Pathogenic Fungi Genomics, Evolu6on and Epidemiology

Transcription

1 Pathogenic Fungi Genomics, Evolu6on and Epidemiology

2 Pathogenic Fungi Genomics, Evolu6on and Epidemiology Richard Benne= Brown University, USA Geraldine Butler Antonis Rokas Li-Jun Ma Guilhem Janbon Norman Pavelka University College Dublin, Ireland Vanderbilt University, USA Umass Amherst, USA Ins6tut Pasteur, Paris, France A*Star, Singapore

3 FUNGI 101 True pathogen Opportunistic Blastomyces dermatitidis Coccidiodes immitis 25 C 37 C Candida albicans Budding yeast Pseudohyphae Hyphae Histoplasma capsulatum Cryptococcus neoformans Capsule Paracoccidioides brasiliensis Aspergillus fumigatus Conidia Adapted from Romani, Nat Rev Immun, 2004

4 FUNGI 101 True pathogen Opportunistic Blastomyces dermatitidis Coccidiodes immitis 25 C 37 C Candida albicans Budding yeast Pseudohyphae Hyphae Histoplasma capsulatum Cryptococcus neoformans Capsule Paracoccidioides brasiliensis Aspergillus fumigatus Conidia Adapted from Romani, Nat Rev Immun, 2004

5 What is the impact of invasive mycoses? Worldwide: Life-threatening Mortality rates infections/yr (%) (1) Cryptococcus >1,000, (=2) Candida >400, (=2) Pneumocystis >400, (4) Aspergillus >200, Brown et al., Sci. Trans. Med., 2012

6 What is the impact of invasive mycoses? Worldwide: Life-threatening Mortality rates infections/yr (%) (=5) Coccidiodomycosis ~25,000 <1-70 (=5) Histoplasmosis ~25, (7) Mucormycosis >10, (8) Penicillosis >8, (9) Paracoccidiodomycosis ~4, (10) Blastomycosis ~3,000 <2-68 Brown et al., Sci. Trans. Med., 2012

7 Phylogeny Cryptococcus neoformans Aspergillus fumigatus Candida albicans Pneumocys7s jirovecii Perez-Nadales et al., Fungal Gene6cs and Biology, 2014

8 Wordle

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10 Improved sequencing technology has pushed forward our understanding of genomes 1976 Bacteriophage MS2 3.5 kp 1995 H. influenzae 1.8 Mbp 1996 S. cerevisiae 12.1 Mbp 2001 H. sapiens 3.2 Gbp

11 Questions in fungal genomics what are the dynamics of genome change? how often do genomes recombine? how does sex impact genome structure? how are aneuploidies tolerated? how does this impact drug resistance? how does host environment impact genomes? how does heterozygosity impact mutation? can GWAS and QTL mapping be applied?

12 Genome Diversity of Candida Species Geraldine Butler, UCD, Ireland Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species Schroder et al., 2016, PloS Gen

13 Hybridization drives emergence of new isolates / species : Saccharomyces pastorianus The interspecific hybrid S. pastorianus is the most commonly used yeast in brewery fermentations worldwide. Diego Libkind et al. PNAS, 2011; Walter et al., G3, 2014; Peris et al., PLoS Gen, 2016

14 Genomics and the making of fungal metabolic diversity Antonis Rokas, Vanderbilt University, Tennessee

15 Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data to uncover the gene.c basis of yeast metabolic diversity. Shen et al., G3, 2016.

16 Fusariosis is the top emerging opportunistic mycosis in immunocompromised individuals* Li-Jun Ma, UMASS Amherst Fusariosis: - Caused by Fusarium species, ubiquitous in environments - Highly invasive, causing disseminated diseases: hepatitis, meningitis - Mostly refractory to existing antifungals resulting in high mortality rate * Severe Fungal Infections, Decision Resources; Montone 2009, AJCP

17 Fusarium wilt of banana, popularly known as Panama disease, is a lethal fungal disease caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc).

18 Transcriptome dynamics in C. neoformans Guilhem Janbon, Pasteur Virulence factors Transcriptome structure Fungal fitness How is the regula.on of the transcriptome achieved in human fungal pathogens? And how does this regula.on impact their biology and virulence?

19 Recognition of seven species in the Cryptococcus gattii/cryptococcus neoformans species complex Hagen et al., Fung. Gen. Biol., 2015 Hybrids!!! A B Cryptococcus neoformans var. neoformans CBS1930 CBS10865 CBS8684 CBS10089 HEC11102 CBS10090 A1M-R265 A1M-F3016 A1M-F2866 WM178 CBS11687 WM728 WM161 CBS8755 CBS6993 CBS5758 CBS C CBS6996 WM276 CBS7748 RV54130 D WM179 CBS A CBS6998 CBS1622 WM779 E B5742 C16528 A47496 M27055 WM721 ICB176 P152 CBS8336 WM148 CBS8710 F CBS879 AMC CBS9172 Bt130 CBS10512 Bt63 G Bt27 Bt206 Bt1 WM714 H PAH21b AMC RKI-M318/90 CBS6900 CBS6886 CBS918 I BD5 CBS882 CBS5728 CBS10511 C C. deuteroga;i C. deuterogattii C. decagattii C. bacillisporus C. gattii C. tetragattii C. decaga;i C. bacillisporus C. ga;i C. tetraga;i C. neoformans C. neoformans C. deneoformans C. deneoformans

