Harnessing Whole Genome Sequencing in Medical Mycology

被引：17
作者：
Cuomo C.A. [1 ]
机构：
[1] Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA
来源：
Current Fungal Infection Reports | 2017年 / 11卷 / 2期
基金：
美国国家卫生研究院;
关键词：
Fungal infections; Genome sequencing; Human fungal pathogens; Medical mycology; Review; Whole genome sequencing;
D O I：
10.1007/s12281-017-0276-7
中图分类号：
学科分类号：
摘要：
Purpose of Review: Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically important fungal pathogens. Recent Findings: Genomes for some important fungal pathogens were only recently assembled, revealing gene family expansions in many species and extreme gene loss in one obligate species. The scale and scope of species sequenced is rapidly expanding, leveraging technological advances to assemble and annotate genomes with higher precision. By using iteratively improved reference assemblies or those generated de novo for new species, recent studies have compared the sequence of isolates representing populations or clinical cohorts. Whole genome approaches provide the resolution necessary for comparison of closely related isolates, for example, in the analysis of outbreaks or sampled across time within a single host. Summary: Genomic analysis of fungal pathogens has enabled both basic research and diagnostic studies. The increased scale of sequencing can be applied across populations, and new metagenomic methods allow direct analysis of complex samples. © 2017, Springer Science+Business Media New York.
引用
收藏
页码：52 / 59
页数：7
相关论文
共 61 条
  • [1] Ma L., Chen Z., Huang D.W., Kutty G., Ishihara M., Wang H., Et al., Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts, Nat Commun, 7, (2016)
  • [2] Munoz J.F., Farrer R.A., Desjardins C.A., Gallo J.E., Sykes S., Sakthikumar S, et al, Genome diversity, recombination, and virulence across the major lineages of Paracoccidioides. mSphere., (2016)
  • [3] Chibucos M.C., Soliman S., Gebremariam T., Lee H., Daugherty S., Orvis J., Et al., An integrated genomic and transcriptomic survey of mucormycosis-causing fungi, Nat Commun, 7, (2016)
  • [4] Braun B.R., van Het Hoog M., d'Enfert C., Martchenko M., Dungan J., Kuo A., Et al., A human-curated annotation of the Candida albicans genome, PLoS Genet, 1, pp. 36-57, (2005)
  • [5] Cisse O.H., Pagni M., Hauser P.M., De novo assembly of the Pneumocystis jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient, MBio, 4, pp. e00412-e004128, (2012)
  • [6] Galagan J.E., Calvo S.E., Cuomo C., Ma L.J., Wortman J.R., Batzoglou S., Et al., Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae, Nature, 438, pp. 1105-1115, (2005)
  • [7] O'Gorman C.M., Fuller H.T., Dyer P.S., Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus, Nature, 457, pp. 471-474, (2009)
  • [8] Liu O.W., Chun C.D., Chow E.D., Chen C., Madhani H.D., Noble S.M., Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans, Cell, 135, pp. 174-188, (2008)
  • [9] Roemer T., Jiang B., Davison J., Ketela T., Veillette K., Breton A., Et al., Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery, Mol Microbiol, 50, pp. 167-181, (2003)
  • [10] Vyas V.K., Barrasa M.I., Fink G.R., A Candida albicans CRISPR system permits genetic engineering of essential genes and gene families, Sci Adv, 1, (2015)
1234567