The world of fungi includes a wide range of organisms, such as mushrooms, molds, and yeast, that are common outdoors in water, soil, and air; indoors on surfaces; and on our skin and inside our bodies. Although many fungi are helpful—or even delicious, like some mushrooms—there are many others which can cause disease. Some fungal infections are more common in people with weakened immune systems or hospitalized individuals, while other fungal infections can infect anyone, including otherwise healthy people. According to the Centers for Disease Control and Prevention (CDC), more than one billion people worldwide get a fungal infection each year. There are four main classes of antifungal drugs, and the rising rate of antimicrobial resistance is limiting and complicating existing treatment options. Currently, there are no approved vaccines to prevent fungal infections.

NIAID conducts and supports basic, translational, and clinical research to understand how fungal pathogens cause disease and how the immune system responds to infection. NIAID researchers are exploring how fungal susceptibility and infection impact the function of immune cells. The following are examples of ongoing clinical trials supported by NIAID through the investigator-initiated clinical trial funding mechanism investigating various aspects of fungal disease. 

Stewardship in AMR – Examining a shorter treatment course for children

Immunocompromised patients are at risk for the development of fungal infections. Hospitalized patients can get severe, often deadly, fungal diseases like candidemia, a bloodstream infection caused by the Candida fungus. According to the CDC, candidemia is one of the most common bloodstream infections in the U.S. with an estimated 25,000 cases each year. The current treatment guidelines for invasive candidemia recommend 14 days of antifungal therapy.  This guideline is based on expert opinion rather than comparative data and the optimal treatment duration remains unknown. NIAID-funded researchers Drs. William J. Steinbach and Brian T. Fisher are conducting a clinical trial (NCT05763251) to examine whether a shorter 7-day treatment strategy is just as safe and effective as current practice. This trial is only enrolling pediatric patients at the study-site hospitals with uncomplicated cases of candidemia. A shorter treatment would significantly reduce the burden of care on sick and recovering pediatric patients, allowing families to come home earlier from the hospital, and could help combat the rising rates of antimicrobial resistance. This is the first randomized control trial to explore the efficacy of a shorter course treatment for any invasive fungal disease. The trial is supported through NIAID grant funding R01 AI 170385. 

Cryptococcus neoformans contributing to HIV/AIDS-related mortality 

Cryptococcus neoformans is a fungal pathogen that can cause cryptococcal meningitis. Those most at risk are immunocompromised, such as people/persons living with HIV/AIDS. Although Antiretroviral therapy (ART) has significantly reduced the incidence of HIV/AIDS in the United States, regions of the world with limited access to ART are still seeing tens of thousands of cases. According to the CDC, each year an estimated 152,000 people living with HIV experience cases of cryptococcal meningitis, of which an estimated 112,000 deaths occur, most in sub-Saharan Africa. In the weeks prior to the onset of meningitis, the cryptococcal antigen (CrAg) is detectable in the blood and is a good predictor of meningitis and death. NIAID-funded researcher Dr. Radha Rajasingham is leading a clinical trial (NCT03002012) to examine whether the treatment combination of liposomal amphotericin (AmBisome) and fluconazole for those who receive a positive CrAg antigen test effectively prevents cryptococcal meningitis and death. Dr. Rajasingham’s lab at the University of Minnesota is dedicated to improving cryptococcal meningitis treatment strategies and outcomes for people/persons living with HIV/AIDS and is supported through NIAID grant funding U01 AI 174978 and R01 AI162181. 

Though these conditions can be severe, they are not the only fungal diseases of concern for NIAID. From aspergillosis to Valley Fever, NIAID is committed to researching new treatments, diagnostics, and preventative measures for a wide array of fungal diseases, especially in the face of rising antifungal resistance.

Mosquitoes are considered one of the most dangerous animals on earth because of their broad distribution and the many pathogens they transmit to humans. Some of the most important human diseases in tropical and temperate regions of the planet are caused by mosquito-borne pathogens. Malaria, dengue, and filariasis, among other mosquito-borne diseases, kill or sicken millions of people worldwide every year.

Mosquito-borne pathogens are transmitted to the vertebrate host, such as a human, when the mosquito bites the host in search of blood. The proteins found in blood are essential for female mosquitoes: without it, they lack the resources to create eggs. Greater knowledge of the biological processes involved in the mosquito life cycle could lead to new or improved strategies to control mosquito populations.     

Dr. Patricia Scaraffia, Associate Professor at the Tulane University School of Public Health and Tropical Medicine, has dedicated her career to understanding the metabolism of the mosquito Aedes aegypti that carries the pathogens responsible for dengue, Zika, chikungunya, and yellow fever to humans. NIAID reached out to Dr. Scaraffia about her team’s research. 

What got you interested in studying mosquito metabolism?

