aspergillus antigen testing, culture and microscopy. Patients who test positive require anti-Aspergillus therapy, and the BAL fluid sample should be fast-tracked for azole resistance testing by PCR (and culture when positive) in regions with high (\u003e 5%) azole resistance rates [34]. This would enable diagnostic assessment and initiation of adequate antifungal therapy within 24–48 h of ICU admission. Diagnostic workup for IAPA may be repeated in patients deteriorating while on antivirals and/or appropriate antibiotics or when initiating corticosteroid treatment is unavoidable."}

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T19","span":{"begin":1518,"end":1539},"obj":"Phenotype"},{"id":"T20","span":{"begin":2084,"end":2087},"obj":"Phenotype"}],"attributes":[{"id":"A19","pred":"hp_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/HP_0002113"},{"id":"A20","pred":"hp_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/HP_0020103"}],"text":"Clinical presentation and diagnosis of IAPA\nA retrospective Belgian study of influenza patients admitted to ICU between September 2009 and March 2011 showed that 9 of 40 (23%) patients had IAPA. Four cases (44%) were proven despite not being immunocompromised according to the EORTC/MSGERC consensus definitions [7]. The median time between influenza diagnosis and IAPA was 2 days (range 0–4 days). All IAPA patients had positive BAL GM, and 78% had positive serum GM, despite not being neutropenic. Eighty-nine percent of patients had Aspergillus growth in BAL culture (almost exclusively Aspergillus fumigatus), and 55% of patients had endobronchial lesions observed during bronchoscopy, possibly indicating invasive tracheobronchitis [7]. Similar performance characteristics of BAL GM and culture were reported in two other cohort studies [8, 9]. BAL sampling is thus an important diagnostic procedure as serum GM can be negative and sputum/tracheal aspirate cultures can remain sterile.\nLesions that are suggestive of invasive mold disease on imaging in neutropenic patients, such as the halo sign, are often absent in critically ill patients. However, in some IAPA patients with autopsy-confirmed Aspergillus tracheobronchitis, chest CT demonstrated peribronchial infiltrates. The main diagnostic clue for airway-invasive Aspergillus tracheobronchitis is epithelial plaques, pseudomembranes or ulcers that can be visualized via bronchoscopy, as radiological features may be subtle [31]. Worsening of radiographic pulmonary infiltrates in patients with influenza is often attributed to progression of ARDS or bacterial infection, leading to a change of antimicrobial therapy without performing diagnostic procedures [32]. Patients who survived IAPA received antifungal therapy much earlier than those who did not (2 days after diagnosis of influenza among survivors versus 9 days among non-survivors) [8], suggesting that early diagnosis and administration of antifungal therapy may be important. Lateral flow tests have recently become available as an alternative for diagnosing IPA (AspLFD, OLM Diagnostics and the sōna Aspergillus GM, IMMY) showing overall good performance in hematology patients [33]. The very quick assessment, with results available within 30–45 min, makes this type of test very attractive for the management of IAPA and use in clinical trials. However, lateral flow tests have not yet been validated in the ICU population.\nIAPA needs to be considered in patients admitted to the ICU with influenza and where indicated these patients should undergo early BAL for Aspergillus antigen testing, culture and microscopy. Patients who test positive require anti-Aspergillus therapy, and the BAL fluid sample should be fast-tracked for azole resistance testing by PCR (and culture when positive) in regions with high (\u003e 5%) azole resistance rates [34]. This would enable diagnostic assessment and initiation of adequate antifungal therapy within 24–48 h of ICU admission. Diagnostic workup for IAPA may be repeated in patients deteriorating while on antivirals and/or appropriate antibiotics or when initiating corticosteroid treatment is unavoidable."