Candida Genotyping of Blood Culture Isolates from Patients Admitted to 16 Hospitals in Madrid: Genotype Spreading during the COVID-19 Pandemic Driven by Fluconazole-Resistant C. parapsilosis
Abstract
1. Introduction
2. Materials and Methods
2.1. Isolates Collected and Studied during the CANDIMAD Study
2.2. Microsatellite Genotyping
3. Results
3.1. Genotypes Found in Blood Cultures and Comparisons with Intra-Abdominal Genotypes
3.2. Genotypes Involving Antifungal-Resistant Isolates
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Hospital Code | Clinical Source and No. Isolates | ||||||
---|---|---|---|---|---|---|---|
Blood Cultures | Intra-Abdominal Samples | Overall | |||||
C. albicans | C. parapsilosis | C. tropicalis | C. albicans | C. parapsilosis | C. tropicalis | ||
1 | 90 | 32 | 16 | 88 | 18 | 12 | 256 |
2 | 34 | 20 | 5 | 104 | 9 | 16 | 188 |
3 | 42 | 22 | 2 | 85 | 9 | 8 | 168 |
4 | 75 | 57 | 6 | 18 | 4 | 1 | 161 |
5 | 30 | 13 | 3 | 44 | 13 | 4 | 107 |
6 | 21 | 4 | 3 | 67 | 4 | 10 | 109 |
7 | 57 | 36 | 8 | 5 | 2 | 0 | 108 |
8 | 25 | 5 | 2 | 57 | 11 | 4 | 104 |
9 | 41 | 35 | 4 | 19 | 5 | 3 | 107 |
10 | 20 | 8 | 2 | 39 | 6 | 4 | 79 |
11 | 21 | 12 | 2 | 6 | 0 | 2 | 43 |
12 | 11 | 9 | 2 | 7 | 0 | 1 | 30 |
13 | 4 | 7 | 1 | 8 | 1 | 1 | 22 |
14 | 6 | 6 | 1 | 2 | 0 | 1 | 16 |
15 | 5 | 5 | 0 | 2 | 1 | 1 | 14 |
16 | 7 | 0 | 0 | 1 | 0 | 0 | 8 |
Overall | 489 | 271 | 57 | 552 | 83 | 68 | 1520 * |
C. albicans | C. parapsilosis | C. tropicalis | |
---|---|---|---|
Isolates/patients | 489 | 271 | 57 |
Genotypes | 399 | 182 | 47 |
Singleton, n (%) | 346 (86.7%) | 158 (86.8%) | 41 (87.2%) |
Cluster, n (%) | 53 (13.3%) | 24 (13.2%) | 6 (12.8%) |
Isolates/patients in cluster, n (%) | 143 (29.2%) | 113 (41.7%) | 16 (28.1%) |
Range of isolates/patients per cluster | 2–15 | 2–37 | 2–4 |
Intra-hospital cluster, n (%) | 14 (26.4%) | 6 (25.0%) | 0 (0.0%) |
Widespread cluster, n (%) * | 39 (73.6%) | 18 (75.0%) | 6 (100%) |
Hospital Code | Frequencies of Combinations of Widespread Genotypes | Numbers of Widespread Genotypes | |||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | C. albicans | C. parapsilosis | Total | |
1 | 3 | 2 | 6 | 2 | 0 | 7 | 1 | 4 | 0 | 3 | 2 | 1 | 0 | 0 | 1 | 15 | 5 | 20 | |
2 | 2 | 0 | 3 | 1 | 1 | 3 | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 2 | 8 | 4 | 12 | |
3 | 1 | 0 | 2 | 1 | 0 | 0 | 2 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 4 | 6 | 10 | |
4 | 3 | 3 | 1 | 4 | 1 | 4 | 3 | 3 | 0 | 5 | 0 | 0 | 1 | 0 | 1 | 17 | 7 | 24 | |
5 | 3 | 2 | 1 | 3 | 1 | 1 | 1 | 1 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 7 | 7 | 14 | |
6 | 1 | 1 | 0 | 1 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 3 | 1 | 4 | |
7 | 1 | 1 | 2 | 2 | 2 | 1 | 0 | 1 | 1 | 3 | 1 | 1 | 1 | 0 | 1 | 12 | 6 | 18 | |
8 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 4 | 1 | 5 | |
9 | 3 | 3 | 3 | 3 | 4 | 1 | 3 | 0 | 0 | 2 | 1 | 1 | 0 | 0 | 0 | 6 | 8 | 14 | |
