Certain species of fungi are responsible for many common infections including yeast infections, ringworm, thrush, and athlete’s foot. While these diseases may not lead to serious outcomes for most healthy individuals, fungal infections can be deadly, especially for patients with weakened immune systems. One fungal pathogen, Candida auris, is an emerging healthcare-associated infection of growing public health concern. The first case of Candida auris was reported in 2009 in Japan, where it was isolated from a patient’s ear (Auris is Latin for “ear”). Outbreaks have since emerged rapidly around the globe. In the United States, C. auris infections have been increasing over the past few years, with more than 1460 cases reported in 2021. C. auris is typically found in hospitals and other healthcare settings and can cause serious bloodstream and wound infections.

Like other Candida species, C. auris is a type of yeast. However, unlike its yeasty cousins, this pathogen can colonize patients’ skin and persist for long periods of time on environmental surfaces. Another challenge is that C. auris is often resistant to one or more of the major classes of drugs that are typically used to treat fungal infections. While most C. auris infections can be treated with a class of antifungals called echinocandins, resistance to these drugs has also been reported, making some infections difficult to treat. C. auris is the only fungal pathogen identified as an ‘urgent’ threat in CDC’s Antibiotic Resistance Threat Report.

Back to basics

NIAID supports several researchers who are asking fundamental questions about the biology of C. auris. Today’s NIAID Now post features insights from NIAID-funded researchers, Jeniel Nett, M.D., Ph.D., associate professor of medicine and medical microbiology and immunology at University of Wisconsin-Madison, and Christina Cuomo, Ph.D., associate director of the Genomic Center of Infectious Diseases at the Broad Institute of Massachusetts Institute of Technology and Harvard University.

How is C. auris able to colonize the skin and persist in the environment?

C. auris can live and grow on the skin or in the body without causing illness. However, people who are colonized with C. auris may spread the pathogen to others and are at risk of getting sick later on if they develop infections. One important question to understanding C. auris outbreaks is: how is the fungus able to colonize skin so effectively and to persist in the environment? Dr. Nett’s research group is tackling this question by studying C. auris growth in the lab using two different systems. The first is designed to mimic human sweat and skin. Nett noted, “we think that this represents skin to some degree but also when surfaces get contaminated with skin and sweat components.” The other system is pig skin. “Pigs have similar skin to humans in terms of skin thickness and some of the cell types,” Nett explained. Using these systems, Nett and colleagues have shown that C. auris is able to readily grow on skin. “It really seems to mirror what we’re seeing patients,” said Nett. They’ve found that when the fungus is grown in the synthetic sweat medium, it forms multi-layered plaques, or biofilms, both on the pig skin as well as on hard surfaces. Compared to other Candida species, the biofilms are thicker and contain more viable organisms. C. auris biofilms can also persist on surfaces without drying out for up to two weeks in the lab.

Jeniel Nett, M.D., Ph.D., associate professor of medicine and medical microbiology and immunology at University of Wisconsin-Madison

Credit: Dr. Jeniel Nett

Nett’s research demonstrates the ability of the fungus to colonize skin and form persistent biofilms on environmental surfaces, which has implications for transmission in healthcare settings. “This really becomes important with reusable medical equipment that goes room to room,” Nett emphasized. The systems Nett’s group has developed to study C. auris in the lab can also inform potential strategies to remove C. auris from the skin of patients. Nett’s research has shown that while antiseptics are somewhat effective, they are not as active against C. auris when the fungus is growing in the skin environment compared to when it is growing without the skin present. In a published manuscript, Nett and colleagues demonstrated that the commonly used topical antiseptic chlorhexidine does not fully remove C. auris from the skin of patients. They also showed that by adding isopropanol, as well as some essential oils, including tea tree and lemongrass, to chlorhexidine, they were able to improve the activity of the antiseptic. Her group is still investigating what specific components of skin and sweat are triggering biofilm growth in C. auris. Understanding this could lead to better, more specific strategies to disrupt skin colonization.

How did C. auris outbreaks emerge around the world, and how has the fungus become multidrug-resistant?

Soon after it was first identified, outbreaks of C. auris arose in four distinct locations—South Asia, East Asia, Africa, and South America—nearly simultaneously. Dr. Cuomo and colleagues are using a genomics approach to better understand this phenomenon. 
“One fundamental question genomics can answer is, what has been the history of the pathogen over time?” Cuomo explained. “We can take isolates from different patients, and by comparing them we can infer back in time to where they have a common connection.”

Christina Cuomo, Ph.D., associate director of the Genomic Center of Infectious Diseases at the Broad Institute of Massachusetts Institute of Technology and Harvard University

Credit: Dr. Christina Cuomo

Together with colleagues at the Centers for Disease Control and Prevention, Cuomo’s group helped confirm that the different outbreaks were caused by distinct genetic groups, or ‘clades.’ As cases have continued to spread around the globe, researchers have been able to trace new C. auris isolates back to these four major clades, allowing them to understand how the different outbreaks are connected.