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T64","span":{"begin":0,"end":43},"obj":"Sentence"},{"id":"T65","span":{"begin":44,"end":194},"obj":"Sentence"},{"id":"T66","span":{"begin":195,"end":316},"obj":"Sentence"},{"id":"T67","span":{"begin":317,"end":398},"obj":"Sentence"},{"id":"T68","span":{"begin":399,"end":499},"obj":"Sentence"},{"id":"T69","span":{"begin":500,"end":741},"obj":"Sentence"},{"id":"T70","span":{"begin":742,"end":849},"obj":"Sentence"},{"id":"T71","span":{"begin":850,"end":990},"obj":"Sentence"},{"id":"T72","span":{"begin":991,"end":1147},"obj":"Sentence"},{"id":"T73","span":{"begin":1148,"end":1281},"obj":"Sentence"},{"id":"T74","span":{"begin":1282,"end":1491},"obj":"Sentence"},{"id":"T75","span":{"begin":1492,"end":1725},"obj":"Sentence"},{"id":"T76","span":{"begin":1726,"end":2000},"obj":"Sentence"},{"id":"T77","span":{"begin":2001,"end":2209},"obj":"Sentence"},{"id":"T78","span":{"begin":2210,"end":2372},"obj":"Sentence"},{"id":"T79","span":{"begin":2373,"end":2451},"obj":"Sentence"},{"id":"T80","span":{"begin":2452,"end":2643},"obj":"Sentence"},{"id":"T81","span":{"begin":2644,"end":2873},"obj":"Sentence"},{"id":"T82","span":{"begin":2874,"end":2992},"obj":"Sentence"},{"id":"T83","span":{"begin":2993,"end":3172},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Clinical presentation and diagnosis of IAPA\nA retrospective Belgian study of influenza patients admitted to ICU between September 2009 and March 2011 showed that 9 of 40 (23%) patients had IAPA. Four cases (44%) were proven despite not being immunocompromised according to the EORTC/MSGERC consensus definitions [7]. The median time between influenza diagnosis and IAPA was 2 days (range 0–4 days). All IAPA patients had positive BAL GM, and 78% had positive serum GM, despite not being neutropenic. Eighty-nine percent of patients had Aspergillus growth in BAL culture (almost exclusively Aspergillus fumigatus), and 55% of patients had endobronchial lesions observed during bronchoscopy, possibly indicating invasive tracheobronchitis [7]. Similar performance characteristics of BAL GM and culture were reported in two other cohort studies [8, 9]. BAL sampling is thus an important diagnostic procedure as serum GM can be negative and sputum/tracheal aspirate cultures can remain sterile.\nLesions that are suggestive of invasive mold disease on imaging in neutropenic patients, such as the halo sign, are often absent in critically ill patients. However, in some IAPA patients with autopsy-confirmed Aspergillus tracheobronchitis, chest CT demonstrated peribronchial infiltrates. The main diagnostic clue for airway-invasive Aspergillus tracheobronchitis is epithelial plaques, pseudomembranes or ulcers that can be visualized via bronchoscopy, as radiological features may be subtle [31]. Worsening of radiographic pulmonary infiltrates in patients with influenza is often attributed to progression of ARDS or bacterial infection, leading to a change of antimicrobial therapy without performing diagnostic procedures [32]. Patients who survived IAPA received antifungal therapy much earlier than those who did not (2 days after diagnosis of influenza among survivors versus 9 days among non-survivors) [8], suggesting that early diagnosis and administration of antifungal therapy may be important. Lateral flow tests have recently become available as an alternative for diagnosing IPA (AspLFD, OLM Diagnostics and the sōna Aspergillus GM, IMMY) showing overall good performance in hematology patients [33]. The very quick assessment, with results available within 30–45 min, makes this type of test very attractive for the management of IAPA and use in clinical trials. However, lateral flow tests have not yet been validated in the ICU population.\nIAPA needs to be considered in patients admitted to the ICU with influenza and where indicated these patients should undergo early BAL for Aspergillus antigen testing, culture and microscopy. Patients who test positive require anti-Aspergillus therapy, and the BAL fluid sample should be fast-tracked for azole resistance testing by PCR (and culture when positive) in regions with high (\u003e 5%) azole resistance rates [34]. This would enable diagnostic assessment and initiation of adequate antifungal therapy within 24–48 h of ICU admission. Diagnostic workup for IAPA may be repeated in patients deteriorating while on antivirals and/or appropriate antibiotics or when initiating corticosteroid treatment is unavoidable."}

