Evolution and pathogenicity in the deadly chytrid pathogen of amphibians Erica Bree Rosenblum UC Berkeley
Emerging infectious disease
Emerging infectious disease EID events have risen significantly over time after controlling for reporting bias - Jones et al. Nature 2008 # EID events 100 50 0 1940 1970 2000 Decade Host Pathogen Environment Why are EID events on the rise?
EIDs can be due to changes in Disease outcome depends on host-pathogen-environment interaction The Pathogen The Host The Environment
Novelty in the microbial pathogen world But what is novelty?
Novelty in the microbial pathogen world * Novel pathogens don t just appear - they evolve Importance of studying a pathogen s evolutionary history
Novelty in the microbial pathogen world * Novel pathogens can be novel in multiple ways (changes in host range, changes in virulence, etc) Importance of studying novelty at multiple levels
Novelty in the microbial pathogen world Evolutionary and functional novelty in an emerging fungal pathogen of amphibians
Bd and amphibian declines
Bd and amphibian declines
Bd and amphibian declines Frog photo: Joel Sartore
Bd and amphibian declines Bd occurs on every continent with amphibians, infecting >500 species Published occurrence Unpublished occurrence Map courtesy of www.spatialepidemiology.net
Bd and amphibian declines Genetic and spatio-temporal data demonstrate that Bd is a novel, emerging pathogen, which has spread around the world quickly
Bd and amphibian declines Chytrids are basal fungi and are mostly sapbrobes Bd is the only chytrid that infects vertebrates Ascomycota Basidiomycota Zygomycota Chytridiomycota Metazoa
Bd and amphibian declines Bd kills frogs by disrupting the structure and function of their skin Bd may also have an immune evasion/ suppression strategy Rosenblum et al. 2009 PLoS ONE Rosenblum et al. 2012. Molecular Ecology
Novelty in the microbial pathogen world But there are persistent unanswered questions about the origin and spread of Bd and the interaction between Bd and its amphibian hosts Where did Bd come from and what makes it so deadly?
Genomics in non-model species Many of our questions cannot be answered using ecological approaches, and we cannot manipulate Bd to use cellular approaches So we are using genomics approaches to understand Bd evolution and pathogenicity
Genomics in non-model species
Genomics and EIDs With technological advances we can conduct genomic studies even for timecritical studies in non-model species
Genomics and EIDs Comparative genomics Functional genomics AGTCGTAGCCGCTATC! AGTCGTAGCCGCTATC! AGCCGTAGCCGCTATG! AGCCGTAACTGCTTTG! CGCTGCAACTGCTTTG! CGCTTCAACTGCTTTG! DNA transcription RNA Gene expression: (microarrays, RNAseq)
Using genomics to understand novelty Understanding evolutionary and functional novelty in Bd
Using genomics to understand novelty Understanding evolutionary and functional novelty in Bd
Novelty at the phylogenetic level It vs They? Bd has a single species name, but there may be important genetic and/or functional variation
Novelty at the phylogenetic level Sequence genomes of 28 Bd isolates from around the world and the genome of the closest known non-pathogenic chytrid 7 6 1 4 1 8 1 JGI genome project backbone, Illumina resequencing ~30x coverage per isolate, ~25Mb genomes
Novelty at the phylogenetic level Dummy Data: Expectations given Bd s recent discovery and spread * * * * N. America (West) N. America (East) Latin America Asia Africa * Bullfrog isolate
Novelty at the phylogenetic level Rooted tree based on >100,000 SNPs N. America (West) N. America disomy (East) Latin America trisomy Asia tetrasomy Africa * Bullfrog isolate 0.07 LOH 5: 1.3 LOH 1: 0.6 LOH 1: 2.4 LOH 5: 1.0 LFT001_10 UM142 CJB5.2 CJB7 JEL271 JEL627 CLFT021 CLFT023 JEL275 JEL433 CLFT024 EV001 JEL408 NCRC106979 LBAbercrom JEL310 JEL427 JEL429 JEL289 SRS812 MexMkt CLFT026 JEL267 JEL359 JEL238 TST75 MLA1 CJB4 * * * * Bd s evolutionary history is more complicated than expected No clear pointsource for origin or linear history of spread chromosome 1 2 3 9 1 1 1 1 5 8 7 1 6 1 4 4 1 2 0 5 3
