Genotype, Antifungal Susceptibility, and Virulence of Clinical South African Cryptococcus neoformans Strains from National Surveillance, 2005–2009
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Design and Sample Selection
2.2. Subculture and Identification of Surveillance Isolates
2.3. Multi Locus Sequence typing (MLST) Experiments and Data Analysis
2.4. Fluconazole Susceptibility Testing
2.5. Virulence Studies
2.6. Whole Genome Sequencing and Phylogenetic Analysis
2.7. Statistical Analyses
2.8. Ethics Approval
3. Results
3.1. Descriptive Analysis of National Laboratory-Based Surveillance
3.2. Genotyping of 251 Clinical C. neoformans Isolates
3.3. Association between Patients’ Clinical Characteristics and Genotype
3.4. Association between Genotype and In-Hospital Mortality
3.5. Fluconazole Susceptibility Testing
3.6. Virulence and Whole Genome Sequencing (WGS) of 15 C. neoformans Isolates with the VNB Molecular Type
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Molecular Type | Total | MIC Value | MIC50 | MIC90 | Geometric Mean | Range | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0.125 | 0.25 | 0.5 | 1 | 2 | 4 | 8 | 16 | 32 | 64 | ||||||
VNI | 60 | 0 | 2 | 10 | 20 | 19 | 3 | 5 | 0 | 1 | 0 | 1 | 6 | 1.43 | 0.25–32 |
VNB | 15 | 0 | 1 | 2 | 6 | 3 | 3 | 0 | 0 | 0 | 0 | 1 | 4 | 1.26 | 0.25–4 |
VNII | 25 | 0 | 0 | 5 | 15 | 4 | 1 | 0 | 0 | 0 | 0 | 1 | 2 | 1.03 | 0.5–4 |
VNIV | 5 | 0 | 0 | 0 | 0 | 5 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 2 | 2 |
Total | 105 | 0 | 3 | 17 | 41 | 31 | 7 | 5 | 0 | 1 | 0 | 1 | 4 | 1.32 | 0.25–32 |
Strain | Median Survival Time | p Value |
---|---|---|
H99 * | 2 | NA |
5873 | 2 | 0.54 |
205 | 3 | 0.02 |
2887 | 3 | 0.01 |
3438 | 3 | 0.24 |
1597 | 3 | 0.01 |
907 | 3 | 0.02 |
1239 | 3 | 0.04 |
3783 | 3 | 0.01 |
130 | 3 | 0.01 |
1543 | 3 | 0.01 |
637 | 4 | 0.02 |
1817 | 4 | 0.002 |
892 | 4 | 0.003 |
2890 | 4 | 0.001 |
1408 | 5 | 0.001 |
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Naicker, S.D.; Magobo, R.E.; Maphanga, T.G.; Firacative, C.; van Schalkwyk, E.; Monroy-Nieto, J.; Bowers, J.; Engelthaler, D.M.; Shuping, L.; Meyer, W.; et al. Genotype, Antifungal Susceptibility, and Virulence of Clinical South African Cryptococcus neoformans Strains from National Surveillance, 2005–2009. J. Fungi 2021, 7, 338. https://doi.org/10.3390/jof7050338
Naicker SD, Magobo RE, Maphanga TG, Firacative C, van Schalkwyk E, Monroy-Nieto J, Bowers J, Engelthaler DM, Shuping L, Meyer W, et al. Genotype, Antifungal Susceptibility, and Virulence of Clinical South African Cryptococcus neoformans Strains from National Surveillance, 2005–2009. Journal of Fungi. 2021; 7(5):338. https://doi.org/10.3390/jof7050338
Chicago/Turabian StyleNaicker, Serisha D., Rindidzani E. Magobo, Tsidiso G. Maphanga, Carolina Firacative, Erika van Schalkwyk, Juan Monroy-Nieto, Jolene Bowers, David M. Engelthaler, Liliwe Shuping, Wieland Meyer, and et al. 2021. "Genotype, Antifungal Susceptibility, and Virulence of Clinical South African Cryptococcus neoformans Strains from National Surveillance, 2005–2009" Journal of Fungi 7, no. 5: 338. https://doi.org/10.3390/jof7050338