LitCovid-sentences  

PMC:7394275 / 6721-20735 JSONTXT 13 Projects

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Id Subject Object Predicate Lexical cue
T40 0-84 Sentence denotes Clinical and Diagnostic Perspective of COVID-19 Associated with Fungal Co-infections
T41 85-175 Sentence denotes As the ongoing COVID-19 pandemic, more and more experts are aware of fungal co-infections.
T42 176-301 Sentence denotes The French High Council for Public Health recommended to systematically screen for fungal pathogens in COVID-19 patients [6].
T43 302-528 Sentence denotes Lanjuan Li academician and her colleagues who have accumulated experience with severe COVID-19 treatment, reminded clinicians should focus on patients’ fungal infections, especially severely ill or immunocompromised ones [22].
T44 529-648 Sentence denotes At the early phase of the disease or with extrapulmonary fungal infections, it may present with atypical chest imaging.
T45 649-1255 Sentence denotes Hence, it is necessary for severely ill patients to receive fungal pathogens surveillance, including (i) etiological examination: direct microscopy and culture; (ii) histopathology; (iii) serology: antigen and antibody, (1,3)-β-d-glucan (BDG) [23] and galactomannan (GM) detection by serum are also need to be tested for suspicious patients, while bronchoalveolar lavage fluid (BALF) and tracheal aspirate (TA) sampling for culture and biomarker testing should be performed under well-protected conditions due to the risk of aerosol spreading and health care worker infections [24]; (iv) PCR-based methods:
T46 1256-1395 Sentence denotes Real-time polymerase chain reaction (PCR) techniques and molecular identification can be performed to identify pathogens if necessary [25].
T47 1396-1526 Sentence denotes After identifying the pathogen, the antifungal susceptibility testing (AST) can be performed to select sensitive antifungal drugs.
T48 1527-1594 Sentence denotes If the AST cannot be carried out, it should be treated empirically.
T49 1595-1702 Sentence denotes The main fungal pathogens for fungal co-infections in severe COVID-19 patients are Aspergillus and Candida.
T50 1703-1834 Sentence denotes Other infrequent opportunistic pathogenic fungus caused lung infections also need to be considered, such as Mucor and Cryptococcus.
T51 1836-1863 Sentence denotes Invasive Aspergillosis (IA)
T52 1864-2007 Sentence denotes Aspergillus species could be an important cause of life-threatening infection in COVID-19 patients, especially in those with high risk factors.
T53 2008-2326 Sentence denotes The potential risk factors for the patients include GC use, prolonged neutropenia, chronic obstructive pulmonary disease (COPD), allogeneic hematopoietic stem cell transplant (allo-HSCT) [26], solid organ transplant (SOT) [27], inherited immunodeficiencies, hemopoietic malignancy (HM), cystic fibrosis (CF) [28], etc.
T54 2327-2586 Sentence denotes The diagnosis of IA requires a microbiologic and/or histopathologic evidence, although specimen acquisition is challenging in many patients because lung biopsy might be contraindicated in patients with coagulation disorders or severe respiratory failure [13].
T55 2587-3065 Sentence denotes Histopathologic examination mainly rely on finding special fungal stains on lung fluid or tissue when a fungal infection is suspected and may reveal the characteristic acute angle branching septate hyphae of Aspergillus spp., and Grocott-Gomori’s methenamine-silver stain (GMS) and periodic acid-Schiff (PAS) stains of fixed tissue will helpful, while it is difficult to distinguish Aspergillus spp. from other filamentous fungi such as Fusarium spp. and Scedosporium spp. [29].
T56 3066-4415 Sentence denotes Therefore, it is necessary to have a definitive confirmation by culture or nonculture technique, including (i) direct microscopic examination with the optical brightener methods, Calcofluor or Blankophor, which may increase the sensitivity and specificity for detecting Aspergillus-like features; (ii) culture on fungal-specific media at 37 °C for 2–5 days, if positive, morphological features of Aspergillus can be identified under the microscope or the DNA sequencing may be used in reference laboratories to identify the species accurately, but usually culture yield is low and a negative result does not exclude the diagnosis of IA; (iii) molecular assays targeting ribosomal DNA (rDNA) sequences can also be used for detection of Aspergillus in tissues or BALF, especially PCR-based assays can be used to detect Aspergillus spp. and CYP51A resistance mutations in A. fumigatus, although these methods have not been standardized or limited by laboratory conditions or proven commercial reagents in some countries [30]; (iv) serum and BALF GM testing are also recommended as an early and accurate marker using less invasive techniques for the diagnosis, especially in neutropenic patients, with advantages of less injury and time-efficient, though sometimes this test in blood samples are less sensitive than cultures of respiratory samples [25].
T57 4416-4699 Sentence denotes The treatment recommendations can be supported by the 2016 Update guideline by the Infectious Diseases Society of America that the prophylaxis, therapeutic medication, combined, and alternative medication of aspergillus infection have been given more detailed guidance opinions [30].