Novelty at the phylogenetic level Rooted tree based on >100,000 SNPs N. America (West) N. America disomy (East) Latin America trisomy Asia tetrasomy Africa * Bullfrog isolate 0.07 LOH 5: 1.3 LOH 1: 0.6 LOH 1: 2.4 LOH 5: 1.0 LFT001_10 UM142 CJB5.2 CJB7 JEL271 JEL627 CLFT021 CLFT023 JEL275 JEL433 CLFT024 EV001 JEL408 NCRC106979 LBAbercrom JEL310 JEL427 JEL429 JEL289 SRS812 MexMkt CLFT026 JEL267 JEL359 JEL238 TST75 MLA1 CJB4 * * * * No geographic or host specific population structure Confirms rapid spread and broad host range chromosome 1 2 3 9 1 1 1 1 5 8 7 1 6 1 4 4 1 2 0 5 3
Novelty at the phylogenetic level Rooted tree based on >100,000 SNPs N. America (West) N. America disomy (East) Latin America trisomy Asia tetrasomy Africa * Bullfrog isolate 0.07 LOH 5: 1.3 LOH 1: 0.6 LOH 1: 2.4 LOH 5: 1.0 LFT001_10 UM142 CJB5.2 CJB7 JEL271 JEL627 CLFT021 CLFT023 JEL275 JEL433 CLFT024 EV001 JEL408 NCRC106979 LBAbercrom JEL310 JEL427 JEL429 JEL289 SRS812 MexMkt CLFT026 JEL267 JEL359 JEL238 TST75 MLA1 CJB4 * * * * Tree has more structure than expected There are 2 highly divergent Bd lineages chromosome 1 2 3 9 1 1 1 1 5 8 7 1 6 1 4 4 1 2 0 5 3
Novelty at the phylogenetic level Rooted tree based on >100,000 SNPs N. America (West) N. America disomy (East) Latin America trisomy Asia tetrasomy Africa * Bullfrog isolate 0.07 LOH 5: 1.3 LOH 1: 0.6 LOH 1: 2.4 LOH 5: 1.0 LFT001_10 UM142 CJB5.2 CJB7 JEL271 JEL627 CLFT021 CLFT023 JEL275 JEL433 CLFT024 EV001 JEL408 NCRC106979 LBAbercrom JEL310 JEL427 JEL429 JEL289 SRS812 MexMkt CLFT026 JEL267 JEL359 JEL238 TST75 MLA1 CJB4 * * * * Basal lineage with isolates from Latin America Large clade with most of the global diversity Likely more diversity to be discovered with more sampling chromosome 1 2 3 9 1 1 1 1 5 8 7 1 6 1 4 4 1 2 0 5 3
Using genomics to understand Bd novelty Understanding evolutionary and functional novelty in Bd
Chytrid comparative genomics Massive expansions of gene families in Bd Ascomycota Basidiomycota Zygomycota Bd is a unique chytrid with functions no other chytrid has acquired Chytridiomycota Metazoa
Chytrid comparative genomics Massive expansions of protease gene families in Bd Fungalysin metallopeptidase Serine protease Rosenblum et al. 2008 PNAS
Chytrid functional genomics vs Zoospores Sporangia vs Lab broth Frog skin
Chytrid functional genomics Many proteases are induced by exposure to host tissue Fungalysin metallopeptidase Serine protease zoospore sporangia frog skin
Chytrid comparative genomics When did the gene family expansions occur? Ascomycota Basidiomycota Zygomycota Chytridiomycota Metazoa
Chytrid comparative genomics
Chytrid comparative genomics Confirmed that Hp does not degrade host tissue Negative control Hp treatment Bd treatment Joneson, Stajich, Shiu, Rosenblum. 2010. PLoS Pathogens
Chytrid comparative genomics Demonstrated that the dramatic protease gene family expansions are recent and mostly Bd-specific Fungalysin peptidase Serine protease Aspartyl protease Crinkler Joneson, Stajich, Shiu, Rosenblum. 2010. PLoS Pathogens
Using genomics to understand Bd novelty Genomics approaches have been key for: Understanding Bd s complex history & identifying key evolutionary transition points Identifying candidate Bd pathogenicity factors & understanding Bd s novel functions Understanding evolution of pathogens and mechanisms of pathogenesis can inform strategies for addressing microbial threats
Acknowledgements NSF-NIH EID Program (EF-0723871) NIH COBRE Program (P20 RR016448-07S2) NSF CAREER Program (DEB-1054062) Key Rosenblum Lab Personnel Thomas Poorten Suzanne Joneson Jamie Voyles Lydia Gentry Karen Pohl Image: Tom Poorten Additional Collaborators Jason Stajich Shin-Han Shiu Timothy James Kelly Zamudio Katy Richards-Hrdlicka Dan Ilut David Rodriguez Michael Eisen Matt Settles Joint Genome Institute