Candida albicans is both a member of the healthy human microbiome
and a major pathogen in immunocompromised individuals. Infections are typically
treated with azole inhibitors of ergosterol biosynthesis often leading to drug
resistance. Studies in clinical isolates have implicated multiple mechanisms in
resistance, but have focused on large-scale aberrations or candidate genes, and do
not comprehensively chart the genetic basis of adaptation. Here, we leveraged
next-generation sequencing to analyze 43 isolates from 11 oral candidiasis patients.
We detected newly selected mutations, including single-nucleotide polymorphisms
(SNPs), copy-number variations and loss-of-heterozygosity (LOH) events. LOH events
were commonly associated with acquired resistance, and SNPs in 240 genes may be
related to host adaptation. Conversely, most aneuploidies were transient and did not
correlate with drug resistance. Our analysis also shows that isolates also varied in
adherence, filamentation, and virulence. Our work reveals new molecular mechanisms
underlying the evolution of drug resistance and host adaptation.
Nearly all humans are infected with the fungus Candida albicans. In
most people, the infection does not produce any symptoms because their immune system
is able to counteract the fungus' attempts to spread around the body. However, if the
balance between fungal attack and body defence fails, the fungus is able to spread,
which can lead to serious disease that is fatal in 42% of cases.
How does C. albicans outcompete the body's defences to cause
disease? This is a pertinent question because the most effective antifungal
medicines—including the drug fluconazole—do not kill the fungus; they
only stop it from growing. This gives the fungus time to develop resistance to the
drug by becoming able to quickly replace the fungal proteins the drug destroys, or to
efficiently remove the drug from its cells.
In this study, Ford et al. studied the changes that occur in the DNA of C.
albicans over time in patients who are being treated with fluconazole.
Ford et al. took 43 samples of C. albicans from 11 patients with
weakened immune systems. The experiments show that the fungus samples collected early
on were more sensitive to the drug than the samples collected later.
In most cases, the genetic data suggest that the infections begin with a single
fungal cell; the cells in the later samples are its offspring. Despite this, there is
a lot of genetic variation between samples from the same patient, which indicates
that the fungus is under pressure to become more resistant to the drug. There were
240 genes—including those that can alter the surface on the fungus cells to
make it better at evading the host immune system—in which small changes
occurred over time in three or more patients. Laboratory tests revealed that many of
these genes are likely important for the fungus to survive in an animal host in the
presence of the drug.
C. albicans cells usually have two genetically distinct copies of
every gene. Ford et al. found that for some genes—including some that make
surface components or are involved in expelling drugs from cells—the loss of
genetic information from one copy, so that both copies become identical, is linked to
resistance to fluconazole. However, the gain of whole or partial
chromosomes—which contain large numbers of genes—is not linked to
resistance, but may provide additional genetic material for generating diversity in
the yeast population that may help the cells to evolve resistance in the future.
These experiments have identified many new candidate genes that are important for
drug resistance and evading the host immune system, and which could be used to guide
the development of new therapeutics to treat these life-threatening infections.