Expanding on this initial work, Cuomo’s group is looking more closely at the different C. auris clades and identifying key genetic differences both within and between these groups as well as among C. auris and other related Candida species. From this analysis, they have generated hypotheses about which genes in the fungus are important for contributing to disease in humans. Such studies provide important insight into the biology of C. auris and can help identify potential targets for new drugs.

Researchers are also actively trying to understand how this fungal species has evolved to become resistant to certain antifungal drugs. Combining clinical data and experimental evolution studies, Cuomo’s group has identified specific mutations, or genetic changes, contributing to resistance to the major classes of antifungal drugs, including echinocandins. Cuomo explained that a single change in one of the C. auris proteins causes the fungus to go from sensitive to resistant, which explains why patients will sometimes stop responding in the middle of treatment with echinocandins.

The genomic resources that Cuomo and her group have developed are used by public health laboratories to help assess the frequency of drug resistance in C. auris. Understanding what genetic changes are associated with drug resistance can also help inform patient treatment. “That’s the kind of information we want to be marrying to traditional diagnostics, to think about how can we best type resistance across the course of a patient’s treatment,” Cuomo noted. “We know that resistance can arise while on treatment. We’d like to detect that as soon as it emerges, and not when the patient succumbs to a very high fever or other devastating symptoms.”

From knowledge to solutions

Working on a novel pathogen is a challenging effort. Both Drs. Nett and Cuomo have forged into relatively new scientific territory, and have had to develop new tools, methods, and resources to study C. auris. However, their work has the potential to make a significant impact against this emerging disease. While the scientific questions they both are tackling are fundamental in nature, the answers are of critical importance to patient care and public health interventions.

Learn more about this research by reading recent papers from Dr. Nett, Dr. Cuomo, and colleagues:

CJ, Johnson et al. Modeling Candida auris skin colonization: Mice, swine, and humans. PLOS Pathogens. DOI: 10.1371/journal.ppat.1010730 (2022)

JM Rybak et al. In vivo emergence of high-level resistance during treatment reveals the first identified mechanism of amphotericin B resistance in Candida auris. Clin Microbiology Infect. DOI:10.1016/j.cmi.2021.11.024 (2022). 

C Johnson et al. Augmenting the Activity of Chlorhexidine for Decolonization of Candida auris from Porcine skin. J Fungi. DOI: : 10.3390/jof7100804 (2021).

J Muñoz et al. Clade-specific chromosomal rearrangements and loss of subtelomeric adhesins in Candida auris. Genetics. DOI: : 10.1093/genetics/iyab029 (2021). 

N Chow et al. Tracing the Evolutionary History and Global Expansion of Candida auris Using Population Genomic Analyses. mBio. DOI: : 10.1128/mBio.03364-19 (2020). 

M Horton et al. Candida auris Forms High-Burden Biofilms in Skin Niche Conditions and on Porcine Skin. mSphere. DOI : 10.1128/mSphere.00910-19 (2020).

S Lockhard et al. Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses. Clin Infect Dis. DOI: 10.1093/cid/ciw691 (2017) 

Eix EF, CJ Johnson, KM Wartman, JF Kernien, JJ Meudt, D Shanmuganayagam, ALF Gibson, JE Nett. 2022. Ex vivo human and porcine skin effectively model C. auris colonization, differentiating robust and poor fungal colonizers. J Infect Dis. PMID: 35267041

Cornell Professor: Environment Drives Mosquito-borne Diseases

NIAID Recognizes World Mosquito Day on Saturday, Aug. 20 

The World Health Organization (WHO) estimates that vector-borne illnesses account for more than 17% of all infectious diseases worldwide and are responsible for more than 700,000 deaths annually. Mosquitoes, which some may argue are the most nefarious among the creepy-crawly swarm of vectors, spread diseases like malaria, dengue, and Zika to humans, causing devastating disease and death worldwide. WHO reports that malaria caused 627,000 deaths in 2020, with the majority being in children younger than five years old. Dengue, also known as breakbone fever, adds another 40,000 to the annual death toll (WHO).

With the growing threat of climate change, researchers are examining how mosquitoes will adapt to warming temperatures and what impact this may have on their ability to transmit pathogens, or disease-causing organisms, to humans.

NIAID-supported researcher Courtney Murdock, Ph.D., associate professor in the Department of Entomology at Cornell University in New York, is researching environmental drivers of malaria transmission and is examining interactions among vectors, pathogens, and vertebrate hosts. She has found that climate change may increase the economic and health burden of vector-borne diseases by altering vectors’ immune responses, increasing their geographic distribution, and modifying their behavior. NIAID spoke with Dr. Murdock to learn more about her research team’s work.

