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PMC:7344504 / 9128-14430 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T21 194-198 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T22 2956-2961 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T23 3170-3175 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T24 3276-3281 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T25 3533-3538 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T15 2956-2961 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T16 3170-3175 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T17 3276-3281 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T18 3533-3538 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
250 174-186 Species denotes A. fumigatus Tax:746128
251 232-239 Species denotes patient Tax:9606
252 379-387 Species denotes patients Tax:9606
253 612-620 Species denotes patients Tax:9606
254 42-47 Chemical denotes azole MESH:D001393
255 155-160 Chemical denotes azole MESH:D001393
256 438-443 Chemical denotes azole MESH:D001393
257 652-660 Chemical denotes triazole MESH:D014230
258 393-419 Disease denotes azole-resistant infections MESH:D007239
259 204-208 Mutation denotes L98H p.L98H
272 794-806 Species denotes A. fumigatus Tax:746128
273 966-978 Species denotes A. fumigatus Tax:746128
274 1033-1046 Species denotes mixed culture Tax:1306155
275 1127-1139 Species denotes A. fumigatus Tax:746128
276 1219-1232 Species denotes mixed culture Tax:1306155
277 877-882 Chemical denotes azole MESH:D001393
278 899-904 Chemical denotes azole MESH:D001393
279 1109-1114 Chemical denotes azole MESH:D001393
280 1337-1349 Chemical denotes itraconazole MESH:D017964
281 1373-1385 Chemical denotes voriconazole MESH:D065819
282 934-943 Disease denotes infection MESH:D007239
283 1306-1310 Mutation denotes L98H p.L98H
297 1620-1627 Species denotes patient Tax:9606
298 1719-1726 Species denotes patient Tax:9606
299 1902-1910 Species denotes patients Tax:9606
300 2139-2147 Species denotes patients Tax:9606
301 2181-2189 Species denotes patients Tax:9606
302 2249-2257 Species denotes patients Tax:9606
303 2417-2424 Species denotes patient Tax:9606
304 2448-2460 Species denotes A. fumigatus Tax:746128
305 2735-2747 Species denotes A. fumigatus Tax:746128
306 2622-2627 Chemical denotes azole MESH:D001393
307 2755-2767 Chemical denotes voriconazole MESH:D065819
308 1669-1692 Disease denotes invasive fungal disease MESH:D000072742
309 2130-2138 Disease denotes COVID-19 MESH:C000657245
328 3061-3069 Species denotes patients Tax:9606
329 3136-3144 Species denotes patients Tax:9606
330 3593-3600 Species denotes patient Tax:9606
331 4000-4008 Species denotes patients Tax:9606
332 3411-3422 Species denotes Aspergillus Tax:746128
333 2962-2975 Chemical denotes galactomannan MESH:C012990
334 3176-3189 Chemical denotes galactomannan MESH:C012990
335 3282-3295 Chemical denotes galactomannan MESH:C012990
336 3392-3402 Chemical denotes β-d-glucan
337 3539-3549 Chemical denotes β-d-glucan
338 3675-3685 Chemical denotes β-d-glucan
339 4031-4041 Chemical denotes β-d-glucan
340 3092-3114 Disease denotes invasive aspergillosis MESH:D055744
341 3499-3507 Disease denotes COVID-19 MESH:C000657245
342 3648-3663 Disease denotes invasive fungal MESH:D000072742
343 3851-3874 Disease denotes invasive fungal disease MESH:D000072742
344 3959-3981 Disease denotes invasive aspergillosis MESH:D055744
345 3985-3999 Disease denotes critically ill MESH:D016638
354 4426-4434 Species denotes patients Tax:9606
355 4737-4744 Species denotes patient Tax:9606
356 5008-5016 Species denotes patients Tax:9606
357 4342-4355 Chemical denotes galactomannan MESH:C012990
358 4365-4375 Chemical denotes β-d-glucan
359 4540-4553 Chemical denotes galactomannan MESH:C012990
360 4830-4843 Chemical denotes galactomannan MESH:C012990
361 4993-5007 Disease denotes critically ill MESH:D016638
366 5097-5104 Species denotes patient Tax:9606
367 5152-5164 Species denotes A. fumigatus Tax:746128
368 5110-5115 Chemical denotes azole MESH:D001393
369 5179-5187 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T37 58-62 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T38 409-419 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T39 602-611 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T40 934-943 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T41 1607-1611 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T42 1897-1901 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T43 2130-2138 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T44 3092-3114 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T45 3101-3114 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T46 3499-3507 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T47 3959-3981 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T48 3968-3981 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T49 5126-5130 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T50 5179-5187 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T51 5279-5283 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T61 133-134 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T62 174-175 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T63 194-198 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T64 240-243 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T65 580-583 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T66 794-795 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T67 825-831 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T68 966-967 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T69 1031-1032 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 1127-1128 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T71 1185-1186 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 1217-1218 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T73 1315-1316 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 1479-1481 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T75 1764-1770 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T76 2066-2069 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T77 2077-2078 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 2448-2449 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T79 2479-2487 http://purl.obolibrary.org/obo/OBI_0100026 denotes organism
