Genomic Diversity Analysis Reveals a Strong Population Structure in Histoplasma capsulatum LAmA (Histoplasma suramericanum)
Abstract
1. Introduction
2. Materials and Methods
2.1. Fungal Isolation and Culture Conditions
2.2. Patient’s Information
2.3. DNA Extraction
2.4. Whole Genome Sequencing and SNP Variant Calling
2.5. Phylogenetic Trees Using Whole Genomes
2.6. Population Structure and Admixture
2.7. Clinical Differences between RJ and Non-RJ Samples
2.8. Strain Genotyping Using Multi Locus Sequencing Type (MLST) Analysis
3. Results
3.1. Phylogenomic Diversity
3.2. Population Structure within H. Suramericanum
3.3. MLST Is Sufficient to Identify the RJ Clade
3.4. Multiple Infections Caused by Histoplasma spp.
4. Discussion
4.1. Histoplasma Genotypes from Southeast Brazil, Rio de Janeiro
4.2. Strong Population Structure in H. suramericanum in South America
4.3. South America Harbors at Least Two Different Species of Histoplasma
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Patient | Isolate | Origin | Specimen | Clinical Features | Phylogenetic Species |
---|---|---|---|---|---|
1 | 13H | Human | Blood Culture | HIV+/Disseminated | NE |
2 | 129H | Human | Blood Culture | HIV+/Disseminated | NE |
3 | 20231 | Human | Tongue Scraping | HIV+/Disseminated | Unknown1 |
- | 11354 | Human | Blood Culture | HIV+/Disseminated | Unknown1 |
4 | 3416 | Human | Sputum | HIV−/Chronic Pulmonary | RJ |
- | 3612 | Human | Lung Biopsy | HIV+/Disseminated | RJ |
- | 39439 | Human | Bone Marrow Aspirate | HIV+/Disseminated | RJ |
- | 39942 | Human | Biopsy | NA | Panama |
5 | 6503 | Human | Ganglion Biopsy | HIV+/Opportunistic | RJ |
- | 84502 | Human | Blood Culture | HIV+/Disseminated | NE |
- | 84564 | Human | Skin Biopsy | HIV+/Disseminated | NE |
- | AC 05 | Environmental | Soil | NA | RJ |
- | CÃO 4 | Animal/Dog | Liver and Spleen | NA | RJ |
- | CO4 | Environmental | Soil | NA | RJ |
- | EP 02 | Environmental | Soil | NA | RJ |
1 | HC 18 | Human | Blood Culture | HIV+/Disseminated | RJ |
6 | 40039 | Human | Bone Marrow Aspirate | HIV+/Disseminated | RJ |
- | IGS 19 | Environmental | Soil | NA | RJ |
- | IGS 4/5 | Environmental | Soil | NA | RJ |
7 | INI 01/16 | Human | Bone Marrow Aspirate | HIV+/Disseminated | NE |
8 | INI 02/16 | Human | Skin Biopsy | HIV+/Disseminated | LAmB1 |
8 | INI 03/16 | Human | Bone Marrow Aspirate | HIV+/Disseminated | LAmB1 |
9 | INI 04/16 | Human | Sputum | HIV-/Disseminated | NE |
9 | INI 05/16 | Human | Ganglion Fragment | HIV-/Disseminated | RJ |
10 | INI 06/16 | Human | Bone Marrow Aspirate | HIV+/Disseminated | RJ |
11 | INI 07/16 | Human | Bone Marrow Aspirate | HIV+/Disseminated | Unknown1 |
12 | 01_12 | Human | Bone Marrow Aspirate | HIV+/Disseminated | RJ |
13 | 01_13 | Human | Blood Culture | HIV+/Disseminated | RJ |
- | 02_13 | Animal/Dog | Blood Culture | NA | RJ |
14 | 02_14 | Human | Skin Biopsy | HIV+/Disseminated | RJ |
15 | 04_12 | Human | Bone Marrow Aspirate | HIV+/Disseminated | RJ |
16 | 04_14 | Human | Bone Marrow Aspirate | HIV+/Disseminated | RJ |
- | 05_12 | Animal/Cat | Lesion Exudate | NA | RJ |
17 | 06_12 | Human | Bone Marrow Aspirate | HIV+/Disseminated | RJ |
