Emergence and Genomic Characterization of Multidrug Resistant Candida auris in Nigeria, West Africa
Abstract
:1. Introduction
1.1. The Cases
1.1.1. Case 1
1.1.2. Case 2
1.1.3. Case 3
1.1.4. Case 4
2. Materials and Methods
2.1. DNA Extraction and Library Preparation
2.2. Whole Genome Sequencing and Bioinformatics Analysis
2.3. Phylogenetic Analysis
3. Results
3.1. Antifungal Susceptibility Test (AFST)
3.2. Genome Analysis
3.3. Variant Analysis
3.4. Phylogenetic Analysis
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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Case | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Date | February, 2021 | February, 2021 | March, 2021 | April, 2021 |
Gender, age (years) | Male, 60 | Female, 67 | Male, 74 | Female, 48 |
Underlying disease | Diabetes mellitus, Hypertension | Diabetes mellitus, Hypertension, COVID-19 | Prostate cancer | Systemic Lupus Erythematosus (SLE) |
Country visited in the previous year | Unknown | Unknown | Dubai, UAE | No travel |
Recent intake of broad-spectrum antibiotics | Yes | Yes | Yes | Yes |
Vascular surgery | No | No | No | No |
Total parenteral nutrition | No | No | No | Yes |
Dialysis | Yes | No | No | Yes |
Urinary catheterization | Yes | Yes | Yes | Yes |
Postoperative drain placement | Yes | No | No | No |
Type of invasive candidiasis infection | Bloodstream infection (also isolated from sputum and urine) | Bloodstream infection | Bloodstream (probable skin colonization) | Bloodstream |
Antifungal Treatment | Voriconazole | None | None | Fluconazole, voriconazole |
Outcome | Death | Death | Discharged | Death |
Antifungal (Minimal Inhibitory Concentration mg/L) | |||||||
---|---|---|---|---|---|---|---|
Fluconazole | Voriconazole | Posaconazole | Amphotericin B | Caspofungin | Micafungin | Anidulafungin | |
Tentative MIC breakpoints | ≥32 | NA * | NA * | ≥2 | ≥2 | ≥4 | ≥4 |
Case 1 | 16 | 0.25 | 0.016 | 1 | 0.06 | 0.063 | 0.031 |
Case 2 | 64 | 1 | 0.031 | 0.5 | 0.06 | 0.125 | 0.25 |
Case 3 | 1 | 0.016 | <0.016 | 0.25 | 0.06 | 0.125 | 0.25 |
Case 4 | 32 | 1 | 0.031 | 0.5 | 0.06 | 0.125 | 0.25 |
Isolate | Change | Type of Change | Gene ID | Ortholog |
---|---|---|---|---|
Case 1 | a1004g | Asn335Ser | snp; missense | CJI97_001156 | ERG11 |
a1029c | Glu343Asp | snp; missense | CJI97_001156 | ERG11 | |
Case 2 | a395t | Tyr132Phe | snp; missense | CJI97_001156 | ERG11 |
ctc374_376ttt | Leu125Phe | complex; missense | CJI97_001156 | ERG11 | |
c4453a | Leu148Ile | snp; missense | CJI97_000983 | FKS1 | |
a2811t | Arg937Ser | snp; missense | CJI97_000983 | FKS1 | |
ca2100ag | Ile701Val | indel; missense | CJI97_000983 | FKS1 | |
a2080g | Ile694Val | snp; missense | CJI97_000983 | FKS1 | |
Case 3 | a530g | Lys177Arg | snp; missense | CJI97_001156 | ERG11 |
a1004g | Asn335Ser | snp; missense | CJI97_001156 | ERG11 | |
a1029c | Glu343Asp | snp; missense | CJI97_001156 | ERG11 | |
Case 4 | ctc374_376ttt | Leu125Phe | complex; missense | CJI97_001156 | ERG11 |
a395t | Tyr132Phe | snp; missense | CJI97_001156 | ERG11 | |
a117c | Glu39Asp | snp; missense | CJI97_005027 | ERG2 |
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Oladele, R.; Uwanibe, J.N.; Olawoye, I.B.; Ettu, A.-W.O.; Meis, J.F.; Happi, C.T. Emergence and Genomic Characterization of Multidrug Resistant Candida auris in Nigeria, West Africa. J. Fungi 2022, 8, 787. https://doi.org/10.3390/jof8080787
Oladele R, Uwanibe JN, Olawoye IB, Ettu A-WO, Meis JF, Happi CT. Emergence and Genomic Characterization of Multidrug Resistant Candida auris in Nigeria, West Africa. Journal of Fungi. 2022; 8(8):787. https://doi.org/10.3390/jof8080787
Chicago/Turabian StyleOladele, Rita, Jessica N. Uwanibe, Idowu B. Olawoye, Abdul-Wahab O. Ettu, Jacques F. Meis, and Christian T. Happi. 2022. "Emergence and Genomic Characterization of Multidrug Resistant Candida auris in Nigeria, West Africa" Journal of Fungi 8, no. 8: 787. https://doi.org/10.3390/jof8080787