How do environmental factors affect mosquitoes and their ability to transmit disease-causing pathogens?

Because mosquitoes are ectothermic, or cold-blooded, temperature is going to have a big impact on basically all aspects of their life cycle. This is because their internal body temperatures are going to quickly track changes in the ambient temperature. This is going to have important implications for their metabolic rates, physiology, development, survival, activity, and their environments, as well as their overall fitness.

Humidity is also going to be important. Temperature and humidity will affect the desiccation (removal of moisture) stress that an organism experiences. Adult mosquitoes, for example, living in warm, arid environments are going to be subject to more desiccation stress if water is limited than those living in humid, warm environments. In general, the availability of water and temperature constraints are important determinants of mosquito distribution across the globe. If environments are climatically suitable for mosquitoes, mosquito populations could, in theory, be larger. They could persist for longer, and potentially be active for longer periods of the day or season.

Why are warming temperatures expected to expose so many new people to mosquito-borne diseases?

If we’re just talking about temperature and thermal suitability, we would expect that, as temperatures warm in northern latitudes, those environments would become more suitable for disease transmission. But which mosquito-borne diseases will be most affected by climate change? I would expect that it’s going to be diseases that are transmitted by vectors that are active during the daytime—such as Aedes mosquitoes, the vector for dengue, Zika, and other diseases —and not likely at as high of transmission rates as we may see currently in the tropics.

For example, in the U.S, I don’t anticipate malaria becoming a problem in the future because Anopheles mosquitoes bite at night. We have housing with air conditioning, and screens that make it hard for those vectors to get in and get out. So, we interact with mosquitoes in our environments differently than in other areas of the world where vector-borne diseases are currently a big problem, and we have fairly wide access to healthcare resources. Now, in areas where temperatures are currently optimal for transmission, if those temperatures move away from being optimal, you could make predictions that mosquito-borne diseases would decline.

What are the greatest challenges to modeling the effects of warming on mosquito-borne disease transmission?

One of the greatest challenges is the lack of high-quality data that can go into informing some of these models. Specifically, we lack data from a diversity of systems on how environmental variation will impact traits that govern mosquito population dynamics and disease transmission. There are statistical models that are good at prediction for a certain set of scenarios, but these models might breakdown when those scenarios change. Then there are mechanistic models which build in the biology of the system and known relationships, that are good at predicting under change, but are really data hungry. It’s trying to balance the data-hungry nature of these models with the lack of high-quality data that’s a real challenge.

How does your research benefit public health?

I guess the pie-in-the-sky goal for my research program is that the data we generate on how key environmental variables impact mosquito populations and disease transmission will allow us to build more accurate and precise predictive models. These models could then be used in combination with intervention efforts to proactively mobilize intervention efforts or target intervention efforts to regions of the world, or even at a finer scale within a city, to enhance disease control.

Which research projects are you currently working on that you are most excited about?

I have one NIAID-supported project right now that I’m very excited about. It investigates how temperature and relative humidity interact to affect urban malaria transmission. There’s been a lot of work done with temperature, but not other environmental variables. And there’s even less work done looking at how environmental variables interact, and they most definitely will interact. This grant is exciting because it combines large-scale environmental experiments in the lab with the vector and the parasite geared toward defining environmental relationships. We’re then taking these data and putting them into novel, mechanistic models to predict how urban malaria varies seasonally and spatially within a city. The output of this work will help local municipalities be more informed on control efforts.

NIAID is supporting research on climate change’s impact on health.  Funding opportunities can be found on the NIAID website.

How Children are Helping Scientists Battle a ‘List of Bad Viruses’
EV-D68 Pilot Project Could Guide Future Pandemic Preparedness

A group of children who recently began participating in a pilot study of a single rare viral disease could eventually provide NIAID scientists and colleagues with the recipe to help slow or stop future viral pandemics.

Researchers at four United States locations are enrolling children 10 and younger in a minimum 3-year study of enterovirus D68 (EV-D68), which evidence suggests can cause a polio-like neurologic disease in children called acute flaccid myelitis, or AFM. The disease was first identified in 2014 with most cases occurring every-other year in children during late summer and early fall. In 2018, physicians reported 238 AFM cases in the United States. Most cases involve fever and breathing difficulty that progress to sudden onset of limb weakness, loss of muscle tone, and loss of reflexes.

More broadly, the study is a test case for how some scientists think nations could plan for viral pandemics, using a two-step approach of meshing human immunology with virus sequence surveillance.

The national EV-D68 pilot study is part of PREMISE, the Pandemic Response Repository through Microbial and Immune Surveillance and Epidemiology. PREMISE is an initiative from NIAID’S Vaccine Research Center (VRC) that began in early 2021.