T80 2479-2487 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organism
T81 2547-2553 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T82 2735-2736 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T83 2976-2983 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T84 2984-2987 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T85 3005-3006 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 3216-3219 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T87 3235-3237 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T88 3445-3451 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T89 3620-3621 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T90 3686-3693 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T91 3697-3698 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 3720-3723 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T93 3831-3843 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonization
T94 3919-3920 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T95 4167-4169 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T96 4256-4259 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T97 4273-4274 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T98 4357-4359 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T99 4490-4491 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T100 4554-4561 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T101 4599-4600 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T102 4635-4638 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T103 4707-4713 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T104 5152-5153 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T72 42-47 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T73 155-160 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T74 393-398 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T75 438-443 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T76 652-660 Chemical denotes triazole http://purl.obolibrary.org/obo/CHEBI_38597
T77 877-882 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T78 899-904 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T79 1109-1114 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T80 1337-1349 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T81 1350-1353 Chemical denotes MIC http://purl.obolibrary.org/obo/CHEBI_59059
T82 1373-1385 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T83 1386-1389 Chemical denotes MIC http://purl.obolibrary.org/obo/CHEBI_59059
T84 1484-1487 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T86 1825-1828 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T87 2206-2209 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T88 2304-2307 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T89 2622-2627 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T90 2755-2767 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T91 2938-2941 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T93 2962-2975 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T94 3176-3189 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T95 3282-3295 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T96 3396-3402 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T97 3453-3456 Chemical denotes LFD http://purl.obolibrary.org/obo/CHEBI_73571
T98 3492-3495 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T100 3543-3549 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T101 3679-3685 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T102 4027-4030 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T103 4035-4041 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T104 4176-4179 Chemical denotes LFD http://purl.obolibrary.org/obo/CHEBI_73571
T105 4319-4322 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T106 4342-4355 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T107 4369-4375 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T108 4384-4387 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T110 4465-4468 Chemical denotes LFD http://purl.obolibrary.org/obo/CHEBI_73571
T111 4540-4553 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T112 4565-4568 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T113 4830-4843 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T114 5110-5115 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T3 2962-2975 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T4 3176-3189 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T5 3282-3295 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T6 4342-4355 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T7 4540-4553 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T8 4830-4843 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T78 0-2 Sentence denotes 3.
T79 3-13 Sentence denotes Discussion
T80 14-169 Sentence denotes We report the first case of azole-resistant CAPA, which occurred in an immunocompetent host during ICU support without a previous history of azole therapy.
T81 170-462 Sentence denotes The A. fumigatus cyp51A gene TR34/L98H mutation found in this patient has been well described as an environmentally acquired mutation [16], which is in line with data from clinical studies where two-thirds of patients with azole-resistant infections had no history of azole pretreatment [10].