I have studied the metabolism of insects that are vectors of pathogens causing human diseases since I was a graduate student at the Universidad Nacional de Cordoba, in Argentina. My Ph.D. dissertation was focused on the energy metabolism in Triatomine insects, vectors of Trypanosoma cruzi, the etiological agent of Chagas´ disease. After my dissertation, I participated as a speaker in a two-week course for PhD students entitled Biochemistry and molecular biology of insects of importance for public health. During the course, Argentinian professors encouraged me to contact the late Dr. Michael A. Wells, a leader in insect metabolism, and apply for a postdoctoral training in his lab. Soon after, I joined Dr. Wells´s lab at the University of Arizona as a research associate and opened a new line of investigation in his lab. Since then, I have never stopped working on A. aegypti mosquito metabolism. I am passionate and curious about the tremendous complexity of mosquito metabolism. It is a fascinating puzzle to work on. It constantly challenges me and my research team to think outside the box when trying to decipher the unknowns related to mosquito metabolism.

Dr. Patricia Scaraffia's work focuses on the secrets of mosquito metabolism.

Credit: Dr. Patricia Scaraffia

What are the metabolic challenges faced by mosquitoes after feeding on blood?

Female mosquitoes are a very captivating biological system. It is during blood feeding that female mosquitoes can transmit dangerous, and sometimes lethal, pathogens to humans. Interestingly, the blood that the females take could be twice their body weight, which is impressive. Female mosquitoes have evolved efficient mechanisms to digest blood meals, eliminate excess water, absorb and transport nutrients, synthesize new molecules, metabolize excess nitrogen, remove nitrogen waste, and successfully lay eggs within 72 hours! Despite significant progress in understanding how females overcome these metabolic challenges, we have not yet fully elucidated the intricate metabolic pathways, networks, and signaling cascades, nor the molecular and biochemical bases underlying the multiple regulatory mechanisms that may exist in blood-fed female mosquitoes. 

What are the greatest potential benefits of understanding mosquito metabolism?

Metabolism is a complicated process that involves the entire set of chemical transformations present in an organism. A metabolic challenge faced by mosquitoes is how to break down ammonia that results from digesting a blood meal and is toxic to the mosquito. With NIAID support, we found that in the absence of a functional metabolic cycle to detoxify ammonia, A. aegypti mosquitoes use specific metabolic pathways that were believed to be non-existent in insects. This discovery has opened a new field of study. 

A better understanding of mosquito metabolism and its mechanisms of regulation in A. aegypti and other mosquito species could lead us to the discovery of common and novel metabolic targets and/or metabolic regulators. It would also provide a strong foundation for the development and implementation of more effective biological, chemical and/or genetic strategies to control mosquito populations around the world. 

What are the biggest challenges to studying mosquito metabolism?

We have often observed that genetic silencing or knockdown—a technique to prevent or reduce gene expression—of one or more genes encoding specific proteins involved in mosquito nitrogen metabolism results in a variety of unpredictable phenotypes based on our knowledge of vertebrate nitrogen metabolism. Notably, female mosquitoes get control of the deficiency of certain key proteins by downregulating or upregulating one or multiple metabolic pathways simultaneously and at a very high speed. This highlights the tremendous adaptive capacity of blood-fed mosquitoes to avoid deleterious effects and survive.

We have been collaborating closely with scientists that work at the University of Texas MD Anderson Cancer Center Metabolomics Core Facility, and more recently, with bioanalytical chemists that work in the Microbiome Center’s Metabolomics and Proteomics Mass Spectrometry Laboratory in Texas Children’s Hospital in Houston. Our projects are not turn-key type of projects with quick turn-round times. We have to invest considerable time and effort to successfully develop and/or optimize methods before analyzing mosquito samples. Despite these challenges, our research work keeps motivating us to unlock the metabolic mysteries that female mosquitoes hold.

Your research has focused on Aedes aegypti, the main vector of dengue, Zika, etc.  Why did you choose to study this mosquito species rather than others that are also important vectors of malaria and other diseases?

My research has focused on Aedes aegypti not only because it is a vector of pathogens that pose public health threats, but also because it is genetically one of the best-characterized insect species. The availability of the Aedes aegypti genome is a great resource for a wide range of investigations. In addition, Aedes aegypti is relatively simple to rear and maintain in the lab. In my lab, we are interested in expanding our metabolic studies to other mosquito species by working in collaboration with scientists with expertise in the biology of different vectors.

What important questions remain unanswered about mosquito metabolism?

Many important questions remain unanswered about mosquito metabolism. I’d like to highlight a few of them that may help us enhance our knowledge of the mosquito as a whole organism rather than as a linear sum of its parts. For example, what are the genetic and biochemical mechanisms that drive metabolic fluxes in mosquitoes in response to internal or external alterations? How do key proteins interact with each other, and how are they post-translationally regulated to maintain mosquito metabolism? How are the metabolic networks regulated in noninfected and pathogen-infected mosquitoes? What are the critical regulatory points within the mosquito metabolism and the vector-host-pathogen interface? 