“We have to start somewhere,” Dr. Daniel Douek said about the EV-D68 pilot study, then explained the ultimate objective of PREMISE: “It sounds a little cheeky, but the aspirational goal is to measure immunity in every single human being on Earth against every single potential pathogen on Earth.” Douek is a VRC physician and researcher who oversees a program studying human immunology.

He is also co-director of PREMISE with VRC colleague Dr. Adrian McDermott. The PREMISE initiative comprises a network of investigators that aim to collect samples from groups of people to detect immunity against viruses of pandemic potential. PREMISE will also sequence samples from animals known to carry diseases that can transmit to people and people with symptoms to detect viruses. 

Douek said the PREMISE initiative grew out of weekly discussions he and McDermott had with epidemiologist colleagues at Princeton University, Bryan Grenfell and C. Jessica Metcalf, a year before the COVID-19 pandemic began.

“They are disease ecologists, interested in population susceptibility, who wanted to know more from us about immunology,” Douek said. When COVID-19 hit, the group realized “we don’t need to just measure immunology, we need to translate that knowledge into products.”

They and collaborators are hoping PREMISE will show that, as Douek explained, it is possible to select a virus, learn how it infects, replicates and mutates; learn what makes certain people susceptible to infection; learn what protects other people from infection; and then use that data to inform the development and testing of vaccines and antibody products to have “waiting on the shelf” if needed. He said retired VRC scientist Dr. Barney Graham suggested EV-D68 as the perfect virus for a pilot study: the virus is a priority pathogen, it affects children, and scientists need to understand its transmission patterns post-COVID-19.

As of May 18, the EV-D68 study had enrolled 117 children. Participating sites include the University of North Carolina in Chapel Hill, University of Colorado/Colorado Children’s Hospital in Aurora, Weill Cornell Medical College in New York, and the University of Alabama-Birmingham.

The pilot study will monitor participants for EV-D68 and other infectious diseases of interest using blood samples, and possibly a nasal swab, that are screened in the lab for beneficial immune-system proteins. Study findings will aid in understanding the seroepidemiology – for example which antibodies are most helpful – of EV-D68 and other infectious diseases. The resulting analyses will be shared to pre-emptively generate research and data resources for early detection and diagnosis, and to inform the identification of monoclonal antibody therapies and immunogens for vaccine discovery and development. These data will help guide the future of PREMISE.

If the EV-D68 pilot project is effective, Douek says researchers would apply the concept to a “list of bad viruses,” which includes hantaviruses, coronaviruses, influenza and various hemorrhagic fever viruses among others – all priority pathogens considered to have pandemic potential.

He is confident in the PREMISE concept because a related project with another Princeton team already is producing intriguing results from the Turkana region of Kenya. Douek says scientists are screening local participant samples against all known coronaviruses.

“We’re seeing some interesting things,” he said, adding that once the data are analyzed and interpreted, scientists plan to publish results that could help better understand how pathogens circulate among isolated populations. “Then it’s a question of pre-positioning with products that can benefit people.”

References: 

H Nguyen-Tran, et al. Enterovirus D68: A Test Case for the Use of Immunologic Surveillance to Develop Tools to Mitigate the Pandemic Potential of Emerging Pathogens. The Lancet Microbe. (2022).

MJ Mina, et al. A Global lmmunological Observatory to meet a time of pandemics. Elife. (2020).

Although pregnant people are at higher risk for severe COVID-19, pregnant volunteers were not included in the initial clinical trials to evaluate the efficacy of vaccines against SARS-CoV-2 infection, which causes COVID-19. To address the gap in knowledge about COVID-19 vaccination during pregnancy, NIAID-supported researchers enrolled 131 individuals of reproductive age, including 84 pregnant, 31 lactating, and 16 nonpregnant individuals in a cohort study to evaluate the immune response generated by the COVID-19 messenger RNA vaccines. Researchers compared the immune responses in individuals who were pregnant and vaccinated with vaccinated non-pregnant participants, and with the immune responses of those who had been naturally infected with COVID-19 while pregnant. Results showed that vaccine-induced antibody responses were equal between pregnant and lactating individuals compared with nonpregnant participants. Antibody levels after vaccination were significantly higher than those induced by natural infection during pregnancy. Vaccine-generated antibodies were also present in all umbilical cord blood and breastmilk samples. Thus, messenger RNA vaccines induced robust immunity in pregnant and lactating individuals, and this immunity was transferred to newborns via the placenta and breastmilk.

Reference: Gray KJ, Bordt EA, Atyeo C, et al. Coronavirus disease 2019 vaccine response in pregnant and lactating women: a cohort study. Am J Obstet Gynecol 2021; 225: 303.e1-17.