T82 463-680 Sentence denotes This case underscores the importance of early diagnosis and the need for resistance surveillance, comparable to what has been described in influenza patients [9,17], given the emergence of triazole resistance [18,19].
T83 681-949 Sentence denotes The sensitivity for detection of resistance in primary cultures with the VIPcheck plate depends on the number of A. fumigatus colonies that are tested, as clinical cultures may contain both mixed azole-susceptible and azole-resistant isolates during an infection [20].
T84 950-1147 Sentence denotes We suspect that A. fumigatus isolated in the first tracheal aspirate was already a mixed culture but was missed in initial fungal cultures due to abundance of azole-susceptible A. fumigatus spores.
T85 1148-1296 Sentence denotes Molecular detection could have given a suggestion to the presence of a mixed culture [21] but PCR could not be performed due to absence of material.
T86 1297-1483 Sentence denotes The TR34/L98H had a phenotype with high itraconazole MIC (>16 mg/L) and low voriconazole MIC (2 mg/L), similar to strains which have been described only recently in the Netherlands [22].
T87 1484-1564 Sentence denotes IPA is known to be problematic to diagnose in the non-neutropenic ICU host [23].
T88 1565-1841 Sentence denotes Regardless of the compelling evidence for CAPA in this patient, the EORTC/MSGERC [24] host criteria for invasive fungal disease were not met, nor did the patient meet the AspICU algorithm because we tested tracheal aspirates instead of bronchoalveolar lavage (BAL) fluid [25].
T89 1842-1972 Sentence denotes This is in line with findings from other groups, where CAPA patients did not meet the EORTC/MSGERC host criteria either [3,4,5,6].
T90 1973-2205 Sentence denotes In addition, the American Association for Bronchology and Interventional Pulmonology (AABIP) has issued a statement advising against routine bronchoscopy in COVID-19 patients, as it poses substantial risk to patients and staff [26].
T91 2206-2355 Sentence denotes BAL should only be considered in intubated patients if upper respiratory samples are negative and BAL would significantly change clinical management.
T92 2356-2496 Sentence denotes Tracheal aspirate cultures, as performed twice weekly in our patient, repeatedly identified A. fumigatus as the only micro-organism present.
T93 2497-2644 Sentence denotes In the first positive culture, five colonies were tested for resistance with the VIPcheck plate as is recommended to exclude azole resistance [15].
T94 2645-2915 Sentence denotes When surveillance cultures of tracheal aspirates were persistently cultured positive with A. fumigatus during voriconazole therapy, we suspected the selection of resistant isolates which were probably already present in the first samples, albeit in undetectable numbers.
T95 2916-2955 Sentence denotes An autopsy to confirm IPA was not done.
T96 2956-3123 Sentence denotes Serum galactomannan testing has been shown to be a fairly sensitive diagnostic tool (70%) in neutropenic patients with pathology-proven invasive aspergillosis [27,28].
T97 3124-3379 Sentence denotes However, in patients who are non-neutropenic, serum galactomannan sensitivity of around 25% has been reported [27], which may explain the low number of serum galactomannan positive findings in recently published case reports [6,7] and case series [3,4,5].
T98 3380-3532 Sentence denotes The role of β-d-glucan and the Aspergillus-specific lateral flow device (LFD) as an adjunct to the diagnosis of IPA in COVID-19 is not yet clear [2,23].
T99 3533-3627 Sentence denotes Serum β-d-glucan was persistently strongly positive in this patient over the course of a week.
T100 3628-3875 Sentence denotes The specificity for invasive fungal disease of β-d-glucan testing in a mixed ICU population has been shown to be high (86%), with two consecutive positive results [29] compared to those with only fungal colonization and no invasive fungal disease.
