Natural mismatch repair mutations mediate phenotypic diversity and drug resistance inCryptococcus deuterogattii

Abstract

Pathogenic microbes confront a constant evolutionary conflict between the pressure to maintain genome stability and the need to adapt to mounting external stresses. Prokaryotes often respond with elevated mutation rates, but to date little evidence exists of stable eukaryotic hypermutators in nature.Whole genome resequencing of the human fungal pathogen Cryptococcus deuterogattii identified an outbreak lineage characterized by a nonsense mutation in MSH2. This defect in mismatch repair results in a moderate mutation rate increase in typical genes, and a larger increase in genes containing homopolymer runs. This allows facile inactivation of genes with coding homopolymer runs including FRR1, which encodes the target of the immunosuppresive antifungal drugs FK506 and rapamycin. Our study identifies a eukaryotic hypermutator lineage spread over two continents and suggests that pathogenic eukaryotic microbes may experience similar selection pressures on mutation rate as bacterial pathogens, particularly during long periods of clonal growth or while expanding into new environments.

5-fluorocytosine resistance is associated with hypermutation and alterations in capsule biosynthesis in Cryptococcus

“…Evolutionary theory predicts that hypermutators should be rare in eukaryotic microbes because sex unlinks mutator alleles from the mutations they generate, eliminating the advantage of an elevated mutation rate and leaving only the general decrease in fitness from introduced mutations 34 . This result lends further support to the recent appreciation that mismatch repair mutants may be common in pathogenic fungi in part because treatment with antifungal drugs increases selection for mutations that generate resistance 13,14,16,17 .…”

“…In previous studies, mutator alleles in C. deuterogattii were not found to be generally advantageous in rich media 13 . However, under stressful conditions, such as drug challenge with FK506 and rapamycin, mutator alleles were highly beneficial.…”

“…Hypermutation mediates resistance to 5FC. In a previous study, we demonstrated that mismatch repair mutations conferred increased rates of resistance to the antifungal drugs FK506 and rapamycin 13 . Because these hypermutator strains are found among both environmental and clinical isolates, here we tested if a hypermutator state could also confer resistance to one of the front-line drugs used to treat Cryptococcosis: 5-fluorocytosine (5FC).…”

“…Recent work has demonstrated one source of increased rates of resistance to antifungal drugs in Cryptococcus: defects in the DNA mismatch repair pathway 13,14 . Natural isolates with DNA mismatch repair defects have been identified in both an outbreak population of Cryptococcus deuterogattii 13,15 and in Cryptococcus neoformans 14,16 . Defects in mismatch repair are also common in other human fungal pathogens, including Candida glabrata 17 .…”

New pathogens, new tricks: emerging, drug‐resistant fungal pathogens and future prospects for antifungal therapeutics

“…Cryptococcus species are not susceptible to the echinocandin class of antifungals; therefore, additional antifungal drug resistance severely limits treatment options. Additionally, mismatch‐repair defective mutator strains have been identified for Cryptococcus species and are associated with high rates of mutations and antifungal drug resistance …”