Antifungal Drug Susceptibility and Genetic Characterization of Fungi Recovered from COVID-19 Patients
Abstract
:1. Introduction
2. Materials and Methods
2.1. Fungal Isolates and Culture Conditions
2.2. DNA Extraction
2.3. Antifungal Susceptibility Testing
2.4. Sequencing of FKS1 and ERG11
2.5. Karyotyping of C. albicans Isolates
2.6. Multilocus Sequence Typing (MLST) of C. albicans Isolates
2.7. Typing of A. fumigatus Isolates
2.8. Clinical Data Review
3. Results
3.1. Species Distribution of Fungal Isolates Recovered from COVID-19 Patients
3.2. Antifungal Susceptibility Testing and Molecular Resistance Determinants Analysis
3.3. Relatedness of the Clinical Isolates
3.4. Clinical Data Review
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Isolate | Specimen | Identification | MIC [mg/L] * | FKS1 | Erg11/Cyp51A | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Original (at HUMC) | Species Confirmation (rDNA seq) | MCF | FLC | VRC | ITR | POS | ISA | ||||
MB 004 | Blood | C. albicans | C. albicans | <0.03 | <0.25 | 0.03 | <0.03 | <0.03 | <0.03 | WT | E266D |
MB 013 | Blood | C. albicans | C. albicans | <0.03 | 0.25 | 0.03 | 0.03 | 0.03 | 0.03 | WT | V437I |
MB 026 | Blood | C. albicans | C. albicans | <0.03 | 0.25 | 0.03 | <0.03 | <0.03 | <0.03 | WT | E266D, H283H/L, K342K/R |
MB 030 | Blood | C. albicans | C. albicans | <0.03 | 0.25 | 0.03 | 0.03 | <0.03 | <0.03 | WT | V437V/I |
MB 044 | Sputum | yeast | C. albicans | <0.03 | 0.25 | 0.03 | 0.03 | <0.03 | <0.03 | WT | K128K/T |
MB 047 | Sputum | yeast | C. albicans | <0.03 | 0.25 | 0.03 | 0.03 | <0.03 | <0.03 | WT | K128K/T |
MB 056 | Sputum | yeast | C. albicans | <0.03 | 0.25 | 0.03 | 0.03 | <0.03 | <0.03 | WT | V437V/I |
MB 059 | Sputum | yeast (not Cryptococcus) | C. albicans | <0.03 | 0.25 | 0.03 | 0.03 | <0.03 | <0.03 | WT | K128K/T |
MB 060 | Sputum | yeast | C. albicans | <0.03 | 0.25 | 0.03 | 0.03 | <0.03 | <0.03 | WT | K128K/T |
MB 064 | Sputum | yeast (not Cryptococcus) | C. albicans | <0.03 | 0.25 | 0.03 | 0.03 | <0.03 | <0.03 | WT | D116D/E, E266E/D |
MB 092 | Blood | C. albicans | C. albicans | <0.03 | <0.25 | 0.03 | 0.03 | <0.03 | <0.03 | WT | V437V/I |
MB 096 | Blood | C. albicans | C. albicans | <0.03 | 0.25 | 0.03 | 0.03 | <0.03 | <0.03 | WT | D116E, K128K/T |
MB 114 | Blood | C. albicans | C. albicans | <0.03 | 0.25 | 0.03 | 0.03 | <0.03 | <0.03 | WT | E266E/D, V437V/I |
MB 167 | Blood | C. albicans | C. albicans | <0.03 | 0.25 | 0.03 | 0.03 | <0.03 | <0.03 | WT | D116E, K128T |
MB 168 | Blood | C. albicans | C. albicans | <0.03 | 0.25 | 0.03 | 0.03 | <0.03 | <0.03 | WT | V437V/I |
MB 179 | Sputum | yeast (not Cryptococcus) | C. albicans | <0.03 | 0.25 | 0.03 | 0.03 | <0.03 | <0.03 | WT | D116D/E, K128K/T, V159V/I |
MB 180 | Sputum | yeast (not Cryptococcus) | C. albicans | <0.03 | <0.25 | 0.06 | <0.03 | <0.03 | <0.03 | WT | D116D/E, K128K/T |