10 | 0 | 1 | 1 | 0 | 0 | 0 | 2 | 0 | 2 | 0 | 0 | 0 | 0 | 1 | 0 | 4 | 3 | 7 | |
11 | 2 | 1 | 0 | 1 | 2 | 1 | 1 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 1 | 8 | 3 | 11 | |
12 | 1 | 0 | 2 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 3 | 3 | 6 | |
13 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 2 | |
14 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 1 | 4 | |
15 | 1 | 2 | 0 | 2 | 1 | 1 | 1 | 0 | 2 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 2 | 3 | |
16 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 0 | 4 |
Hospital Code | Candidaemia Incidence (Cases per 100,000 Hospital Admissions) | |||||
---|---|---|---|---|---|---|
Overall (No. of Admissions) * | C. albicans (2019/2020/2021) | C. parapsilosis (2019/2020/2021) | C. tropicalis (2019/2020/2021) | |||
2019 | 2020 | 2021 | ||||
1 α | 114.8 (47,048) | 155.5 (42,444) | 135.7 (35,377) | 53.1/69.6/70.7 α | 31.9/16.5/28.3 | 10.6/14.1/14.1 |
2 | 50.7 (45,357) | 63.0 (39,669) | 78.3 (39,607) | 22.0/35.3/25.2 | 15.4/7.6/25.2 | 4.4/2.5/5.0 |
3 β | 83.2 (32,442) | 51.4 (60,348) | 83.3 (40,832) | 40.1/24.9/34.3 | 21.6/13.3/17.1 | 0.0/0.0/4.9 |
4 γ | 152.9 (31,399) | 201.1 (27,841) | 231.6 (28,067) | 86.0/89.9/81.9 | 38.2/53.9/106.9 β,γ | 12.7/3.6/3.6 |
5 | 130.7 (16,064) | 208.8 (13,886) | 137.2 (13,848) | 49.8/108.0/50.5 | 37.4/43.2/7.2 | 0.0/7.2/14.4 |
6 α | 53.6 (18,671) | 125.3 (16,755) | 77.4 (16,786) | 16.1/53.7/53.6 | 10.7/11.9/0.0 | 0.0/11.9/6.0 |
7 α,γ | 65.6 (48,757) | 131.2 (44,196) | 109.0 (44,949) | 20.5/58.8/46.7 α,γ | 16.4/45.3/17.8 α, β | 4.1/2.3/11.1 |
8 β | 104.8 (15,268) | 129.1 (13,940) | 55.6 (14,388) | 58.9/71.7/41.7 | 13.1/14.3/7.0 | 0.0/7.2/7.0 |
9 | 117.7 (26,348) | 171.8 (24,454) | 130.2 (24,577) | 45.5/102.2/16.3 α, β | 26.6/40.9/73.2 γ | 11.4/4.1/0.0 |
10 α,γ | 61.3 (13,049) | 150.6 (11,288) | 124.1 (11,283) | 30.7/88.6/53.2 | 7.7/17.7/44.3 | 15.3/0.0/0.0 |
11 | 87.4 (16,012) | 94.3 (15,902) | ND | 50.0/44.0/ND | 25.0/6.3/ND | 6.2/6.3/ND |
12 | 44.2 (15,826) | 86.8 (14,969) | 51.6 (15,501) | 19.0/33.4/19.4 | 19.0/33.4/6.5 | 0.0/13.4/0.0 |
13 α | 11.1 (9045) | 80.9 (8656) | ND | 0.0/23.1/ND | 11.1/34.7/ND | 0.0/11.6/ND |
14 | 34.9 (11,471) | 83.2 (9620) | ND | 26.2/10.4/ND | 8.7/31.2/ND | 0.0/10.4/ND |
15 | 86.2 (8116) | 14.4 (6946) | ND | 37.0/14.4/ND | 24.6/0.0/ND | 0.0/0.0/ND |
16 | 88.8 (4504) | 0.0 (4146) | ND | 66.6/0.0/ND | 0.0/0.0/ND | 0.0/0.0/ND |
Overall α,γ | 85.4 (359,377) | 114.6 (355,060) | 112.9 (285,215) ** | 39.2/58.0/44.9 α, β | 21.7/24.5/31.9 γ | 5.3/5.4/6.7 |
Species | Genotype | Hospitals Involved | Patients Involved | No. of Isolates and Source | Phenotypic Resistance | FKSp Substitution | ERG11p Substitution | |
---|---|---|---|---|---|---|---|---|
Blood | Intra -Abdominal | |||||||
C. albicans | CA-0056 * | H9 | 1 | 0 | 1 | Echinocandin | F641L FKS1 HS1 | ND |
CA-0511 | H6 | 2 | 1 | 1 | Echinocandin | S645P FKS1 HS1 | ND | |
CA-1341 | H6 | 1 | 0 | 1 | Echinocandin | S645P FKS1 HS1 | ND | |
