Researchers Have Fully Sequenced The Deadly Human Pathogen Cryptococcus

Image Caption: Scanning electron micrograph shows infectious spores produced by the deadly fungi Cryptococcus neoformans. Credit: Duke University

By Marla Vacek Broadfoot, Duke University

Ten-year effort yields map for finding weaknesses in the fungus

Within each strand of DNA lies the blueprint for building an organism, along with the keys to its evolution and survival. These genetic instructions can give valuable insight into why pathogens like Cryptococcus neoformans a fungus responsible for a million cases of pneumonia and meningitis every year are so malleable and dangerous.

Now researchers have sequenced the entire genome and all the RNA products of the most important pathogenic lineage of Cryptococcus neoformans, a strain called H99. The results, which appear April 17 in PLOS Genetics, also describe a number of genetic changes that can occur after laboratory handling of H99 that make it more susceptible to stress, hamper its ability to sexually reproduce and render it less virulent.

The study provides a playbook that can be used to understand how the pathogen causes disease and develop methods to keep it from evolving into even deadlier strains.

We are beginning to get a grasp on what makes this organism tick. By having a carefully annotated genome of H99, we can investigate how this and similar organisms can change and mutate and begin to understand why they arent easily killed by antifungal medications, said study coauthor John Perfect, M.D., a professor of medicine at Duke who first isolated H99 from a patient with cryptococcal meningitis 36 years ago.

The fungus Cryptococcus neoformans is a major human pathogen that primarily infects individuals with compromised immune systems, such as patients undergoing transplant or those afflicted with HIV/AIDS. Researchers have spent many years conducting genetic, molecular and virulence studies on Cryptococcus neoformans, focusing almost exclusively on the H99 strain originally isolated at Duke. Interestingly, investigators have noticed that over time, the strain became less and less virulent as they grew it in the laboratory.

Virulence, or the ability of this organism to cause disease in mice or humans, is not very stable. It changes, and can rapidly be lost or gained. When the organism is in the host it is in one state, but when we take it out of the host and begin growing it in the laboratory it begins mutating, said Fred Dietrich, senior study author and associate professor of molecular genetics and microbiology at Duke University School of Medicine.

Dietrich and his colleagues decided that the best way to investigate how the virulence of this pathogen could change over time was to develop a carefully annotated genomic map of the H99 strain, both in its original state as well as after it had been cultured. In an effort that took ten years and dozens of collaborators, the researchers sequenced the original H99 and nine other cultured variants, analyzing both the genome, the genetic code written in the DNA, as well as the transcriptome, the RNA molecules that occupy the second step in the flow of genetic information from DNA to RNA to protein.