While basic science will continue to be crucial in answering these questions, to successfully fight against mosquitoes, we must work together as part of a multidisciplinary team of scientists to tightly coordinate our efforts and close the gap between basic and applied science. 

NIAID Funds Cutting-Edge Genomics and Bioinformatics Programs 

NIAID has announced six awards to continue the Genomics Centers for Infectious Diseases (GCIDs) and Bioinformatics Resource Centers (BRCs) for Infectious Diseases, both important data science networks offering critical resources for the scientific community. NIAID expects to commit approximately $19.1 million per year to fund the five-year programs. The awards mark the 20^th anniversaries of the GCID and BRC programs and extend NIAID's history of investing in cutting-edge pathogen genomics and bioinformatics research – the relatively new field of using patient gene sequences and computer analysis to identify, predict and prevent disease. 

The GCIDs and BRCs provide public access to high-quality genomic data and data analytics technologies, tools, and training to facilitate discoveries by researchers studying viruses, bacteria, fungi, parasites, other eukaryotic pathogens, and vectors. In addition, in the event of an infectious disease outbreak, the GCID and BRC programs offer network expertise and resources and provide a coordinated research response.

For example, the GCIDs use innovative, large-scale genomics technology and bioinformatics tools to find specific genetic sequences to explain how pathogens cause disease and whether pathogens are resistant to available treatments. GCID studies can enhance understanding of infection mechanisms, track pathogen transmission dynamics, and improve detection – all leading to better diagnostics, prevention, treatment, and pathogen elimination strategies.

For more information, visit the GCID program website. 

The BRCs are publicly accessible online resources that include data on pathogens, vectors, and hosts. The newly funded BRCs will have four primary objectives: 

1. To provide integrated data and bioinformatics resources for infectious diseases.
2. To develop advanced innovative bioinformatics technologies, software, and tools to accelerate basic and applied human infectious diseases research.
3. To offer state-of-the-art bioinformatics trainings, educational materials, and other community outreach activities for the infectious diseases research community in the United States and globally.
4. To offer cutting-edge bioinformatics resources and analytics in response to emerging needs, outbreaks, and public health emergencies consistent with NIAID’s mission.

The newly funded BRCs will align with the NIH Strategic Plan for Data Science and incorporate globally distributed repositories and analytical capabilities that will be strengthened by a program-wide commitment to FAIR data principles and collaborative work. All three funded centers will conduct activities and advance research across all four programmatic objectives and will become operational soon after the awards are made. Two centers, the Bioinformatics Resource Analytics Center (BRC.analytics) and the Pathogen Data Network will address all pathogen types relevant to the NIAID mission and will continue to make available bioinformatics data compiled during previous funding periods from eukaryotic pathogens and vectors, and from bacteria and viruses. Both centers will have a specific focus on advancing the knowledge base and tools for bioinformatics analysis of eukaryotic genomes but will also advance technologies for bacterial and viral bioinformatics. The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) will continue its focus on bacterial and viral pathogens, and bioinformatics data compiled for bacteria and viruses during previous funding periods will be found on its site.

Bioinformatics infrastructure advances anticipated include: providing uniform and easy access to numerous pathogen-relevant external resources; integrating infectious diseases data with additional human and clinical data; and providing large-scale automated bioinformatics workflows and dataset management.

The BRC program is expected to enhance NIAID’s outbreak and pandemic preparedness response by offering accessible platforms that integrate public health, pathogen and other data.  For more information, visit the BRC program website.

GCID award recipients are:

The Center for Advancing Genomic, Transcriptomic and Functional Approaches to Combat Globally Important and Emerging Pathogens

• Principal Investigator/Director: Daniel Neafsey, Ph.D.
• Institute: Broad Institute, Boston, Massachusetts

The Center for Integrated Genomics of Mucosal Infections

• Principal Investigator/Director: Joseph Petrosino, Ph.D.
• Institute: Baylor College of Medicine, Houston, Texas

The Michigan Infectious Disease Genomics (MIDGE) Center

• Principal Investigator/Director: Adam Lauring, M.D., Ph.D.
• Institute: The University of Michigan, Ann Arbor, Michigan

BRC award recipients are: 

The Bacterial and Viral Bioinformatics Resource Center (BV-BRC)  

• Principal Investigator/Director: Rick Stevens, Ph.D.
• Institute: University of Chicago, Chicago, Illinois
• Website: https://www.bv-brc.org/

The Bioinformatics Resource Analytics Center (BRC.analytics)  

• Principal Investigator/Director: Anton Nekrutenko, Ph.D.
• Institute: Pennsylvania State University, University Park, Pennsylvania 
• Website: https://brc-analytics.org/

The Pathogen Data Network 

• Principal Investigator/Director: Aitana Neves, Ph.D.
• Institute: Swiss Institute of Bioinformatics, Lausanne, Switzerland
• Website: https://pathogendatanetwork.org/