- | 07_12 | Animal/Dog | Lymph Node Biopsy | NA | RJ |
18 | 09_12 | Human | Bronchoalveolar Lavage | Chronic Pulmonary | NE |
19 | 11_12 | Human | Skin Biopsy | HIV+/Disseminated | LAmB1 |
13 | 23_11 | Human | Blood Culture | HIV+/Disseminated | Unknown1 |
- | 24_11 | Human | Blood Culture | HIV+/Disseminated | RJ |
- | 26_11 | Human | Bone Marrow Aspirate | HIV+/Disseminated | RJ |
20 | 27_11 | Human | Oropharyngeal Swab | HIV+/Disseminated | RJ |
20 | 28_11 | Human | Bone Marrow Aspirate | HIV+/Disseminated | RJ |
- | IT 04 | Environmental | Soil | NA | RJ |
- | RPS 35 | Environmental | Soil | NA | RJ |
- | RPS 45 | Environmental | Soil | NA | RJ |
- | RPS 51 | Environmental | Soil | NA | RJ |
- | RS 36 | Wild Animal | NA | NA | RJ |
- | TI 01 | Environmental | Soil | NA | RJ |
- | TI 05 | Environmental | Soil | NA | RJ |
- | 36GAL | Human | Blood | HIV+/Disseminated | Unknown1 |
Clinical Data | Genotype | Power | p-Value | Corrected p-Value | |
---|---|---|---|---|---|
RJ | Others | ||||
Fever | 9 (90%) | 5 (71.4%) | 0.166 | ||
Weight Loss | 6 (60%) | 5 (71.4%) | 0.078 | ||
Cough | 6 (60%) | 6 (85.7%) | 0.226 | ||
Dyspnea | 3 (30%) | 1 (14.2%) | 0.122 | ||
Abdominal Pain | 3 (30%) | 2 (28.5%) | 0.050 | ||
Diarrhea | 1 (10%) | 4 (57.1%) | 0.584 | 0.119 | 0.476 |
Vomit | 3 (30%) | 3 (42.8%) | 0.085 | ||
Asthenia | 3 (30%) | 5 (71.4%) | 0.411 | 0.234 | 0.701 |
Headache | 0 (0%) | 2 (28.5%) | 0.629 | 0.301 | 0.701 |
Hepatomegaly | 4 (40%) | 2 (28.5%) | 0.078 | ||
Splenomegaly | 5 (50%) | 4 (57.1%) | 0.060 | ||
Acute Renal Failure | 7 (70%) | 2 (28.5%) | 0.411 | 0.234 | 0.701 |
Hemorrhage | 3 (30%) | 1 (14.2%) | 0.122 | ||
Skin Lesion | 4 (40%) | 3 (42.8%) | 0.0516 | ||
Adenomegaly | 6 (60%) | 4 (57.1%) | 0.0516 |
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Almeida-Silva, F.; de Melo Teixeira, M.; Matute, D.R.; de Faria Ferreira, M.; Barker, B.M.; Almeida-Paes, R.; Guimarães, A.J.; Zancopé-Oliveira, R.M. Genomic Diversity Analysis Reveals a Strong Population Structure in Histoplasma capsulatum LAmA (Histoplasma suramericanum). J. Fungi 2021, 7, 865. https://doi.org/10.3390/jof7100865
Almeida-Silva F, de Melo Teixeira M, Matute DR, de Faria Ferreira M, Barker BM, Almeida-Paes R, Guimarães AJ, Zancopé-Oliveira RM. Genomic Diversity Analysis Reveals a Strong Population Structure in Histoplasma capsulatum LAmA (Histoplasma suramericanum). Journal of Fungi. 2021; 7(10):865. https://doi.org/10.3390/jof7100865
Chicago/Turabian StyleAlmeida-Silva, Fernando, Marcus de Melo Teixeira, Daniel R. Matute, Marcela de Faria Ferreira, Bridget M. Barker, Rodrigo Almeida-Paes, Allan J. Guimarães, and Rosely M. Zancopé-Oliveira. 2021. "Genomic Diversity Analysis Reveals a Strong Population Structure in Histoplasma capsulatum LAmA (Histoplasma suramericanum)" Journal of Fungi 7, no. 10: 865. https://doi.org/10.3390/jof7100865
APA StyleAlmeida-Silva, F., de Melo Teixeira, M., Matute, D. R., de Faria Ferreira, M., Barker, B. M., Almeida-Paes, R., Guimarães, A. J., & Zancopé-Oliveira, R. M. (2021). Genomic Diversity Analysis Reveals a Strong Population Structure in Histoplasma capsulatum LAmA (Histoplasma suramericanum). Journal of Fungi, 7(10), 865. https://doi.org/10.3390/jof7100865