MB 025 | Blood | C. parapsilosis | C. parapsilosis | 2 | 0.5 | 0.125 | <0.03 | <0.03 | <0.03 | WT ** | F215S |
MB 099 | Blood | C. parapsilosis | C. parapsilosis | 2 | 0.5 | 0.125 | <0.03 | <0.03 | <0.03 | WT ** | F215S |
MB 097 | Sputum | A. fumigatus | A. fumigatus | 0.06 | >64 | 0.25 | 0.5 | 0.03 | 0.125 | N/A | WT |
MB 098 | Sputum | A. fumigatus | A. fumigatus | 0.06 | >64 | 0.25 | 0.5 | 0.03 | 0.125 | N/A | WT |
Gene | Organism | Primer Name | Sequence | Use | Reference |
---|---|---|---|---|---|
rDNA | Candida spp. | Fun-rDNAF | GGTCATTTAGAGGAAGTAAAAGTCG | PCR + seq | S. Katiyar, personal communication |
Fun-rDNAR | YGATATGCTTAAGTTCAGCGGGTA | PCR + seq | |||
β-tubulin | Aspergillus spp. | btub2F | TTCACCTTCAGACCGGT | PCR + seq | [33] |
btub4R | AGTTGTCGGGACGGAATAG | PCR + seq | |||
FKS1 | C. albicans | F2426 | CATTGCTGTGGCCACTTTAG | PCR + seq | [34] |
R2919 | GATTTCCATTTCCGTGGTAGC | PCR | |||
F4590 | TACTATGGTCATCCAGGTTTCC | PCR + seq | |||
R4954 | GGTCAAATCAGTGAAAACCG | PCR | |||
C. parapsilosis | CparF | CTCCAAGTCCTCATATGCAC | PCR + seq | ||
CparR | AGATGTTTCTCCATGGTGTC | PCR | |||
F4500 | AAGATTGGTGCTGGTATGGG | PCR + seq | [35] | ||
R5112 | TAATGGTGCTTGCCAATGAG | PCR | |||
ERG11 | C. albicans | Ca_ERG11_F | ATG GCT ATT GTT GAA ACT GTC ATT G | PCR | This study * |
Ca_ERG11_R | TTA AAA CAT ACA AGT TTC TCT TTT TTC CC | PCR | |||
Ca_ERG11_731-750_F | GGA GAC GTG ATG CTG CTC AA | seq | |||
Ca_ERG11_918-938_R | GCA GAA GTA TGT TGA CCA CCC | seq | |||
C. parapsilosis | Cpara_erg11_F1 | TCCCTACCTTCGTTCATC | PCR + seq | ||
Cpara_erg11_R1 | CGAGGTGAGTCAACAAAG | PCR + seq | |||
Cpara_erg11_F2 | AGAGACGGGTGACATTG | seq | |||
Cpara_erg11_R2 | TGGCACTAGTATGCTGTC | seq | |||
CYP51A promoter | A. fumigatus | A5 | CTT TTT CGA CTG CCG CGC | PCR + seq | [28] |
A7 | TCA TAT GTT GCT CAG CGG | PCR + seq | |||
CYP51A | A. fumigatus | P450.1 | ATG GTG CCG ATG CTA TGG | PCR | |
P450.2 | CTG TCT CAC TTG GAT GTG | PCR | |||
CypA1 | CTT ACG GCC TAC ATG GCC | seq | |||
CypA2 | TTC GAC CGC TTC TCC CAG | seq | |||
A3 | TAG TCC ATT GAC GAC CCC | seq | |||
TRESPERG genotyping | A. fumigatus | CSP1F | TTGGGTGGCATTGTGCCAA | PCR + seq | [32] |
CSP2R | GAGCATGACAACCCAGATACCA | PCR + seq | |||
MP2A | ATGCGGTTCTCTGCGTTA | PCR | |||
MP2B | CAGCAACAGTGCAAATGC | PCR | |||
MP2_P1 | CTCGAACTTGGCTACGAC | seq | |||
MP2_P2 | AGGTAGTGGAGGTCACTG | seq | |||
CFEMA | ATGAAGGCCTCTGTGTC | PCR + seq | |||
CFEMB | AGGATAATCAAGGCAGCG | PCR + seq | |||
ERG4B_P1 | ATGACTGTCACACGCTCC | PCR + seq | |||
ERG4B_P2 | TAGACGGCACCAATCCAC | PCR + seq |
Isolate | Specimen | AAT1a | ACC1 | ADP1 | MPI | SYA1 | VPS13 | ZWF1b | ST |
---|---|---|---|---|---|---|---|---|---|
MB004 | Blood | 43 | 14 | 8 | 4 | 7 | 10 | 8 | 927 |
MB013 | Blood | 117 | 7 | 21 | 34 | * 238 | 24 | 6 | New ST, A |
MB026 | Blood | 25 | 7 | 6 | 3 | 6 | 27 | 37 | 90 |
MB030 | Blood | 20 | 3 | 6 | 2 | 51 | 132 | 5 | New ST, B |
MB044 | Sputum | 2 | 5 | 5 | 2 | 2 | 6 | 20 | 485 |