T58 4700-4924 Sentence denotes Generally, drugs recommended for the treatment and prophylaxis of IA include triazoles (itraconazole, voriconazole, posaconazole, esaconazole), Amphotericin B and its liposomes and echinococcins (micafungin or carpofenjing).
T59 4925-5114 Sentence denotes Most patients can choose triazole drugs to treat IA, however, therapeutic drug monitoring (TDM) is recommended and the interaction between azoles and other drugs should be fully considered.
T60 5116-5141 Sentence denotes Invasive Candidiasis (IC)
T61 5142-5471 Sentence denotes For the severe COVID-19 patients who have more opportunities to be treat with broad-spectrum antibacterial drugs, parenteral nutrition and invasive examinations, or the patients accompanied with prolonged neutropenia and other immune impairment factors, the risk of infection with Candida species may significantly increase [31].
T62 5472-5860 Sentence denotes Diagnosis of IC depends on culture methods including culture of blood or other samples collected under sterile conditions which are usually considered as gold standards for IC, and nonculture diagnostic tests including mannan and antimannan IgG tests, C. albicans germ tube antibody (CAGTA), BDG and PCR-based assays, which are now entering clinical practice as adjuncts to cultures [32].
T63 5861-6388 Sentence denotes There are mainly two disadvantages about blood culture, on the one hand, the blood culture time is long, because the average positive alarm time is 2–3 days (range 1 to ≥ 7 days), plus identification and susceptibility test duration 4 to 6 days, on the other hand, it is not sensitive than PCR with much lower detection limit when Candida concentration is ≤ 1 CFU/mL and easy to have failure to detect in extremely low concentrations of candidiasis, intermittent candidiasis or deep Candida infection has not entered the blood.
T64 6389-6536 Sentence denotes Hence, several nonculture diagnostic tests are recommended, but also there is widespread uncertainty about their utility in clinical practice [31].
T65 6537-6814 Sentence denotes BDG is a major cell wall constituent of Candida and most pathogenic fungi, excluding Cryptococcus species, Blastomyces species, and Mucorales, which is widely used in clinical and well recommended by detecting serum, but cannot distinguish between Candida and other fungi [25].
T66 6815-7005 Sentence denotes Besides, mannan and antimannan IgG tests, CAGTA are employed at many European centers, and higher sensitivity and specificity by a combination with mannan/antimannan assay are observed [33].
T67 7006-7283 Sentence denotes There are promising PCR tests, including multiplex-PCR platforms, at the same time, it exists some limitations for a lack of multicenter validation of assay performance, so there are no FDA-cleared PCR assays for Candida, but commercial and in-house tests are widely available.
T68 7284-7445 Sentence denotes Further, T2 magnetic resonance is also can be used by amplifying and detecting Candida DNA, but its feasibility in early diagnosis of candidemia remains unclear.
T69 7446-7784 Sentence denotes MALDI-TOF technology is available in more hospitals with the biggest advantage of its promptness taking no more than 5 min to identify a microorganism from isolated colonies, even researchers have developed protocols to identify yeasts directly from positive blood culture bottles within half an hour without performing a subculture [32].
T70 7785-8074 Sentence denotes Overall, not only it is necessary to fully realize the benefits of combining culture and nonculture methods, but also, clinicians must take the types of IC, the strengths and limitations of each assay and the context of the clinical setting into account to have a judicious interpretation.
T71 8075-8234 Sentence denotes Besides, susceptibility test is recommended for all blood-stream and other clinically relevant Candida isolates, especially for C. glabrata or C. parapsilosis.
T72 8235-8483 Sentence denotes The treatment recommendations can be supported by the 2016 Update guideline by the Infectious Diseases Society of America that the therapeutic and alternative medication of candidiasis infection have been given more detailed guidance opinions [34].
T73 8484-8796 Sentence denotes Generally, patients who are suspected or confirmed with IC should be treated with echinocandin (caspofungin, micafungin, and anidulafungin), azoles (fluconazole, voriconazole, itraconazole), and Amphotericin B and its liposomes, what’s more, TDM for azoles should be used to optimize efficacy and limit toxicity.
T74 8798-8819 Sentence denotes Invasive Mucormycosis
T75 8820-8965 Sentence denotes COVID-19 patients with trauma, diabetes mellitus, GC use, HM, prolonged neutropenia, allo-HSCT, SOT are more likely to develop mucormycosis [35].
T76 8966-9224 Sentence denotes Mucormycosis is usually suspected based on results of direct microscopy or plus fluorescent brighteners from clinical specimens such as sputum, BALF, and skin lesions that Mucorales hyphae are non-septate or pauci-septatethe with a variable width of 6–16 μm.
T77 9225-9385 Sentence denotes To confirm the diagnosis, non-pigmented hyphae showing tissue invasion should be shown in tissue sections stained with hematoxylin–eosin (HE), PAS, or GMS [36].
T78 9386-9481 Sentence denotes Culture of specimens is strongly recommended for identification of genus and species, also AST.
