Novel Research Shedding Light on Fungal Infections

BY DAVID WILD

A Candida tropicalis fungal colony. Source: CDC/ Dr. Hardin

Novel diagnostics are helping clinicians identify fungal infections where conventional methods have proven insufficient, and new technologies are revealing that fungi interact with pathogenic bacteria in ways that can exacerbate infections.

“There is an increased understanding that while many types of chronic wounds, including diabetic foot ulcers, are polymicrobial in nature, traditional culture methods might underrepresent the vast diversity of chronic wound microbiomes, including fungal populations,” explained Lindsay Kalan, PhD, an assistant professor, Departments of Medical Microbiology and Immunology and Medicine, Division of Infectious Disease, University of Wisconsin–Madison.

Advanced techniques have uncovered fungi in roughly 80% of diabetic foot ulcers, whereas traditional culturing methods identify fungi in only 5% of wounds, Dr. Kalan noted (mBio 2016;7[5]:e0158-16. doi:10.1128/mBio.01058-16).

Better understanding of the role that fungal populations play in these infections could help pinpoint those patients who are most likely to develop nonhealing foot wounds, she said, noting that the presence of other organisms, such as Staphylococcus aureus, has not been a very good prognostic marker in this regard.

“We have found some interesting things by studying microbial communities instead of a single pathogen within a single wound sample and looking at how community diversity changes before and after an intervention,” Dr. Kalan said.

For example, she and her colleagues found that diabetic foot wounds that heal after debridement exhibit a significant drop in the overall microbial diversity, while unhealed or amputated wounds have a much larger proportion of fungi on a community level (mBio 2016;7[5]:e0158-16. doi:10.1128/mBio.01058-16).

“Additionally, looking at highly necrotic tissue, we’ve seen a really striking increase in the proportion of pathogenic fungi that grow alongside anaerobic bacteria, suggesting there are bacterial–fungal networks forming within these wounds and leading to poor outcomes,” she said.

Indeed, using a diabetic foot ulcer lab model, her team demonstrated that bacteria and fungi “jointly synergize to contribute to pathogenesis,” she said. They cultured Candida albicans along with S. aureus and Citrobacter freundii, a species of anaerobic gram-negative bacteria, and found that when C. albicans colonized first, C. freundii outcompeted S. aureus by inducing growth of fungal hyphae and binding to C. albicans (ISME J 2021;15:2012-2027). They also found significantly

higher levels of neutrophil cell death in mixed fungal–bacterial biofilms, compared with when there was a single species, Dr. Kalan said, noting these insights could identify “important markers for predicting the healing trajectory and possibly finding targets for intervention as well.”

Fungal Lung Infections in Cystic Fibrosis

Fungal Lung Infections in COVID-19

Fungi also have gained recognition as pulmonary pathogens among patients with COVID-19, Martin Hoenigl, MD, an associate professor, Division of Infectious Diseases and Global Public Health, University of California, San Diego and the Medical University of Graz, in Austria.

He noted that 3.1% of the overall COVID19 population develops COVID-19–associated pulmonary aspergillosis (CAPA), with the number rising to 8.9% among ICU patients with COVID-19 and to 10% to 15% in ICU patients with COVID-19 who require mechanical ventilation (Clin Microbiol Infect 2021 Aug 26. doi:10.1016/j.cmi.2021.08.014).

While CAPA is an ominous diagnosis, associated with a 51.8% mortality rate, it can be a challenge to diagnose, Dr. Hoenigl explained.

Although “the classical neutropenic patient at risk for invasive aspergillosis who develops primarily angioinvasive disease” can display the typical radiological signs of infection, “things get a little bit more complicated once we move a little bit up the spectrum to non-neutropenic patients who develop primary airway–invasive disease first,” he said.

In these more complicated cases, the typical radiological signs of infection may not be present, and bronchoalveolar lavage (BAL) samples from the site of infection are needed to confirm a diagnosis.

Many clinicians are reluctant to employ bronchoscopy to diagnose lung infections in COVID-19 patients because the procedure generates aerosols, but recent consensus criteria offer a number of possible alternatives to BAL-based diagnosis, he said (Lancet Infect Dis 2021;21[6]:e149-e162).

One such alternative is diagnostic lateral flow assay (LFA) testing for galactomannan, which Dr. Hoenigl and his colleagues have studied. In a recent multicenter trial, they found “a very good predictive value for diagnosing invasive aspergillosis” with the device they used (Aspergillus GM LFA; IMMY) (J Clin Microbiol 2021 Oct 13. doi:10.1128/JCM.0168921). Specifically, they documented an area under the curve of greater than 0.8 for the same device for diagnosing CAPA in respiratory specimens, indicating a high level of accuracy.

“It also seems to work very well for distinguishing CAPA from non-CAPA,” Dr. Hoenigl noted.

There is growing interest in the role of fungi in other lung infections, such as those in patients with cystic fibrosis (CF), according to Deborah Hogan, PhD, a professor in the Geisel School of Medicine at Dartmouth, in Hanover, N.H. Although lung infections in patients with CF are most often dominated by bacteria, “it’s becoming increasingly appreciated that these infections also contain fungi, such as Candida and Aspergillus,” she said. “What we’re finding is that the fungi might be under-detected through clinical laboratory practices, where selective media specific to fungi are not always used,” Dr. Hogan said. Candida lusitaniae. Indeed, advanced analytical tools have revealed that some lung infections are dominated by fungi, and these technologies have uncovered “some interesting dynamics between bacteria and fungi, including increased fungal burden after antibiotics are used,” Dr. Hogan said. One recent insight with important research and potentially clinical implications is that fungi live in the lungs of CF patients chronically, she told meeting attendees. “Using banked samples in our CF center here at Dartmouth, we’ve been able to determine that Candida lusitaniae can be present for months or years in some individuals with CF and that these isolates can become phenotypically heterogenous, with drug-resistant subpopulations,” she said. Some C. lusitaniae isolates are resistant to fluconazole while others are not, she said. Thus, “depending on what isolate is chosen for phenotyping, the clinician might choose a different antifungal therapy. “Clinicians need to consider more than one isolate, or perhaps whole populations, when thinking about drug therapies for particularly chronic infections,” she said. ■ Dr. Hoenigl reported receiving grant or research support from Astellas, F2G, Gilead, Pfizer and Scynexis. Dr. Hogan reported no relevant financial disclosures.