LitCovid-PMC-OGER-BB

2_test

{"project":"2_test","denotations":[{"id":"32572532-22895826-47963419","span":{"begin":313,"end":314},"obj":"22895826"},{"id":"32572532-22895826-47963420","span":{"begin":738,"end":739},"obj":"22895826"},{"id":"32572532-28387526-47963421","span":{"begin":843,"end":844},"obj":"28387526"},{"id":"32572532-30076119-47963422","span":{"begin":846,"end":847},"obj":"30076119"},{"id":"32572532-31102782-47963423","span":{"begin":1487,"end":1489},"obj":"31102782"},{"id":"32572532-27177530-47963424","span":{"begin":1721,"end":1723},"obj":"27177530"},{"id":"32572532-28387526-47963425","span":{"begin":1906,"end":1907},"obj":"28387526"},{"id":"32572532-31292663-47963426","span":{"begin":2205,"end":2207},"obj":"31292663"},{"id":"32572532-30580035-47963427","span":{"begin":2869,"end":2871},"obj":"30580035"},{"id":"T80169","span":{"begin":313,"end":314},"obj":"22895826"},{"id":"T27000","span":{"begin":738,"end":739},"obj":"22895826"},{"id":"T8508","span":{"begin":843,"end":844},"obj":"28387526"},{"id":"T93633","span":{"begin":846,"end":847},"obj":"30076119"},{"id":"T30112","span":{"begin":1487,"end":1489},"obj":"31102782"},{"id":"T25822","span":{"begin":1721,"end":1723},"obj":"27177530"},{"id":"T48506","span":{"begin":1906,"end":1907},"obj":"28387526"},{"id":"T39271","span":{"begin":2205,"end":2207},"obj":"31292663"},{"id":"T67090","span":{"begin":2869,"end":2871},"obj":"30580035"}],"text":"Clinical presentation and diagnosis of IAPA\nA retrospective Belgian study of influenza patients admitted to ICU between September 2009 and March 2011 showed that 9 of 40 (23%) patients had IAPA. Four cases (44%) were proven despite not being immunocompromised according to the EORTC/MSGERC consensus definitions [7]. The median time between influenza diagnosis and IAPA was 2 days (range 0–4 days). All IAPA patients had positive BAL GM, and 78% had positive serum GM, despite not being neutropenic. Eighty-nine percent of patients had Aspergillus growth in BAL culture (almost exclusively Aspergillus fumigatus), and 55% of patients had endobronchial lesions observed during bronchoscopy, possibly indicating invasive tracheobronchitis [7]. Similar performance characteristics of BAL GM and culture were reported in two other cohort studies [8, 9]. BAL sampling is thus an important diagnostic procedure as serum GM can be negative and sputum/tracheal aspirate cultures can remain sterile.\nLesions that are suggestive of invasive mold disease on imaging in neutropenic patients, such as the halo sign, are often absent in critically ill patients. However, in some IAPA patients with autopsy-confirmed Aspergillus tracheobronchitis, chest CT demonstrated peribronchial infiltrates. The main diagnostic clue for airway-invasive Aspergillus tracheobronchitis is epithelial plaques, pseudomembranes or ulcers that can be visualized via bronchoscopy, as radiological features may be subtle [31]. Worsening of radiographic pulmonary infiltrates in patients with influenza is often attributed to progression of ARDS or bacterial infection, leading to a change of antimicrobial therapy without performing diagnostic procedures [32]. Patients who survived IAPA received antifungal therapy much earlier than those who did not (2 days after diagnosis of influenza among survivors versus 9 days among non-survivors) [8], suggesting that early diagnosis and administration of antifungal therapy may be important. Lateral flow tests have recently become available as an alternative for diagnosing IPA (AspLFD, OLM Diagnostics and the sōna Aspergillus GM, IMMY) showing overall good performance in hematology patients [33]. The very quick assessment, with results available within 30–45 min, makes this type of test very attractive for the management of IAPA and use in clinical trials. However, lateral flow tests have not yet been validated in the ICU population.\nIAPA needs to be considered in patients admitted to the ICU with influenza and where indicated these patients should undergo early BAL for Aspergillus antigen testing, culture and microscopy. Patients who test positive require anti-Aspergillus therapy, and the BAL fluid sample should be fast-tracked for azole resistance testing by PCR (and culture when positive) in regions with high (\u003e 5%) azole resistance rates [34]. This would enable diagnostic assessment and initiation of adequate antifungal therapy within 24–48 h of ICU admission. Diagnostic workup for IAPA may be repeated in patients deteriorating while on antivirals and/or appropriate antibiotics or when initiating corticosteroid treatment is unavoidable."}

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