MB047 | Sputum | 8 | 5 | * 6 | 2 | 2 | 6 | 5 | New ST, C |
MB056 | Sputum | 33 | 14 | 38 | 2 | * 136 | 122 | 15 | New ST, D |
MB059 | Sputum | 2 | 5 | 5 | 2 | 2 | 6 | 20 | 485 |
MB060 | Sputum | 8 | 3 | 6 | 2 | 2 | 6 | 49 | New ST, E |
MB064 | Sputum | 13 | 7 | 15 | 6 | 7 | 55 | 15 | 1830 |
MB092 | Blood | 33 | 7 | 6 | 2 | 78 | 122 | 15 | New ST, F |
MB096 | Blood | 8 | 5 | * 6 | 2 | 2 | 6 | 5 | New ST, C |
MB114 | Blood | 13 | 10 | 15 | 6 | 7 | 15 | 15 | New ST, G |
MB167 | Blood | 2 | 2 | 5 | 2 | 2 | 68 | 5 | New ST, H |
MB168 | Blood | 33 | 3 | 38 | 2 | 78 | 122 | 22 | New ST, I |
MB179 | Sputum | 8 | 2 | 5 | 9 | 2 | 6 | 5 | 285 |
MB180 | Sputum | 2 | 3 | 5 | 2 | 2 | 6 | 5 | 66 |
Characteristic | Values |
---|---|
Age | 60 (55–69) (49–84) |
BMI | 29.3 (24.96–37.34) (22.91–58.5) |
≥30 | 8 (42.1%) |
Sex | |
Male | 13 (68.4%) |
Female | 6 (31.6%) |
Comorbidities | |
Diabetes | 7 (36.8%) |
Asthma | 3 (15.8%) |
COPD | 1 (5.3%) |
Hypertension | 12 (63.2%) |
Cancer | 0 |
Hypercholesterolemia | 5 (26.3%) |
Hyperlipidemia | 2 (10.5%) |
Arthritis | 4 (21.1%) |
Treatment | |
Antibiotics | 19 (100%) |
Antifungals | 12 (63.2%) |
Corticosteroids | 18 (94.7%) |
Hydroxychloroquine | 14 (73.7%) |
Remdesivir | 3 (15.8%) |
Lopinavir-ritonavir | 1 (5.3%) |
Sarilumab | 1 (5.3%) |
Fungal culture | |
Day of the first blood culture | 14 (11–19) (8–28) |
Day of the first sputum culture | 12 (6–18) (1–40) |
Fungal culture only | 6 (31.6%) |
Fungal and bacterial culture | 13 (68.4%) |
Hospitalization | |
Days of hospital stay | 29 (15–33) (9–81) |
ICU admission | 6 (31.6%) |
Days in ICU | 24 (8.25–41.25) (0–54) |
Ventilation | 18 (94.7%) * |
Days on ventilator | 24 (11–31.25) (7–81) |
Death | 17 (89.5%) |
Respiratory failure | 14/17 (82.3%) |
Cardiac failure | 2/17 (11.8%) |
No data | 1/17 (5.9%) |
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Share and Cite
Kordalewska, M.; Guerrero, K.D.; Garcia-Rubio, R.; Jiménez-Ortigosa, C.; Mediavilla, J.R.; Cunningham, M.H.; Hollis, F.; Hong, T.; Chow, K.F.; Kreiswirth, B.N.; et al. Antifungal Drug Susceptibility and Genetic Characterization of Fungi Recovered from COVID-19 Patients. J. Fungi 2021, 7, 552. https://doi.org/10.3390/jof7070552
Kordalewska M, Guerrero KD, Garcia-Rubio R, Jiménez-Ortigosa C, Mediavilla JR, Cunningham MH, Hollis F, Hong T, Chow KF, Kreiswirth BN, et al. Antifungal Drug Susceptibility and Genetic Characterization of Fungi Recovered from COVID-19 Patients. Journal of Fungi. 2021; 7(7):552. https://doi.org/10.3390/jof7070552
Chicago/Turabian StyleKordalewska, Milena, Kevin D. Guerrero, Rocio Garcia-Rubio, Cristina Jiménez-Ortigosa, José R. Mediavilla, Marcus H. Cunningham, Frank Hollis, Tao Hong, Kar Fai Chow, Barry N. Kreiswirth, and et al. 2021. "Antifungal Drug Susceptibility and Genetic Characterization of Fungi Recovered from COVID-19 Patients" Journal of Fungi 7, no. 7: 552. https://doi.org/10.3390/jof7070552