CA-1872 | H2 | 1 | 1 | 0 | Echinocandin | R1361H FKS1 HS2 | ND | |
CA-0313 ** | H1 | 1 | 1 | 0 | Fluconazole | ND | None | |
CA-1283 | H7 | 1 | 1 | 0 | Fluconazole | ND | D115E, K128T, F145L, I471L/I | |
CA-1505 | H2 | 1 | 0 | 1 | Fluconazole | ND | A114S, Y257H | |
CA-1674 | H1 | 1 | 0 | 1 | Fluconazole | ND | None | |
CA-1762 | H9 | 1 | 1 | 0 | Fluconazole | ND | D116E/D, D153E/D | |
C. parapsilosis | CP-540 | H9 | 1 | 0 | 1 | Echinocandin | None | ND |
CP-451 | H2, H4, H9, H15 | 39 | 37 | 2 | Fluconazole | ND | Y132F, R398I | |
CP-673 | H4 | 2 | 2 | 0 | Fluconazole | ND | Y132F, R398I | |
CP-674 | H4 | 2 | 2 | 0 | Fluconazole | ND | Y132F, R398I | |
CP-675 | H10 | 5 | 4 | 1 | Fluconazole | ND | G458S | |
C. tropicalis | CT-031 *** | H10 | 1 | 0 | 1 | Echinocandin | S654P/S FKS1 HS1 + V1352I/V, V1404I/V FKS1 | ND |
CT-081 | H6 | 1 | 0 | 1 | Fluconazole | ND | None | |
CT-313 | H7 | 1 | 1 | 0 | Fluconazole | ND | F449V |
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Díaz-García, J.; Gómez, A.; Machado, M.; Alcalá, L.; Reigadas, E.; Sánchez-Carrillo, C.; Pérez-Ayala, A.; de la Pedrosa, E.G.-G.; González-Romo, F.; Cuétara, M.S.; et al. Candida Genotyping of Blood Culture Isolates from Patients Admitted to 16 Hospitals in Madrid: Genotype Spreading during the COVID-19 Pandemic Driven by Fluconazole-Resistant C. parapsilosis. J. Fungi 2022, 8, 1228. https://doi.org/10.3390/jof8111228
Díaz-García J, Gómez A, Machado M, Alcalá L, Reigadas E, Sánchez-Carrillo C, Pérez-Ayala A, de la Pedrosa EG-G, González-Romo F, Cuétara MS, et al. Candida Genotyping of Blood Culture Isolates from Patients Admitted to 16 Hospitals in Madrid: Genotype Spreading during the COVID-19 Pandemic Driven by Fluconazole-Resistant C. parapsilosis. Journal of Fungi. 2022; 8(11):1228. https://doi.org/10.3390/jof8111228
Chicago/Turabian StyleDíaz-García, Judith, Ana Gómez, Marina Machado, Luis Alcalá, Elena Reigadas, Carlos Sánchez-Carrillo, Ana Pérez-Ayala, Elia Gómez-García de la Pedrosa, Fernando González-Romo, María Soledad Cuétara, and et al. 2022. "Candida Genotyping of Blood Culture Isolates from Patients Admitted to 16 Hospitals in Madrid: Genotype Spreading during the COVID-19 Pandemic Driven by Fluconazole-Resistant C. parapsilosis" Journal of Fungi 8, no. 11: 1228. https://doi.org/10.3390/jof8111228
APA StyleDíaz-García, J., Gómez, A., Machado, M., Alcalá, L., Reigadas, E., Sánchez-Carrillo, C., Pérez-Ayala, A., de la Pedrosa, E. G.-G., González-Romo, F., Cuétara, M. S., García-Esteban, C., Quiles-Melero, I., Zurita, N. D., Algarra, M. M., Durán-Valle, M. T., Sánchez-García, A., Muñoz, P., Escribano, P., Guinea, J., & on behalf of the CANDIMAD Study Group. (2022). Candida Genotyping of Blood Culture Isolates from Patients Admitted to 16 Hospitals in Madrid: Genotype Spreading during the COVID-19 Pandemic Driven by Fluconazole-Resistant C. parapsilosis. Journal of Fungi, 8(11), 1228. https://doi.org/10.3390/jof8111228