20 Pavelka lab Norman Pavelka, A Star, Singapore The Pavelka lab is focused on understanding the ecological and evolu6onary forces that govern the threeway interac6on between C. albicans, GI bacteria and the immune system. C. albicans GI colonization fecal pellet isolation YPD, 30 C systemic infection kidney isolation

21 β-glucan Exposure on the Fungal Cell Wall Tightly Correlates with Competitive Fitness of Candida Species in the Mouse Gastrointestinal Tract XiaoHui Sem, Giang T. T. Le, Alrina S. M. Tan, Gloria Tso, Marina Yurieva, Webber W. P. Liao, Josephine Lum, Kandhadayar G. Srinivasan, Michael Poidinger, Francesca Zolezzi and Norman Pavelka * ORIGINAL RESEARCH published: 22 December 2016 doi: /fcimb C. glabrata C. albicans

22 Genetic and phenotypic intra-species variation in Candida albicans Matthew P. Hirakawa, 1 Diego A. Martinez, 2,5 Sharadha Sakthikumar, 2,5 Matthew Z. Anderson, 1,3 Aaron Berlin, 2 Sharvari Gujja, 2 Qiandong Zeng, 2 Ethan Zisson, 1 Joshua M. Wang, 1 Joshua M. Greenberg, 1 Judith Berman, 3,4 Richard J. Bennett, 1,5 and Christina A. Cuomo 2,5 * Genome Research 21 genomes x SNP/indel muta6ons 8 heterozygous chromosomes in diploid genome Loss of heterozygosity (LOH) Hirakawa et al., 2015, Genome Research Aneuploidy

23 How does intra-species diversity affect phenotypes such as virulence? L26 GC75 P37005 P57072 P60002 Survival (%) 19F P97 12C P94015* P Survival (%) Time (Days) Wu et al., Mol Micro, 2007

24 A P94015 P94015 SC5314 SC5314 B BB % Filamentous Cells % Filamentous Cells The role of EFG1 in P94015? P94015+EFG1 (2) P94015+EFG1 (1) Contains a homozygous, premature stop codon in EFG1 P94015+EFG1(2) (2) P94015+EFG1(1) (1) P94015+EFG1 P94015+EFG1 1 (2) * * 5 DDD ) 00 0 G 1 (2 ) ( Days Days5Post PostInfection Infection 1010 Days Infection Days Post Post Infection Frequency Days 0Po Days Da P94015 P94015 vs.vs. vs.vs.vs P94015 P94015 P94015 P94015+EFG1 (1) P94015+EFG1 (2) s (%)Strain elative StrainFrequency Frequency ative Feces(%) (%) ininfeces y D 0 10 E Restoring EFG1 increased filamentation and virulenceff E E F Hirakawa et al., 2015, Genome Research P94015 P94015 P94015+EFG1 P94015+EFG1(1) (1) P94015 P94015+EFG1 P94015+EFG1(2) (2) P E F G P E F P in Kidney (%) 10 P9 4 P E 15P F +9E4G1 F0G1 (1 15+)E ( Increased Virulence CC % Survival % Filamentous Cells Relative Strain Frequency Relative in Strain KidneyFrequency (%) RelativeinStrain Frequency Kidney (%) Increased Filamentation % Survival Survival % B * P94015 Relative Strain Frequency RelativeinStrain Frequency Organs (%) * train Frequency in Organs (%) rgans (%) aa P9 P P9 4 APSES DNAbinding domain P94015 SC5314 % Filamentous Cells A vs

25 Does reintroduction of a functional EFG1 allele into P94015 alter commensal fitness? Restoring EFG1 reduced fitness in the commensal GI model

26 Natural isolates show preferential specificity for different host niches Strains biased towards a more commensal lifestyle Loss of EFG1 function Strains biased towards a more pathogenic lifestyle A natural polymorphism impacts commensal fitness and virulence Hirakawa et al., Genome Res, 2015

27 A note of caution with genomes! Finding a Missing Gene: EFG1 Regulates Morphogenesis in Candida tropicalis Eugenio Mancera,* Allison M. Porman, Christina A. Cuomo, Richard J. Bennett, and Alexander D. Johnson*, *Department of Microbiology and Immunology and Department of Biochemistry and Biophysics, Unive My data suggests that the genes is located in Supercon6g_3.1 in the gap spanning from 887,643 to 888,943

28 What about sex? opaque opaque C. albicans 2N a α 2N white white 2N a a/α α 2N 4N 2N a 2N+1 a Spo11/ DSBs α 2N+1 α 2N 2N+2 a α 2N+2 Recombinant parasexual products

29 More genomes and genome resources. and tools h=p://1000.fungalgenomes.org/home/about/

30 Pathogenic Fungi Genomics, Evolu6on and Epidemiology Geraldine Butler Antonis Rokas Li-Jun Ma Guilhem Janbon Norman Pavelka University College Dublin, Ireland Vanderbilt University, USA Umass Amherst, USA Ins6tut Pasteur, Paris, France A*Star, Singapore