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Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort
Emerging infections caused by fungi have become a widely recognized global phenomenon and are causing an increasing burden of disease. Genomic techniques are providing new insights into the structure of fungal populations, revealing hitherto undescribed fine‐scale adaptations to environments and hos...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5412878/ https://www.ncbi.nlm.nih.gov/pubmed/27862555 http://dx.doi.org/10.1111/mec.13891 |
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author | Vanhove, Mathieu Beale, Mathew A. Rhodes, Johanna Chanda, Duncan Lakhi, Shabir Kwenda, Geoffrey Molloy, Sile Karunaharan, Natasha Stone, Neil Harrison, Thomas S. Bicanic, Tihana Fisher, Matthew C. |
author_facet | Vanhove, Mathieu Beale, Mathew A. Rhodes, Johanna Chanda, Duncan Lakhi, Shabir Kwenda, Geoffrey Molloy, Sile Karunaharan, Natasha Stone, Neil Harrison, Thomas S. Bicanic, Tihana Fisher, Matthew C. |
author_sort | Vanhove, Mathieu |
collection | PubMed |
description | Emerging infections caused by fungi have become a widely recognized global phenomenon and are causing an increasing burden of disease. Genomic techniques are providing new insights into the structure of fungal populations, revealing hitherto undescribed fine‐scale adaptations to environments and hosts that govern their emergence as infections. Cryptococcal meningitis is a neglected tropical disease that is responsible for a large proportion of AIDS‐related deaths across Africa; however, the ecological determinants that underlie a patient's risk of infection remain largely unexplored. Here, we use genome sequencing and ecological genomics to decipher the evolutionary ecology of the aetiological agents of cryptococcal meningitis, Cryptococcus neoformans and Cryptococcus gattii, across the central African country of Zambia. We show that the occurrence of these two pathogens is differentially associated with biotic (macroecological) and abiotic (physical) factors across two key African ecoregions, Central Miombo woodlands and Zambezi Mopane woodlands. We show that speciation of Cryptococcus has resulted in adaptation to occupy different ecological niches, with C. neoformans found to occupy Zambezi Mopane woodlands and C. gattii primarily recovered from Central Miombo woodlands. Genome sequencing shows that C. neoformans causes 95% of human infections in this region, of which over three‐quarters belonged to the globalized lineage VNI. We show that VNI infections are largely associated with urbanized populations in Zambia. Conversely, the majority of C. neoformans isolates recovered in the environment belong to the genetically diverse African‐endemic lineage VNB, and we show hitherto unmapped levels of genomic diversity within this lineage. Our results reveal the complex evolutionary ecology that underpins the reservoirs of infection for this, and likely other, deadly pathogenic fungi. |
format | Online Article Text |
id | pubmed-5412878 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-54128782017-05-15 Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort Vanhove, Mathieu Beale, Mathew A. Rhodes, Johanna Chanda, Duncan Lakhi, Shabir Kwenda, Geoffrey Molloy, Sile Karunaharan, Natasha Stone, Neil Harrison, Thomas S. Bicanic, Tihana Fisher, Matthew C. Mol Ecol Insights on Microbial Adaptation from Patterns of Local Adaptation in Nature Emerging infections caused by fungi have become a widely recognized global phenomenon and are causing an increasing burden of disease. Genomic techniques are providing new insights into the structure of fungal populations, revealing hitherto undescribed fine‐scale adaptations to environments and hosts that govern their emergence as infections. Cryptococcal meningitis is a neglected tropical disease that is responsible for a large proportion of AIDS‐related deaths across Africa; however, the ecological determinants that underlie a patient's risk of infection remain largely unexplored. Here, we use genome sequencing and ecological genomics to decipher the evolutionary ecology of the aetiological agents of cryptococcal meningitis, Cryptococcus neoformans and Cryptococcus gattii, across the central African country of Zambia. We show that the occurrence of these two pathogens is differentially associated with biotic (macroecological) and abiotic (physical) factors across two key African ecoregions, Central Miombo woodlands and Zambezi Mopane woodlands. We show that speciation of Cryptococcus has resulted in adaptation to occupy different ecological niches, with C. neoformans found to occupy Zambezi Mopane woodlands and C. gattii primarily recovered from Central Miombo woodlands. Genome sequencing shows that C. neoformans causes 95% of human infections in this region, of which over three‐quarters belonged to the globalized lineage VNI. We show that VNI infections are largely associated with urbanized populations in Zambia. Conversely, the majority of C. neoformans isolates recovered in the environment belong to the genetically diverse African‐endemic lineage VNB, and we show hitherto unmapped levels of genomic diversity within this lineage. Our results reveal the complex evolutionary ecology that underpins the reservoirs of infection for this, and likely other, deadly pathogenic fungi. John Wiley and Sons Inc. 2016-11-08 2017-04 /pmc/articles/PMC5412878/ /pubmed/27862555 http://dx.doi.org/10.1111/mec.13891 Text en © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Insights on Microbial Adaptation from Patterns of Local Adaptation in Nature Vanhove, Mathieu Beale, Mathew A. Rhodes, Johanna Chanda, Duncan Lakhi, Shabir Kwenda, Geoffrey Molloy, Sile Karunaharan, Natasha Stone, Neil Harrison, Thomas S. Bicanic, Tihana Fisher, Matthew C. Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort |
title | Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort |
title_full | Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort |
title_fullStr | Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort |
title_full_unstemmed | Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort |
title_short | Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort |
title_sort | genomic epidemiology of cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an african hiv/aids cohort |
topic | Insights on Microbial Adaptation from Patterns of Local Adaptation in Nature |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5412878/ https://www.ncbi.nlm.nih.gov/pubmed/27862555 http://dx.doi.org/10.1111/mec.13891 |
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