Comparative Genomics of Serial Isolates of Cryptococcus neoformans Reveals Gene Associated With Carbon Utilization and Virulence

Abstract

The opportunistic fungal pathogen Cryptococcus neoformans is a leading cause of mortality among the human immunodeficiency virus/acquired immunodeficiency syndrome population and is known for frequently causing life-threatening relapses. To investigate the potential contribution of in-host microevolution to persistence and relapse, we have analyzed two serial isolates obtained from a patient with acquired immunodeficiency syndrome who suffered an initial and relapse episode of cryptococcal meningoencephalitis. Despite being identical by multilocus sequence typing, the isolates differ phenotypically, exhibiting changes in key virulence factors, nutrient acquisition, metabolic profiles, and the ability to disseminate in an animal model. Whole-genome sequencing uncovered a clonal relationship, with only a few unique differences. Of these, two key changes are expected to explain the phenotypic differences observed in the relapse isolate: loss of a predicted AT-rich interaction domain protein and changes in copy number of the left and right arms of chromosome 12. Gene deletion of the predicted transcriptional regulator produced changes in melanin, capsule, carbon source use, and dissemination in the host, consistent with the phenotype of the relapse isolate. In addition, the deletion mutant displayed altered virulence in the murine model. The observed differences suggest the relapse isolate evolved subsequent to penetration of the central nervous system and may have gained dominance following the administration of antifungal therapy. These data reveal the first molecular insights into how the Cryptococcus neoformans genome changes during infection of humans and the manner in which microevolution progresses in this deadly fungal pathogen.

Whole-Genome Comparison of Aspergillus fumigatus Strains Serially Isolated from Patients with Aspergillosis

“…In contrast, few WGS-based studies have been carried out for pathogenic fungi. The only such study recently published identified five loci that showed genetic variation between the genomes of two Cryptococcus neoformans strains serially isolated 77 days apart (42). One of these five mutations was associated with phenotypic differences in virulence factors, indicating that the WGS comparison is a powerful tool to investigate intraclonal isolates of pathogenic fungi.…”

Ploidy dynamics and evolvability in fungi

“…Many more examples of aneuploidies that rescued the lethal phenotypes of deletions of essential genes were recently identified in a genome-wide screen [46]. Similarly, cells resistant to the Hsp90 inhibitor radicicol emerged from an extra copy of ChrXV, owing to elevated expression of two genes ( STI1 and PDR5 ) on that chromosome [47]; and resistance to 4-nitroquinoline- N -oxide (4NQO) is conferred by an extra copy of chromosome ChrXIII, and therefore an extra copy of ATR1 [48,49]. Improved survival on caspofungin is seen in cells with Chr5 monosomy [50].…”

Refractory and/or Relapsing Cryptococcosis Associated with Acquired Immune Deficiency Syndrome: Clinical Features, Genotype, and Virulence Factors of Cryptococcus spp. Isolates

“…grubii may undergo discrete genotypic modifications in the host, eventually accompanied by changes in the expression of virulence factors and of susceptibility to azole drugs. 37,38 Multiple factors may be involved in the persistence and relapse of cryptococcal infection. In the present study, these complications were more related to the host and the extent of infection than to the causal agent.…”