T79 9482-9755 Sentence denotes What’s more, it is suggested to be cultured at 30 °C and 37 °C separately that typically cottony white or grayish black colony usually will be found, afterward morphological identification of fungi or DNA sequencing based on bar code genes, such as 18S, ITS, 28 s, or rDNA.
T80 9756-9912 Sentence denotes MALDI-TOF identification is just moderately supported because it depends mainly on in-house databases, and many laboratories do not have this capacity [37].
T81 9913-10123 Sentence denotes Further, it is promising to detect fungi DNA, in serum as well as in other body fluids, even in paraffin-embedded tissue, however, because of lack of standardization supported it is only with moderate strength.
T82 10124-10480 Sentence denotes The treatment recommendations can be supported by the global guideline for the diagnosis and management of mucormycosis in 2019 by European Confederation of Medical Mycology (ECMM) and Mycoses Study Group Education and Research Consortium that the therapeutic and alternative medication of mucormycosis have been given more detailed guidance opinions [35].
T83 10481-10631 Sentence denotes Generally, it strongly supports an early complete surgical treatment for mucormycosis whenever possible, in addition to systemic antifungal treatment.
T84 10632-10772 Sentence denotes In neutropenic patients, those with graft-versus-host disease or high risk factor, primary prophylaxis with posaconazole may be recommended.
T85 10773-10978 Sentence denotes Amphotericin B lipid complex, liposomal Amphotericin B and posaconazole oral suspension are treated as the first-line antifungal monotherapy, while isavuconazole is strongly supported as salvage treatment.
T86 10979-11113 Sentence denotes There are no convincing data to guide the use of antifungal combination therapy of polyenes and azoles or polyenes plus echinocandins.
T87 11115-11138 Sentence denotes Invasive Cryptococcosis
T88 11139-11394 Sentence denotes COVID-19 patients with human immunodeficiency virus (HIV) infection accompanied by CD4 + T-lymphocyte count < 200 cells/μL, allo-HSCT, SOT, or other immune impaired are susceptible to cryptococcosis which predominantly present as meningoencephalitis [38].
T89 11395-11658 Sentence denotes Given the complexities surrounding the diagnosis of cryptococcosis and identification of Cryptococcus species including C. neoformans and C. gattii species, the diagnosis of cryptococcosis is usually based on a combination of clinical and laboratory confirmation.
T90 11659-11783 Sentence denotes The methods used to confirm the infection are culture, direct microscopy, histopathology, serology, and molecular detection.
T91 11784-12026 Sentence denotes To diagnose cryptococcosis, specimen from cerebrospinal fluid (CSF) can be mixed with India ink and observed under a microscope that the distinctive structure for Cryptococcus spp. with narrow budding encapsulated yeasts usually can be found.
T92 12027-12154 Sentence denotes Samples for culture should be placed on Sabouraud dextrose agar at 30 °C for 7 days, in aerobic conditions, and observed daily.
T93 12155-12252 Sentence denotes Moreover, cultures from patients receiving systemic antifungal therapy might need longer to grow.
T94 12253-12300 Sentence denotes Cryptococcus appears as mucoid creamy colonies.
T95 12301-12438 Sentence denotes Capsular polysaccharides of Cryptococcus can be detected and quantified from body fluids such as serum, CSF, BAL, or pathological tissue.
T96 12439-12637 Sentence denotes Three formats of cryptococcal antigen (CrAg) detection tests are currently available: the latex agglutination test (LAT), the enzyme-linked immunoassay (EIA), and the lateral flow immunoassay (LFA).
T97 12638-12788 Sentence denotes These methods are rapid, sensitive, and specific, but have not been standardized for respiratory specimens such as BAL, pleural fluid, or sputum [32].
T98 12789-12942 Sentence denotes Molecular detection of Cryptococcus is required in specific situations where other diagnostic tools have failed to confirm a diagnosis of cryptococcosis.
T99 12943-13102 Sentence denotes These molecular methods include pan-fungal PCR, DNA sequencing for identification, multiplex PCR, isothermal amplification method, and probe-based microarrays.
T100 13103-13261 Sentence denotes Once a diagnosis cryptococcosis is made, a lumbar puncture and cerebrospinal fluid (CSF) examination (including antigen) are recommended in all patients [39].
T101 13262-13355 Sentence denotes Cryptococcus can disseminate into the central nervous system causing cryptococcal meningitis.
T102 13356-13646 Sentence denotes The treatment recommendations can be supported by guidelines for the diagnosis, prevention, and management of cryptococcal disease in HIV-infected adults, adolescents, and children in 2018 by World Health Organization (from: https://www.who.int/hiv/pub/guidelines/cryptococcal-disease/en/).
T103 13647-14014 Sentence denotes Generally, the following is recommended as the preferred regimen: (i) Induction phase for amphotericin B deoxycholate and + flucytosine, followed by fluconazole; alternative options for fluconazole + flucytosine or amphotericin B deoxycholate + fluconazole. (ii) Consolidation phase for fluconazole. (iii) Maintenance (or secondary prophylaxis) phase for fluconazole.