T101 3876-4026 Sentence denotes In addition, multiple other studies report a good sensitivity for the diagnosis of invasive aspergillosis in critically ill patients [30,31,32,33,34].
T102 4027-4171 Sentence denotes BAL β-d-glucan in the ICU setting is, however, not recommended, due to its poor specificity and confounders causing false positive results [35].
T103 4172-4252 Sentence denotes The LFD is particularly interesting in the ICU due to its short turnaround time.
T104 4253-4435 Sentence denotes It has demonstrated a higher sensitivity but lower specificity in BAL fluids compared to galactomannan [36] and β-d-glucan [37] in IPA-probable and proven immunocompromised patients.
T105 4436-4584 Sentence denotes In the ICU setting, however, LFD is suggested to have a lower sensitivity but comparable specificity to galactomannan testing in BAL fluids [35,38].
T106 4585-4677 Sentence denotes Noteworthily, a negative predictive value of >96% has been reported in the ICU setting [39].
T107 4678-4851 Sentence denotes We used the OLM lateral flow device (AspLFD) on sequential patient tracheal aspirates, yielding positive results on all samples confirming the positive galactomannan result.
T108 4852-5030 Sentence denotes Although suitable for its negative predictive value or as an additional diagnostic measure, further evaluation of lateral flow technology in critically ill patients is warranted.
T109 5031-5131 Sentence denotes Altogether, we describe the clinical course of the first reported patient with azole-resistant CAPA.
T110 5132-5302 Sentence denotes The contribution of A. fumigatus to this fatal COVID-19 course is highly likely, although autopsy was not performed, as in all previously reported CAPA cases [3,4,5,6,7].

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T18 1484-1487 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T19 2938-2941 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T20 3492-3495 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T21 4384-4387 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103

2_test

Id Subject Object Predicate Lexical cue
32517166-24204249-60114387 305-307 24204249 denotes 16
32517166-32297377-60114388 622-623 32297377 denotes 9
32517166-29570855-60114389 624-626 29570855 denotes 17
32517166-28911045-60114390 673-675 28911045 denotes 18
32517166-30580035-60114391 676-678 30580035 denotes 19
32517166-25326091-60114392 945-947 25326091 denotes 20
32517166-31361683-60114393 1560-1562 31361683 denotes 23
32517166-31802125-60114394 1647-1649 31802125 denotes 24
32517166-22517788-60114395 1837-1839 22517788 denotes 25
32517166-32396381-60114396 1963-1964 32396381 denotes 3
32517166-32339350-60114397 1967-1968 32339350 denotes 5
32517166-32195687-60114398 2201-2203 32195687 denotes 26
32517166-29544767-60114399 2640-2642 29544767 denotes 15
32517166-17885264-60114400 3116-3118 17885264 denotes 27
32517166-11015433-60114401 3119-3121 11015433 denotes 28
32517166-17885264-60114402 3235-3237 17885264 denotes 27
32517166-32396381-60114403 3372-3373 32396381 denotes 3
32517166-32339350-60114404 3376-3377 32339350 denotes 5
32517166-31361683-60114405 3528-3530 31361683 denotes 23
32517166-28384600-60114406 3792-3794 28384600 denotes 29
32517166-20825441-60114407 4010-4012 20825441 denotes 30
32517166-21811868-60114408 4013-4015 21811868 denotes 31
32517166-30015290-60114409 4016-4018 30015290 denotes 32
32517166-21880959-60114410 4019-4021 21880959 denotes 33
32517166-27475024-60114411 4022-4024 27475024 denotes 34
32517166-25903568-60114412 4357-4359 25903568 denotes 36
32517166-24671798-60114413 4377-4379 24671798 denotes 37
32517166-30565352-60114414 4580-4582 30565352 denotes 38
32517166-25927915-60114415 4673-4675 25927915 denotes 39
32517166-32396381-60114416 5291-5292 32396381 denotes 3
32517166-32339350-60114417 5295-5296 32339350 denotes 5